@article {pmid36983491,
year = {2023},
author = {Du, Z and Li, Y and Wang, XC and Wang, K and Yao, YJ},
title = {Re-Examination of the Holotype of Ganoderma sichuanense (Ganodermataceae, Polyporales) and a Clarification of the Identity of Chinese Cultivated Lingzhi.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {3},
pages = {},
doi = {10.3390/jof9030323},
pmid = {36983491},
issn = {2309-608X},
abstract = {The widely cultivated Chinese Lingzhi is a famous fungus with significant medicinal and economic value, which has commonly been misidentified as Ganoderma lucidum for a long period of time. The scientific binomial of the fungus is always a hotly debated question that revolves around G. lingzhi and G. sichuanense. To interpret the species concept of the taxon, six specific primers for G. sichuanense and one universal primer were designed. Through directed and nested PCRs, we obtained nine ITS sequences from the holotype (HMAS 42798) of G. sichuanense. By genome sequencing, the ITS sequence of the first cultivated Lingzhi (HMAS 25103) was assembled. Based on a phylogenetic study of the genus Ganoderma, the correct name for widely cultivated Ganoderma species in China was confirmed as G. sichuanense, and G. lingzhi should be a later synonym.},
}

@article {pmid36979054,
year = {2023},
author = {Żabicka, J and Kirschey, T and Migdałek, G and Słomka, A and Kuta, E},
title = {Genetic Variation versus Morphological Variability in European Peatland Violets (Viola epipsila-V. palustris Group).},
journal = {Biology},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/biology12030362},
pmid = {36979054},
issn = {2079-7737},
abstract = {In Europe, the V. epipsila-V. palustris group comprises V. epipsila Ledeb., V. palustris L., V. pubifolia (Kuta) G. H. Loos (=V. palustris subsp. pubifolia Kuta), interspecific hybrids, and putative introgressants. The genetic affinity of V. pubifolia to V. palustris, and their shared origin via hybridization followed by polyploidization, were confirmed using inter simple sequence repeat (ISSR) markers, restriction site-associated DNA sequencing (RAD-Seq), and a low-copy nuclear gene, GPI, which encodes glucose-6-phosphate isomerase. The other taxa of subsect. Stolonosae were not identified as putative parents of V. pubifolia by GPI. Our analyses indicated that V. pubifolia can be included in the morphological and genetic variation of V. palustris. The ISSR, RAD-Seq, and genome size value separated well V. palustris from V. epipsila and hybrids. The results also reopen the discussion on intraspecific variation in the context of taxa ranks and species concepts. The reduced tolerance of V. epipsila in Europe to changing environmental conditions might result from low genetic differentiation and heterozygosity, as well as the increased number of interspecific hybrids (V. epipsila × V. palustris), and eventually can possibly lead to its extinction. The disappearance of populations/individuals of this species may indicate anthropogenic changes occurring in peatlands.},
}

@article {pmid36944262,
year = {2023},
author = {Milner, DS and Galindo, LJ and Irwin, NAT and Richards, TA},
title = {Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-032421-115538},
pmid = {36944262},
issn = {1545-3251},
abstract = {Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the functional factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire. Expected final online publication date for the Annual Review of Microbiology, Volume 77 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid36920650,
year = {2023},
author = {Konashev, MB},
title = {The Russian Backdrop to Dobzhansky's Genetics and the Origin of Species.},
journal = {Journal of the history of biology},
volume = {},
number = {},
pages = {},
pmid = {36920650},
issn = {1573-0387},
abstract = {Theodosius Dobzhansky was one of the principal 'founding fathers' of the modern 'synthetic theory of evolution' and the 'biological species' concept, first set forth in his classic book, Genetics and the Origin of Species (1937). Much of the discussion of Dobzhansky's work by historians has focused on English-accessible sources, and has emphasized the roles of the Morgan School, and figures such as Sewall Wright, and Leslie C. Dunn. This article uses Dobzhansky's Russian articles that are unknown to English-speaking readers, and his late 1920s to early 1930s correspondence with colleagues and friends in the Soviet Union, to clarify some of the Russian influences on Dobzhansky's evolving evolutionary views, particularly the development of his views on species and speciation. For Dobzhansky, as for Darwin, the problem of species and speciation was crucial for his theoretical explanation of evolution.},
}

@article {pmid36890896,
year = {2023},
author = {Bai, S and Han, X and Feng, D},
title = {Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1139744},
pmid = {36890896},
issn = {1664-462X},
abstract = {High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.},
}

@article {pmid36876315,
year = {2023},
author = {Wang, MZ and Fan, XK and Zhang, YH and Wu, J and Mao, LM and Zhang, SL and Cai, MQ and Li, MH and Zhu, ZS and Zhao, MS and Liu, LX and Cameron, KM and Li, P},
title = {Phylogenomics and integrative taxonomy reveal two new species of Amana (Liliaceae).},
journal = {Plant diversity},
volume = {45},
number = {1},
pages = {54-68},
pmid = {36876315},
issn = {2468-2659},
abstract = {Until now the genus Amana (Liliaceae), known as 'East Asian tulips', has contained just seven species. In this study, a phylogenomic and integrative taxonomic approach was used to reveal two new species, Amana nanyueensis from Central China and A. tianmuensis from East China. A. nanyueensis resembles Amana edulis in possessing a densely villous-woolly bulb tunic and two opposite bracts, but differs in its leaves and anthers. Amana tianmuensis resembles Amana erythronioides in possessing three verticillate bracts and yellow anthers, but differs in aspects of its leaves and bulbs. These four species are clearly separated from each other in principal components analysis based on morphology. Phylogenomic analyses based on plastid CDS further support the species delimitation of A. nanyueensis and A. tianmuensis and suggests they are closely related to A. edulis. Cytological analysis shows that A. nanyueensis and A. tianmuensis are both diploid (2n = 2x = 24), different from A. edulis, which is either diploid (northern populations) or tetraploid (southern populations, 2n = 4x = 48). The pollen morphology of A. nanyueensis is similar to other Amana species (single-groove germination aperture), but A. tianmuensis is quite different because of the presence of a sulcus membrane, which creates the illusion of double grooves. Ecological niche modelling also revealed a niche differentiation between A. edulis, A. nanyueensis and A. tianmuensis.},
}

@article {pmid36876113,
year = {2023},
author = {Anderson, BD and Bisanz, JE},
title = {Challenges and opportunities of strain diversity in gut microbiome research.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1117122},
pmid = {36876113},
issn = {1664-302X},
abstract = {Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than de novo mutations. As such, the conserved portion of the genome is often a fraction of the pangenome which gives rise to significant phenotypic variation, particularly in traits which are important in host microbe interactions. In this review, we discuss the mechanisms that give rise to strain variation and methods that can be used to study it. We identify that while strain diversity can act as a major barrier in interpreting and generalizing microbiome data, it can also be a powerful tool for mechanistic research. We then highlight recent examples demonstrating the importance of strain variation in colonization, virulence, and xenobiotic metabolism. Moving past taxonomy and the species concept will be crucial for future mechanistic research to understand microbiome structure and function.},
}

@article {pmid36845931,
year = {2023},
author = {Zuo, J and Zhu, E and Yin, W and Yao, C and Liao, J and Ping, X and Zhu, Y and Cai, X and Rao, Y and Feng, H and Zhang, K and Qian, Z},
title = {Long-term spatiotemporal and highly specific imaging of the plasma membrane of diverse plant cells using a near-infrared AIE probe.},
journal = {Chemical science},
volume = {14},
number = {8},
pages = {2139-2148},
pmid = {36845931},
issn = {2041-6520},
abstract = {Fluorescent probes are valuable tools to visualize plasma membranes intuitively and clearly and their related physiological processes in a spatiotemporal manner. However, most existing probes have only realized the specific staining of the plasma membranes of animal/human cells within a very short time period, while almost no fluorescent probes have been developed for the long-term imaging of the plasma membranes of plant cells. Herein, we designed an AIE-active probe with NIR emission to achieve four-dimensional spatiotemporal imaging of the plasma membranes of plant cells based on a collaboration approach involving multiple strategies, demonstrated long-term real-time monitoring of morphological changes of plasma membranes for the first time, and further proved its wide applicability to plant cells of different types and diverse plant species. In the design concept, three effective strategies including the similarity and intermiscibility principle, antipermeability strategy and strong electrostatic interactions were combined to allow the probe to specifically target and anchor the plasma membrane for an ultralong amount of time on the premise of guaranteeing its sufficiently high aqueous solubility. The designed APMem-1 can quickly penetrate cell walls to specifically stain the plasma membranes of all plant cells in a very short time with advanced features (ultrafast staining, wash-free, and desirable biocompatibility) and the probe shows excellent plasma membrane specificity without staining other areas of the cell in comparison to commercial FM dyes. The longest imaging time of APMem-1 can be up to 10 h with comparable performance in both imaging contrast and imaging integrity. The validation experiments on different types of plant cells and diverse plants convincingly proved the universality of APMem-1. The development of plasma membrane probes with four-dimensional spatial and ultralong-term imaging ability provides a valuable tool to monitor the dynamic processes of plasma membrane-related events in an intuitive and real-time manner.},
}

@article {pmid36842092,
year = {2023},
author = {Kious, BM},
title = {Suffering and the dilemmas of pediatric care: a response to Tyler Tate.},
journal = {Theoretical medicine and bioethics},
volume = {},
number = {},
pages = {},
pmid = {36842092},
issn = {1573-0980},
abstract = {In a recent article, Tyler Tate argues that the suffering of children - especially children with severe cognitive impairments - should be regarded as the antithesis of flourishing, where flourishing is relative to one's individual characteristics and essentially involves receiving care from others. Although initially persuasive, Tate's theory is ambiguous in several ways, leading to significant conceptual problems. By identifying flourishing with receiving care, Tate raises questions about the importance of care that he does not address, giving rise to a bootstrapping problem. By making flourishing relative to an individual's circumstances, Tate is forced to confront questions about exactly how relative it can be, suggesting the possibility that, on his view, to flourish is simply to be however one is. In an attempt to surmount these problems, I offer a revision and restatement of Tate's view that defines the relationship between individualized flourishing and the more conventional, species-relative concept, and describe more clearly the role that care should play with respect to flourishing - one that is instrumental and not merely constitutive. Even this restated view, however, fails to answer difficult questions about how one should respond to the medical needs of some children, highlighting the fact that a conceptual analysis of suffering may do little, in the end, to untangle ethical dilemmas in the care of severely ill children.},
}

@article {pmid36793683,
year = {2023},
author = {Korshunova, T and Lundin, K and Malmberg, K and Martynov, A},
title = {Narrowly defined taxa on a global scale: The phylogeny and taxonomy of the genera Catriona and Tenellia (Nudibranchia, Trinchesiidae) favours fine-scale taxonomic differentiation and dissolution of the "lumpers & splitters" dilemma.},
journal = {Evolutionary applications},
volume = {16},
number = {2},
pages = {428-460},
pmid = {36793683},
issn = {1752-4571},
abstract = {By applying morphological and molecular data on two genera of the nudibranch molluscs it is shown that the tension between taxonomic practice and evolutionary processes persists. A review of the related genera Catriona and Tenellia is used to demonstrate that the fine-scale taxonomic differentiation is an important tool in the integration of morphological and molecular data. This is highlighted by the hidden species problem and provides strong argument that the genus must be kept as a maximally narrowly-defined entity. Otherwise, we are forced to compare a highly disparate species under the putatively lumped name "Tenellia". We demonstrate this in the present study by applying a suite of delimitation methods and describing a new species of Tenellia from the Baltic Sea. The new species possesses fine-scale morphological distinguishing features, which were not investigated before. The true, narrowly defined genus Tenellia represents a peculiar taxon with a clearly expressed paedomorphic characters and predominantly brackish-water habitats. The phylogenetically related genus Catriona, of which three new species are described here, clearly demonstrates different features. A lumping decision to call many morphologically and evolutionary different taxa as "Tenellia" will downgrade the taxonomic and phylogenetic resolution of the entire family Trinchesiidae to just a single genus. The dissolution of the dilemma of "lumpers & splitters", which still significantly affects taxonomy, will further help to make systematics a true evolutionary discipline.},
}

@article {pmid36775928,
year = {2023},
author = {Sherratt, E and Kraatz, B},
title = {Multilevel analysis of integration and disparity in the mammalian skull.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpad020},
pmid = {36775928},
issn = {1558-5646},
abstract = {Biological variation is often considered in a scalable hierarchy, e.g., within the individual, within the populations, above the species level. Morphological integration, the concept of covariation among constituent parts of an organism, is also hierarchical; the degree to which these 'modules' covary is a matter of the scale of the study as well as underlying processes driving the covariation. Multilevel analyses of trait covariation are a valuable tool to infer the origins and historical persistence of morphological diversity. Here we investigate concordance in patterns of integration and modularity across three biological levels of variation: within a species, within two genera-level radiations, and among species at the family level. We demonstrate this approach using the skull of mammalian family Leporidae (rabbits and hares), which is morphologically diverse and has a rare-among-mammals functional signal of locomotion adaptation. We tested three alternative hypotheses of modularity; from the most supported we investigated disparity and integration of each module to infer which is most responsible for patterns of cranial variation across these levels, and whether variation is partitioned consistently across levels. We found a common pattern of modularity underlies leporid cranial diversity, though there is inconsistency across levels in each module's disparity and integration. The face module contributes the most to disparity at all levels, which we propose is facilitating evolutionary diversity in this clade. Therefore, the distinctive facial tilt of leporids is an adaptation to locomotory behavior facilitated by a modular system that allows lineages to respond differently to selection pressures.},
}

@article {pmid36765984,
year = {2023},
author = {Fraiture, MA and D'aes, J and Guiderdoni, E and Meunier, AC and Delcourt, T and Hoffman, S and Vandermassen, E and De Keersmaecker, SCJ and Vanneste, K and Roosens, NHC},
title = {Targeted High-Throughput Sequencing Enables the Detection of Single Nucleotide Variations in CRISPR/Cas9 Gene-Edited Organisms.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/foods12030455},
pmid = {36765984},
issn = {2304-8158},
abstract = {Similar to genetically modified organisms (GMOs) produced by classical genetic engineering, gene-edited (GE) organisms and their derived food/feed products commercialized on the European Union market fall within the scope of European Union Directive 2001/18/EC. Consequently, their control in the food/feed chain by GMO enforcement laboratories is required by the competent authorities to guarantee food/feed safety and traceability (2003/1829/EC; 2003/1830/EC). However, their detection is potentially challenging at both the analytical and interpretation levels since this requires methodological approaches that can target and detect a specific single nucleotide variation (SNV) introduced into a GE organism. In this study, we propose a targeted high-throughput sequencing approach, including (i) a prior PCR-based enrichment step to amplify regions of interest, (ii) a sequencing step, and (iii) a data analysis methodology to identify SNVs of interest. To investigate if the performance of this targeted high-throughput sequencing approach is compatible with the performance criteria used in the GMO detection field, several samples containing different percentages of a GE rice line carrying a single adenosine insertion in OsMADS26 were prepared and analyzed. The SNV of interest in samples containing the GE rice line could successfully be detected, both at high and low percentages. No impact related to food processing or to the presence of other crop species was observed. The present proof-of-concept study has allowed us to deliver the first experimental-based evidence indicating that the proposed targeted high-throughput sequencing approach may constitute, in the future, a specific and sensitive tool to support the safety and traceability of the food/feed chain regarding GE plants carrying SNVs.},
}

@article {pmid36761452,
year = {2022},
author = {Sharkey, MJ and Tucker, EM and Baker, A and Smith, MA and Ratnasingham, S and Manjunath, R and Hebert, P and Hallwachs, W and Janzen, D},
title = {More discussion of minimalist species descriptions and clarifying some misconceptions contained in Meier et al. 2021.},
journal = {ZooKeys},
volume = {1110},
number = {},
pages = {135-149},
pmid = {36761452},
issn = {1313-2989},
abstract = {This is a response to a preprint version of "A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science", https://www.biorxiv.org/content/10.1101/2021.04.28.441626v2. Meier et al. strongly criticized Sharkey et al.'s publication in which 403 new species were deliberately minimally described, based primarily on COI barcode sequence data. Here we respond to these criticisms. The following points are made: 1) Sharkey et al. did not equate BINs with species, as demonstrated in several examples in which multiple species were found to be in single BINs. 2) We reiterate that BINs were used as a preliminary sorting tool, just as preliminary morphological identification commonly sorts specimens based on color and size into unit trays; despite BINs and species concepts matching well over 90% of species, this matching does not equate to equality. 3) Consensus barcodes were used only to provide a diagnosis to conform to the rules of the International Code of Zoological Nomenclature just as consensus morphological diagnoses are. The barcode of a holotype is definitive and simply part of its cellular morphology. 4) Minimalist revisions will facilitate and accelerate future taxonomic research, not hinder it. 5) We refute the claim that the BOLD sequences of Plesiocoelusvanachterbergi are pseudogenes and demonstrate that they simply represent a frameshift mutation. 6) We reassert our observation that morphological evidence alone is insufficient to recognize species within species-rich higher taxa and that its usefulness lies in character states that are congruent with molecular data. 7) We show that in the cases in which COI barcodes code for the same amino acids in different putative species, data from morphology, host specificity, and other ecological traits reaffirm their utility as indicators of genetically distinct lineages.},
}

@article {pmid36761113,
year = {2022},
author = {Brunke, AJ},
title = {A world generic revision of Quediini (Coleoptera, Staphylinidae, Staphylininae), part 1. Early diverging Nearctic lineages.},
journal = {ZooKeys},
volume = {1134},
number = {},
pages = {129-170},
pmid = {36761113},
issn = {1313-2989},
abstract = {Several phylogenetically isolated, early diverging lineages of rove beetle tribe Quediini, all endemic to the western Nearctic, have recently been revealed by phylogenomic systematics. These three lineages, currently treated as either Quedius (Raphirus) or Q. (Paraquedius) warrant recognition at the genus level in the ongoing effort to achieve reciprocal monophyly of genera in Quediini. The three lineages were each morphologically studied in detail, with the following results: Paraquedius Casey, stat. res. is re-elevated to genus rank, Quediellus Casey, stat. res. is resurrected from synonymy and redefined, and Iratiquedius gen. nov. is described for the species of the Amabilis and Prostans groups. A morphological diagnosis is provided for each genus at both the global and regional (Nearctic) level. Species level revisions, with keys, are provided for Iratiquedius, Paraquedius, and Quediellus with the following results: Iratiquediusuncifer sp. nov. and Paraquediusmarginicollis sp. nov. are described, Quediellusnanulus Casey is treated as syn. nov. of Quediellusdebilis (Horn), and I.amabilis (Smetana), I.mutator (Smetana), and P.puncticeps (Horn) are substantially redefined. Where possible, CO1 barcode sequence data are integrated with the morphological species concepts used herein and their clusters were found to be congruent.},
}

@article {pmid36761034,
year = {2022},
author = {Boza Espinoza, TE and Kessler, M},
title = {A monograph of the genus Polylepis (Rosaceae).},
journal = {PhytoKeys},
volume = {203},
number = {},
pages = {1-274},
pmid = {36761034},
issn = {1314-2011},
abstract = {We present a monograph of the high Andean tree genus Polylepis (Rosaceae), based on a species concept considering morphological, climatic and biogeographic distinctness as indicators of evolutionary independence. In total, we recognize 45 species of Polylepis, grouped in five sections. Polylepissect.Sericeae is represented by 15 species in four subsections, P.sect.Reticulatae by seven species, P.sect.Subsericantes by three species, P.sect.Australes by two species and P.sect.Incanaee by three subsections with 18 species. We describe seven new species, one from Colombia (P.frontinensis), one from Ecuador (P.simpsoniae) and five from Peru (P.acomayensis, P.fjeldsaoi, P.occidentalis, P.pilosissima and P.sacra). Three species from Peru (P.albicans, P.pallidistigma and P.serrata) are re-instated as valid species. Two taxa from Bolivia (P.incanoides and P.nana) are elevated from subspecies to species rank. The morphology, habitat, distribution, ecology and conservation status of each species are documented. We also provide an identification key to the species of the genus and general introductions on taxonomic history, morphology, evolution, ecology and conservation.},
}

@article {pmid36760461,
year = {2022},
author = {Sklenář, F and Glässnerová, K and Jurjević, Ž and Houbraken, J and Samson, RA and Visagie, CM and Yilmaz, N and Gené, J and Cano, J and Chen, AJ and Nováková, A and Yaguchi, T and Kolařík, M and Hubka, V},
title = {Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability.},
journal = {Studies in mycology},
volume = {102},
number = {},
pages = {53-93},
pmid = {36760461},
issn = {0166-0616},
abstract = {Aspergillus series Versicolores members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (CaM) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (benA, CaM, RPB2, Mcm7, Tsr1). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series Versicolores to four species, namely A. versicolor, A. creber, A. sydowii and A. subversicolor, and the remaining species are synonymized with either A. versicolor or A. creber. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between A. versicolor and A. creber. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied Aspergillus species complexes and other fungal genera. Citation: Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson RA, Visagie CM, Yilmaz N, Gené J, Cano J, Chen AJ, Nováková A, Yaguchi T, Kolařík M, Hubka V (2022). Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Studies in Mycology 102 : 53-93. doi: 10.3114/sim.2022.102.02.},
}

@article {pmid36719249,
year = {2023},
author = {Rivi, V and Benatti, C and Rigillo, G and Blom, JMC},
title = {Invertebrates as models of learning and memory: investigating neural and molecular mechanisms.},
journal = {The Journal of experimental biology},
volume = {226},
number = {3},
pages = {},
doi = {10.1242/jeb.244844},
pmid = {36719249},
issn = {1477-9145},
abstract = {In this Commentary, we shed light on the use of invertebrates as model organisms for understanding the causal and conserved mechanisms of learning and memory. We provide a condensed chronicle of the contribution offered by mollusks to the studies on how and where the nervous system encodes and stores memory and describe the rich cognitive capabilities of some insect species, including attention and concept learning. We also discuss the use of planarians for investigating the dynamics of memory during brain regeneration and highlight the role of stressful stimuli in forming memories. Furthermore, we focus on the increasing evidence that invertebrates display some forms of emotions, which provides new opportunities for unveiling the neural and molecular mechanisms underlying the complex interaction between stress, emotions and cognition. In doing so, we highlight experimental challenges and suggest future directions that we expect the field to take in the coming years, particularly regarding what we, as humans, need to know for preventing and/or delaying memory loss. This article has an associated ECR Spotlight interview with Veronica Rivi.},
}

@article {pmid36716112,
year = {2023},
author = {Manoj, KM},
title = {Murburn posttranslational modifications of proteins: Cellular redox processes and murzyme-mediated metabolo-proteomics.},
journal = {Journal of cellular physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jcp.30954},
pmid = {36716112},
issn = {1097-4652},
abstract = {Murburn concept constitutes the thesis that diffusible reactive species or DRS are obligatorily involved in routine metabolic and physiological activities. Murzymes are defined as biomolecules/proteins that generate/modulate/sustain/utilize DRS. Murburn posttranslational modifications (PTMs) result because murburn/murzyme functionalism is integral to cellular existence. Cells must incorporate the inherently stochastic nature of operations mediated by DRS. Due to the earlier/inertial stigmatic perception that DRS are mere agents of chaos, several such outcomes were either understood as deterministic modulations sponsored by house-keeping enzymes or deemed as unregulated nonenzymatic events resulting out of "oxidative stress". In the current review, I dispel the myths around DRS-functions, and undertake systematic parsing and analyses of murburn modifications of proteins. Although it is impossible to demarcate all PTMs into the classical or murburn modalities, telltale signs of the latter are evident from the relative inaccessibility of the locus, non-specificities and mechanistic details. It is pointed out that while many murburn PTMs may be harmless, some others could have deleterious or beneficial physiological implications. Some details of reversible/irreversible modifications of amino acid residues and cofactors that may be subjected to phosphorylation, halogenation, glycosylation, alkylation/acetylation, hydroxylation/oxidation, etc. are listed, along with citations of select proteins where such modifications have been reported. The contexts of these modifications and their significance in (patho)physiology/aging and therapy are also presented. With more balanced explorations and statistically verified data, a definitive understanding of normal versus pathological contexts of murburn modifications would be obtainable in the future.},
}

@article {pmid36714688,
year = {2022},
author = {Chang, JT and Chao, CT and Nakamura, K and Liu, HL and Luo, MX and Liao, PC},
title = {Corrigendum: Divergence with gene flow and contrasting population size blur the species boundary in Cycas Sect. Asiorientales, as inferred from morphology and RAD-seq data.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1081728},
doi = {10.3389/fpls.2022.1081728},
pmid = {36714688},
issn = {1664-462X},
abstract = {[This corrects the article DOI: 10.3389/fpls.2022.824158.].},
}

@article {pmid36700086,
year = {2021},
author = {Yoshimura, Y and Hamada, A and Augey, Y and Akiyama, M and Sakakibara, Y},
title = {Genomic style: yet another deep-learning approach to characterize bacterial genome sequences.},
journal = {Bioinformatics advances},
volume = {1},
number = {1},
pages = {vbab039},
pmid = {36700086},
issn = {2635-0041},
abstract = {MOTIVATION: Biological sequence classification is the most fundamental task in bioinformatics analysis. For example, in metagenome analysis, binning is a typical type of DNA sequence classification. In order to classify sequences, it is necessary to define sequence features. The k-mer frequency, base composition and alignment-based metrics are commonly used. On the other hand, in the field of image recognition using machine learning, image classification is broadly divided into those based on shape and those based on style. A style matrix was introduced as a method of expressing the style of an image (e.g. color usage and texture).

RESULTS: We propose a novel sequence feature, called genomic style, inspired by image classification approaches, for classifying and clustering DNA sequences. As with the style of images, the DNA sequence is considered to have a genomic style unique to the bacterial species, and the style matrix concept is applied to the DNA sequence. Our main aim is to introduce the genomics style as yet another basic sequence feature for metagenome binning problem in replace of the most commonly used sequence feature k-mer frequency. Performance evaluations showed that our method using a style matrix has the potential for accurate binning when compared with state-of-the-art binning tools based on k-mer frequency.

The source code for the implementation of this genomic style method, along with the dataset for the performance evaluation, is available from https://github.com/friendflower94/binning-style.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.},
}

@article {pmid36696515,
year = {2023},
author = {Le Bras, Z and Bouchet, S and Winkel, LHE},
title = {Sensitive and High-Throughput Analysis of Volatile Organic Species of S, Se, Br, and I at Trace Levels in Water and Atmospheric Samples by Thermal Desorption Coupled to Gas Chromatography and Inductively Coupled Plasma Mass Spectrometry.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.2c04751},
pmid = {36696515},
issn = {1520-6882},
abstract = {Emissions of volatile organic sulfur (S), selenium (Se), bromine (Br), and iodine (I) species from aquatic ecosystems represent an important source of these elements into the atmosphere. Available methods to measure these species are either not sensitive enough or not automated, which hinder a full understanding of species distribution and production mechanisms. Here, we present a sensitive and high-throughput method for the simultaneous and comprehensive quantification of S, Se, Br, and I volatile organic species in atmospheric and aqueous samples using a preconcentration step onto sorbent tubes and subsequent analysis by thermal desorption coupled to gas chromatography and inductively coupled plasma mass spectrometry (TD-GC-ICP-MS). Selected commercially available sorbent tubes, consisting of mixed porous polymer and graphitized black carbon, offered the highest trapping capacity and lowest loss of species when stored at -20 °C for 28 days after sampling. After optimization of the TD-GC-ICP-MS method, absolute detection limits were better than 3.8 pg, 9.1 fg, 313 fg, and 50 fg, respectively, for S, Se, Br, and I species. As a proof of concept, the concentrations of target species were determined in aqueous and continuously collected atmospheric samples during a cruise in the Baltic and North Seas. Moreover, unknown S, Br, and I volatile species were detected in both aqueous and atmospheric samples demonstrating the full potential of the method.},
}

@article {pmid36696419,
year = {2023},
author = {Chen, SW and Zheng, ZY and Mahfut, FB and Yang, Y and Ogino, M and Okada, K and Sato, K and Zhang, W},
title = {Leveraging an advanced simulated moving bed approach to achieve 3-component separation for enhanced impurity removal in a non-affinity cation exchange capture step.},
journal = {PloS one},
volume = {18},
number = {1},
pages = {e0280760},
doi = {10.1371/journal.pone.0280760},
pmid = {36696419},
issn = {1932-6203},
abstract = {One of the key challenges in downstream bioprocessing is to obtain products of high purity in a productive fashion through the effective removal of process and product related impurities. While a classical simulated moving bed (SMB) system operation can typically achieve a 2-component separation between the weakly bound impurities and target species, here we present an advanced SMB approach that can achieve a 3-component separation, including the removal of the strongly bound impurities from the target species. As a proof-of-concept, we demonstrate the enhanced removal of strongly bound host cell proteins (HCP) from the target monoclonal antibody (mAb) through the utilisation of the advanced SMB approach in a non-affinity cation exchange (CEX) capture step. In this way, 1 less polishing step was required to achieve the therapeutic requirements of < 100 ppm HCP and the overall process recovery was increased by ~ 6% compared to the corresponding process that utilised a batch CEX operation. The non-affinity CEX capture platform technology established through the utilisation of the advanced SMB approach presented here can potentially be further applied to address the downstream processing challenges presented by other challenging biotherapeutic modalities to yield a final target product with improved purity and recovery.},
}

@article {pmid36671828,
year = {2023},
author = {Bateman, RM and Rudall, PJ},
title = {Morphological Continua Make Poor Species: Genus-Wide Morphometric Survey of the European Bee Orchids (Ophrys L.).},
journal = {Biology},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/biology12010136},
pmid = {36671828},
issn = {2079-7737},
abstract = {Despite (or perhaps because of) intensive multidisciplinary research, opinions on the optimal number of species recognised within the Eurasian orchid genus Ophrys range from nine to at least 400. The lower figure of nine macrospecies is based primarily on seeking small but reliable discontinuities in DNA 'barcode' regions, an approach subsequently reinforced and finessed via high-throughput sequencing studies. The upper figure of ca. 400 microspecies reflects the morphological authoritarianism of traditional taxonomy combined with belief in extreme pollinator specificity caused by reliance on pollination through pseudo-copulation, enacted by bees and wasps. Groupings of microspecies that are less inclusive than macrospecies are termed mesospecies. Herein, we present multivariate morphometric analyses based on 51 characters scored for 457 individual plants that together span the full morphological and molecular diversity within the genus Ophrys, encompassing 113 named microspecies that collectively represent all 29 mesospecies and all nine macrospecies. We critique our preferred morphometric approach of accumulating heterogeneous data and analysing them primarily using principal coordinates, noting that our conclusions would have been strengthened by even greater sampling and the inclusion of data describing pseudo-pheromone cocktails. Morphological variation within Ophrys proved to be exceptionally multidimensional, lacking strong directional trends. Multivariate clustering of plants according to prior taxonomy was typically weak, irrespective of whether it was assessed at the level of macrospecies, mesospecies or microspecies; considerable morphological overlap was evident even between subsets of the molecularly differentiable macrospecies. Characters supporting genuine taxonomic distinctions were often sufficiently subtle that they were masked by greater and more positively correlated variation that reflected strong contrasts in flower size, tepal colour or, less often, plant size. Individual macrospecies appear to represent morphological continua, within which taxonomic divisions are likely to prove arbitrary if based exclusively on morphological criteria and adequately sampled across their geographic range. It remains unclear how much of the mosaic of subtle character variation among the microspecies reflects genetic versus epigenetic or non-genetic influences and what proportion of any contrasts observed in gene frequencies can be attributed to the adaptive microevolution that is widely considered to dictate speciation in the genus. Moreover, supplementing weak morphological criteria with extrinsic criteria, typically by imposing constraints on geographic location and/or supposed pollinator preference, assumes rather than demonstrates the presence of even the weakest of species boundaries. Overall, it is clear that entities in Ophrys below the level of macrospecies have insufficiently structured variation, either phenotypic or genotypic, to be resolved into discrete, self-circumscribing ("natural") entities that can legitimately be equated with species as delimited within other less specialised plant genera. Our search for a non-arbitrary (meso)species concept competent to circumscribe an intermediate number of species has so far proven unsuccessful.},
}

@article {pmid36657627,
year = {2023},
author = {Dai, C and Feng, P},
title = {Multiple concordant cytonuclear divergences and potential hybrid speciation within a species complex in Asia.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {107709},
doi = {10.1016/j.ympev.2023.107709},
pmid = {36657627},
issn = {1095-9513},
abstract = {Various environmental factors impact the distribution, population structure, demography and evolutionary trajectory of a bird species, leading to genetic and morphological divergences between populations across its distribution. The Paradoxornis webbianus species complex is found throughout much of East Asia, where its geographically distinct populations exhibit dramatic morphological variation. This has resulted in a hotly debated taxonomy. This study intended to identify genetic divergence patterns and their underlying contributing factors for this species complex. We collected 243 birds, whose data was combined with those available in GenBank to perform phylogeographic analyses using one mitochondrial and six nuclear loci. Six mitochondrial clades were observed in the species complex, while individual-based Bayesian clustering using nuclear markers showed multiple congruent breaks. Overall, the six molecular lineages could be recognized as independent species under the lineage species concept in view of genetic divergence, clade-specific morphological changes and distribution: P. webbianus, P. w. bulomachus, P. alphonsianus, P. a. ganluoensis, P. brunneus brunneus and P. b. ricketti. The estimated divergence times range from 0.46 to 3.36 million years ago, suggesting it was likely impacted by paleoclimatic changes. Interestingly, P. alphonsianus carries two divergent mitochondrial lineages shared with P. webbianus and P. a. ganluoensis, respectively, and analyses based on nuclear loci found a similar pattern. We discussed the various hypotheses for this pattern and argued that P. alphonsianus was likely the result of hybridization between P. webbianus and P. a. ganluoensis. Further data on genome, transcriptome and breeding ecology are needed to address the hypothesis of hybrid speciation and its underlying mechanisms.},
}

@article {pmid36655041,
year = {2023},
author = {Kim, JG and Cho, K and Yoon, SM and Lee, J},
title = {Taxonomic review of the genus Stenocaris Sars (Copepoda, Harpacticoida, Cylindropsyllidae), with (re)descriptions of two Stenocaris species from the Far East.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e14623},
pmid = {36655041},
issn = {2167-8359},
abstract = {The taxonomic concept of the genus Stenocaris Sars, 1909 is uncertain because none of the synapomorphies for the species of Stenocaris are defined. Detailed comparison of previous records of Stenocaris minor (T. Scott, 1892) from different localities reveals that this species represents a species complex composed of two species, S. minor s. str. and S. minor sensu Cottarelli & Venanzetti, 1989. Because the latter species has fundamental differences in the nature of the fifth leg in females and the sexual dimorphism of the second leg in males, we propose a new species for S. minor sensu Cottarelli & Venanzetti, 1989, S. figaroloensis sp. nov. We also suggest that S. minor sensu Apostolov, 1971, S. minor sensu Marinov, 1971, and S. minor sensu Apostolov & Marinov, 1988 from the Black Sea and S. minor sensu Wilson, 1932 from North America should be relegated to species inquirenda in the genus. Taxonomic review of the morphology of all Stenocaris species indicated that the generic concept must be restricted to accommodate S. minor s. str., S. gracilis Sars, 1909, S. intermedia Itô, 1972, S. figaroloensis sp. nov., and the South Korean new species, S. marcida sp. nov., based on the synapomorphic condition of the confluent fifth leg in males. As a result of our analysis, two Stenocaris species, S. baltica Arlt, 1983 and S. pygmaea Noodt, 1955, are transferred to the genus Vermicaris Kornev & Chertoprud, 2008 as V. baltica (Arlt, 1983) comb. nov. and V. pygmaea (Noodt, 1955) comb. nov. based on the synapomorphic characters of a reduced condition of the second and fifth legs. Additionally, S. arenicola Wilson, 1932 and S. kliei (Kunz, 1938) are allocated to a new genus, Huysicaris gen. nov., mainly characterized by obvious caudal rami with a recurved dorsal spinous process and convex inner margins, as H. arenicola (Wilson, 1932) comb. nov. and H. kliei (Kunz, 1938) comb. nov. A marine interstitial harpacticoid collected from the subtidal substrate off Dok-do Island in the East Sea of South Korea is proposed as S. marcida sp. nov. and the distribution of S. intermedia, originally known from its type locality in Japanese waters only, is extended to the East Sea of Korea and Russia. We provide their detailed descriptions and illustrations and discuss the morphological characters supporting their identities.},
}

@article {pmid36622661,
year = {2022},
author = {Bolnick, DI and Hund, AK and Nosil, P and Peng, F and Ravinet, M and Stankowski, S and Subramanian, S and Wolf, JBW and Yukilevich, R},
title = {A multivariate view of the speciation continuum.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpac004},
pmid = {36622661},
issn = {1558-5646},
support = {/ERC_/European Research Council/International ; },
abstract = {The concept of a "speciation continuum" has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.},
}

@article {pmid36620432,
year = {2021},
author = {Hajdari, A and Pulaj, B and Schmiderer, C and Mala, X and Wilson, B and Lluga-Rizani, K and Mustafa, B},
title = {A phylogenetic analysis of the wild Tulipa species (Liliaceae) of Kosovo based on plastid and nuclear DNA sequence.},
journal = {Advanced genetics (Hoboken, N.J.)},
volume = {2},
number = {3},
pages = {e202100016},
pmid = {36620432},
issn = {2641-6573},
abstract = {In Kosovo, the genus Tulipa is represented by eight taxa, most of which form a species complex surrounding Tulipa scardica. To investigate the phylogenetic relationship of these Tulipa species a Bayesian analysis was undertaken using the ITS nuclear marker and trnL-trnF, rbcL and psbA-trnH plastid markers. The resulting phylogenetic trees show that Kosovarian Tulipa species consistently group into two main clades, the subgenera Eriostemones and Tulipa. Furthermore, our analyses provide some evidence that the subspecies of Tulipa sylvestris are genetically distinguishable, however not significantly enough to support their reclassification as species. In contrast, the markers provide some novel information to reassess the species concepts of the T. scardica complex. Our data provide support for the synonymisation of Tulipa luanica and Tulipa kosovarica under the species Tulipa serbica. Resolution and sampling limitations hinder any concrete conclusion about whether Tulipa albanica and T. scardica are true species, yet our data do provide some support that these are unique taxa and therefore should continue to be treated as such until further clarification. Overall, our work shows that genetic data will be important in determining species concepts in this genus, however, even with a molecular perspective pulling apart closely related taxa can be extremely challenging.},
}

@article {pmid36585846,
year = {2022},
author = {Cobo-Simón, M and Hart, R and Ochman, H},
title = {Escherichia coli: What is and Which are?.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msac273},
pmid = {36585846},
issn = {1537-1719},
abstract = {Escherichia coli have served as important model organisms for over a century-used to elucidate key aspects of genetics, evolution, molecular biology, and pathogenesis. However, defining which strains actually belong to this species is erratic and unstable due to shifts in the characters and criteria used to distinguish bacterial species. Additionally, many isolates designated as E. coli are genetically more closely related to strains of Shigella than to other E. coli, creating a situation in which the entire genus of Shigella and its four species are encompassed within the single species E. coli. We evaluated all complete genomes assigned to E. coli and its closest relatives according to the Biological Species Concept (BSC), using evidence of reproductive isolation and gene flow (i.e., homologous recombination in the case of asexual bacteria) to ascertain species boundaries. The BSC establishes a uniform, consistent and objective principle that allows species-level classification across all Domains of Life and does not rely on either phenotypic or genotypic similarity to a defined type-specimen for species membership. Analyzing a total of 1887 sequenced genomes and comparing our results to other genome-based classification methods, we found few barriers to gene flow among the strains, clades, phylogroups or species within E. coli and Shigella. Due to the utility in recognizing which strains constitute a true biological species, we designate genomes that form a genetic cohesive group as members of E. coliBIO.},
}

@article {pmid36558823,
year = {2022},
author = {Carrillo-Bilbao, G and Navarro, JC and Martin-Solano, S and Chávez-Larrea, MA and Cholota-Iza, C and Saegerman, C},
title = {First Molecular Identification of Trypanosomes and Absence of Babesia sp. DNA in Faeces of Non-Human Primates in the Ecuadorian Amazon.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
pmid = {36558823},
issn = {2076-0817},
abstract = {Trypanosomes are a group of pathogens distributed in the continents of Africa, America, Asia and Europe, and they affect all vertebrates including the neotropical primate group. Information about the trypanosome's diversity, phylogeny, ecology and pathology in non-human primates (NHPs) from the neotropical region is scarce. The objective of the study was to identify Trypanosoma and Babesia molecularly in NHPs under the phylogenetic species concept. We extracted DNA from a total of 76 faecal samples collected between 2019 and 2021, from a total of 11 non-human primate species of which 46 are from captive NHPs and 30 are free-living NHPs in the Western Amazon region of Ecuador. We did not detect DNA of Babesia sp. by polymerase chain reaction test in any of the faecal samples. However, the nested-PCR-based method revealed Trypanosoma parasites by ITS gene amplification in two faecal samples; one for the species Leontocebus lagonotus (from the captive population) and a second one for Cebus albifrons (from the free-ranging population). Maximum parsimony and likelihood methods with the Kimura2+G+I model inferred the evolutionary history of the two records, which showed an evolutionary relationship with the genus Trypanosoma. Two sequences are monophyletic with Trypanosoma. However, the number of sequences available in GenBank for their species identification is limited. The two samples present different molecular identifications and evolutionary origins in the tree topology. We are most likely referring to two different species, and two different localities of infection. We suggest that health management protocols should be implemented to prevent the transmission of blood-borne pathogens such as Trypanosoma sp. among captive populations. In addition, these protocols also protect the personnel of wildlife rehabilitation centers working in close proximity to NHPs and vice versa.},
}

@article {pmid36511814,
year = {2022},
author = {Deepak, V and Gower, DJ and Cooper, N},
title = {Diet and habit explain head-shape convergences in natricine snakes.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jeb.14139},
pmid = {36511814},
issn = {1420-9101},
abstract = {The concept of ecomorphs, whereby species with similar ecologies have similar phenotypes regardless of their phylogenetic relatedness, is often central to discussions regarding the relationship between ecology and phenotype. However, some aspects of the concept have been questioned, and sometimes species have been grouped as ecomorphs based on phenotypic similarity without demonstrating ecological similarity. Within snakes, similar head shapes have convergently evolved in species living in comparable environments and/or with similar diets. Therefore, ecomorphs could exist in some snake lineages, but this assertion has rarely been tested for a wide-ranging group within a single framework. Natricine snakes (Natricinae) are ecomorphologically diverse and currently distributed in Asia, Africa, Europe and north-central America. They are primarily semiaquatic or ground-dwelling terrestrial snakes, but some are aquatic, burrowing or aquatic and burrowing in habit and may be generalist or specialist in diet. Thus, natricines present an interesting system to test whether snakes from different major habit categories represent ecomorphs. We quantify morphological similarity and disparity in head shape among 191 of the ca. 250 currently recognized natricine species and apply phylogenetic comparative methods to test for convergence. Natricine head shape is largely correlated with habit, but in some burrowers is better explained by dietary specialism. Convergence in head shape is especially strong for aquatic burrowing, semiaquatic and terrestrial ecomorphs and less strong for aquatic and burrowing ecomorphs. The ecomorph concept is useful for understanding natricine diversity and evolution, though would benefit from further refinement, especially for aquatic and burrowing taxa.},
}

@article {pmid36502470,
year = {2022},
author = {Manoj, KM and Gideon, DA and Bazhin, NM and Tamagawa, H and Nirusimhan, V and Kavdia, M and Jaeken, L},
title = {Na,K-ATPase: A murzyme facilitating thermodynamic equilibriums at the membrane-interface.},
journal = {Journal of cellular physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jcp.30925},
pmid = {36502470},
issn = {1097-4652},
abstract = {The redox metabolic paradigm of murburn concept advocates that diffusible reactive species (DRS, particularly oxygen-centric radicals) are mainstays of physiology, and not mere pathological manifestations. The murburn purview of cellular function also integrates the essential principles of bioenergetics, thermogenesis, homeostasis, electrophysiology, and coherence. In this context, any enzyme that generates/modulates/utilizes/sustains DRS functionality is called a murzyme. We have demonstrated that several water-soluble (peroxidases, lactate dehydrogenase, hemogoblin, etc.) and membrane-embedded (Complexes I-V in mitochondria, Photosystems I/II in chloroplasts, rhodopsin/transducin in rod cells, etc.) proteins serve as murzymes. The membrane protein of Na,K-ATPase (NKA, also known as sodium-potassium pump) is the focus of this article, owing to its centrality in neuro-cardio-musculo electrophysiology. Herein, via a series of critical queries starting from the geometric/spatio-temporal considerations of diffusion/mass transfer of solutes in cells to an update on structural/distributional features of NKA in diverse cellular systems, and from various mechanistic aspects of ion-transport (thermodynamics, osmoregulation, evolutionary dictates, etc.) to assays/explanations of inhibitory principles like cardiotonic steroids (CTS), we first highlight some unresolved problems in the field. Thereafter, we propose and apply a minimalist murburn model of trans-membrane ion-differentiation by NKA to address the physiological inhibitory effects of trans-dermal peptide, lithium ion, volatile anesthetics, confirmed interfacial DRS + proton modulators like nitrophenolics and unsaturated fatty acid, and the diverse classes of molecules like CTS, arginine, oximes, etc. These explanations find a pan-systemic connectivity with the inhibitions/uncouplings of other membrane proteins in cells.},
}

@article {pmid36470606,
year = {2022},
author = {Tester, PA and Litaker, RW and Soler-Onís, E and Fernández-Zabala, J and Berdalet, E},
title = {Using artificial substrates to quantify Gambierdiscus and other toxic benthic dinoflagellates for monitoring purposes.},
journal = {Harmful algae},
volume = {120},
number = {},
pages = {102351},
doi = {10.1016/j.hal.2022.102351},
pmid = {36470606},
issn = {1878-1470},
mesh = {*Dinoflagellida ; Ecosystem ; Biomass ; },
abstract = {Collecting methods generally used to determine cell abundances of toxic benthic dinoflagellates (BHAB) use cells dislodged from either macrophytes or artificial substrates. This article compares the advantages of the macrophyte and artificial substrate methods and discusses which method is more appropriate for use in monitoring programs that focus on toxic BHAB species identification and quantification. The concept of benthic dinoflagellate "preference" for specific macrophytes was also reviewed. Examination of data from 75 field studies showed macrophytes with higher surface area per unit biomass harbored higher concentrations of Gambierdiscus cells. There was no definitive evidence that cells were actively selecting one macrophyte over another. This observation supports the use of artificial substrates (AS) as a means of assessing cell abundances in complex habitats because cell counts are normalized to a standardized surface area, not macrophyte biomass. The artificial substrate method represents the most robust approach, currently available, for collecting toxic, benthic dinoflagellates for a cell-based early warning system.},
}

*Dinoflagellida
Ecosystem
Biomass

@article {pmid36465531,
year = {2022},
author = {Hohenwallner, K and Troppmair, N and Panzenboeck, L and Kasper, C and El Abiead, Y and Koellensperger, G and Lamp, LM and Hartler, J and Egger, D and Rampler, E},
title = {Decoding Distinct Ganglioside Patterns of Native and Differentiated Mesenchymal Stem Cells by a Novel Glycolipidomics Profiling Strategy.},
journal = {JACS Au},
volume = {2},
number = {11},
pages = {2466-2480},
pmid = {36465531},
issn = {2691-3704},
abstract = {Gangliosides are an indispensable glycolipid class concentrated on cell surfaces with a critical role in stem cell differentiation. Nonetheless, owing to the lack of suitable methods for scalable analysis covering the full scope of ganglioside molecular diversity, their mechanistic properties in signaling and differentiation remain undiscovered to a large extent. This work introduces a sensitive and comprehensive ganglioside assay based on liquid chromatography, high-resolution mass spectrometry, and multistage fragmentation. Complemented by an open-source data evaluation workflow, we provide automated in-depth lipid species-level and molecular species-level annotation based on decision rule sets for all major ganglioside classes. Compared to conventional state-of-the-art methods, the presented ganglioside assay offers (1) increased sensitivity, (2) superior structural elucidation, and (3) the possibility to detect novel ganglioside species. A major reason for the highly improved sensitivity is the optimized spectral readout based on the unique capability of two parallelizable mass analyzers for multistage fragmentation. We demonstrated the high-throughput universal capability of our novel analytical strategy by identifying 254 ganglioside species. As a proof of concept, 137 unique gangliosides were annotated in native and differentiated human mesenchymal stem cells including 78 potential cell-state-specific markers and 38 previously unreported gangliosides. A general increase of the ganglioside numbers upon differentiation was observed as well as cell-state-specific clustering based on the ganglioside species patterns. The combination of the developed glycolipidomics assay with the extended automated annotation tool enables comprehensive in-depth ganglioside characterization as shown on biological samples of interest. Our results suggest ganglioside patterns as a promising quality control tool for stem cells and their differentiation products. Additionally, we believe that our analytical workflow paves the way for probing glycolipid-based biochemical processes shedding light on the enigmatic processes of gangliosides and glycolipids in general.},
}

@article {pmid36461060,
year = {2022},
author = {Alcántara-Salinas, G and Hunn, ES and Ibáñez-Bravo, ME and Aldasoro-Maya, EM and Flores-Hernández, N and Pérez-Sato, JA and Real-Luna, N and Trujillo, RAM and Lope-Alzina, D and Rivera-Hernández, JE},
title = {Bird conservation status and cultural values in Indigenous Mexican communities: towards a bioculturally informed conservation policy.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {18},
number = {1},
pages = {69},
pmid = {36461060},
issn = {1746-4269},
mesh = {Humans ; Animals ; Mexico ; *Birds ; *Policy ; Biodiversity ; Endangered Species ; },
abstract = {BACKGROUND: We summarize comparative ethnoornithological data for ten Mexican Indigenous communities, an initial step towards a comprehensive archive of the avian diversity conserved within Mexico's Indigenous territories. We do so by counting highlighted species listed for bird conservation status on widely recognized "red lists" and their cultural value to build biocultural policies in Mexico for their conservation.

METHODS: Indigenous bird names for each study site were determined to allow calculation of the "Scientific Species Recognition Ratio" (SSRR) for high cultural value birds obtained across communities. This demonstrated patterns of cultural prominence. A matrix of 1275 bird versus seven biocultural values was analysed using a correspondence analysis (InfoStat/L-v2020) to illustrate patterns of concordance between bird conservation status and cultural values.

RESULTS: This paper contributes to quantitative and qualitative data on the role of ethnoornithology and ethnobiology in biocultural conservation. The areas studied provide refugia for almost 70% of the Mexican avifauna within a fraction of 1% of the national territory, that is 769 bird species recorded for all communities. The global correspondence of regions of biological and linguistic megadiversity is well established, while linguistic diversity is widely accepted as a good proxy for general cultural diversity. Our correspondence analysis explained 81.55% of the variation, indicating a strong relation between cultural importance and bird conservation status. We propose three main categories to establish a bioculturally informed public policy in Mexico for the conservation of what we described as high, medium, and bioculturally prominent bird species all include cultural value in any material or symbolic aspect. High are those species appearing on any threatened list, but also considered in any endemic status, while medium include threatened listed species. The last category included species not necessarily listed on any threat list, but with a wide range of social and cultural uses. We suggest that the concept might be extended to other species of biocultural importance.

CONCLUSIONS: We argue that bird conservation policies should be biocultural, that is they should recognize birds of cultural value on a par with bird species "of special interest" because they are most critical for biodiversity conservation. The desire of local people to protect their traditional community lands and livelihoods can be an effective biodiversity conservation strategy, which should be recognized in national biocultural policies.},
}

Humans
Animals
Mexico
*Birds
*Policy
Biodiversity
Endangered Species

@article {pmid36449568,
year = {2022},
author = {Stagg, O and Morris, K and Townsend, LT and Kvashnina, KO and Baker, ML and Dempsey, RL and Abrahamsen-Mills, L and Shaw, S},
title = {Sulfidation and Reoxidation of U(VI)-Incorporated Goethite: Implications for U Retention during Sub-Surface Redox Cycling.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.2c05314},
pmid = {36449568},
issn = {1520-5851},
abstract = {Over 60 years of nuclear activity have resulted in a global legacy of contaminated land and radioactive waste. Uranium (U) is a significant component of this legacy and is present in radioactive wastes and at many contaminated sites. U-incorporated iron (oxyhydr)oxides may provide a long-term barrier to U migration in the environment. However, reductive dissolution of iron (oxyhydr)oxides can occur on reaction with aqueous sulfide (sulfidation), a common environmental species, due to the microbial reduction of sulfate. In this work, U(VI)-goethite was initially reacted with aqueous sulfide, followed by a reoxidation reaction, to further understand the long-term fate of U species under fluctuating environmental conditions. Over the first day of sulfidation, a transient release of aqueous U was observed, likely due to intermediate uranyl(VI)-persulfide species. Despite this, overall U was retained in the solid phase, with the formation of nanocrystalline U(IV)O2 in the sulfidized system along with a persistent U(V) component. On reoxidation, U was associated with an iron (oxyhydr)oxide phase either as an adsorbed uranyl (approximately 65%) or an incorporated U (35%) species. These findings support the overarching concept of iron (oxyhydr)oxides acting as a barrier to U migration in the environment, even under fluctuating redox conditions.},
}

@article {pmid36447513,
year = {2022},
author = {Stork, S and Jalinsky, J and Neiman, M},
title = {Evidence for stronger discrimination between conspecific and heterospecific mating partners in sexual vs. asexual female freshwater snails.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14470},
pmid = {36447513},
issn = {2167-8359},
abstract = {Once-useful traits that no longer contribute to fitness tend to decay over time. Here, we address whether the expression of mating-related traits that increase the fitness of sexually reproducing individuals but are likely less useful or even costly to asexual counterparts seems to exhibit decay in the latter. Potamopyrgus antipodarum is a New Zealand freshwater snail characterized by repeated transitions from sexual to asexual reproduction. The frequent coexistence of sexual and asexual lineages makes P. antipodarum an excellent model for the study of mating-related trait loss. Under the presumption (inherent in the Biological Species Concept) that failure to discriminate between conspecific and heterospecific mating partners represents a poor mate choice, we used a mating choice assay including sexual and asexual P. antipodarum females and conspecific (presumed better choice) vs. heterospecific (presumed worse choice) males to evaluate the loss of behavioral traits related to sexual reproduction. We found that sexual females engaged in mating behaviors with conspecific mating partners more frequently and for a greater duration than with heterospecific mating partners. By contrast, asexual females mated at similar frequency and duration as sexual females, but did not mate more often or for longer duration with conspecific vs. heterospecific males. While further confirmation will require inclusion of a more diverse array of sexual and asexual lineages, these results are consistent with a scenario where selection acting to maintain effective mate discrimination in asexual P. antipodarum is weak or ineffective relative to sexual females and, thus, where asexual reproduction is associated with the evolutionary decay of mating-related traits in this system.},
}

@article {pmid36398197,
year = {2022},
author = {Bergmann, A and Burchardt, LS and Wimmer, B and Kugelschafter, K and Gloza-Rausch, F and Knörnschild, M},
title = {The soundscape of swarming: Proof of concept for a noninvasive acoustic species identification of swarming Myotis bats.},
journal = {Ecology and evolution},
volume = {12},
number = {11},
pages = {e9439},
pmid = {36398197},
issn = {2045-7758},
abstract = {Bats emit echolocation calls to orientate in their predominantly dark environment. Recording of species-specific calls can facilitate species identification, especially when mist netting is not feasible. However, some taxa, such as Myotis bats can be hard to distinguish acoustically. In crowded situations where calls of many individuals overlap, the subtle differences between species are additionally attenuated. Here, we sought to noninvasively study the phenology of Myotis bats during autumn swarming at a prominent hibernaculum. To do so, we recorded sequences of overlapping echolocation calls (N = 564) during nights of high swarming activity and extracted spectral parameters (peak frequency, start frequency, spectral centroid) and linear frequency cepstral coefficients (LFCCs), which additionally encompass the timbre (vocal "color") of calls. We used this parameter combination in a stepwise discriminant function analysis (DFA) to classify the call sequences to species level. A set of previously identified call sequences of single flying Myotis daubentonii and Myotis nattereri, the most common species at our study site, functioned as a training set for the DFA. 90.2% of the call sequences could be assigned to either M. daubentonii or M. nattereri, indicating the predominantly swarming species at the time of recording. We verified our results by correctly classifying the second set of previously identified call sequences with an accuracy of 100%. In addition, our acoustic species classification corresponds well to the existing knowledge on swarming phenology at the hibernaculum. Moreover, we successfully classified call sequences from a different hibernaculum to species level and verified our classification results by capturing swarming bats while we recorded them. Our findings provide a proof of concept for a new noninvasive acoustic monitoring technique that analyses "swarming soundscapes" by combining classical acoustic parameters and LFCCs, instead of analyzing single calls. Our approach for species identification is especially beneficial in situations with multiple calling individuals, such as autumn swarming.},
}

@article {pmid36349407,
year = {2022},
author = {Hu, J and Vandenkoornhuyse, P and Khalfallah, F and Causse-Védrines, R and Mony, C},
title = {Ecological corridors homogenize plant root endospheric mycobiota.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.18606},
pmid = {36349407},
issn = {1469-8137},
abstract = {Ecological corridors promote species coexistence in fragmented habitats where dispersal limits species fluxes. The corridor concept was developed and investigated with macroorganisms in mind while microorganisms, the invisible majority of biodiversity, were disregarded. We analyzed the effect of corridors on the dynamics of endospheric fungal assemblages associated with plant roots at the scale of one meter over two years (i.e. at five time points) by combining an experimental corridor-mesocosm with high-throughput amplicon sequencing. We show that the plant root endospheric mycobiota was sensitive to corridor effects when the corridors were set up at a small spatial scale. The endospheric mycobiota of connected plants had higher species richness, lower beta-diversity, and more deterministic assembly than the mycobiota of isolated plants. These effects became more pronounced with the development of host plants. Biotic corridors composed of host plants may thus play a key role in the spatial dynamics of microbial communities and may influence microbial diversity and related ecological functions.},
}

@article {pmid36324542,
year = {2022},
author = {Portillo, JTDM and Barbo, FE and Sawaya, RJ},
title = {Climatic niche breadths of the Atlantic Forest snakes do not increase with increasing latitude.},
journal = {Current zoology},
volume = {68},
number = {5},
pages = {535-540},
pmid = {36324542},
issn = {1674-5507},
abstract = {The climatic niche is a central concept for understanding species distribution, with current and past climate interpreted as strong drivers of present and historical-geographical ranges. Our aim is to understand whether Atlantic Forest snakes follow the general geographical pattern of increasing species climatic niche breadths with increasing latitude. We also tested if there is a tradeoff between temperature and precipitation niche breadths of species in order to understand if species with larger breadths of one niche dimension have stronger dispersal constraints by the other due to narrower niche breadths. Niche breadths were calculated by the subtraction of maximal and minimal values of temperature and precipitation across species ranges. We implemented Phylogenetic Generalized Least Squares to measure the relationship between temperature and precipitation niche breadths and latitude. We also tested phylogenetic signals by Lambda statistics to analyze the degree of phylogenetic niche conservatism to both niche dimensions. Temperature niche breadths were not related to latitude. Precipitation niche breadths decreased with increasing latitude and presented a high phylogenetic signal, that is, significant phylogenetic niche conservatism. We rejected the tradeoff hypotheses of temperature and precipitation niche breadths. Our results also indicate that precipitation should be an important ecological constraint affecting the geographical distribution of snake lineages across the South American Atlantic Forest. We then provide a general view of how phylogenetic niche conservatism could impact the patterns of latitudinal variation of climatic niches across this biodiversity hotspot.},
}

@article {pmid36307232,
year = {2022},
author = {Berns, GS},
title = {Deciphering the dog brain with fMRI.},
journal = {Trends in neurosciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tins.2022.10.005},
pmid = {36307232},
issn = {1878-108X},
abstract = {fMRI has been increasingly used to study brain function in domestic dogs trained to lie still in MRI scanners. These studies highlight both similarities and differences between dogs and humans when presented with the same stimuli, raising intriguing questions about the concept of functional homologies in a coevolved species that shares the human environment.},
}

@article {pmid36294662,
year = {2022},
author = {Peçanha, PM and Peçanha-Pietrobom, PM and Grão-Velloso, TR and Rosa Júnior, M and Falqueto, A and Gonçalves, SS},
title = {Paracoccidioidomycosis: What We Know and What Is New in Epidemiology, Diagnosis, and Treatment.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {10},
pages = {},
pmid = {36294662},
issn = {2309-608X},
abstract = {Paracoccidioidomycosis (PCM) is a systemic mycosis endemic to Latin America caused by thermodimorphic fungi of the genus Paracoccidioides. In the last two decades, enhanced understanding of the phylogenetic species concept and molecular variations has led to changes in this genus' taxonomic classification. Although the impact of the new species on clinical presentation and treatment remains unclear, they can influence diagnosis when serological methods are employed. Further, although the infection is usually acquired in rural areas, the symptoms may manifest years or decades later when the patient might be living in the city or even in another country outside the endemic region. Brazil accounts for 80% of PCM cases worldwide, and its incidence is rising in the northern part of the country (Amazon region), owing to new settlements and deforestation, whereas it is decreasing in the south, owing to agriculture mechanization and urbanization. Clusters of the acute/subacute form are also emerging in areas with major human intervention and climate change. Advances in diagnostic methods (molecular and immunological techniques and biomarkers) remain scarce, and even the reference center's diagnostics are based mainly on direct microscopic examination. Classical imaging findings in the lungs include interstitial bilateral infiltrates, and eventually, enlargement or calcification of adrenals and intraparenchymal central nervous system lesions are also present. Besides itraconazole, cotrimoxazole, and amphotericin B, new azoles may be an alternative when the previous ones are not tolerated, although few studies have investigated their use in treating PCM.},
}

@article {pmid36290373,
year = {2022},
author = {Ali, F and Khan, N and Rahmonov, O},
title = {Ecosystem Services and Linkages of Naturally Managed Monotheca buxifolia (Falc.) A. DC. Forests with Local Communities across Contiguous Mountainous Ranges in Pakistan.},
journal = {Biology},
volume = {11},
number = {10},
pages = {},
pmid = {36290373},
issn = {2079-7737},
abstract = {The local community of the Suleiman and Hindukush mountain systems in Pakistan has largely depended on the natural resources of the environment since ancient times. The ecosystem of these regions is under huge pressure due to a lack of awareness and the uncontrolled interference of communal, commercial, security, political, and ecological conditions. The present study was designed to illuminate the link between mountain society and the consumption of the benefits from Monotheca phytocoenoses using the ecosystem services concept from the sphere of the socio-ecological system to cultural relations. The use of this approach is very important due to the visible role and dominant status of Monotheca vegetation within the ecological system of the region. M. buxifolia is strongly connected with both local and cultural traditions and is counted as a key species, particularly for high-mountain inhabitants. We report that Monotheca phytocoenoses provide several services including shelter, food, fodder, medicines, and wood, etc., to the indigenous community and is highly valued in the local culture because of the poor economic condition of the society. The concept of this cultural keystone species is crucial for understanding ecosystem services and must be considered for the protection and conservation of these habitats. The results of field and social studies have shown that the stable maintenance of Monotheca phytocoenosis forests ensures the existence of key species as the most important providers of ecosystem services, e.g., provisioning, regulation, maintenance and cultural services, indicating the close relations between society and the protection of mountain areas. According to the results obtained, the mountains community of the studied area believes that tree species like M. buxifolia, F. palmata, O. ferruginea, P. granatum, A. modesta, J. regia, etc., are the key components contributing to the function of both the mountain ecosystem and communities' well-being. This approach will be extremely useful for ensuring an inclusive management of the socio-ecological system of the Hindukush and Suleiman Mountain ranges of Pakistan.},
}

@article {pmid36273538,
year = {2023},
author = {Lamattina, D and Salomón, OD},
title = {Triatoma infestans, to be or not to be autogenic?.},
journal = {Acta tropica},
volume = {237},
number = {},
pages = {106727},
doi = {10.1016/j.actatropica.2022.106727},
pmid = {36273538},
issn = {1873-6254},
mesh = {Animals ; Female ; *Triatoma ; *Triatominae ; Nymph ; Feeding Behavior ; Nutritional Status ; },
abstract = {Autogeny, the ability to develop eggs without a meal in the adult stage, has been described in several groups of arthropods, especially hematophagous Diptera Nematocera. In obligate hematophagous hemimetabolous insects that feed on blood in all their instars, such as Triatominae, this concept gives rise to species with apparently facultative autogeny, such as Triatoma infestans. Generalized linear models were applied to explain egg production by the predictor variables molting weight as a proxy of nymphal accumulated reserves and digested blood weight as an indicator of adult reserve in fasted, incompletely fed and engorged at repletion females. The relationship between these indicators of nutritional status and egg development turned out to be a continuous function in which, with molting weights greater than 254 mg, the insects are autogenic, but for the first batch of eggs with molting weights between 132 and 253 mg, they require one adult meal of at least 202 mg, and with molting weights less than 131 mg at least two meals are required. Both molting weight and blood intake could determine oocyte production in an additive manner, thus the concept of autogeny as a switch on-off phenomenon is not directly applicable to Triatominae. Nevertheless, autogenic ability would allow Triatominae with relatively long cycles to accelerate population growth under favorable or low competition conditions during colonization or recovery after a control intervention.},
}

Animals
Female
*Triatoma
*Triatominae
Nymph
Feeding Behavior
Nutritional Status

@article {pmid36255144,
year = {2022},
author = {Wang, S and Qian, YQ and Zhao, RP and Chen, LL and Song, JM},
title = {Graph-based pan-genome: increased opportunities in plant genomics.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erac412},
pmid = {36255144},
issn = {1460-2431},
abstract = {Due to the development of sequencing technology and the great reduction in sequencing costs, the genomes of an increasing number of plant species have been assembled, and the numerous genomes have revealed large amounts of variation. However, a single reference genome does not allow the exploration of species diversity; therefore, the concept of the pan-genome was developed. A pan-genome is a collection of all sequences available for a species, including a large number of consensus sequences, large structural variations (SVs), and small variations, including single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). A simple linear pan-genome does not allow these SVs to be intuitively characterized, so graph-based pan-genomes have been developed. These pan-genomes store sequence and SV information in the form of nodes and paths to store and display species variation information in a more intuitive manner. The key role of graph-based pan-genome is to expand the coordinate system of the linear reference genome to accommodate more regions of genetic diversity. Here, we review the origin and development of graph-based pan-genomes, explore their application in plant research, and further highlight the application of graph-based pan-genomes for future plant breeding.},
}

@article {pmid36247363,
year = {2022},
author = {Rocchini, D and Santos, MJ and Ustin, SL and Féret, JB and Asner, GP and Beierkuhnlein, C and Dalponte, M and Feilhauer, H and Foody, GM and Geller, GN and Gillespie, TW and He, KS and Kleijn, D and Leitão, PJ and Malavasi, M and Moudrý, V and Müllerová, J and Nagendra, H and Normand, S and Ricotta, C and Schaepman, ME and Schmidtlein, S and Skidmore, AK and Šímová, P and Torresani, M and Townsend, PA and Turner, W and Vihervaara, P and Wegmann, M and Lenoir, J},
title = {The Spectral Species Concept in Living Color.},
journal = {Journal of geophysical research. Biogeosciences},
volume = {127},
number = {9},
pages = {e2022JG007026},
pmid = {36247363},
issn = {2169-8953},
abstract = {Biodiversity monitoring is an almost inconceivable challenge at the scale of the entire Earth. The current (and soon to be flown) generation of spaceborne and airborne optical sensors (i.e., imaging spectrometers) can collect detailed information at unprecedented spatial, temporal, and spectral resolutions. These new data streams are preceded by a revolution in modeling and analytics that can utilize the richness of these datasets to measure a wide range of plant traits, community composition, and ecosystem functions. At the heart of this framework for monitoring plant biodiversity is the idea of remotely identifying species by making use of the 'spectral species' concept. In theory, the spectral species concept can be defined as a species characterized by a unique spectral signature and thus remotely detectable within pixel units of a spectral image. In reality, depending on spatial resolution, pixels may contain several species which renders species-specific assignment of spectral information more challenging. The aim of this paper is to review the spectral species concept and relate it to underlying ecological principles, while also discussing the complexities, challenges and opportunities to apply this concept given current and future scientific advances in remote sensing.},
}

@article {pmid36240488,
year = {2022},
author = {Tong, KKH and Riisom, M and Leung, E and Hanif, M and Söhnel, T and Jamieson, SMF and Hartinger, CG},
title = {Impact of Coordination Mode and Ferrocene Functionalization on the Anticancer Activity of N-Heterocyclic Carbene Half-Sandwich Complexes.},
journal = {Inorganic chemistry},
volume = {61},
number = {43},
pages = {17226-17241},
doi = {10.1021/acs.inorgchem.2c02832},
pmid = {36240488},
issn = {1520-510X},
mesh = {Metallocenes/pharmacology ; *Coordination Complexes/pharmacology ; Reactive Oxygen Species ; Methane/pharmacology ; *Antineoplastic Agents/pharmacology ; Ligands ; },
abstract = {The substitution of phenyl rings in established drugs with ferrocenyl moieties has been reported to yield compounds with improved biological activity and alternative modes of action, often involving the formation of reactive oxygen species (ROS). Translating this concept to N-heterocyclic carbene (NHC) complexes, we report here organometallics with a piano-stool structure that feature di- or tridentate ligand systems. The ligands impacted the cytotoxic activity of the NHC complexes, but the coordination modes seemed to have a limited influence, which may be related to the propensity of forming the same species in solution. In general, the stability of the complexes in an aqueous environment and their reactivity to selected biomolecules were largely dominated by the nature of the metal center. While the complexes promoted the formation of ROS, the levels did not correlate with their cytotoxic activity. However, the introduction of ferrocenyl moieties had a significant impact on the antiproliferative potency of the complexes and, in particular, some of the ferrocenyl-functionalized compounds yielded IC50 values in the low μM range.},
}

Metallocenes/pharmacology
*Coordination Complexes/pharmacology
Reactive Oxygen Species
Methane/pharmacology
*Antineoplastic Agents/pharmacology
Ligands

@article {pmid36223598,
year = {2022},
author = {Bradshaw, MJ and Braun, U and Pfister, DH},
title = {Phylogeny and taxonomy of the genera of Erysiphaceae, part 1: Golovinomyces.},
journal = {Mycologia},
volume = {114},
number = {6},
pages = {964-993},
doi = {10.1080/00275514.2022.2115419},
pmid = {36223598},
issn = {1557-2536},
mesh = {Phylogeny ; *Plant Diseases/microbiology ; DNA, Fungal/genetics ; *Ascomycota/genetics ; DNA, Ribosomal/genetics ; Plants/microbiology ; },
abstract = {Powdery mildews are a monophyletic group of obligate plant pathogenic fungi in the family Erysiphaceae. Powdery mildews are economically important in that they cause damage to many agriculturally significant crops and plants in ecologically important habitats. In this contribution, we introduce a new series of publications focusing on the phylogeny and taxonomy of this group, with an emphasis on specimens collected from North America. The first part of the series focuses on the genus Golovinomyces and includes a section detailing the powdery mildew species concept. We conducted analyses of Golovinomyces spp. with available rDNA sequence data from GenBank and supplemented the data set with rDNA (ITS, 28S, IGS) as well as protein-coding (GAPDH) data from 94 North American collections. Many of the species evaluated are included in phylogenetic and morphological analyses for the first time, including the American species G. americanus, G. brunneopunctatus, G. californicus, G. greeneanus, G. hydrophyllacearum, and G. sparsus. A special emphasis was placed on acquiring ex-type or ex-epitype sequences or presenting reference sequences for phylogenetic-taxonomic purposes. Three new species, G. eurybiarum, G. galiorum, and G. malvacearum, are described, and the new combinations G. fuegianus, G. mutisiae, and G. reginae are introduced. Ex-holotype sequences of Erysiphe sparsa (≡ G. sparsus) reveal that it should be reduced to synonymy with G. ambrosiae, and ex-epitype sequences of G. valerianae reveal that it should be reduced to synonymy with G. orontii. Multiple epitypes are designated with ex-epitype sequences.},
}

Phylogeny
*Plant Diseases/microbiology
DNA, Fungal/genetics
*Ascomycota/genetics
DNA, Ribosomal/genetics
Plants/microbiology

@article {pmid36211486,
year = {2022},
author = {Wallingford, JC and Neve Myers, P and Barber, CM},
title = {Effects of addition of 2-fucosyllactose to infant formula on growth and specific pathways of utilization by Bifidobacterium in healthy term infants.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {961526},
pmid = {36211486},
issn = {2296-861X},
abstract = {Oligosaccharides in human milk support health via intestinal microbiome. We studied effects of addition of 2-fucosyllactose (2'FL) to the infant formula on infant growth, occurrence of adverse events (AE), and infant microbiome, including expression of microbial genes that metabolize 2'FL. Our hypothesis was that while 2'FL would not affect growth, it would cause changes in microbiome metabolism. In a double-blinded randomized controlled study fashion, the infant formula ± 2'FL or human milk was fed to healthy term infants for 16 weeks. Fecal samples obtained at baseline and week 16 were analyzed for microbial populations, metagenomic species concept (MGS), and genetics of gut metabolic modules (GMMs). There were no effects of addition of 2'FL on growth or AEs. There were no significant differences by feeding group in MGS richness or Shannon diversity at baseline, but formula groups each had significantly greater richness (p < 0.05) and diversity (p < 0.05) after 16 weeks of feeding than the breastfed group. While two glycosyl hydrolase (GH) families (GH42 and GH112) were significantly increased, two other GH families (GH20 and GH2) were significantly decreased in the test formula group compared to the control formula group; although modest, addition of 2'FL resulted in changes in microbiome in the direction of breastfed infants, consistent with internal metabolism of HMOs by Bifidobacterium.},
}

@article {pmid36203732,
year = {2022},
author = {Oppong, SO and Twum, F and Hayfron-Acquah, JB and Missah, YM},
title = {A Novel Computer Vision Model for Medicinal Plant Identification Using Log-Gabor Filters and Deep Learning Algorithms.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {1189509},
pmid = {36203732},
issn = {1687-5273},
mesh = {Algorithms ; Artificial Intelligence ; *Deep Learning ; Humans ; Neural Networks, Computer ; *Plants, Medicinal ; },
abstract = {Computer vision is the science that enables computers and machines to see and perceive image content on a semantic level. It combines concepts, techniques, and ideas from various fields such as digital image processing, pattern matching, artificial intelligence, and computer graphics. A computer vision system is designed to model the human visual system on a functional basis as closely as possible. Deep learning and Convolutional Neural Networks (CNNs) in particular which are biologically inspired have significantly contributed to computer vision studies. This research develops a computer vision system that uses CNNs and handcrafted filters from Log-Gabor filters to identify medicinal plants based on their leaf textural features in an ensemble manner. The system was tested on a dataset developed from the Centre of Plant Medicine Research, Ghana (MyDataset) consisting of forty-nine (49) plant species. Using the concept of transfer learning, ten pretrained networks including Alexnet, GoogLeNet, DenseNet201, Inceptionv3, Mobilenetv2, Restnet18, Resnet50, Resnet101, vgg16, and vgg19 were used as feature extractors. The DenseNet201 architecture resulted with the best outcome of 87% accuracy and GoogLeNet with 79% preforming the worse averaged across six supervised learning algorithms. The proposed model (OTAMNet), created by fusing a Log-Gabor layer into the transition layers of the DenseNet201 architecture achieved 98% accuracy when tested on MyDataset. OTAMNet was tested on other benchmark datasets; Flavia, Swedish Leaf, MD2020, and the Folio dataset. The Flavia dataset achieved 99%, Swedish Leaf 100%, MD2020 99%, and the Folio dataset 97%. A false-positive rate of less than 0.1% was achieved in all cases.},
}

Algorithms
Artificial Intelligence
*Deep Learning
Humans
Neural Networks, Computer
*Plants, Medicinal

@article {pmid36182674,
year = {2022},
author = {Zheng, W and Chen, Y and Fu, H and Yan, Z and Lei, Z and Duan, W and Feng, C},
title = {Reactive species conversion into [1]O2 promotes substantial inhibition of chlorinated byproduct formation during electrooxidation of phenols in Cl[-]-laden wastewater.},
journal = {Water research},
volume = {225},
number = {},
pages = {119143},
doi = {10.1016/j.watres.2022.119143},
pmid = {36182674},
issn = {1879-2448},
mesh = {Waste Water/chemistry ; Chlorine/chemistry ; *Water Purification/methods ; Phenol/chemistry ; Hydrogen Peroxide/chemistry ; Phenols ; Halogens/chemistry ; Oxidation-Reduction ; Chlorides ; *Water Pollutants, Chemical/chemistry ; Ultraviolet Rays ; },
abstract = {The generation of chlorinated byproducts during the electrochemical oxidation (EO) of Cl[-]-laden wastewater is a significant concern. We aim to propose a concept of converting reactive species (e.g., reactive chlorines and HO[•] resulting from electrolysis) into [1]O2 via the addition of H2O2, which substantially alleviates chlorinated organic formation. When phenol was used as a model organic compound, the results showed that the H2O2-involving EO system outperformed the H2O2-absent system in terms of higher rate constants (5.95 × 10[-2] min[-1]vs. 2.97 × 10[-2] min[-1]) and a much lower accumulation of total organic chlorinated products (1.42 mg L[-1]vs. 8.18 mg L[-1]) during a 60 min operation. The rate constants of disappearance of a variety of phenolic compounds were positively correlated with the Hammett constants (σ), suggesting that the reactive species preferred oxidizing phenols with electron-rich groups. After the identification of [1]O2 that was abundant in the bulk solution with the use of electron paramagnetic resonance and computational kinetic simulation, the routes of [1]O2 generation were revealed. Despite the consensus as to the contribution of reaction between H2O2 and ClO[-] to [1]O2 formation, we conclude that the predominant pathway is through H2O2 reaction with electrogenerated HO[•] or chlorine radicals (Cl[•] and Cl2[•][-]) to produce O2[•][-], followed by self-combination. Density functional theory calculations theoretically showed the difficulty in forming chlorinated byproducts for the [1]O2-initiated phenol oxidation in the presence of Cl[-], which, by contrast, easily occurred for the Cl[•]-or HO[•]-initiated phenol reaction. The experiments run with real coking wastewater containing high-concentration phenols further demonstrated the superiority of the H2O2-involving EO system. The findings imply that this unique method for treating Cl[-]-laden organic wastewater is expected to be widely adopted for generalizing EO technology for environmental applications.},
}

Waste Water/chemistry
Chlorine/chemistry
*Water Purification/methods
Phenol/chemistry
Hydrogen Peroxide/chemistry
Phenols
Halogens/chemistry
Oxidation-Reduction
Chlorides
*Water Pollutants, Chemical/chemistry
Ultraviolet Rays

@article {pmid36121444,
year = {2022},
author = {Rauf, S and Hanif, MB and Mushtaq, N and Tayyab, Z and Ali, N and Shah, MAKY and Motola, M and Saleem, A and Asghar, MI and Iqbal, R and Yang, C and Xu, W},
title = {Modulating the Energy Band Structure of the Mg-Doped Sr0.5Pr0.5Fe0.2Mg0.2Ti0.6O3-δ Electrolyte with Boosted Ionic Conductivity and Electrochemical Performance for Solid Oxide Fuel Cells.},
journal = {ACS applied materials & interfaces},
volume = {14},
number = {38},
pages = {43067-43084},
pmid = {36121444},
issn = {1944-8252},
abstract = {Achieving fast ionic conductivity in the electrolyte at low operating temperatures while maintaining the stable and high electrochemical performance of solid oxide fuel cells (SOFCs) is challenging. Herein, we propose a new type of electrolyte based on perovskite Sr0.5Pr0.5Fe0.4Ti0.6O3-δ for low-temperature SOFCs. The ionic conducting behavior of the electrolyte is modulated using Mg doping, and three different Sr0.5Pr0.5Fe0.4-xMgxTi0.6O3-δ (x = 0, 0.1, and 0.2) samples are prepared. The synthesized Sr0.5Pr0.5Fe0.2Mg0.2Ti0.6O3-δ (SPFMg0.2T) proved to be an optimal electrolyte material, exhibiting a high ionic conductivity of 0.133 S cm[-1] along with an attractive fuel cell performance of 0.83 W cm[-2] at 520 °C. We proved that a proper amount of Mg doping (20%) contributes to the creation of an adequate number of oxygen vacancies, which facilitates the fast transport of the oxide ions. Considering its rapid oxide ion transport, the prepared SPFMg0.2T presented heterostructure characteristics in the form of an insulating core and superionic conduction via surface layers. In addition, the effect of Mg doping is intensively investigated to tune the band structure for the transport of charged species. Meanwhile, the concept of energy band alignment is employed to interpret the working principle of the proposed electrolyte. Moreover, the density functional theory is utilized to determine the perovskite structures of SrTiO3-δ and Sr0.5Pr0.5Fe0.4-xMgxTi0.6O3-δ (x = 0, 0.1, and 0.2) and their electronic states. Further, the SPFMg0.2T with 20% Mg doping exhibited low dissociation energy, which ensures the fast and high ionic conduction in the electrolyte. Inclusively, Sr0.5Pr0.5Fe0.4Ti0.6O3-δ is a promising electrolyte for SOFCs, and its performance can be efficiently boosted via Mg doping to modulate the energy band structure.},
}

@article {pmid36101245,
year = {2022},
author = {Moravec, JI and Wiesner, J and Jocque, M},
title = {New or rare Madagascar tiger beetles26. A new species of the genus Pogonostoma Klug from northwestern Madagascar and a revised key to the Pogonostoma (P.) srnkai species-group (Coleoptera: Cicindelidae).},
journal = {Zootaxa},
volume = {5169},
number = {2},
pages = {165-176},
doi = {10.11646/zootaxa.5169.2.4},
pmid = {36101245},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Coleoptera ; Madagascar ; },
abstract = {A new species of the genus Pogonostoma Klug, 1835, P. (Pogonostoma) mahimborondrense Moravec Wiesner sp. nov. is described as new to science from the Mahimborondro protected area in Northern Highlands, northwestern Madagascar. By its unique complex of diagnostic characters, the new species is incomparable to any other species within the genus. It is placed here into the Pogonostoma (P.) srnkai species-group (in the concept presented in the monograph of the genus by Moravec 2007). A revised key to species of the species-group is presented in order to supplement the key in the monograph. Habitus and diagnostic characters of the new species are illustrated in colour photographs. Maps and photos of the occurrence of the new species in Mahimborondro are also presented.},
}

Animal Distribution
Animals
*Coleoptera
Madagascar

@article {pmid36095810,
year = {2022},
author = {Lair, X and Ropars, L and Skevington, JH and Kelso, S and Geslin, B and Minssieux, E and Nve, G},
title = {Revision of the genus Pelecocera Meigen, 1822 (Diptera: Syrphidae) from France: taxonomy, ecology and distribution.},
journal = {Zootaxa},
volume = {5141},
number = {1},
pages = {1-24},
doi = {10.11646/zootaxa.5141.1.1},
pmid = {36095810},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; France ; },
abstract = {The occurrence and distribution of the various species of the genus Pelecocera Meigen, 1822 (Diptera: Syrphidae) occurring in France are revised and a new species, Pelecocera garrigae Lair Nve, 2022 sp. nov., is described from Mediterranean France. Distribution and ecological data of the six French species of Pelecocera are provided and an identification key is given to all these species. Sequences of the cytochrome c oxidase subunit I (COI) from all European Pelecocera species support the morphological species concept, except for Pelecocera scaevoides (Falln, 1817). The binomen Pelecocera lugubris Perris, 1839 is recovered to name the Pelecocera lusitanica (Mik, 1898) of authors in France.},
}

Animals
*Diptera
France

@article {pmid36095753,
year = {2022},
author = {Philips, TK and Mudge, AD and Orozco, J and Neidlinger, R and Beinhundner, G and Joly, C},
title = {A rich and diverse fauna: an illustrated guide to the cetoniines of Ghana with comparisons to Ivory Coast and Benin (Coleoptera: Scarabaeidae: Cetoniinae).},
journal = {Zootaxa},
volume = {5150},
number = {2},
pages = {151-188},
doi = {10.11646/zootaxa.5150.2.1},
pmid = {36095753},
issn = {1175-5334},
mesh = {Animals ; Benin ; *Coleoptera ; Cote d'Ivoire ; Ghana ; },
abstract = {The currently known cetoniine fauna of Ghana is discussed and illustrated. It now includes 60 genera and 148 taxa, including 9 subspecies. Comparison to the adjacent countries of Ivory Coast and nearby Benin gives evidence that the faunas of all three countries surprisingly may still be grossly under-sampled and hence poorly known for what is considered a relatively well-known group of beetles. At least 22 species known from both Ivory Coast and Benin are expected to be found in Ghana but still have yet to be reported. Notes on several species concepts and the alternate use of names are also given to clarify the taxonomy of the taxa known from this area.},
}

Animals
Benin
*Coleoptera
Cote d'Ivoire
Ghana

@article {pmid36093929,
year = {2022},
author = {Green, WH},
title = {Concluding remarks: Faraday Discussion on unimolecular reactions.},
journal = {Faraday discussions},
volume = {238},
number = {0},
pages = {741-766},
doi = {10.1039/d2fd00136e},
pmid = {36093929},
issn = {1364-5498},
abstract = {This Faraday Discussion, marking the centenary of Lindemann's explanation of the pressure-dependence of unimolecular reactions, presented recent advances in measuring and computing collisional energy transfer efficiencies, microcanonical rate coefficients, and pressure-dependent (phenomenological) rate coefficients, and the incorporation of these rate coefficients in kinetic models. Several of the presentations featured systems where breakdown of the Born-Oppenheimer approximation is key to understanding the measured rates/products. Many of the reaction systems presented were quite complex, which can make it difficult to go from "plausible proposed explanation" to "quantitative agreement between model and experiment". This complexity highlights the need for better automation of the calculations, better documentation and benchmarking to catch any errors and to make the calculations more easily reproducible, and continued (and even closer) cooperation of experimentalists and modelers. In some situations the correct definition of a "species" is debatable, since the population distributions and time evolution are so distorted from the perfect-Boltzmann Lewis-structure zero-order concept of a chemical species. Despite all these challenges, the field has made tremendous advances, and several cases were presented which demonstrated both excellent understanding of very complicated reaction chemistry and quantitatively accurate predictions of complicated experiments. Some of the interesting contributions to this Discussion are highlighted here, with some comments and suggestions for next steps.},
}

@article {pmid36079936,
year = {2022},
author = {Polivtseva, S and Kois, J and Kruzhilina, T and Kaupmees, R and Klopov, M and Molaiyan, P and van Gog, H and van Huis, MA and Volobujeva, O},
title = {Solution-Mediated Inversion of SnSe to Sb2Se3 Thin-Films.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {12},
number = {17},
pages = {},
pmid = {36079936},
issn = {2079-4991},
abstract = {New facile and controllable approaches to fabricating metal chalcogenide thin films with adjustable properties can significantly expand the scope of these materials in numerous optoelectronic and photovoltaic devices. Most traditional and especially wet-chemical synthetic pathways suffer from a sluggish ability to regulate the composition and have difficulty achieving the high-quality structural properties of the sought-after metal chalcogenides, especially at large 2D length scales. In this effort, and for the first time, we illustrated the fast and complete inversion of continuous SnSe thin-films to Sb2Se3 using a scalable top-down ion-exchange approach. Processing in dense solution systems yielded the formation of Sb2Se3 films with favorable structural characteristics, while oxide phases, which are typically present in most Sb2Se3 films regardless of the synthetic protocols used, were eliminated. Density functional theory (DFT) calculations performed on intermediate phases show strong relaxations of the atomic lattice due to the presence of substitutional and vacancy defects, which likely enhances the mobility of cationic species during cation exchange. Our concept can be applied to customize the properties of other metal chalcogenides or manufacture layered structures.},
}

@article {pmid36072310,
year = {2022},
author = {Doyle, JJ},
title = {Cell types as species: Exploring a metaphor.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {868565},
pmid = {36072310},
issn = {1664-462X},
abstract = {The concept of "cell type," though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, "species." In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the "cell types as species" metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.},
}

@article {pmid36065479,
year = {2022},
author = {Lachance, MA},
title = {Phylogenies in yeast species descriptions: In defense of neighbor-joining.},
journal = {Yeast (Chichester, England)},
volume = {39},
number = {10},
pages = {513-520},
doi = {10.1002/yea.3812},
pmid = {36065479},
issn = {1097-0061},
mesh = {*Algorithms ; Evolution, Molecular ; *Models, Genetic ; Phylogeny ; },
abstract = {The neighbor-joining (NJ) method of tree inference is examined, with special attention to its use in yeast species descriptions. How the often-vilified method works is often misunderstood. More importantly, given the right kind of data, its output is a phylogram that illustrates a hypothetical phylogeny that is just as credible as that obtained by any other method. And as with any other method, the result is greatly affected by sampling intensity, particularly the number of aligned positions used for analysis. I address various allegations, including the claim that the method is phenetic, and, therefore, not phylogenetic. I argue that NJ is the most suitable tree inference method to use in yeast species descriptions, primarily because it is best at visually preserving the extent of sequence divergence between close relatives, which continues to be the primary criterion for yeast species delineation. The relevance of bootstraps in the application of the phylogenetic species concept is discussed.},
}

*Algorithms
Evolution, Molecular
*Models, Genetic
Phylogeny

@article {pmid36063161,
year = {2022},
author = {Mallet, J and Mullen, SP},
title = {Reproductive isolation is a heuristic, not a measure: a commentary on Westram et al., 2022.},
journal = {Journal of evolutionary biology},
volume = {35},
number = {9},
pages = {1175-1182},
doi = {10.1111/jeb.14052},
pmid = {36063161},
issn = {1420-9101},
mesh = {Gene Flow ; *Genetic Speciation ; Heuristics ; *Reproductive Isolation ; Sympatry ; },
abstract = {Reproductive isolation is the heuristic basis of the biological species concept, but what is it? Westram et al. (this issue) propose that it is a measurable quantity, "barrier strength," that prevents gene flow among populations. However, their attempt to make the concept of reproductive isolation more scientific is unlikely to satisfy the diverse opinions of all evolutionary biologists. There are many different opinions about the nature of species, even under the biological species concept. Complete reproductive isolation, where gene flow is effectively zero, is regarded by some biologists as an important end point of speciation. Others, including Westram et al., argue for a more nuanced approach, and they also suggest that reproductive isolation may differ in different parts of the genome due to variation in genetic linkage to divergently selected loci. In contrast to both these approaches, we favour as a key criterion of speciation the stable coexistence of divergent populations in sympatry. Obviously, such populations must be reproductively isolated in some sense, but neither the fraction of the genome that is exchanged, nor measures of overall barrier strength acting on neutral variation will yield very precise predictions as to species status. Although an overall measure of reproductive isolation is virtually unattainable for these reasons, its early generation components, such as assortative mating, divergent selection, or hybrid inviability and sterility are readily measurable and remain informative. For example, we can make the prediction that to remain divergent in sympatry, almost all sexual species will require strong assortative mating, as well as some sort of ecological or intrinsic selection against hybrids and introgressed variants.},
}

Gene Flow
*Genetic Speciation
Heuristics
*Reproductive Isolation
Sympatry

@article {pmid36027870,
year = {2022},
author = {Kudryavtsev, A},
title = {From Argentine Abyssal Plain to farmed turbot in Spain: A ubiquitous amoeba species Vannella robusta sp. nov. (Amoebozoa, Vannellida).},
journal = {European journal of protistology},
volume = {85},
number = {},
pages = {125912},
doi = {10.1016/j.ejop.2022.125912},
pmid = {36027870},
issn = {1618-0429},
mesh = {Amebiasis/*veterinary/virology ; Amoebozoa/classification/*isolation & purification ; Animals ; Argentina ; Atlantic Ocean ; Electron Transport Complex IV/genetics ; Fish Diseases/*virology ; Flatfishes/genetics/*parasitology ; Phylogeny ; RNA, Ribosomal/genetics ; Seawater/parasitology ; Sequence Analysis, DNA ; Spain ; Species Specificity ; },
abstract = {A strain with the characters of the genus Vannella was isolated from the water layer immediately above the deep-sea sediment collected in the south-western Atlantic Ocean, ca. 4.6 km deep. Small-subunit ribosomal RNA (SSU rRNA) and cytochrome c oxidase (Cox1) gene phylogenetic analyses showed that the new strain branches within the clade of previously isolated unnamed Vannella strains from different marine fish and invertebrate hosts. Although the SSU rRNA gene sequences of these strains show variability within 2% of all nucleotide positions without any regular pattern, the available Cox1 gene sequences from within this clade are identical. Given the morphological homogeneity of the revealed clade, all of its strains can be assigned under the same species name, and the variation of their SSU rRNA is comparable to its intragenomic variation, as shown by molecular cloning of the PCR amplicons. High variability of the SSU rRNA gene sequences within and between independently isolated morphologically identical strains in combination with highly conserved Cox1 gene sequences may be a feature in some clades of Vannella, but is not a general rule for this genus, as SSU rRNA genes conserved between different morphospecies occur in several other clades within Vannella.},
}

Amebiasis/*veterinary/virology
Amoebozoa/classification/*isolation & purification
Animals
Argentina
Atlantic Ocean
Electron Transport Complex IV/genetics
Fish Diseases/*virology
Flatfishes/genetics/*parasitology
Phylogeny
RNA, Ribosomal/genetics
Seawater/parasitology
Sequence Analysis, DNA
Spain
Species Specificity

@article {pmid36004556,
year = {2022},
author = {Pizzato, J and Tang, W and Bernabeu, S and Bonnin, RA and Bille, E and Farfour, E and Guillard, T and Barraud, O and Cattoir, V and Plouzeau, C and Corvec, S and Shahrezaei, V and Dortet, L and Larrouy-Maumus, G},
title = {Discrimination of Escherichia coli, Shigella flexneri, and Shigella sonnei using lipid profiling by MALDI-TOF mass spectrometry paired with machine learning.},
journal = {MicrobiologyOpen},
volume = {11},
number = {4},
pages = {e1313},
pmid = {36004556},
issn = {2045-8827},
support = {105603/Z/14/Z/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Bacteria ; Escherichia coli ; *Escherichia coli Infections ; Humans ; Lipids ; Machine Learning ; RNA, Ribosomal, 16S ; *Shigella ; Shigella flexneri ; Shigella sonnei ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a staple in clinical microbiology laboratories. Protein-profiling of bacteria using this technique has accelerated the identification of pathogens in diagnostic workflows. Recently, lipid profiling has emerged as a way to complement bacterial identification where protein-based methods fail to provide accurate results. This study aimed to address the challenge of rapid discrimination between Escherichia coli and Shigella spp. using MALDI-TOF MS in the negative ion mode for lipid profiling coupled with machine learning. Both E. coli and Shigella species are closely related; they share high sequence homology, reported for 16S rRNA gene sequence similarities between E. coli and Shigella spp. exceeding 99%, and a similar protein expression pattern but are epidemiologically distinct. A bacterial collection of 45 E. coli, 48 Shigella flexneri, and 62 Shigella sonnei clinical isolates were submitted to lipid profiling in negative ion mode using the MALDI Biotyper Sirius® system after treatment with mild-acid hydrolysis (acetic acid 1% v/v for 15 min at 98°C). Spectra were then analyzed using our in-house machine learning algorithm and top-ranked features used for the discrimination of the bacterial species. Here, as a proof-of-concept, we showed that lipid profiling might have the potential to differentiate E. coli from Shigella species using the analysis of the top five ranked features obtained by MALDI-TOF MS in the negative ion mode of the MALDI Biotyper Sirius® system. Based on this new approach, MALDI-TOF MS analysis of lipids might help pave the way toward these goals.},
}

Bacteria
Escherichia coli
*Escherichia coli Infections
Humans
Lipids
Machine Learning
RNA, Ribosomal, 16S
*Shigella
Shigella flexneri
Shigella sonnei
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

@article {pmid35993885,
year = {2022},
author = {Chambers, EA and Marshall, TL and Hillis, DM},
title = {The Importance of Contact Zones for Distinguishing Interspecific from Intraspecific Geographic Variation.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syac056},
pmid = {35993885},
issn = {1076-836X},
abstract = {With limited sampling, geographic variation within a single species can be difficult to distinguish from interspecific variation, confounding our ability to draw accurate species boundaries. We argue that thorough sampling and analysis of contact zones between putative taxa can determine if assortative mating or selection against hybrids exists (supporting the presence of two distinct species), or alternatively if mating is random among genotypes and admixture among adjacent populations is gradual and continuous (supporting geographic variation within a single species). Here, we test two alternative hypotheses for two pairs of named taxa at contact zones within the American milksnake (Lampropeltis triangulum) complex. A prior morphological analysis found areas of gradual intergradation among named taxa, and concluded that the taxa represented geographical races of a single polytypic species. In contrast, a subsequent analysis of gene sequence data, but with limited sampling near the contact zones, hypothesized distinct boundaries between species at the contact zones. At the contact zone between proposed species L. triangulum and L. gentilis, we examined a ∼700 km-wide transect across the states of Kansas and Missouri, with thorough sampling and reduced-representation genomic-level sequencing, to test the two opposing taxonomic hypotheses. Our transect analyses included examinations of population structure, fixed differences, cline-fitting, and an admixture index analysis. These analyses all supported a gradual and continuous geographic cline across a broad intergrade zone between two geographic forms of L. triangulum, thus providing strong support for a single species in this region (and no support for the recognition of L. gentilis as a distinct species). At a second contact zone between proposed species L. triangulum and L. elapsoides (but variously treated as species or subspecies by different researchers) in Kentucky and Tennessee, we re-evaluated morphological data. In this case, the contact zone analysis indicated sympatry and reproductive isolation of the two taxa, and thus strongly supported L. triangulum and L. elapsoides as distinct species. We conclude that detailed studies of contact zones, based on either genetic or morphological data, are essential for distinguishing intraspecific from interspecific variation in the case of widely and continuously distributed taxa.},
}

@article {pmid35988118,
year = {2022},
author = {Kekäläinen, J},
title = {Cryptic female choice within individual males - A neglected component of the postmating sexual selection?.},
journal = {Journal of evolutionary biology},
volume = {35},
number = {11},
pages = {1407-1413},
doi = {10.1111/jeb.14081},
pmid = {35988118},
issn = {1420-9101},
mesh = {Male ; Female ; Animals ; *Sexual Selection ; *Semen ; Fertilization ; Spermatozoa ; Reproduction ; },
abstract = {Cryptic female choice (CFC) is commonly assumed to act only in polyandrous mating systems, which allows females to bias fertilization towards the sperm of particular males. However, accumulated evidence has demonstrated that sperm show significant phenotypic and genotypic variation also within single ejaculates, which have important consequences for offspring phenotype and fitness. Here, I argue that these neglected sources of intra-male sperm variation often allow CFC to act also within individual males and facilitate fertilization bias towards genetically compatible (or otherwise preferred) sperm haplotypes. In this article, I explain prerequisites for within-male CFC, the criteria for demonstrating it and summarize accumulated evidence for this emerging selection process. Then, I evaluate prevalence of within-male CFC and review its potential evolutionary consequences. The aim of this article is to broaden the current definition of CFC by demonstrating that CFC has potential to act in all mating systems, in both internally and externally fertilizing species. Incorporation of the within-male CFC concept into the current models of sexual selection may provide novel insights into the deeper understanding of selective factors driving the evolution of mating systems and reproductive proteins. Finally, within-male CFC towards particular sperm haplotypes may increase our understanding of non-Mendelian inheritance.},
}

Male
Female
Animals
*Sexual Selection
*Semen
Fertilization
Spermatozoa
Reproduction

@article {pmid35963148,
year = {2022},
author = {Harbuzov, Z and Farberova, V and Tom, M and Pallavicini, A and Stanković, D and Lotan, T and Lubinevsky, H},
title = {Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition.},
journal = {Marine genomics},
volume = {65},
number = {},
pages = {100980},
doi = {10.1016/j.margen.2022.100980},
pmid = {35963148},
issn = {1876-7478},
mesh = {Base Composition ; Gene Library ; *High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; },
abstract = {The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470-490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using the Illumina 300 × 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 reads. Five quality scores (q = 35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs for the DADA2 software, ending with five reference ASV libraries. Each of these libraries was clustered, applying 3% dissimilarity threshold, revealed an average number of 1.38 ± 0.078 ASVs / cluster. Hence, demonstrating high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs / cluster, strongly indicated fair representation of the actual number of the underlying species. Hence, the q = 25 library was selected to be used as metabarcoding reference library. It contained 461 ASVs and 342-3% clusters with average number of 1.34 ± 1.036 ASV / cluster and their BLASTN annotation elucidated a variety of expected meiofaunal taxa. The sixteen assemblies of sample-specific paired reads were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and clustered.},
}

Base Composition
Gene Library
*High-Throughput Nucleotide Sequencing
Polymerase Chain Reaction

@article {pmid35952411,
year = {2022},
author = {Qi, L and Qiao, J},
title = {Progress of chiral ligand-exchange capillary electrophoresis for enantioseparation.},
journal = {Journal of chromatography. A},
volume = {1679},
number = {},
pages = {463381},
doi = {10.1016/j.chroma.2022.463381},
pmid = {35952411},
issn = {1873-3778},
mesh = {*Electrophoresis, Capillary ; Ligands ; Stereoisomerism ; },
abstract = {Chiral ligand exchange capillary electrophoresis (CLE-CE) has become an area of tremendous interest in chiral separation science, particularly in life science and pharmaceutical, due to its notable simplicity, tunable migration order, and outstanding performance. This approach effectively separates enantiomers in drugs, food products and bio-samples. Nevertheless, the main challenges in CLE-CE are the limited chiral ligand-species, unclear mechanism of thermodynamic enantioseparation and unsatisfactory enantioseparation efficiency, which restrict its applications. Designing desirable chiral ligand-species and exploring profitable central metal ions are considered to be efficient strategies for addressing these obstacles, which can improve the performance of CLE-CE and expand its application in living bio-systems. This review introduces the concept of desirable chiral ligand species and highlights the latest CLE-CE research in the last decade, with special emphasis on boosting its enantioseparation efficiency and expanding its cutting-edge application. Moreover, further research in the CLE-CE field is prospected.},
}

*Electrophoresis, Capillary
Ligands
Stereoisomerism

@article {pmid35923138,
year = {2022},
author = {Zhou, H and Lu, X and Du, C and Zhou, Z and Feng, J and Liang, Z and Xu, Y and Qiu, X and Shen, Z},
title = {Cycloacceleration of Reactive Oxygen Species Generation Based on Exceedingly Small Magnetic Iron Oxide Nanoparticles for Tumor Ferroptosis Therapy.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {18},
number = {35},
pages = {e2202705},
doi = {10.1002/smll.202202705},
pmid = {35923138},
issn = {1613-6829},
mesh = {Cell Line, Tumor ; Contrast Media ; *Ferroptosis ; Humans ; Magnetic Iron Oxide Nanoparticles ; *Nanoparticles ; *Neoplasms/diagnostic imaging/drug therapy/pathology ; Reactive Oxygen Species ; Tumor Microenvironment ; },
abstract = {Because of the insufficiency of hydrogen peroxide, the relatively low rate of Fenton reaction, and the active glutathione (GSH) peroxidase 4 (GPX4) in tumor cells, it is difficult to achieve a desirable efficacy of ferroptosis therapy (FT) for tumors based on nanomaterials. Inspired by the concept of "cyclotron" in physics, in this study, a new concept of cycloacceleration of reactive oxygen species (ROS) generation in tumor cells to realize high-performance FT of tumors is proposed. Typically, a magnetic resonance imaging (MRI) contrast agent of dotted core-shell Fe3 O4 /Gd2 O3 hybrid nanoparticles (FGNPs) is prepared based on exceedingly small magnetic iron oxide nanoparticles (ES-MIONs). Sorafenib (SFN) is loaded and poly(ethylene glycol) methyl ether-poly(propylene sulfide)-NH2 (mPEG-PPS-NH2) is grafted on the surface of FGNP to generate SA-SFN-FGNP via self-assembly. The results of in vitro and in vivo demonstrate SA-SFN-FGNP can work with the acidic tumor microenvironment and endosomal conditions, Fenton reaction and system XC [-] , and generate cyclic reactions in tumor cells, resulting in specific cycloacceleration of ROS generation for high-performance FT of tumors. The very high longitudinal relaxivity (r1 , 33.43 mM[-1] s[-1] , 3.0 T) makes sure that the SA-SFN-FGNP can be used for MRI-guided FT of tumors.},
}

Cell Line, Tumor
Contrast Media
*Ferroptosis
Humans
Magnetic Iron Oxide Nanoparticles
*Nanoparticles
*Neoplasms/diagnostic imaging/drug therapy/pathology
Reactive Oxygen Species
Tumor Microenvironment

@article {pmid35906926,
year = {2022},
author = {Leducq, JB and Sneddon, D and Santos, M and Condrain-Morel, D and Bourret, G and Martinez-Gomez, NC and Lee, JA and Foster, JA and Stolyar, S and Shapiro, BJ and Kembel, SW and Sullivan, JM and Marx, CJ},
title = {Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity.},
journal = {Genome biology and evolution},
volume = {14},
number = {8},
pages = {},
pmid = {35906926},
issn = {1759-6653},
mesh = {Ecosystem ; *Methylobacterium ; Phylogeny ; Plant Leaves ; Plants/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfer (HGT). We showed that Methylobacterium contains four evolutionarily distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content, and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition to recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), whose early branching in Methylobacterium history has been heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandonment of Methylorubrum.},
}

Ecosystem
*Methylobacterium
Phylogeny
Plant Leaves
Plants/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid35890512,
year = {2022},
author = {Ott, T and Schall, M and Vogt, R and Oberprieler, C},
title = {The Warps and Wefts of a Polyploidy Complex: Integrative Species Delimitation of the Diploid Leucanthemum (Compositae, Anthemideae) Representatives.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {14},
pages = {},
pmid = {35890512},
issn = {2223-7747},
abstract = {Species delimitation-owing to the paramount role of the species rank in evolutionary, ecological, and nature conservation studies-is an essential contribution of taxonomy to biodiversity research. In an 'integrative taxonomy' approach to species delimitation on the diploid level, we searched for evolutionary significant units (the warps and wefts) that gave rise to the polyploid complex of European ox-eye daisies (Leucanthemum; Compositae-Anthemideae). Species discovery and validation methods based on genetic, ecological, geographical, and morphometric datasets were applied to test the currently accepted diploid morpho-species, i.e., morphologically delimited species, in Leucanthemum. Novel approaches were taken in the analyses of RADseq data (consensus clustering), morphometrics of reconstructed leaf silhouettes from digitized herbarium specimens, and quantification of species-distribution overlaps. We show that 17 of the 20 Leucanthemum morpho-species are supported by genetic evidence. The taxonomic rank of the remaining three morpho-species was resolved by combining genealogic, ecologic, geographic, and morphologic data in the framework of von Wettstein's morpho-geographical species concept. We herewith provide a methodological pipeline for the species delimitation in an 'integrative taxonomy' fashion using sources of evidence from genealogical, morphological, ecological, and geographical data in the philosophy of De Queiroz's "Unified Species Concept".},
}

@article {pmid35868886,
year = {2022},
author = {Connolly, JB and Romeis, J and Devos, Y and Glandorf, DCM and Turner, G and Coulibaly, MB},
title = {Gene drive in species complexes: defining target organisms.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2022.06.013},
pmid = {35868886},
issn = {1879-3096},
abstract = {Engineered gene drives, which bias their own inheritance to increase in frequency in target populations, are being developed to control mosquito malaria vectors. Such mosquitoes can belong to complexes of both vector and nonvector species that can produce fertile interspecific hybrids, making vertical gene drive transfer (VGDT) to sibling species biologically plausible. While VGDT to other vectors could positively impact human health protection goals, VGDT to nonvectors might challenge biodiversity ones. Therefore, environmental risk assessment of gene drive use in species complexes invites more nuanced considerations of target organisms and nontarget organisms than for transgenes not intended to increase in frequency in target populations. Incorporating the concept of target species complexes offers more flexibility when assessing potential impacts from VGDT.},
}

@article {pmid35860537,
year = {2022},
author = {Smith, LT and Magdalena, C and Przelomska, NAS and Pérez-Escobar, OA and Melgar-Gómez, DG and Beck, S and Negrão, R and Mian, S and Leitch, IJ and Dodsworth, S and Maurin, O and Ribero-Guardia, G and Salazar, CD and Gutierrez-Sibauty, G and Antonelli, A and Monro, AK},
title = {Revised Species Delimitation in the Giant Water Lily Genus Victoria (Nymphaeaceae) Confirms a New Species and Has Implications for Its Conservation.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {883151},
pmid = {35860537},
issn = {1664-462X},
abstract = {Reliably documenting plant diversity is necessary to protect and sustainably benefit from it. At the heart of this documentation lie species concepts and the practical methods used to delimit taxa. Here, we apply a total-evidence, iterative methodology to delimit and document species in the South American genus Victoria (Nymphaeaceae). The systematics of Victoria has thus far been poorly characterized due to difficulty in attributing species identities to biological collections. This research gap stems from an absence of type material and biological collections, also the confused diagnosis of V. cruziana. With the goal of improving systematic knowledge of the genus, we compiled information from historical records, horticulture and geography and assembled a morphological dataset using citizen science and specimens from herbaria and living collections. Finally, we generated genomic data from a subset of these specimens. Morphological and geographical observations suggest four putative species, three of which are supported by nuclear population genomic and plastid phylogenomic inferences. We propose these three confirmed entities as robust species, where two correspond to the currently recognized V. amazonica and V. cruziana, the third being new to science, which we describe, diagnose and name here as V. boliviana Magdalena and L. T. Sm. Importantly, we identify new morphological and molecular characters which serve to distinguish the species and underpin their delimitations. Our study demonstrates how combining different types of character data into a heuristic, total-evidence approach can enhance the reliability with which biological diversity of morphologically challenging groups can be identified, documented and further studied.},
}

@article {pmid35845367,
year = {2022},
author = {Burbrink, FT and Crother, BI and Murray, CM and Smith, BT and Ruane, S and Myers, EA and Pyron, RA},
title = {Empirical and philosophical problems with the subspecies rank.},
journal = {Ecology and evolution},
volume = {12},
number = {7},
pages = {e9069},
pmid = {35845367},
issn = {2045-7758},
abstract = {Species-level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species "concepts." These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what "kind" of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.},
}

@article {pmid35842034,
year = {2022},
author = {Kurtz, MA and Khullar, P and Gilbert, JL},
title = {Cathodic activation and inflammatory species are critical to simulating in vivo Ti-6Al-4V selective dissolution.},
journal = {Acta biomaterialia},
volume = {149},
number = {},
pages = {399-409},
doi = {10.1016/j.actbio.2022.07.020},
pmid = {35842034},
issn = {1878-7568},
mesh = {*Alloys ; Corrosion ; Humans ; *Hydrogen Peroxide ; Materials Testing/methods ; Solubility ; Surface Properties ; Titanium ; },
abstract = {In vivo retrievals of metallic orthopedic implants have shown selective dissolution of Ti-6Al-4V, where the vanadium-rich β phase preferentially corrodes from the surface. This damage, typically observed in crevices, is not directly caused by wear mechanics and the underlying electrochemical mechanism remains poorly understood. Previous studies show that fretting corrosion can cause negative potential drops, resulting in a decrease in surface oxide passivation resistance and the electrochemical generation of reactive oxygen species (ROS) at metallic surfaces. In this study, we combine cathodic activation and hydrogen peroxide to induce selective dissolution in vitro. After a 600 s -1 V hold and 4 h recovery in 20 °C 1 M H2O2 solution, the Ti-6Al-4V β phase was preferentially dissolved. An initial activation threshold of -0.5 V induced a significant increase in β dissolution (p = 0.000). Above this threshold, little selective dissolution occurred. In an Arrhenius-like fashion, decreasing solution concentration to 0.1 M required 72 h to generate β dissolution instead of 4 h at 1 M. Heating 0.1 M solution to body temperature (37 °C) resulted in a decrease in the time needed to replicate a similar level of β dissolution (>90%). Electrochemical impedance shows that both cathodic activation and inflammatory species are necessary to induce selective dissolution, where the combinatorial effect causes a significant drop in oxide passivation resistance from 106 to 102 (p = 0.000). STATEMENT OF SIGNIFICANCE: Though hip arthroplasties are considered a successful procedure, revision rates of 2-4% result in tens of thousands of additional surgeries within the United States, subjecting patients to increased risk of complications. Corrosion is associated with implant failure and retrieval studies show that titanium and its alloys can severely corrode in vivo in ways not yet duplicated in vitro. Here, we reproduce selective dissolution of Ti-6Al-4V β phase simulating key characteristics of in vivo degradation observed in orthopedic retrievals. We establish both cathodically activated corrosion, a relatively unexplored concept, and the presence of inflammatory species as prerequisites, furthering our understanding of this clinically relevant damage mode. We introduce an Arrhenius-based approach to assess the concentration-temperature-time interactions present.},
}

*Alloys
Corrosion
Humans
*Hydrogen Peroxide
Materials Testing/methods
Solubility
Surface Properties
Titanium

@article {pmid35837745,
year = {2022},
author = {Barrett, CF and Santee, MV and Fama, NM and Freudenstein, JV and Simon, SJ and Sinn, BT},
title = {Lineage and role in integrative taxonomy of a heterotrophic orchid complex.},
journal = {Molecular ecology},
volume = {31},
number = {18},
pages = {4762-4781},
pmid = {35837745},
issn = {1365-294X},
support = {U54 GM104942/GM/NIGMS NIH HHS/United States ; P20 GM121299/GM/NIGMS NIH HHS/United States ; P20 GM103434/GM/NIGMS NIH HHS/United States ; },
mesh = {*Orchidaceae/genetics ; Oregon ; Phylogeny ; Species Specificity ; },
abstract = {Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data-ISSRseq-demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach.},
}

*Orchidaceae/genetics
Oregon
Phylogeny
Species Specificity

@article {pmid35837665,
year = {2022},
author = {Brunke, AJ},
title = {Revision of rove beetle genus Bolitogyrus Chevrolat (Staphylininae, Cyrtoquediini). Supplement 1.},
journal = {ZooKeys},
volume = {1096},
number = {},
pages = {1-16},
pmid = {35837665},
issn = {1313-2989},
abstract = {Bolitogyrus is a moderately diverse genus of 78 species that are widely disjunct in the subtropical and tropical forests of the Neotropical and Oriental regions. Following recent revisions of both the Neotropical and Oriental species, this study provides new distributional data, a revised species concept for Bolitogyrusstrigifrons (Wendeler) sensu nov., and the description of B.pseudostrigifrons sp. nov. and B.nigropolitoides sp. nov., bringing the total number of Bolitogyrus species to 80. Several keys are updated to reflect the newly available data and new species.},
}

@article {pmid35780503,
year = {2022},
author = {Wang, M and Mao, X and Liu, J and Deng, B and Deng, S and Jin, S and Li, W and Gong, J and Deng, R and Zhu, J},
title = {A Versatile 3D-Confined Self-Assembly Strategy for Anisotropic and Ordered Mesoporous Carbon Microparticles.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {9},
number = {25},
pages = {e2202394},
pmid = {35780503},
issn = {2198-3844},
mesh = {*Carbon/chemistry ; Catalysis ; *Metal Nanoparticles/chemistry ; Platinum/chemistry ; Polymers/chemistry ; },
abstract = {Mesoporous carbon microparticles (MCMPs) with anisotropic shapes and ordered structures are attractive materials that remain challenging to access. In this study, a facile yet versatile route is developed to prepare anisotropic MCMPs by combining neutral interface-guided 3D confined self-assembly (3D-CSA) of block copolymer (BCP) with a self-templated direct carbonization strategy. This route enables pre-engineering BCP into microparticles with oblate shape and hexagonal packing cylindrical mesostructures, followed by selective crosslinking and decorating of their continuous phase with functional species (such as platinum nanoparticles, Pt NPs) via in situ growth. To realize uniform in situ growth, a "guest exchange" strategy is proposed to make room for functional species and a pre-crosslinking strategy is developed to preserve the structural stability of preformed BCP microparticles during infiltration. Finally, Pt NP-loaded MCMPs are derived from the continuous phase of BCP microparticles through selective self-templated direct carbonization without using any external carbon source. This study introduces an effective concept to obtain functional species-loaded and N-doped MCMPs with oblate shape and almost hexagonal structure (p6mm), which would find important applications in fuel cells, separation, and heterogeneous catalysis.},
}

*Carbon/chemistry
Catalysis
*Metal Nanoparticles/chemistry
Platinum/chemistry
Polymers/chemistry

@article {pmid35775956,
year = {2022},
author = {Fang, G and Chen, H and Shao, X and Wang, H and Zhan, D and Wang, R and Meng, P and Fang, H and Liu, F and Ling, P and Wu, Z and Diao, J and Yao, Q and Chen, Q},
title = {Single Image Capture of Bioactive Ion Crosstalk within Inter-Organelle Membrane Contacts at Nanometer Resolution.},
journal = {Small methods},
volume = {6},
number = {8},
pages = {e2200321},
doi = {10.1002/smtd.202200321},
pmid = {35775956},
issn = {2366-9608},
mesh = {Cell Physiological Phenomena ; *Lysosomes/metabolism ; Mitochondria ; Mitochondrial Membranes ; *Organelles/chemistry ; },
abstract = {Rapid bioactive ion exchange is a form of communication that regulates a wide range of biological processes. Despite advances in super-resolution optical microscopy, visualizing ion exchange remains challenging due to the extremely fast nature of these events. Here, a "converting a dynamic event into a static image construction" (CDtSC) strategy is developed that uses the color transformation of a single dichromatic molecular probe to visualize bioactive ion inter-organelle exchange in live cells. As a proof of concept, a reactive sulfur species (RSS) is analyzed at the mitochondria-lysosome contact sites (MLCs). A non-toxic and sensitive probe based on coumarin-hemicyanine structure is designed that responds to RSS localized in both mitochondria and lysosomes while fluorescing different colors. Using this probe, RSS give-and-take at MLCs is visualized, thus providing the first evidence that RSS is involved in inter-organelle contacts and communication. Taken together, the CDtSC provides a strategy to visualize and analyze rapid inter-organelle ion exchange events in live cells at nanometer resolution.},
}

Cell Physiological Phenomena
*Lysosomes/metabolism
Mitochondria
Mitochondrial Membranes
*Organelles/chemistry

@article {pmid35760130,
year = {2022},
author = {Sreedhar, A and Hoai Ta, QT and Noh, JS},
title = {Role of p-n junction initiated mixed-dimensional 0D/2D, 1D/2D, and 2D/2D BiOX (X = Cl, Br, and I)/TiO2 nanocomposite interfaces for environmental remediation applications: A review.},
journal = {Chemosphere},
volume = {305},
number = {},
pages = {135478},
doi = {10.1016/j.chemosphere.2022.135478},
pmid = {35760130},
issn = {1879-1298},
mesh = {Catalysis ; *Environmental Restoration and Remediation ; *Nanocomposites ; Titanium ; Water ; },
abstract = {Nowadays, we are critically facing various environmental issues. Among these, water contamination is the foremost issue, which worsens our health and living organisms in the water. Thus, it is necessary to provide an avenue to minimize the toxic matter through the development of facile technique and harmless photocatalyst. In this review, we intended to uncover the findings associated with various 0D, 1D, and 2D nanostructures featured photocatalysts for advancements in interfacial characteristics and toxic matter degradation. In this context, we evaluated the promising mixed-dimensional 0D/2D, 1D/2D, and 2D/2D bismuth oxyhalides BiOX (X = Cl, Br, and I) integrated TiO2 nanostructure interfaces. Tunable mixed-dimensional interfaces highlighted with higher surface area, more heterojunctions, variation in the conduction and valence band potential, narrowed band gap, and built-in electric field formation between BiOX and TiO2, which exhibits remarkable toxic dye, heavy metals, and antibiotics degradation. Further, this review further examines insights into the charge carrier generation, separation, and shortened charge transfer path at reduced recombination. Considering the advantages of type-II, S-scheme, and Z-scheme charge transfer mechanisms in the BiOX/TiO2, we heightened the combination of various reactive species generation. In a word, the concept of mixed-dimensional BiOX/TiO2 heterojunction interface endows toxic matter adsorption and decomposition into useful products. Challenges and future perspectives are also provided.},
}

Catalysis
*Environmental Restoration and Remediation
*Nanocomposites
Titanium
Water

@article {pmid35754287,
year = {2022},
author = {Salvatore, MF and Soto, I and Kasanga, EA and James, R and Shifflet, MK and Doshier, K and Little, JT and John, J and Alphonso, HM and Cunningham, JT and Nejtek, VA},
title = {Establishing Equivalent Aerobic Exercise Parameters Between Early-Stage Parkinson's Disease and Pink1 Knockout Rats.},
journal = {Journal of Parkinson's disease},
volume = {12},
number = {6},
pages = {1897-1915},
pmid = {35754287},
issn = {1877-718X},
mesh = {Animals ; Exercise Test ; Exercise Therapy/methods ; Heart Rate ; Humans ; Infant ; *Parkinson Disease/genetics ; Rats ; },
abstract = {BACKGROUND: Rodent Parkinson's disease (PD) models are valuable to interrogate neurobiological mechanisms of exercise that mitigate motor impairment. Translating these mechanisms to human PD must account for physical capabilities of the patient.

OBJECTIVE: To establish cardiovascular parameters as a common metric for cross-species translation of aerobic exercise impact.

METHOD: We evaluated aerobic exercise impact on heart rate (HR) in 21 early-stage PD subjects (Hoehn Yahr ≤1.5) exercising in non-contact boxing training for ≥3 months, ≥3x/week. In 4-month-old Pink1 knockout (KO) rats exercising in a progressively-increased treadmill speed regimen, we determined a specific treadmill speed that increased HR to an extent similar in human subjects.

RESULTS: After completing aerobic exercise for ∼30 min, PD subjects had increased HR∼35% above baseline (∼63% maximum HR). Motor and cognitive test results indicated the exercising subjects completed the timed up and go (TUG) and trail-making test (TMT-A) in significantly less time versus exercise-naïve PD subjects. In KO and age-matched wild-type (WT) rats, treadmill speeds of 8-10 m/min increased HR up to 25% above baseline (∼67% maximum HR), with no further increases up to 16 m/min. Exercised KO, but not WT, rats showed increased locomotor activity compared to an age-matched exercise-naïve cohort at 5 months old.

CONCLUSION: These proof-of-concept results indicate HR is a cross-species translation parameter to evaluate aerobic exercise impact on specific motor or cognitive functions in human subjects and rat PD models. Moreover, a moderate intensity exercise regimen is within the physical abilities of early-stage PD patients and is therefore applicable for interrogating neurobiological mechanisms in rat PD models.},
}

Animals
Exercise Test
Exercise Therapy/methods
Heart Rate
Humans
Infant
*Parkinson Disease/genetics
Rats

@article {pmid35736076,
year = {2022},
author = {Cavender, JC and Vadell, EM and Perrigo, AL and Landolt, JC and Stephenson, SL and Liu, P},
title = {Four New Species of Dictyostelids from Soil Systems in Northern Thailand.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {6},
pages = {},
pmid = {35736076},
issn = {2309-608X},
abstract = {Dictyostelid cellular slime molds (dictyostelids) are ubiquitous microorganisms found in the uppermost layers of most soils. Reports on the species diversity of dictyostelids in Southeast Asia, particularly Thailand, are few in number. A survey for dictyostelids performed in northern Thailand in 2008 recovered 15 distinctive forms, including several common species and a number of forms morphologically different from anything already described. Five of the latter were formally described as new to science in a previous paper. An additional five isolates appeared to be morphologically distinct, and this was supported by DNA sequence data and phylogenetic analysis. These isolates representing four species are described herein as species new to science. Detailed descriptions and illustrations of these new species are provided.},
}

@article {pmid35718755,
year = {2022},
author = {Estes, JA and Vermeij, GJ},
title = {History's legacy: Why future progress in ecology demands a view of the past.},
journal = {Ecology},
volume = {103},
number = {11},
pages = {e3788},
doi = {10.1002/ecy.3788},
pmid = {35718755},
issn = {1939-9170},
mesh = {Animals ; *Ecosystem ; Food Chain ; Hydrogen-Ion Concentration ; Kelp ; Otters ; Seawater ; *Ecology/methods/standards ; },
abstract = {History has profoundly affected the composition, distribution, and abundances of species in contemporary ecosystems. A full understanding of how ecosystems work and change must therefore take history into account. We offer four well-studied examples illustrating how a knowledge of history has strengthened interpretations of modern systems: the development of molluscan antipredatory defenses in relation to shell-breaking predators; the North Pacific kelp ecosystem with sea otters, smaller predators, sea urchins, and large herbivores; estuarine ecosystems affected by the decline in oysters and other suspension feeders; and the legacy of extinct large herbivores and frugivores in tropical American forests. Many current ecological problems would greatly benefit from a historical perspective. We highlight four of these: soil depletion and tree stunting in forests related to the disappearance of large consumers; the spread of anoxic dead zones in the ocean, which we argue could be mitigated by restoring predator and suspension-feeding guilds; ocean acidification, which would be alleviated by more nutrient recycling by consumers in the aerobic ecosystem; and the relation between species diversity and keystone predators, a foundational concept that is complicated by simplified trophic relationships in modern ecosystems.},
}

Animals
*Ecosystem
Food Chain
Hydrogen-Ion Concentration
Kelp
Otters
Seawater
*Ecology/methods/standards

@article {pmid35705651,
year = {2022},
author = {Sharwani, AA and Narayanan, KB and Khan, ME and Han, SS},
title = {Photocatalytic degradation activity of goji berry extract synthesized silver-loaded mesoporous zinc oxide (Ag@ZnO) nanocomposites under simulated solar light irradiation.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10017},
pmid = {35705651},
issn = {2045-2322},
mesh = {Anti-Bacterial Agents/chemistry/pharmacology ; Catalysis ; Coloring Agents ; Congo Red ; Gram-Negative Bacteria ; Gram-Positive Bacteria ; *Lycium ; *Metal Nanoparticles/chemistry ; Methylene Blue ; *Nanocomposites/chemistry ; Plant Extracts/chemistry/pharmacology ; Silver/chemistry ; Zinc ; *Zinc Oxide/chemistry ; },
abstract = {Different approaches have been developed for the synthesis of various nanostructured materials with unique morphologies. This study demonstrated the photocatalytic and antimicrobial abilities of silver-loaded zinc oxide nanocomposites (Ag@ZnO NCs). Initially, ZnO with a unique mesoporous ellipsoidal morphology in the size range of 0.59 ± 0.11 × 0.33 ± 0.09 µm (length × width) was synthesized using aqueous precipitation in a mild hydrothermal condition (80 °C) with the aqueous fruit extract of goji berry (GB) (as an additive) and calcined in air at 200 °C/2 h and 250 °C/3 h. Powder X-ray diffraction (XRD) revealed the formation of a hexagonal phase of the wurtzite (WZ) structure. The average crystallite size of ZnO was 23.74 ± 4.9 nm as calculated using Debye-Scherrer's equation. It also possesses higher thermal stability with the surface area, pore volume, and pore size of 11.77 m[2]/g, 0.027 cm[3]/g, and 9.52 nm, respectively. Furthermore, different mesoporous Ag@ZnO NCs loaded with face-centered cubic (fcc) silver nanoparticles (Ag NPs) in the range of 90-160 nm were synthesized by GB extract as a reducing and capping agent on the surface of ZnO after calcination in air. The immobilization of Ag NPs was confirmed by XRD, X-ray photoelectron spectroscopy (XPS), field-emission scanning electron microscopy (FE-SEM), FE-transmission electron microscopy (FE-TEM), and energy-dispersive X-ray spectroscopy (EDS). It was found that Ag0.2@ZnO NC (0.2 wt% of Ag) showed excellent photocatalytic degradation of both methylene blue (MB) (cationic) and congo red (CR) (anionic) dyes under simulated solar irradiation. The photocatalytic degradation of 99.3 ± 0.35% MB and 98.5 ± 1.3% CR occurred in 90 and 55 min, respectively, at room temperature by Ag0.2@ZnO NC. Besides, these NCs also showed broad-spectrum antibacterial activity against both Gram-positive and Gram-negative bacteria. The mechanistic concept of generating reactive oxygen species (ROS) by electron and hole charge (e‾/h[+]) carriers seems to be responsible for the photocatalytic degradation of commercial dyes and antibacterial activities by Ag@ZnO NCs. Thus, these silver-loaded mesoporous ellipsoidal ZnO NCs are promising candidates as photocatalysts for industrial/wastewater treatment as well as in antimicrobial therapeutics.},
}

Anti-Bacterial Agents/chemistry/pharmacology
Catalysis
Coloring Agents
Congo Red
Gram-Negative Bacteria
Gram-Positive Bacteria
*Lycium
*Metal Nanoparticles/chemistry
Methylene Blue
*Nanocomposites/chemistry
Plant Extracts/chemistry/pharmacology
Silver/chemistry
Zinc
*Zinc Oxide/chemistry

@article {pmid35644289,
year = {2022},
author = {Sanati, M and Afshari, AR and Kesharwani, P and Sukhorukov, VN and Sahebkar, A},
title = {Recent trends in the application of nanoparticles in cancer therapy: The involvement of oxidative stress.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {348},
number = {},
pages = {287-304},
doi = {10.1016/j.jconrel.2022.05.035},
pmid = {35644289},
issn = {1873-4995},
mesh = {Humans ; *Nanoparticles/chemistry ; Nanotechnology ; *Neoplasms/drug therapy/pathology ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; },
abstract = {In the biomedical area, the interdisciplinary field of nanotechnology has the potential to bring numerous unique applications, including better tactics for cancer detection, diagnosis, and therapy. Nanoparticles (NPs) have been the topic of many research and material applications throughout the last decade. Unlike small-molecule medications, NPs are defined by distinct physicochemical characteristics, such as a large surface-to-volume ratio, which allows them to permeate live cells with relative ease. The versatility of NPs as both therapeutics and diagnostics makes them ideal for a broad spectrum of illnesses, from infectious diseases to cancer. A significant amount of data has been participated in the current scientific publications, emphasizing the concept that NPs often produce reactive oxygen species (ROS) to a larger degree than micro-sized particles. It is important to note that oxidative stress governs a wide range of cell signaling cascades, many of which are responsible for cancer cell cytotoxicity. Here, we aimed to provide insight into the signaling pathways triggered by oxidative stress in cancer cells in response to several types of nanomaterials, such as metallic and polymeric NPs and quantum dots. We discuss recent advances in developing integrated anticancer medicines based on NPs targeted to destroy malignant cells by increasing their ROS setpoint.},
}

Humans
*Nanoparticles/chemistry
Nanotechnology
*Neoplasms/drug therapy/pathology
Oxidative Stress
Reactive Oxygen Species/metabolism

@article {pmid35633899,
year = {2022},
author = {Ali, C and Blackmond, DG and Burés, J},
title = {Kinetic Rationalization of Nonlinear Effects in Asymmetric Catalytic Cascade Reactions under Curtin-Hammett Conditions.},
journal = {ACS catalysis},
volume = {12},
number = {10},
pages = {5776-5785},
pmid = {35633899},
issn = {2155-5435},
abstract = {Observations of nonlinear effects of catalyst enantiopurity on product enantiomeric excess in asymmetric catalysis are often used to infer that more than one catalyst species is involved in one or more reaction steps. We demonstrate here, however, that in the case of asymmetric catalytic cascade reactions, a nonlinear effect may be observed in the absence of any higher order catalyst species or any reaction step involving two catalyst species. We illustrate this concept with an example from a recent report of an organocatalytic enantioselective [10 + 2] stepwise cyclization reaction. The disruption of pre-equilibria (Curtin-Hammett equilibrium) in reversible steps occurring prior to the final irreversible product formation step can result in an alteration of the final product ee from what would be expected based on a linear relationship with the enantiopure catalyst. The treatment accounts for either positive or negative nonlinear effects in systems over a wide range of conditions including "major-minor" kinetics or the more conventional "lock-and-key" kinetics. The mechanistic scenario proposed here may apply generally to other cascade reaction systems exhibiting similar kinetic features and should be considered as a viable alternative model whenever a nonlinear effect is observed in a cascade sequence of reactions.},
}

@article {pmid35630417,
year = {2022},
author = {Melekhin, M and Yakovleva, Y and Lebedeva, N and Nekrasova, I and Nikitashina, L and Castelli, M and Mayén-Estrada, R and Romanovich, AE and Petroni, G and Potekhin, A},
title = {Cryptic Diversity in Paramecium multimicronucleatum Revealed with a Polyphasic Approach.},
journal = {Microorganisms},
volume = {10},
number = {5},
pages = {},
pmid = {35630417},
issn = {2076-2607},
abstract = {Paramecium (Ciliophora) systematics is well studied, and about twenty morphological species have been described. The morphological species may include several genetic species. However, molecular phylogenetic analyses revealed that the species diversity within Paramecium could be even higher and has raised a problem of cryptic species whose statuses remain uncertain. In the present study, we provide the morphological and molecular characterization of two novel Paramecium species. While Paramecium lynni n. sp., although morphologically similar to P. multimicronucleatum, is phylogenetically well separated from all other Paramecium species, Paramecium fokini n. sp. appears to be a cryptic sister species to P. multimicronucleatum. The latter two species can be distinguished only by molecular methods. The number and structure of micronuclei, traditionally utilized to discriminate species in Paramecium, vary not only between but also within each of the three studied species and, thus, cannot be considered a reliable feature for species identification. The geographic distribution of the P. multimicronucleatum and P. fokini n. sp. strains do not show defined patterns, still leaving space for a role of the geographic factor in initial speciation in Paramecium. Future findings of new Paramecium species can be predicted from the molecular data, while morphological characteristics appear to be unstable and overlapping at least in some species.},
}

@article {pmid35621795,
year = {2022},
author = {Ivković, M and Sinclair, BJ and Wahlberg, E},
title = {The Century Old Taxonomic Confusion Surrounding Wiedemannia zetterstedti Fallén and Related Species Is Resolved (Diptera: Empididae): Revision of the W. zetterstedti Group.},
journal = {Insects},
volume = {13},
number = {5},
pages = {},
pmid = {35621795},
issn = {2075-4450},
abstract = {The Wiedemannia zetterstedti species group is revised after examination of all available type specimens and includes one new species (W. ulrichi Ivković & Sinclair sp. nov.) and four redescribed species (W. czernyi (Bezzi), W. longipennis (Mik) stat. rev., W. rufipes (Oldenberg) stat. rev. and W. zetterstedti (Fallén)). The following new synonyms are proposed: W. (Roederella) ouedorum Vaillant, 1952 = W. czernyi (Bezzi, 1905); Paramesia riparia Robert, 1836 = W. zetterstedti (Fallén, 1826). Lectotypes are designated for the following species/subspecies: Atalanta hirtiloba Speiser, Brachystoma escheri Zetterstedt, Clinocera czernyi Bezzi, Clinocera longipennis Mik, Paramesia riparia Robert, and Roederia czernyi rufipes Oldenberg. In addition to morphological evidence, molecular species concepts were investigated using a molecular phylogenetic divergence-based species delimitation (bPTP) and results confirmed the morphological conclusions. A key to species is presented and geographic distributions are mapped.},
}

@article {pmid35621776,
year = {2022},
author = {Liu, T and Geng, X and Tang, Y and Li, B and Zhang, H and Teng, K},
title = {First Report of the Immature Stages of the Leaf-Mining Genus Subclemensia Kozlov, 1987 (Lepidoptera: Incurvariidae), with a Re-Illustration of the Type Species and a Generic Concept Discussion Based on Immature Characters.},
journal = {Insects},
volume = {13},
number = {5},
pages = {},
pmid = {35621776},
issn = {2075-4450},
abstract = {The immature stages of primitive Lepidoptera can provide quite different but often useful morphological evidence and synapomorphies from those of adults. Incurvariidae is one of the most primitive lineages of extant Lepidoptera, which is species-poor but highly diverse, but half of the genera lack any information on immature stages. New knowledge on the immature stages of the family is expected to provide useful morphological evidence and synapomorphies to stabilize the generic nomenclature. Subclemensia Kozlov, 1987 is one of the monotypic genera in Incurvariidae. In this study, the immature stages of the type species of Subclemensia are reported for the first time. The leaf mine, host plant and its biological characteristics are also provided. DNA barcodes were generated to aid the species delimitation. The adult male and female genitalia are re-illustrated by color photography to supplement the original line drawings. The generic concepts of Subclemensia and other related genera are discussed based on immature characters.},
}

@article {pmid35615129,
year = {2022},
author = {Chang, JT and Chao, CT and Nakamura, K and Liu, HL and Luo, MX and Liao, PC},
title = {Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {824158},
pmid = {35615129},
issn = {1664-462X},
abstract = {The divergence process of incipient species is fascinating but elusive by incomplete lineage sorting or gene flow. Species delimitation is also challenging among those morphologically similar allopatric species, especially when lacking comprehensive data. Cycas sect. Asiorientales, comprised of C. taitungensis and C. revoluta in the Ryukyu Archipelago and Taiwan, diverged recently with continuous gene flow, resulting in a reciprocal paraphyletic relationship. Their previous evolutionary inferences are questioned from few genetic markers, incomplete sampling, and incomprehensive morphological comparison by a long-term taxonomic misconception. By whole range sampling, this study tests the geographic mode of speciation in the two species of Asiorientales by approximate Bayesian computation (ABC) using genome-wide single nucleotide polymorphisms (SNPs). The individual tree was reconstructed to delimit the species and track the gene-flow trajectory. With the comparison of diagnostic morphological traits and genetic data, the allopatric speciation was rejected. Alternatively, continuous but spatially heterogeneous gene flow driven by transoceanic vegetative dispersal and pollen flow with contrasting population sizes blurred their species boundary. On the basis of morphological, genetic, and evolutionary evidence, we synonymized these two Cycas species. This study highlights not only the importance of the Kuroshio Current to species evolution but also the disadvantage of using species with geographically structured genealogies as conservation units.},
}

@article {pmid35589052,
year = {2022},
author = {Ennes Silva, F and Valsecchi do Amaral, J and Roos, C and Bowler, M and Röhe, F and Sampaio, R and Cora Janiak, M and Bertuol, F and Ismar Santana, M and de Souza Silva Júnior, J and Rylands, AB and Gubili, C and Hrbek, T and McDevitt, AD and Boubli, JP},
title = {Molecular phylogeny and systematics of bald uakaris, genus Cacajao (Primates: Pitheciidae), with the description of a new species.},
journal = {Molecular phylogenetics and evolution},
volume = {173},
number = {},
pages = {107509},
doi = {10.1016/j.ympev.2022.107509},
pmid = {35589052},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Genome ; Phylogeny ; *Pitheciidae ; },
abstract = {Bald uakaris, genus Cacajao, are Amazonian primates currently classified as one species and four subspecies based on the patterns of pelage coloration. In this study, we test if their current taxonomy is represented by the phylogenetic relationship of the main lineages retrieved from molecular data. We included, for the first time, all bald uakari taxa in a mitochondrial (cytochrome b) and genome-wide (ddRAD) phylogenetic analyses. We also examined the pattern of pelage colouration in specimens from zoological collections. Having determined the number of lineages using Maximum Likelihood and the species tree using coalescent analyses, we test their divergence time using a Bayesian approach. While the cytochrome b analysis only recovered two clades, the ddRAD analysis supported the reciprocal monophyly of five lineages of bald uakaris, with all clades including only individuals with distinct and exclusive diagnostic phenotypic characters. We found that species diversification in Cacajao occurred during the last 300 Kya and may have been influenced by the formation of rivers and flooded forests in western Amazonia. We propose that the four bald uakari subspecies currently recognised can be upgraded to species level and we describe the white uakaris from the basin of the Rio Tarauacá as a new species.},
}

Animals
Bayes Theorem
Cytochromes b/genetics
DNA, Mitochondrial/genetics
Genome
Phylogeny
*Pitheciidae

@article {pmid35575078,
year = {2022},
author = {Lee, J and Willett, CS},
title = {Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids.},
journal = {The Journal of heredity},
volume = {113},
number = {2},
pages = {171-183},
doi = {10.1093/jhered/esab068},
pmid = {35575078},
issn = {1465-7333},
mesh = {Animals ; *Copepoda/genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.},
}

Animals
*Copepoda/genetics
DNA, Mitochondrial/genetics
Genes, Mitochondrial
Haplotypes
Mitochondria/genetics
Phylogeny

@article {pmid35565523,
year = {2022},
author = {Bugarski-Stanojević, V and Stamenković, G and Jojić, V and Ćosić, N and Ćirović, D and Stojković, O and Veličković, J and Savić, I},
title = {Cryptic Diversity of the European Blind Mole Rat Nannospalax leucodon Species Complex: Implications for Conservation.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {9},
pages = {},
pmid = {35565523},
issn = {2076-2615},
abstract = {We explored the cryptic speciation of the Nannospalax leucodon species complex, characterised by intense karyotype evolution and reduced phenotypic variability that has produced different lineages, out of which 25 are described as chromosomal forms (CFs), so many cryptic species remain unnoticed. Although some of them should be classified as threatened, they lack the official nomenclature necessary to be involved in conservation strategies. Reproductive isolation between seven CFs has previously been demonstrated. To investigate the amount and dynamics of genetic discrepancy that follows chromosomal changes, infer speciation levels, and obtain phylogenetic patterns, we analysed mitochondrial 16S rRNA and MT-CYTB nucleotide polymorphism among 17 CFs-the highest number studied so far. Phylogenetic trees delineated 11 CFs as separate clades. Evolutionary divergence values overlapped with acknowledged higher taxonomic categories, or sometimes exceeded them. The fact that CFs with higher 2n are evolutionary older corresponds to the fusion hypothesis of Nannospalax karyotype evolution. To participate in conservation strategies, N. leucodon classification should follow the biological species concept, and proposed cryptic species should be formally named, despite a lack of classical morphometric discrepancy. We draw attention towards the syrmiensis and montanosyrmiensis CFs, estimated to be endangered/critically endangered, and emphasise the need for detailed monitoring and population survey for other cryptic species.},
}

@article {pmid35552760,
year = {2022},
author = {DeRaad, DA and McCormack, JE and Chen, N and Peterson, AT and Moyle, RG},
title = {Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays.},
journal = {Systematic biology},
volume = {71},
number = {6},
pages = {1453-1470},
doi = {10.1093/sysbio/syac034},
pmid = {35552760},
issn = {1076-836X},
mesh = {Animals ; Gene Flow ; Genetic Speciation ; Genetics, Population ; *Passeriformes ; Phylogeny ; *Songbirds/genetics ; },
abstract = {Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-Jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage A. w. texana, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (Aphelocoma californica) and Woodhouse's Scrub-Jay (Aphelocoma woodhouseii) result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting (ILS) to better understand the systematics of other groups with similarly complex evolutionary histories. [Gene flow; genomics; introgression; phylogenomics; population genetics; species delimitation; species trees; systematics.].},
}

Animals
Gene Flow
Genetic Speciation
Genetics, Population
*Passeriformes
Phylogeny
*Songbirds/genetics

@article {pmid35535507,
year = {2022},
author = {Cauz-Santos, LA and Dodsworth, S and Samuel, R and Christenhusz, MJM and Patel, D and Shittu, T and Jakob, A and Paun, O and Chase, MW},
title = {Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility.},
journal = {The Plant journal : for cell and molecular biology},
volume = {111},
number = {1},
pages = {7-18},
pmid = {35535507},
issn = {1365-313X},
mesh = {Australia ; Genomics ; Phylogeny ; *RNA-Dependent RNA Polymerase/genetics ; *Tobacco/genetics ; },
abstract = {One of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. This susceptibility is the result of an insertion and consequent loss of function in the RNA-dependent RNA polymerase 1 (Rdr1) gene. However, the origin and age of LAB and the evolution of N. benthamiana across its wide distribution in Australia remain relatively underexplored. Here, we have used multispecies coalescent methods on genome-wide single nucleotide polymorphisms (SNPs) to assess species limits, phylogenetic relationships and divergence times within N. benthamiana. Our results show that the previous taxonomic concept of this species in fact comprises five geographically, morphologically and genetically distinct species, one of which includes LAB. We provide clear evidence that LAB is closely related to accessions collected further north in the Northern Territory; this species split much earlier, c. 1.1 million years ago, from their common ancestor than the other four in this clade and is morphologically the most distinctive. We also found that the Rdr1 gene insertion is variable among accessions from the northern portions of the Northern Territory. Furthermore, this long-isolated species typically grows in sheltered sites in subtropical/tropical monsoon areas of northern Australia, contradicting the previously advanced hypothesis that this species is an extremophile that has traded viral resistance for precocious development.},
}

Australia
Genomics
Phylogeny
*RNA-Dependent RNA Polymerase/genetics
*Tobacco/genetics

@article {pmid35524916,
year = {2022},
author = {Zhang, B and Chen, H and Deng, M and Li, J and González, AL and Wang, S},
title = {High dimensionality of stoichiometric niches in soil fauna.},
journal = {Ecology},
volume = {103},
number = {9},
pages = {e3741},
doi = {10.1002/ecy.3741},
pmid = {35524916},
issn = {1939-9170},
mesh = {Animals ; Biomass ; Carbon/analysis ; Nitrogen/analysis ; *Phosphorus/analysis ; *Soil/chemistry ; },
abstract = {The ecological niche is a fundamental concept to understand species' coexistence in natural communities. The recently developed framework of the multidimensional stoichiometric niche (MSN) characterizes species' niches using chemical elements in living organisms. Despite the fact that living organisms are composed of multiple elements, stoichiometric studies have so far mostly focused on carbon (C), nitrogen (N), and phosphorus (P), and therefore a quantitative analysis of the dimensionality of the MSN in living organisms is still lacking, particularly for animals. Here we quantified 10 elements composing the biomass of nine soil animal taxa (958 individuals) from three trophic groups. We found that all 10 elements exhibited large variation among taxa, which was partially explained by their phylogeny. Overlaps of MSNs among the nine soil animal taxa were relatively smaller based on 10 elements, compared with those based on only C, N, and P. Discriminant analysis using all 10 elements successfully differentiated among the nine taxa (accuracy: 90%), whereas that using only C, N, and P resulted in a lower accuracy (60%). Our findings provide new evidence for MSN differentiation in soil fauna and demonstrate the high dimensionality of organismal stoichiometric niches beyond C, N, and P.},
}

Animals
Biomass
Carbon/analysis
Nitrogen/analysis
*Phosphorus/analysis
*Soil/chemistry

@article {pmid35498683,
year = {2022},
author = {Xian, X and Zhao, H and Wang, R and Qiao, H and Guo, J and Zhang, G and Liu, W and Wan, F},
title = {Ecological Niche Shifts Affect the Potential Invasive Risk of Rapistrum rugosum (L.) All. in China.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {827497},
pmid = {35498683},
issn = {1664-462X},
abstract = {Ecological niche is a key concept that links species distributions. Ecological niche shifts are expected to affect the potential invasive risk of alien species. Rapistrum rugosum is an invasive agricultural weed in many countries. Wild populations of R. rugosum have been recorded in China, representing a great threat to the regional crops. Based on distribution records from different regions and relevant environmental variables, the present study predicted the potential distribution and estimated the invasive risk of R. rugosum in China. Ecological niche shifts strongly affected the potential invasive risk of R. rugosum in China. The two most important variables were annual temperature range (Bio7) and mean temperature of the coldest quarter (Bio11). The total suitable habitat for the species covered an area of 287.53 × 10[4]km[2] and was mainly distributed in Southwest, Southeast, and Central China. Australia, Canada, Brazil, the United States, and Argentina accounted for over 90% of the inspection records of R. rugosum from Chinese entry ports during 2015-2018. The intercepted R. rugosum was frequently mixed in Glycine max (L.) Merr., Hordeum vulgare L., linseed, Triticum aestivum L., and Sorghum bicolor (L.) Moench. Moreover, 80% interceptions were recorded from Tianjin, Guangdong, Nanjing, and Chengdu customs. Climatic conditions do not limit the establishment capability of R. rugosum in China. Our results provide a theoretical reference for the development of monitoring and control measures for this invasive weed.},
}

@article {pmid35491980,
year = {2022},
author = {Corrêa, LL and de Souza, DC and Adriano, EA},
title = {Relationship of the parasite Rhadinorhynchus plagioscionis (Acanthocephala) with Plagioscion squamosissimus host and its specificity of occurrence in the Brazilian Amazon.},
journal = {Annals of parasitology},
volume = {68},
number = {1},
pages = {177-183},
doi = {10.17420/ap6801.422},
pmid = {35491980},
issn = {2299-0631},
mesh = {*Acanthocephala ; Animals ; Brazil/epidemiology ; *Fish Diseases/epidemiology/parasitology ; *Parasites ; *Perciformes/parasitology ; },
abstract = {Objective was the relationship of the parasite Rhadinorhynchus plagioscionis with its host Plagioscion squamosissimus, providing morphological and morphometric data to prove the specificity of this parasite with its host, with reports occurring only in rivers in the Brazilian Amazon. Rhadinorhynchus plagioscionis infected P. squamosissimus captured in the municipal region of Santarém, in the state of Pará, in the eastern Brazilian Amazon. The specimens were analyzed by light and scanning electron microscopy. Morphological data obtained confirmed conspecificty with R. plagioscionis and supplemental information was added to the morphological concept of this species. The body of R. plagioscionis is cylindrical and milky-coloured with dorsal curvature, a long proboscis displaying ventral curvature with 12 longitudinal rows containing 22 to 24 hooks, which are larger and more prominent towards the end of the ventral curvature, and decrease in size in the posterior extremity of the proboscis. The present study describes, in addition to the morphological and morphometric characteristics of R. plagioscionis, which have host specificity for P. squamosissimus, a relationship being reported exclusively in the Brazilian Amazon.},
}

*Acanthocephala
Animals
Brazil/epidemiology
*Fish Diseases/epidemiology/parasitology
*Parasites
*Perciformes/parasitology

@article {pmid35456404,
year = {2022},
author = {Aggarwal, SK and Singh, A and Choudhary, M and Kumar, A and Rakshit, S and Kumar, P and Bohra, A and Varshney, RK},
title = {Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives.},
journal = {Genes},
volume = {13},
number = {4},
pages = {},
pmid = {35456404},
issn = {2073-4425},
mesh = {Chromosome Mapping ; Humans ; *Plant Breeding ; *Plants/genetics ; },
abstract = {Advances in sequencing technologies and bioinformatics tools have fueled a renewed interest in whole genome sequencing efforts in many organisms. The growing availability of multiple genome sequences has advanced our understanding of the within-species diversity, in the form of a pangenome. Pangenomics has opened new avenues for future research such as allowing dissection of complex molecular mechanisms and increased confidence in genome mapping. To comprehensively capture the genetic diversity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a super-pangenome. Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed. From understanding evolution and adaptation to elucidating host-pathogen interactions, finding novel genes or breeding targets to aid crop improvement to design effective vaccines for human prophylaxis, the increasing availability of the pangenome has revolutionized several aspects of biological research. The future availability of high-resolution pangenomes based on reference-level near-complete genome assemblies would greatly improve our ability to address complex biological problems.},
}

Chromosome Mapping
Humans
*Plant Breeding
*Plants/genetics

@article {pmid35450796,
year = {2022},
author = {Wells, T and Carruthers, T and Scotland, RW},
title = {Heuristics, species, and the analysis of systematic data.},
journal = {Trends in plant science},
volume = {27},
number = {6},
pages = {524-527},
doi = {10.1016/j.tplants.2022.03.013},
pmid = {35450796},
issn = {1878-4372},
support = {T001445/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Heuristics ; },
abstract = {Disagreements over how to define species potentially render them incomparable, yet biologists routinely count and compare species. This 'species problem' persists despite the wealth of data and methods available to contemporary systematists. A heuristic approach to species provides a consistent yet flexible means of selecting, assessing, and integrating different biological data.},
}

*Heuristics

@article {pmid35420714,
year = {2022},
author = {Wang, Z and Zhan, M and Hu, X},
title = {Pulsed Laser Excited Photoacoustic Effect for Disease Diagnosis and Therapy.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {28},
number = {37},
pages = {e202200042},
doi = {10.1002/chem.202200042},
pmid = {35420714},
issn = {1521-3765},
mesh = {Lasers ; Light ; *Photoacoustic Techniques/methods ; Spectrum Analysis ; },
abstract = {Pulsed laser can excite light absorber to generate photoacoustic (PA) effect, that is, when the absorber is irradiated with pulsed laser, the absorbed light energy is converted into local heat to cause rapid thermoelastic expansion and generate acoustic wave. The generated PA signal has been widely employed for the diagnosis of many diseases with superb contrast, high penetrability and sensitivity. In addition, with the increase of pulsed laser energy, the resulting PA shockwave and cavitation can promote efficient drug release at lesion sites to potentiate the resulting therapeutic efficacy. Furthermore, the PA shockwave/cavitation can mechanically inhibit disease and produce reactive species. In this Concept article, the principle and research status of pulsed laser excited disease theranostics are briefly summarized, extra suggestions are proposed to inspire extensive PA probes and photodynamic materials as well as novel methodologies.},
}

Lasers
Light
*Photoacoustic Techniques/methods
Spectrum Analysis

@article {pmid35398511,
year = {2022},
author = {Rajaonison, A and Le Page, S and Maurin, T and Chaudet, H and Raoult, D and Baron, SA and Rolain, JM},
title = {Antilogic, a new supervised machine learning software for the automatic interpretation of antibiotic susceptibility testing in clinical microbiology: proof-of-concept on three frequently isolated bacterial species.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {28},
number = {9},
pages = {1286.e1-1286.e8},
doi = {10.1016/j.cmi.2022.03.035},
pmid = {35398511},
issn = {1469-0691},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Artificial Intelligence ; Bacteria ; Escherichia coli ; Humans ; Microbial Sensitivity Tests ; Software ; Supervised Machine Learning ; },
abstract = {OBJECTIVE: Antibiotic susceptibility testing (AST) is necessary in order to adjust empirical antibiotic treatment, but the interpretation of results requires experience and knowledge. We have developed a machine learning software that is capable of reading AST images without any human intervention and that automatically interprets the AST, based on a database of antibiograms that have been clinically validated with European Committee on Antimicrobial Susceptibility Testing rules.

METHODS: We built a database of antibiograms that were labelled by senior microbiologists for three species: Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. We then developed Antilogic, a Python software based on an original image segmentation module and supervised learning models that we trained against the database. Finally, we blind tested Antilogic against a validation set of 5100 photos of antibiograms.

RESULTS: We trained Antilogic against a database of 18072 pictures of antibiograms. Overall agreement against the validation set reached 97% (16 855/17 281) regarding phenotypes. The severity rate of errors was also evaluated: 1.66% (287/17 281) were major errors and 0.80% (136/17 281) were very major errors. After implementation of uncertainty quantifications, the rate of errors decreased to 0.80% (114/13 451) and 0.42% (51/13 451) for major and very major errors respectively.

DISCUSSION: Antilogic is the first machine learning software that has been developed for AST interpretation. It is based on a novel approach that differs from the typical diameter measurement and expert system approach. Antilogic is a proof of concept that artificial intelligence can contribute to faster and easier diagnostic methods in the field of clinical microbiology.},
}

*Anti-Bacterial Agents/pharmacology
*Artificial Intelligence
Bacteria
Escherichia coli
Humans
Microbial Sensitivity Tests
Software
Supervised Machine Learning

@article {pmid35396623,
year = {2022},
author = {Koide, RT},
title = {On Holobionts, Holospecies, and Holoniches: the Role of Microbial Symbioses in Ecology and Evolution.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35396623},
issn = {1432-184X},
abstract = {My goal in writing this is to increase awareness of the roles played by microbial symbionts in eukaryote ecology and evolution. Most eukaryotes host one or more species of symbiotic microorganisms, including prokaryotes and fungi. Many of these have profound impacts on the biology of their hosts. For example, microbial symbionts may expand the niches of their hosts, cause rapid adaptation of the host to the environment and re-adaptation to novel conditions via symbiont swapping, facilitate speciation, and fundamentally alter our concept of the species. In some cases, microbial symbionts and multicellular eukaryote hosts have a mutual dependency, which has obvious conservation implications. Hopefully, this contribution will stimulate a reevaluation of important ecological and evolutionary concepts including niche, adaptation, the species, speciation, and conservation of multicellular eukaryotes.},
}