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20 Jul 2024 at 01:56
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Bibliography on: Species Concept


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RJR: Recommended Bibliography 20 Jul 2024 at 01:56 Created: 

Species Concept

Wikipedia: The species problem is the set of questions that arises when biologists attempt to define what a species is. Such a definition is called a species concept; there are at least 26 recognized species concepts. A species concept that works well for sexually reproducing organisms such as birds is useless for species that reproduce asexually, such as bacteria. The scientific study of the species problem has been called microtaxonomy. One common, but sometimes difficult, question is how best to decide which species an organism belongs to, because reproductively isolated groups may not be readily recognizable, and cryptic species may be present. There is a continuum from reproductive isolation with no interbreeding, to panmixis, unlimited interbreeding. Populations can move forward or backwards along this continuum, at any point meeting the criteria for one or another species concept, and failing others. Many of the debates on species touch on philosophical issues, such as nominalism and realism, and on issues of language and cognition. The current meaning of the phrase "species problem" is quite different from what Charles Darwin and others meant by it during the 19th and early 20th centuries. For Darwin, the species problem was the question of how new species arose. Darwin was however one of the first people to question how well-defined species are, given that they constantly change.

Created with PubMed® Query: ( ("species concept"[tiab:~6] OR "species concepts"[tiab] OR "species problem") NOT "invasive species" ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2024-07-14

Chen Z, Chen Y, Shi L, et al (2024)

Directional Construction of the Highly Stable Active-Site Ensembles at Sub-2 nm to Enhance Catalytic Activity and Selectivity.

Advanced materials (Deerfield Beach, Fla.) [Epub ahead of print].

Precise control over the size, species, and breakthrough of the activity-selectivity trade-off are great challenges for sub-nano non-noble metal catalysts. Here, for the first time, a "multiheteroatom induced SMSI + in situ P activation" strategy that enables high stability and effective construction of sub-2 nm metal sites for optimizing selective hydrogenation performance is developed. It is synthesized the smallest metal phosphide clusters (<2 nm) including from unary to ternary non-noble metal systems, accompanied by unprecedented thermal stability. In the proof-of-concept demonstration, further modulation of size and species results in the creation of a sub-2 nm site platform, directionally achieving single atom (Ni1), Ni1+metal cluster (Ni1+Nin), or novel Ni1+metal phosphide cluster synergistic sites (Ni1+Ni2Pn), respectively. Based on thorough structure and mechanism investigation, it is found the Ni1+Ni2Pn site is motivated to achieve electronic structure self-optimizing through synergistic SMSI and site coupling effect. Therefore, it speeds up the substrate adsorption-desorption kinetics in semihydrogenation of alkyne and achieves superior catalytic activity that is 56 times higher than the Ni1 site under mild conditions. Compared to traditional active sites, this may represent the highly effective integration of atom utilization, thermal stability, and favorable site requirements for chemisorption properties and reactivities of substrates.

RevDate: 2024-07-09
CmpDate: 2024-07-09

Moreno AA, Tully TN, Liu CC, et al (2024)

Reference Interval Creation for Symmetric Dimethylarginine (SDMA) in Healthy Hispaniolan Amazon Parrots (Amazona ventralis) and Quaker Parrots (Myiopsitta monachus).

Journal of avian medicine and surgery, 38(2):83-90.

Renal disease is often identified as a cause of morbidity and mortality in avian patients. However, currently, early antemortem detection of renal disease in avian patients is difficult. Anatomical and physiological differences between mammals and birds mean the use of commonly employed diagnostic testing (ie, measurement of blood urea nitrogen [BUN] and serum creatinine, urinalysis, and ultrasonography) are either nondiagnostic or difficult to achieve. Symmetric dimethylarginine (SDMA) is considered a more sensitive marker for renal disease in humans, dogs, and cats. However, SDMA has not yet been assessed for diagnostic use in any psittacine species. In this study, we establish reference ranges for SDMA in both Hispaniolan Amazon parrots (Amazona ventralis, HAP) and Quaker parrots (Myiopsitta monachus, QP). Blood was collected from 23 Amazon parrots and 32 Quaker parrots maintained in research facilities. Measurement of SDMA through a commercially available immunoassay (IA-SDMA) as well as creatinine, BUN, uric acid, phosphorus, calcium, sodium, potassium, and chloride were determined through IDEXX Laboratories. Plasma SDMA concentrations ranged from 6 to 15 µg/dL and 3 to 15 µg/dL for the HAP and QP, respectively. Sex was a confounding factor for the QP population, but sex did not have a significant effect on SDMA for the HAP population. No significant correlations were identified between SDMA concentrations and other parameters in either psittacine species. Our results show proof of concept for the IA-SDMA and provide reference intervals for SDMA in HAP and QP. Further investigation is required to determine the validity of this assay and the predictive power of SDMA in the detection of renal impairment for parrots and other common companion birds.

RevDate: 2024-06-27

Carlisle JD, Smith KT, Beck JL, et al (2024)

Beyond overlap: Considering habitat preference and fitness outcomes in the umbrella species concept.

Animal conservation, 27(2):212-225.

Umbrella species and other surrogate-species approaches to conservation provide an appealing framework to extend the reach of conservation efforts beyond single species. For the umbrella species concept to be effective, populations of multiple species of concern must persist in areas protected on behalf of the umbrella species. Most assessments of the concept, however, focus exclusively on geographic overlap among umbrella and background species, and not measures that affect population persistence (e.g., habitat quality or fitness). We quantified the congruence between the habitat preferences and nesting success of a high-profile umbrella species (greater sage-grouse, Centrocercus urophasianus, hereafter "sage-grouse"), and three sympatric species of declining songbirds (Brewer's sparrow Spizella breweri, sage thasher Oreoscoptes montanus, and vesper sparrow Pooecetes gramineus) in central Wyoming, USA during 2012 - 2013. We used machine-learning methods to create data-driven predictions of sage-grouse nest-site selection and nest survival probabilities by modeling field-collected sage-grouse data relative to habitat attributes. We then used field-collected songbird data to assess whether high-quality sites for songbirds aligned with those of sage-grouse. Nest sites selected by songbirds did not coincide with sage-grouse nesting preferences, with the exception that Brewer's sparrows preferred similar nest sites to sage-grouse in 2012. Moreover, the areas that produced higher rates of songbird nest survival were unrelated to those for sage-grouse. Our findings suggest that management actions at local scales that prioritize sage-grouse nesting habitat will not necessarily enhance the reproductive success of sagebrush-associated songbirds. Measures implemented to conserve sage-grouse and other purported umbrella species at broad spatial scales likely overlap the distribution of many species, however, broad-scale overlap may not translate to fine-scale conservation benefit beyond the umbrella species itself. The maintenance of microhabitat heterogeneity important for a diversity of species of concern will be critical for a more-holistic application of the umbrella species concept.

RevDate: 2024-06-27
CmpDate: 2024-06-27

Scopel JM, Medeiros-Neves B, Teixeira HF, et al (2024)

Supercritical Carbon Dioxide Extraction of Coumarins from the Aerial Parts of Pterocaulon polystachyum.

Molecules (Basel, Switzerland), 29(12): pii:molecules29122741.

Pterocaulon polystachyum is a species of pharmacological interest for providing volatile and non-volatile extracts with antifungal and amebicidal properties. The biological activities of non-volatile extracts may be related to the presence of coumarins, a promising group of secondary metabolites. In the present study, leaves and inflorescences previously used for the extraction of essential oils instead of being disposed of were subjected to extraction with supercritical CO2 after pretreatment with microwaves. An experimental design was followed to seek the best extraction condition with the objective function being the maximum total extract. Pressure and temperature were statistically significant factors, and the optimal extraction condition was 240 bar, 60 °C, and pretreatment at 30 °C. The applied mathematical models showed good adherence to the experimental data. The extracts obtained by supercritical CO2 were analyzed and the presence of coumarins was confirmed. The extract investigated for cytotoxicity against bladder tumor cells (T24) exhibited significant reduction in cell viability at concentrations between 6 and 12 μg/mL. The introduction of green technology, supercritical extraction, in the exploration of P. polystachyum as a source of coumarins represents a paradigm shift with regard to previous studies carried out with this species, which used organic solvents. Furthermore, the concept of circular bioeconomy was applied, i.e., the raw material used was the residue of a steam-distillation process. Therefore, the approach used here is in line with the sustainable exploitation of native plants to obtain extracts rich in coumarins with cytotoxic potential against cancer cells.

RevDate: 2024-06-26

Waddle AW, Clulow S, Aquilina A, et al (2024)

Hotspot shelters stimulate frog resistance to chytridiomycosis.

Nature [Epub ahead of print].

Many threats to biodiversity cannot be eliminated; for example, invasive pathogens may be ubiquitous. Chytridiomycosis is a fungal disease that has spread worldwide, driving at least 90 amphibian species to extinction, and severely affecting hundreds of others[1-4]. Once the disease spreads to a new environment, it is likely to become a permanent part of that ecosystem. To enable coexistence with chytridiomycosis in the field, we devised an intervention that exploits host defences and pathogen vulnerabilities. Here we show that sunlight-heated artificial refugia attract endangered frogs and enable body temperatures high enough to clear infections, and that having recovered in this way, frogs are subsequently resistant to chytridiomycosis even under cool conditions that are optimal for fungal growth. Our results provide a simple, inexpensive and widely applicable strategy to buffer frogs against chytridiomycosis in nature. The refugia are immediately useful for the endangered species we tested and will have broader utility for amphibian species with similar ecologies. Furthermore, our concept could be applied to other wildlife diseases in which differences in host and pathogen physiologies can be exploited. The refugia are made from cheap and readily available materials and therefore could be rapidly adopted by wildlife managers and the public. In summary, habitat protection alone cannot protect species that are affected by invasive diseases, but simple manipulations to microhabitat structure could spell the difference between the extinction and the persistence of endangered amphibians.

RevDate: 2024-06-20

Leal-Bertioli SCM, de Blas FJ, Carolina Chavarro M, et al (2024)

Relationships of the wild peanut species, section Arachis: A resource for botanical classification, crop improvement, and germplasm management.

American journal of botany [Epub ahead of print].

PREMISE: Wild species are strategic sources of valuable traits to be introduced into crops through hybridization. For peanut, the 33 currently described wild species in the section Arachis are particularly important because of their sexual compatibility with the domesticated species, Arachis hypogaea. Although numerous wild accessions are carefully preserved in seed banks, their morphological similarities pose challenges to routine classification.

METHODS: Using a high-density array, we genotyped 272 accessions encompassing all diploid species in section Arachis. Detailed relationships between accessions and species were revealed through phylogenetic analyses and interpreted using the expertise of germplasm collectors and curators.

RESULTS: Two main groups were identified: one with A genome species and the other with B, D, F, G, and K genomes. Species groupings generally showed clear boundaries. Structure within groups was informative, for instance, revealing the history of the proto-domesticate A. stenosperma. However, some groupings suggested multiple sibling species. Others were polyphyletic, indicating the need for taxonomic revision. Annual species were better defined than perennial ones, revealing limitations in applying classical and phylogenetic species concepts to the genus. We suggest new species assignments for several accessions.

CONCLUSIONS: Curated by germplasm collectors and curators, this analysis of species relationships lays the foundation for future species descriptions, classification of unknown accessions, and germplasm use for peanut improvement. It supports the conservation and curation of current germplasm, both critical tasks considering the threats to the genus posed by habitat loss and the current restrictions on new collections and germplasm transfer.

RevDate: 2024-06-18

Zhang L, Luo Z, Guo X, et al (2024)

Invasibility framework to predict the early colonization of alien Sonneratia in mangrove: Implications for coastal area management.

Journal of environmental management, 364:121461 pii:S0301-4797(24)01447-6 [Epub ahead of print].

Invasibility, or an ecosystem's susceptibility to invasion, plays a critical role in managing biological invasions but is challenging to quantify due to its dependence on specific ecosystem variables. This limitation restricts the practical application of this concept in the control of alien species. This study aims to simplify invasibility into measurable components and develop an applicable framework to predict early colonization of alien plants within the coastal mangrove ecosystem. We used the unchanneled path length (UPL), a widely applied hydrological connectivity-related indicator, to assess the accessibility of the mangrove. The enhanced vegetation index (EVI), positively correlated with above-ground biomass, was used to evaluate the potential competitive intensity. Firstly, building on existing studies, we developed a four-quadrant concept model integrating the effects of EVI and UPL on the early colonization of the alien species Sonneratia apetala. Our results revealed significant differences in EVI and UPL values between colonized and uncolonized areas, with colonized regions displaying markedly lower values (P < 0.001). Additionally, logistic regression showed a significant negative association between the probability of successful colonization by S. apetala and both indicators (P < 0.001). These results validate the effectiveness of our conceptual model. Furtherly, we identified four key niche opportunities for exotic species in mangrove: mudflats outside the mangrove forest, tidal creeks, canopy gaps, and unmanaged abandoned aquaculture ponds. Overall, this study provides important insight into the ecological processes of alien S. apetala colonization and practical information for management of coastal areas susceptible to invasion. Additionally, it presents a case study on the practical application of the concept of invasibility in the management of alien species.

RevDate: 2024-06-18

Lesur I, Rogier O, Sow MD, et al (2024)

A Strategy for Studying Epigenetic Diversity in Natural Populations: Proof of Concept in Poplar and Oak.

Journal of experimental botany pii:7695861 [Epub ahead of print].

These last 20 years, several techniques have been developed for quantifying DNA methylation, the most studied epigenetic marks in eukaryotes, including the gold standard method, whole-genome bisulphite sequencing (WGBS). WGBS quantifies genome-wide DNA methylation but has several inconveniences rendering it less suitable for population-scale epigenetic studies. The high cost of deep sequencing and the large amounts of data generated prompted us to seek an alternative approach. Restricting studies to parts of the genome would be a satisfactory alternative had there not been a major limitation: the need to select upstream targets corresponding to differentially methylated regions (DMRs) as targets. Given the need to study large numbers of samples, we propose a strategy for investigating DNA methylation variation in natural populations, considering the structural complexity of the genomes with their size and their content in unique as coding regions versus repeated regions as transposable elements. We first identified regions of highly variable DNA methylation in a representative subset of genotypes representative of the biological diversity in the population by WGBS. We then analysed the variations of DNA methylation in these targeted regions at the population level by Sequencing Capture Bisulphite (SeqCapBis). The entire strategy was then validated by applying it to another species. Our strategy was developed as a proof of concept on natural populations of two forest species: Populus nigra and Quercus petraea.

RevDate: 2024-06-16

Goldsmith TC (2024)

Mammal Aging as a Programmed Life Cycle Function - Resolving the Cause and Effect Conundrum.

Advanced biology [Epub ahead of print].

Because aging and internally determined lifespan vary greatly between similar species it is now widely accepted that aging is an evolved trait, resulting in two classes of evolutionary aging theories: aging is programmed by complex biological mechanisms, and aging is not programmed. As recently as 2002 programmed aging is thought to be theoretically impossible. However, genetics discoveries, results of selective breeding, and other direct evidence strongly support the idea that aging creates an evolutionary advantage and that therefore complex biological mechanisms evolved that control aging in mammals and other multiparous organisms. Like life-cycle programs that control reproduction, growth, and menopause the aging program can adjust the aging trait during an individual's life to compensate for temporary or local changes in external conditions that alter the optimum lifespan for a particular species population. Genetics discoveries also strongly support the evolvability concept to the effect that sexually reproducing species can evolve design features that increase their ability to evolve, and that aging is one such feature. Genetics discoveries also prove that biological inheritance involves transmission of organism design information in digital form between parent and descendant of any organism. This has major implications for the evolution process.

RevDate: 2024-06-14

Schmid S, Bachmann Salvy M, Garcia Jimenez A, et al (2024)

Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish.

Molecular ecology [Epub ahead of print].

Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterize the species' population structure, demographic history and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Interestingly, colour patterns differed noticeably among the Indonesian populations and the two populations at the extreme of the sampling distribution (i.e. Maldives and New Caledonia), which exhibited more comparable colour patterns despite their geographic and genetic distances. Our study emphasizes how whole-genome studies can uncover the intricate evolutionary past of wide-ranging species with diverse phenotypes, shedding light on the complex nature of the species concept paradigm.

RevDate: 2024-06-07

Karbstein K, Kösters L, Hodač L, et al (2024)

Species delimitation 4.0: integrative taxonomy meets artificial intelligence.

Trends in ecology & evolution pii:S0169-5347(23)00296-3 [Epub ahead of print].

Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.

RevDate: 2024-05-31

Konstantinidis KT (2023)

Sequence-discrete species for prokaryotes and other microbes: A historical perspective and pending issues.

mLife, 2(4):341-349.

Whether prokaryotes, and other microorganisms, form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying, regulating, and communicating about these organisms. In the past decade, comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters, albeit organisms of intermediate relatedness between the identified clusters are also frequently found. Accumulating evidence suggests, however, that the latter "intermediate" organisms show enough ecological and/or functional distinctiveness to be considered different species. Notably, the area of discontinuity between clusters often-but not always-appears to be around 85%-95% genome-average nucleotide identity, consistently among different taxa. More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well. This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters. The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination, which mediates (successful) horizontal gene transfer, around 95% nucleotide identity. Deviations from the 95% threshold (e.g., species showing lower intraspecies diversity) may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer. While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency (i.e., higher recombination within vs. between groups) is appealing, the supporting evidence remains anecdotal. The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.

RevDate: 2024-05-13

Alves G, Ogurtsov AY, Porterfield H, et al (2024)

Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm.

Journal of the American Society for Mass Spectrometry [Epub ahead of print].

Having fast, accurate, and broad spectrum methods for the identification of microorganisms is of paramount importance to public health, research, and safety. Bottom-up mass spectrometer-based proteomics has emerged as an effective tool for the accurate identification of microorganisms from microbial isolates. However, one major hurdle that limits the deployment of this tool for routine clinical diagnosis, and other areas of research such as culturomics, is the instrument time required for the mass spectrometer to analyze a single sample, which can take ∼1 h per sample, when using mass spectrometers that are presently used in most institutes. To address this issue, in this study, we employed, for the first time, tandem mass tags (TMTs) in multiplex identifications of microorganisms from multiple TMT-labeled samples in one MS/MS experiment. A difficulty encountered when using TMT labeling is the presence of interference in the measured intensities of TMT reporter ions. To correct for interference, we employed in the proposed method a modified version of the expectation maximization (EM) algorithm that redistributes the signal from ion interference back to the correct TMT-labeled samples. We have evaluated the sensitivity and specificity of the proposed method using 94 MS/MS experiments (covering a broad range of protein concentration ratios across TMT-labeled channels and experimental parameters), containing a total of 1931 true positive TMT-labeled channels and 317 true negative TMT-labeled channels. The results of the evaluation show that the proposed method has an identification sensitivity of 93-97% and a specificity of 100% at the species level. Furthermore, as a proof of concept, using an in-house-generated data set composed of some of the most common urinary tract pathogens, we demonstrated that by using the proposed method the mass spectrometer time required per sample, using a 1 h LC-MS/MS run, can be reduced to 10 and 6 min when samples are labeled with TMT-6 and TMT-10, respectively. The proposed method can also be used along with Orbitrap mass spectrometers that have faster MS/MS acquisition rates, like the recently released Orbitrap Astral mass spectrometer, to further reduce the mass spectrometer time required per sample.

RevDate: 2024-05-13

Cejas-Sánchez J, Caminade AM, Kajetanowicz A, et al (2024)

A water-soluble polyphosphorhydrazone Janus dendrimer built by "click" chemistry as support for Ru-complexes in catalysis.

Dalton transactions (Cambridge, England : 2003) [Epub ahead of print].

The field of supported catalysis has experienced increased attention with respect to the development of novel architectures for immobilizing catalytic species, aiming to maintain or enhance their activity while facilitating the easy recovery and reuse of the active moiety. Dendrimers have been identified as promising candidates capable of imparting such properties to catalysts through selective functionalization. The present study details the synthesis of two polyphosphorhydrazone (PPH) dendrons, each incorporating azide or acetylene groups at the core for subsequent coupling through "click" triazole chemistry. Employing this methodology, a novel PPH Janus dendrimer was successfully synthesized, featuring ten polyethylene glycol (PEG) chains on one side of the structure and ten Ru(p-cymene) derivatives on the other. This design was intended to confer dual properties, influencing solubility modulation, and allowing the presence of active catalytic moieties. The synthesized dendrimer underwent testing in the isomerization of allyl alcohols in organic solvents and biphasic solvent mixtures. The results demonstrated a positive dendritic effect compared with model monometallic and bimetallic species, providing a proof-of-concept for the first PPH Janus dendrimer with tested applications in catalysis.

RevDate: 2024-05-07
CmpDate: 2024-05-07

Amstislavsky S, Brusentsev E, Lebedeva D, et al (2024)

Effect of cryopreservation on Odc1 and RhoA genes expression in diapausing mouse blastocysts.

Reproduction in domestic animals = Zuchthygiene, 59(5):e14576.

The possibility of embryo cryopreservation is important for applying the genome resource banking (GRB) concept to those mammalian species that exhibit embryonal diapause in their early development. Odc1 encodes ODC1, which is a key enzyme in polyamine synthesis. RhoA is an essential part of Rho/ROCK system. Both Odc1 and RhoA play an important role in preimplantation embryo development. Studying these systems in mammalian species with obligate or experimentally designed embryonic diapause may provide insight into the molecular machinery underlying embryo dormancy and re-activation. The effect of cryopreservation procedures on the expression of the Odc1 and RhoA in diapausing embryos has not been properly studied yet. The purpose of this work is to address the possibility of cryopreservation diapausing embryos and to estimate the expression of the Odc1 and RhoA genes in diapausing and non-diapausing embryos before and after freeze-thaw procedures using ovariectomized progesterone treated mice as a model. Both diapausing and non-diapausing in vivo-derived embryos continued their development in vitro after freezing-thawing as evidenced by blastocoel re-expansion. Although cryopreservation dramatically decreased the expression of the Odc1 and RhoA genes in non-diapausing embryos, no such effects have been observed in diapausing embryos where these genes were already at the low level before freeze-thaw procedures. Future studies may attempt to facilitate the re-activation of diapausing embryos, for example frozen-thawed ones, specifically targeting Odc1 or Rho/ROCK system.

RevDate: 2024-04-29

Pol S, Kallonen T, Mäklin T, et al (2024)

Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing.

mBio [Epub ahead of print].

UNLABELLED: The nasopharynx is an important reservoir of disease-associated and antimicrobial-resistant bacterial species. This proof-of-concept study assessed the utility of a combined culture, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and targeted metagenomic sequencing workflow for the study of the pediatric nasopharyngeal bacterial microbiota. Nasopharyngeal swabs and clinical metadata were collected from Cambodian children during a hospital outpatient visit and then biweekly for 12 weeks. Swabs were cultured on chocolate and blood-gentamicin agar, and all colony morphotypes were identified by MALDI-TOF MS. Metagenomic sequencing was done on a scrape of all colonies from a chocolate agar culture and processed using the mSWEEP pipeline. One hundred one children were enrolled, yielding 620 swabs. MALDI-TOF MS identified 106 bacterial species/40 genera: 20 species accounted for 88.5% (2,190/2,474) of isolates. Colonization by Moraxella catarrhalis (92.1% of children on ≥1 swab), Haemophilus influenzae (87.1%), and Streptococcus pneumoniae (83.2%) was particularly common. In S. pneumoniae-colonized children, a median of two serotypes [inter-quartile range (IQR) 1-2, range 1-4] was detected. For the 21 bacterial species included in the mSWEEP database and identifiable by MALDI-TOF, detection by culture + MALDI-TOF MS and culture + mSWEEP was highly concordant with a median species-level agreement of 96.9% (IQR 86.8%-98.8%). mSWEEP revealed highly dynamic lineage-level colonization patterns for S. pneumoniae which were quite different to those for S. aureus. A combined culture, MALDI-TOF MS, targeted metagenomic sequencing approach for the exploration of the young child nasopharyngeal microbiome was technically feasible, and each component yielded complementary data.

IMPORTANCE: The human upper respiratory tract is an important source of disease-causing and antibiotic-resistant bacteria. However, understanding the interactions and stability of these bacterial populations is technically challenging. We used a combination of approaches to determine colonization patterns over a 3-month period in 101 Cambodian children. The combined approach was feasible to implement, and each component gave complementary data to enable a better understanding of the complex patterns of bacterial colonization.

RevDate: 2024-04-27

Avila Cartes J, Bonizzoni P, Ciccolella S, et al (2024)

RecGraph: recombination-aware alignment of sequences to variation graphs.

Bioinformatics (Oxford, England) pii:7658945 [Epub ahead of print].

MOTIVATION: Bacterial genomes present more variability than human genomes, which requires important adjustments in computational tools that are developed for human data. In particular, bacteria exhibit a mosaic structure due to homologous recombinations, but this fact is not sufficiently captured by standard read mappers that align against linear reference genomes. The recent introduction of pangenomics provides some insights in that context, as a pangenome graph can represent the variability within a species. However, the concept of sequence-to-graph alignment that captures the presence of recombinations has not been previously investigated.

RESULTS: In this paper, we present the extension of the notion of sequence-to-graph alignment to a variation graph that incorporates a recombination, so that the latter are explicitly represented and evaluated in an alignment. Moreover, we present a dynamic programming approach for the special case where there is at most a recombination-we implement this case as RecGraph. From a modeling point of view, a recombination corresponds to identifying a new path of the variation graph, where the new arc is composed of two halves, each extracted from an original path, possibly joined by a new arc. Our experiments show that RecGraph accurately aligns simulated recombinant bacterial sequences that have at most a recombination, providing evidence for the presence of recombination events.

AVAILABILITY: Our implementation is open source and available at https://github.com/AlgoLab/RecGraph.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2024-04-23

Gillmann SM, Lorenz AW, Kaijser W, et al (2024)

How tolerances, competition and dispersal shape benthic invertebrate colonisation in restored urban streams.

The Science of the total environment pii:S0048-9697(24)02812-2 [Epub ahead of print].

Biotic communities often respond poorly to river restoration activities and the drivers of community recovery after restoration are not fully understood. According to the Asymmetric Response Concept (ARC), dispersal capacity, species tolerances to stressors, and biotic interactions are three key drivers influencing community recovery of restored streams. However, the ARC remains to be tested. Here we used a dataset on benthic invertebrate communities of eleven restored stream sections in a former open sewer system that were sampled yearly over a period of eleven years. We applied four indices that reflect tolerance against chloride and organic pollution, the community's dispersal capacity and strength of competition to the benthic invertebrate taxa lists of each year and site. Subsequently, we used generalised linear mixed models to analyse the change of these indices over time since restoration. Dispersal capacity was high directly after restoration but continuously decreased over time. The initial communities thus consisted of good dispersers and were later joined by more slowly dispersing taxa. The tolerance to organic pollution also decreased over time, reflecting continuous improvement of water quality and an associated increase of sensitive species. On the contrary, chloride tolerances did not change, which could indicate a stable chloride level throughout the sampling period. Lastly, competition within the communities, reflected by interspecific trait niche overlap, increased with time since restoration. We show that recovery follows a specific pattern that is comparable between sites. Benthic communities change from tolerant, fast dispersing generalists to more sensitive, slowly dispersing specialists exposed to stronger competition. Our results lay support to the ARC (increasing role of competition, decreasing role of dispersal) but also underline that certain tolerances may still shape communities a decade after restoration. Disentangling the drivers of macroinvertebrate colonisation can help managers to better understand recovery trajectories and to define more realistic restoration targets.

RevDate: 2024-04-21

Ghodrati S, Lesiczka PM, Zurek L, et al (2024)

Rhipicephalus sanguineus from Hungarian dogs: Tick identification and detection of tick-borne pathogens.

Veterinary parasitology, regional studies and reports, 50:101007.

The brown dog tick, Rhipicephalus sanguineus is a complex of tick species with an unsettled species concept. In Europe, R. sanguineus is considered mainly a Mediterranean tick with sporadic findings in central and northern Europe. R. sanguineus is known as a vector of a range of pathogens of medical and veterinary importance, most of which not yet reported as autochthonous in Hungary. A total of 1839 ticks collected by veterinarians from dogs and cats were obtained in Hungary. The study aims at precise determination of ticks identified as R. sanguineus and detection of pathogens in collected ticks. All ticks were morphologically determined and 169 individuals were identified as R. sanguineus. A subset of 15 ticks was selected for molecular analysis (16S rDNA, 12S rDNA, COI). Phylogenetic analyses invariably placed sequences of all three markers into a single haplotype identified as R. sanguineus sensu stricto. All 169 brown dog ticks were tested for the presence of A. platys, E. canis, R. conorii, B. vogeli and H. canis. None of the investigated ticks was positive for the screened pathogens, though A. phagocytophilum sequence was detected in a single tick.

RevDate: 2024-04-21

Akrokoh J, Bediako JO, Fafanyo K, et al (2024)

Relatedness of hypoxia and hyperthermia tolerances in the Nile tilapia (Oreochromis niloticus) and their relationships with cardiac and gill traits.

Comparative biochemistry and physiology. Part A, Molecular & integrative physiology pii:S1095-6433(24)00075-8 [Epub ahead of print].

In fish, thermal and hypoxia tolerances may be functionally related, as suggested by the oxygen- and capacity-limited thermal tolerance (OCLTT) concept, which explains performance failure at high temperatures due to limitations in oxygen delivery. In this study the interrelatedness of hyperthermia and hypoxia tolerances in the Nile tilapia (Oreochromis niloticus), and their links to cardiorespiratory traits were examined. Different groups of O. niloticus (n = 51) were subjected to hypoxia and hyperthermia challenges and the O2 tension for aquatic surface respiration (ASR pO2) and critical thermal maximum (CTmax) were assessed as measurement endpoints. Gill filament length, total filament number, ventricle mass, length and width were also measured. Tolerance to hypoxia, as evidenced by ASR pO2 thresholds of the individual fish, was highly variable and varied between 0.26 and 3.39 kPa. ASR events increased more profoundly as O2 tensions decreased below 2 kPa. The CTmax values recorded for the O. niloticus individuals ranged from 43.1 to 44.8 °C (Mean: 44.2 ± 0.4 °C). Remarkably, there was a highly significant correlation between ASR pO2 and CTmax in O. niloticus (r = -0.76, p < 0.0001) with ASR pO2 increasing linearly with decreasing CTmax. There were, however, no discernible relationships between the measured cardiorespiratory properties and hypoxia or hyperthermia tolerances. The strong relationship between hypoxia and hyperthermia tolerances in this study may be related to the ability of the cardiorespiratory system to provide oxygen to respiring tissues under thermal stress, and thus provides some support for the OCLTT concept in this species, at least at the level of the entire organism.

RevDate: 2024-04-11

Ranjan R, Koffel T, CA Klausmeier (2024)

The three-species problem: Incorporating competitive asymmetry and intransitivity in modern coexistence theory.

Ecology letters, 27(4):e14426.

While natural communities can contain hundreds of species, modern coexistence theory focuses primarily on species pairs. Alternatively, the structural stability approach considers the feasibility of equilibria, gaining scalability to larger communities but sacrificing information about dynamic stability. Three-species competitive communities are a bridge to more-diverse communities. They display novel phenomena while remaining amenable to mathematical analysis, but remain incompletely understood. Here, we combine these approaches to identify the key quantities that determine three-species competition outcomes. We show that pairwise niche overlap and fitness differences are insufficient to completely characterize competitive outcomes, which requires a strictly triplet-wise quantity: cyclic asymmetry, which underlies intransitivity. Low pairwise niche overlap stabilizes the triplet, while high fitness differences promote competitive exclusion. The effect of cyclic asymmetry on stability is complex and depends on pairwise niche overlap. In summary, we elucidate how pairwise niche overlap, fitness differences and cyclic asymmetry determine three-species competition outcomes.

RevDate: 2024-04-11

Visagie CM, Yilmaz N, Kocsubé S, et al (2024)

A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species.

Studies in mycology, 107:1-66.

The order Eurotiales is diverse and includes species that impact our daily lives in many ways. In the past, its taxonomy was difficult due to morphological similarities, which made accurate identification of species difficult. This situation improved and stabilised with recent taxonomic and nomenclatural revisions that modernised Aspergillus, Penicillium and Talaromyces. This was mainly due to the availability of curated accepted species lists and the publication of comprehensive DNA sequence reference datasets. This has also led to a sharp increase in the number of new species described each year with the accepted species lists in turn also needing regular updates. The focus of this study was to review the 160 species described between the last list of accepted species published in 2020 until 31 December 2022. To review these species, single-gene phylogenies were constructed and GCPSR (Genealogical Concordance Phylogenetic Species Recognition) was applied. Multi-gene phylogenetic analyses were performed to further determine the relationships of the newly introduced species. As a result, we accepted 133 species (37 Aspergillus, two Paecilomyces, 59 Penicillium, two Rasamsonia, 32 Talaromyces and one Xerochrysium), synonymised 22, classified four as doubtful and created a new combination for Paraxerochrysium coryli, which is classified in Xerochrysium. This brings the number of accepted species to 453 for Aspergillus, 12 for Paecilomyces, 535 for Penicillium, 14 for Rasamsonia, 203 for Talaromyces and four for Xerochrysium. We accept the newly introduced section Tenues (in Talaromyces), and series Hainanici (in Aspergillus sect. Cavernicolarum) and Vascosobrinhoana (in Penicillium sect. Citrina). In addition, we validate the invalidly described species Aspergillus annui and A. saccharicola, and series Annuorum (in Aspergillus sect. Flavi), introduce a new combination for Dichlaena lentisci (type of the genus) and place it in a new section in Aspergillus subgenus Circumdati, provide an updated description for Rasamsonia oblata, and list excluded and recently synonymised species that were previously accepted. This study represents an important update of the accepted species lists in Eurotiales. Taxonomic novelties: New sections: Aspergillus section Dichlaena Visagie, Kocsubé & Houbraken. New series: Aspergillus series Annuorum J.J. Silva, B.T. Iamanaka, Frisvad. New species: Aspergillus annui J.J. Silva, M.H.P. Fungaro, Frisvad, M.H. Taniwaki & B.T. Iamanaka; Aspergillus saccharicola J.J. Silva, Frisvad, M.H.P. Fungaro, M.H. Taniwaki & B.T. Iamanaka. New combinations: Aspergillus lentisci (Durieu & Mont.) Visagie, Malloch, L. Kriegsteiner, Samson & Houbraken; Xerochrysium coryli (Crous & Decock) Visagie & Houbraken. Citation: Visagie CM, Yilmaz N, Kocsubé S, Frisvad JC, Hubka V, Samson RA, Houbraken J (2024). A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species. Studies in Mycology 107: 1-66. doi: 10.3114/sim.2024.107.01.

RevDate: 2024-04-08

Huymann LR, Hannecker A, Giovanni T, et al (2024)

Revised taxon definition in European Cortinarius subgenus Dermocybe based on phylogeny, chemotaxonomy, and morphology.

Mycological progress, 23(1):26.

UNLABELLED: Cortinarius (Fr.) Fr. is one of the most species-rich genera in the Agaricales (Basidiomycota). Cortinarius subgen. Dermocybe (Fr.) Trog includes brightly coloured Cortinarii with anthraquinone pigments. The chemotaxonomic approach has always been as important as classical methods for species definition of Dermocybe and helped to improve overall species concepts. However, some species concepts within this group remain unclear. We therefore address this topic based on a combined phylogenetic, morphological, and pigment-chemical approach. For this, sequence data, HPLC-MS pigment profiles and spore sizes were included were included to obtain a better resolution of taxa. The study was based on 173 recent collections and 12 type specimens. A total of 117 rDNA ITS sequences were produced from the collections in this study, 102 sequences were retrieved from databases. We could detect and clearly delimit 19 Dermocybe species occurring in central European habitats, from which 16 are discussed in detail. Additionally, we grouped the detected anthraquinone pigments into four groups. This detailed analysis of dermocyboid Cortinarius species occurring in a restricted number of habitat types confirmed our hypothesis that species diversity is much higher than currently assumed. This high diversity is blurred by too wide and incorrect species concepts of several classical species like C. croceus and C. cinnamomeus. Molecular and chemotaxonomical studies carried out together with careful phenotypical analyses resulted in a good differentiation of species. A key is presented for these taxa to allow a better identification of Cortinarius subgenus Dermocybe spp. occurring in Central Europe mainly in the alpine range.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11557-024-01959-z.

RevDate: 2024-04-04

Tiktak GP, Gabb A, Brandt M, et al (2024)

Genetic identification of three CITES-listed sharks using a paper-based Lab-on-a-Chip (LOC).

PloS one, 19(4):e0300383 pii:PONE-D-23-38097.

Threatened shark species are caught in large numbers by artisanal and commercial fisheries and traded globally. Monitoring both which shark species are caught and sold in fisheries, and the export of CITES-restricted products, are essential in reducing illegal fishing. Current methods for species identification rely on visual examination by experts or DNA barcoding techniques requiring specialist laboratory facilities and trained personnel. The need for specialist equipment and/or input from experts means many markets are currently not monitored. We have developed a paper-based Lab-on-a-Chip (LOC) to facilitate identification of three threatened and CITES-listed sharks, bigeye thresher (Alopias superciliosus), pelagic thresher (A. pelagicus) and shortfin mako shark (Isurus oxyrinchus) at market source. DNA was successfully extracted from shark meat and fin samples and combined with DNA amplification and visualisation using Loop Mediated Isothermal Amplification (LAMP) on the LOC. This resulted in the successful identification of the target species of sharks in under an hour, with a working positive and negative control. The LOC provided a simple "yes" or "no" result via a colour change from pink to yellow when one of the target species was present. The LOC serves as proof-of-concept (PoC) for field-based species identification as it does not require specialist facilities. It can be used by non-scientifically trained personnel, especially in areas where there are suspected high frequencies of mislabelling or for the identification of dried shark fins in seizures.

RevDate: 2024-03-28

Cruz H, Pinheiro M, V Borges (2024)

ReporType: A Flexible Bioinformatics Tool for Targeted Loci Screening and Typing of Infectious Agents.

International journal of molecular sciences, 25(6): pii:ijms25063172.

In response to the pressing need for continuous monitoring of emergence and circulation of pathogens through genomics, it is imperative to keep developing bioinformatics tools that can help in their rapid characterization and classification. Here, we introduce ReporType, a versatile bioinformatics pipeline designed for targeted loci screening and typing of infectious agents. Developed using the snakemake workflow manager, ReporType integrates multiple software for read quality control and de novo assembly, and then applies ABRicate for locus screening, culminating in the production of easily interpretable reports for the identification of pathogen genotypes and/or screening of specific genomic loci. The pipeline accommodates a range of input formats, from Illumina or Oxford Nanopore Technology (ONT) reads (FASTQ) to Sanger sequencing files (AB1), or FASTA files, making it flexible for application in multiple pathogens and with different purposes. ReporType is released with pre-prepared databases for some viruses and bacteria, yet it remains easily configurable to handle custom databases. ReporType performance and functionality were validated through proof-of-concept exercises, encompassing diverse pathogenic species, including viruses such as measles, Newcastle disease virus (NDV), Dengue virus (DENV), influenza, hepatitis C virus (HCV) and Human T-Cell Lymphotropic virus type 1 (HTLV-1), as well as bacteria like Chlamydia trachomatis and Legionella pneumophila. In summary, ReporType emerges as a simple, dynamic and pan-pathogen tool, poised to evolve in tandem with the ever-changing needs of the fields of pathogen genomics, infectious disease epidemiology, and one health bioinformatics. ReporType is freely available at GitHub.

RevDate: 2024-03-20

Duran DP, Laroche RA, Roman SJ, et al (2024)

Species delimitation, discovery and conservation in a tiger beetle species complex despite discordant genetic data.

Scientific reports, 14(1):6617.

In an age of species declines, delineating and discovering biodiversity is critical for both taxonomic accuracy and conservation. In recent years, there has been a movement away from using exclusively morphological characters to delineate and describe taxa and an increase in the use of molecular markers to describe diversity or through integrative taxonomy, which employs traditional morphological characters, as well as genetic or other data. Tiger beetles are charismatic, of conservation concern, and much work has been done on the morphological delineation of species and subspecies, but few of these taxa have been tested with genetic analyses. In this study, we tested morphologically based taxonomic hypotheses of polymorphic tiger beetles in the Eunota circumpicta (LaFerté-Sénectère, 1841) species complex using multilocus genomic and mtDNA analyses. We find multiple cryptic species within the previous taxonomic concept of Eunota circumpicta, some of which were historically recognized as subspecies. We found that the mtDNA and genomic datasets did not identify the same taxonomic units and that the mtDNA was most at odds with all other genetic and morphological patterns. Overall, we describe new cryptic diversity, which raises important conservation concerns, and provide a working example for testing species and subspecies validity despite discordant data.

RevDate: 2024-03-14

Fujita H, Shimada D, Kudo J, et al (2024)

Carbocationoids, a concept for controlling highly reactive cationic species.

Communications chemistry, 7(1):55.

Carbocations, which are positively charged highly electrophilic intermediates, are efficacious for the direct alkylation of low-reactive nucleophiles. The utilization of carbocations in SN1 reactions relies on the activation of their precursors in the presence of a nucleophile. However, undesirable interactions between the nucleophile and the leaving group activator limit the scope of acceptable nucleophiles. Here we report a strategy to conduct SN1 reactions involving unstable carbocations in an alternative stepwise procedure, which was demonstrated by the benzylation of various neutral nucleophiles. In the first step, carbocations were accumulated in a nucleophile-free solution in the form of carbocationoids utilizing the coordinative stabilization of triazinediones. Subsequently, the addition of these solutions in the second step enabled room-temperature alkylation without the need for acidic additives. This methodology overcomes the inherent challenges of carbocations in SN1 reactions.

RevDate: 2024-03-13

Wood TJ (2024)

New Asian Andrena species, with notes on the subgenus Cnemidandrena (Hymenoptera: Andrenidae).

Zootaxa, 5404(1):167-188.

Asia is the worlds largest continent and comprises most of the Holarctic biogeographic region. The genus Andrena is principally distributed through the Holarctic, but it remains understudied in Asia. The subgenus Cnemidandrena Hedicke, 1933 is distributed across Asia with some species reaching south to the Tibetan Plateau. However, some southern members display an unusual morphology, including A. (Cnemidandrena) kishidai chagyabensis Wu, 1982 (newly recorded for Bhutan, India, and Nepal) and A. (Cnemidandrena) granulitergorum Tadauchi & Xu, 2002 (newly recorded for Nepal). The male of A. granulitergorum is described for the first time, A. (Cnemidandrena) rufina Morawitz, 1876 is reported from Kyrgyzstan, Afghanistan, and Kashmir for the first time, and possible senior synonyms for Asian A. (Cnemidandrena) are suggested. To contribute to an improved understanding of localised Asian Andrena diversity, the following new species are described: A. (Cnemidandrena) textrix sp. nov. from China, A. (incertae sedis) liebigi sp. nov. and A. (Troandrena) monfaredi sp. nov. from Iran, and A. (incertae sedis) quercorum sp. nov. from Turkey. These results further confirm that additional taxonomic work is needed to harmonise Andrena species concepts across the different biogeographic regions of Asia.

RevDate: 2024-03-13

Hendrix SV, CR Bartlett (2024)

Redescription and revised genus placement of Oliarus pinicolus Osborn, 1926, with notes on Antillean Pentastirini (Hemiptera: Fulgoromorpha: Cixiidae).

Zootaxa, 5405(2):209-226.

Oliarus pinicolus Osborn, 1926 is a little-known planthopper described from western Cuba on Cuban pine (Pinus cubensis). As part of a review of the sprawling New World cixiid genus Melanoliarus Fennah, 1945, the species is herein redescribed and illustrated for the first time, including the male terminalia. After comparison to similar species in the region, we transfer the species to Nivcentia Holzinger, 2004, as Nivcentia pinicolus comb. nov., based on characteristics of the male terminalia and provide an amended description of the genus. We also designate a lectotype for Oliarus pinicolus to ensure the stability of the species concept described here. A checklist of Antillean Pentastirini is included with taxonomic comments on the species and genera of the region. The pentastirine species of Cuba are illustrated.

RevDate: 2024-03-12

Tembrock LR, Wilson CR, Zink FA, et al (2023)

CO1 barcodes resolve an asymmetric biphyletic clade for Diabrotica undecimpunctata subspecies and provide nucleotide variants for differentiation from related lineages using real-time PCR.

Frontiers in insect science, 3:1168586.

Diabrotica undecimpunctata is a multivoltine polyphagous beetle species that has long been documented as a significant agricultural pest throughout its native range in North America. This beetle can vector bacterial and viral plant pathogens that result in major losses to crops such as cucumber and soybean. Many countries outside the Americas treat D. undecimpunctata as a species of quarantine importance, while in the USA only the subspecies D. u. duodecimnotata is subject to quarantine, to prevent introduction from Mexico. Identification of D. undecimpunctata on the basis of morphology alone can be complicated given the use of conflicting characters in the description of some subspecific taxa. To better understand relationships among D. undecimpunctata subspecies and other related species, we sequenced mitochondrial cytochrome oxidase 1 (CO1) and nuclear internal transcribed spacer 2 (ITS2) DNA from individuals in different subspecific taxa and across different parts of the species range using museum samples and interceptions. When our data were combined with publicly available Diabrotica data, no pattern of divergence consistent with the currently recognized subspecific designations was found. In addition, we compared phylogenetic patterns in CO1 data from the congener D. virgifera to demonstrate the utility of mitochondrial data in resolving subspecies. From the CO1 data, a diagnostic real-time PCR assay was developed that could successfully identify all haplotypes within the large D. undecimpunctata clade for use in surveys and identification at ports of entry. These findings underscore the need to resolve molecular and morphological datasets into cogent, lineage-based groupings. Such efforts will provide an evolutionary context for the study of agriculturally important attributes of Diabrotica such as host preferences, xenobiotic metabolism, and natural and anthropogenic patterns of dispersal.

RevDate: 2024-03-08

Chávez-Tinoco M, García-Ortega LF, E Mancera (2024)

Genetic modification of Candida maltosa, a non-pathogenic CTG species, reveals EFG1 function.

Microbiology (Reading, England), 170(3):.

Candida maltosa is closely related to important pathogenic Candida species, especially C. tropicalis and C. albicans, but it has been rarely isolated from humans. For this reason, through comparative studies, it could be a powerful model to understand the genetic underpinnings of the pathogenicity of Candida species. Here, we generated a cohesive assembly of the C. maltosa genome and developed genetic engineering tools that will facilitate studying this species at a molecular level. We used a combination of short and long-read sequencing to build a polished genomic draft composed of 14 Mbp, 45 contigs and close to 5700 genes. This assembly represents a substantial improvement from the currently available sequences that are composed of thousands of contigs. Genomic comparison with C. albicans and C. tropicalis revealed a substantial reduction in the total number of genes in C. maltosa. However, gene loss seems not to be associated to the avirulence of this species given that most genes that have been previously associated with pathogenicity were also present in C. maltosa. To be able to edit the genome of C. maltosa we generated a set of triple auxotrophic strains so that gene deletions can be performed similarly to what has been routinely done in pathogenic Candida species. As a proof of concept, we generated gene knockouts of EFG1, a gene that encodes a transcription factor that is essential for filamentation and biofilm formation in C. albicans and C. tropicalis. Characterization of these mutants showed that Efg1 also plays a role in biofilm formation and filamentous growth in C. maltosa, but it seems to be a repressor of filamentation in this species. The genome assembly and auxotrophic mutants developed here are a key step forward to start using C. maltosa for comparative and evolutionary studies at a molecular level.

RevDate: 2024-03-05

Moragues-Solanas L, Le-Viet T, McSorley E, et al (2024)

Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection.

BMC medical genomics, 17(1):71.

BACKGROUND: The timely and accurate diagnosis of bloodstream infection (BSI) is critical for patient management. With longstanding challenges for routine blood culture, metagenomics is a promising approach to rapidly provide sequence-based detection and characterisation of bloodborne bacteria. Long-read sequencing technologies have successfully supported the use of clinical metagenomics for syndromes such as respiratory illness, and modified approaches may address two requisite factors for metagenomics to be used as a BSI diagnostic: depletion of the high level of host DNA to then detect the low abundance of microbes in blood.

METHODS: Blood samples from healthy donors were spiked with different concentrations of four prevalent causative species of BSI. All samples were then subjected to a modified saponin-based host DNA depletion protocol and optimised DNA extraction, whole genome amplification and debranching steps in preparation for sequencing, followed by bioinformatical analyses. Two related variants of the protocol are presented: 1mL of blood processed without bacterial enrichment, and 5mL of blood processed following a rapid bacterial enrichment protocol-SepsiPURE.

RESULTS: After first identifying that a large proportion of host mitochondrial DNA remained, the host depletion process was optimised by increasing saponin concentration to 3% and scaling the reaction to allow more sample volume. Compared to non-depleted controls, the 3% saponin-based depletion protocol reduced the presence of host chromosomal and mitochondrial DNA < 10[6] and < 10[3] fold respectively. When the modified depletion method was further combined with a rapid bacterial enrichment method (SepsiPURE; with 5mL blood samples) the depletion of mitochondrial DNA improved by a further > 10X while also increasing detectable bacteria by > 10X. Parameters during DNA extraction, whole genome amplification and long-read sequencing were also adjusted, and subsequently amplicons were detected for each input bacterial species at each of the spiked concentrations, ranging from 50-100 colony forming units (CFU)/mL to 1-5 CFU/mL.

CONCLUSION: In this proof-of-concept study, four prevalent BSI causative species were detected in under 12 h to species level (with antimicrobial resistance determinants) at concentrations relevant to clinical blood samples. The use of a rapid and precise metagenomic protocols has the potential to advance the diagnosis of BSI.

RevDate: 2024-03-04

van der Gulik PTS, Hoff WD, D Speijer (2024)

The contours of evolution: In defence of Darwin's tree of life paradigm.

BioEssays : news and reviews in molecular, cellular and developmental biology [Epub ahead of print].

Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights into widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.

RevDate: 2024-03-04

Yu KP, M Kuntner (2024)

Discovering unknown Madagascar biodiversity: integrative taxonomy of raft spiders (Pisauridae: Dolomedes).

PeerJ, 12:e16781.

Madagascar is a global biodiversity hotspot, but its biodiversity continues to be underestimated and understudied. Of raft spiders, genus Dolomedes Latreille, 1804, literature only reports two species on Madagascar. Our single expedition to humid forests of eastern and northern Madagascar, however, yielded a series of Dolomedes exemplars representing both sexes of five morphospecies. To avoid only using morphological diagnostics, we devised and tested an integrative taxonomic model for Dolomedes based on the unified species concept. The model first determines morphospecies within a morphometrics framework, then tests their validity via species delimitation using COI. It then incorporates habitat preferences, geological barriers, and dispersal related traits to form hypotheses about gene flow limitations. Our results reveal four new Dolomedes species that we describe from both sexes as Dolomedes gregoric sp. nov., D. bedjanic sp. nov., D. hydatostella sp. nov., and D. rotundus sp. nov. The range of D. kalanoro Silva & Griswold, 2013, now also known from both sexes, is expanded to eastern Madagascar. By increasing the known raft spider diversity from one valid species to five, our results merely scratch the surface of the true Dolomedes species diversity on Madagascar. Our integrative taxonomic model provides the framework for future revisions of raft spiders anywhere.

RevDate: 2024-03-01

Dong Y, Zhang Q, Mao Y, et al (2024)

Control of two insect pests by expression of a mismatch corrected double-stranded RNA in plants.

Plant biotechnology journal [Epub ahead of print].

RNA interference (RNAi) has emerged as an efficient technology for pest control by silencing the essential genes of targeted insects. Owing to its nucleotide sequence-guided working mechanism, RNAi has a high degree of species-specificity without impacts on non-target organisms. However, as plants are inevitably under threat by two or more insect pests in nature, the species-specific mode of RNAi-based technology restricts its wide application for pest control. In this study, we artificially designed an intermediate dsRNA (iACT) targeting two β-Actin (ACT) genes of sap-sucking pests Bemisia tabaci and Myzus persicae by mutual correction of their mismatches. When expressing hairpin iACT (hpiACT) from tobacco nuclear genome, transgenic plants are well protected from both B. tabaci and M. persicae, either individually or simultaneously, as evidenced by reduced fecundity and suppressed ACT gene expression, whereas expression of hpRNA targeting BtACT or MpACT in transgenic tobacco plants could only confer specific resistance to either B. tabaci or M. persicae, respectively. In sum, our data provide a novel proof-of-concept that two different insect species could be simultaneously controlled by artificial synthesis of dsRNA with sequence optimization, which expands the range of transgenic RNAi methods for crop protection.

RevDate: 2024-02-29

Monecke S (2024)

Threatened chronotopes: can chronobiology help endangered species?.

Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology [Epub ahead of print].

Pittendrigh and Daan's 1976 article "Pacemaker structure: A clock for all seasons" marks the foundation of modern seasonal chronobiology. It proposed the internal coincidence model comprised of a Morning (M) and Evening (E) oscillator, which are coupled but synchronized separately by dawn and dusk. It has become an attractive model to explain the seasonal adaptation of circadian rhythms. Using the example of the European hamster, this article connects the classical entrainment concept to species decline and, ultimately, conservation concepts. Seasonality of this species is well studied and circannual rhythms have been described in at least 32 parameters. The European hamster is listed as critically endangered on the International Union for Conservation of Nature (IUCN) red list. Changes in the temporal structure of the environment (the chronotope) caused by climate change and light pollution might be responsible for the global decline. The article shows that classical chronobiological concepts such as the internal coincidence model (Pittendrigh and Daan Pittendrigh and Daan, J Comp Physiol [a] 106:333-355, 1976) are helpful to understand the (chronobiological) causes of the decline and can potentially support species conservation. Knowing the species' physiological limitations as well as its adaptation capacities can potentially prevent its extinction at a time when classical conservation concepts have reached their limits.

RevDate: 2024-02-23

Wang S, Jiang N, R Ma (2024)

Morphology and Phylogeny Reveal Three New Species of Cytospora Associated with Tree Cankers in China.

Journal of fungi (Basel, Switzerland), 10(2): pii:jof10020139.

Cytospora (Cytosporaceae, Diaporthales) is a fungal genus that usually inhabits plants as endophytes, saprobes, as well as pathogens. Species of this genus are characterized by possessing allantoid hyaline conidia and ascospores. Samples with typical Cytospora canker symptoms on Prunus davidiana, P. padus and Salix sp. were collected in Tibet and Xinjiang, China. Species were identified using both morphological and molecular approaches of combined loci of internal transcribed spacer region rDNA (ITS), the partial actin (act) region, RNA polymerase II second largest subunit (rpb2), the translation elongation factor 1-alpha (tef1) gene and the partial be-ta-tubulin (tub2) gene. Six isolates in the present study formed three distinct clades from previously known species. Cytospora hejingensis sp. nov. from Salix sp., C. jilongensis sp. nov. from P. davidiana and C. kunsensis from P. padus were proposed herein. The current study improves the understanding of species concept in Cytospora.

RevDate: 2024-02-20

Lukhtanov VA (2024)

Polytypic species concept and subspecies in the genomic era.

Proceedings of the National Academy of Sciences of the United States of America, 121(9):e2317038121.

RevDate: 2024-02-13

Koch Bach R, Murithi HM, Slocum CR, et al (2024)

Remarkably high ITS haplotype diversity of the fungal Select Agent Coniothyrium glycines discovered throughout its range in sub-Saharan Africa.

Phytopathology [Epub ahead of print].

Red leaf blotch of soybean, caused by the fungus Coniothyrium glycines, is a foliar disease characterized by blotching, necrosis, and defoliation, which has only been reported from Africa. The species is listed as a Select Agent by the Federal Select Agent Program due to its potentially devastating impacts to soybean production should it spread to the U.S. Despite its potential import, very few isolates are available for study. Herein, we obtained 96 new C. glycines isolates from six soybean-producing countries throughout sub-Saharan Africa. Along with 12 previously collected ones, we sequenced each at the internal transcribed spacer (ITS) region. Between all isolates, we identified a total of 28 single nucleotide polymorphisms and 23 haplotypes. One hypothesis to explain the tremendous diversity uncovered at the ITS-which is generally conserved within a species-is that our current species concept of C. glycines is too broad, and that there may be multiple species that cause RLB. Zambia contained the highest haplotype diversity, a significant fraction of which remains unsampled. Most haplotypes were specific to a single country, except for two, which were found in Zambia and either neighboring Mozambique or Zimbabwe. This geographic specificity indicates that the ITS region may be useful in identifying source populations or routes of transmission should this pathogen spread beyond Africa. The observed geographic partitioning of this pathogen is likely the result of millions of years of replication on little-studied native hosts, given that soybean has only been cultivated in Africa since the early 1900s.

RevDate: 2024-02-10

Maggisano V, Capriglione F, Mio C, et al (2024)

RNA Profile of Cell Bodies and Exosomes Released by Tumorigenic and Non-Tumorigenic Thyroid Cells.

International journal of molecular sciences, 25(3): pii:ijms25031407.

Tumor cells release exosomes, extracellular vesicle containing various bioactive molecules such as protein, DNA and RNA. The analysis of RNA molecules packaged in exosomes may provide new potential diagnostic or prognostic tumor biomarkers. The treatment of radioiodine-refractory aggressive thyroid cancer is still an unresolved clinical challenge, and the search for biomarkers that are detectable in early phase of the disease has become a fundamental goal for thyroid cancer research. By using transcriptome analysis, this study aimed to analyze the gene expression profiles of exosomes secreted by a non-tumorigenic thyroid cell line (Nthy-ori 3.1-exo) and a papillary thyroid cancer (TPC-1-exo) cell line, comparing them with those of cell bodies (Nthy-ori 3.1-cells and TPC-1-cells). A total of 9107 transcripts were identified as differentially expressed when comparing TPC-1-exo with TPC-1-cells and 5861 when comparing Nthy-ori 3.1-exo with Nthy-ori 3.1-cells. Among them, Sialic acid-binding immunoglobulin-like lectins 10 and 11 (SIGLEC10, SIGLEC11) and Keratin-associated protein 5 (KRTAP5-3) transcripts, genes known to be involved in cancer progression, turned out to be up-regulated only in TPC-1-exo. Gene ontology analysis revealed significantly enriched pathways, and only in TPC-1-exo were the differential expressed genes associated with an up-regulation in epigenetic processes. These findings provide a proof of concept that some mRNA species are specifically packaged in tumor-cell-derived exosomes and may constitute a starting point for the identification of new biomarkers for thyroid tumors.

RevDate: 2024-02-09

Smith JE, FP Gabbaï (2023)

Are Ar3SbCl2 Species Lewis Acidic? Exploration of the Concept and Pnictogen Bond Catalysis Using a Geometrically Constrained Example.

Organometallics, 42(3):240-245.

As part of our investigations into the Lewis acidic behavior of antimony derivatives, we have decided to study the properties of 5-phenyl-5,5-dichloro-λ[5]-dibenzostibole (1), a dichlorostiborane with an antimony atom confined to a five-membered heterocycle. Our work shows that the resulting geometrical constraints elevate the Lewis acidity of the antimony atom, as confirmed by the crystal structure of 1-THF and the solution study of the interaction of 1 with Ph3PO. The enhanced Lewis acidic properties of 1, which exceed those of simple dichlorostiboranes such as Ph3SbCl2, also become manifest in pnictogen bonding catalysis experiments involving the reductions of imines with Hantzsch ester. The influence of geometrical constraints in the chemistry of this compound is also supported by a computational activation strain analysis as well as by an energy decomposition analysis of a model Me3PO adduct.

RevDate: 2018-12-20
CmpDate: 2018-12-20

Gippoliti S, CP Groves (2018)

Overlooked mammal diversity and conservation priorities in Italy: Impacts of taxonomic neglect on a Biodiversity Hotspot in Europe.

Zootaxa, 4434(3):511-528 pii:zootaxa.4434.3.7.

For more than half a century, little taxonomic revisionary work has been directed towards extant European mammals so that the limits of most geographically widespread polytypic species remained scientifically untested. Occasionally, taxonomic changes have been proposed and several new species have been resurrected / discovered in the last decades mainly on the basis of genetic studies, often considered the only tool to establish objective species boundaries. Nevertheless, the precise details of species boundaries, subspecific variation and phylogenetic relationships remain unknown for several European mammal taxa. The inadequacies of outdated, incomplete taxonomic knowledge reach an extreme in southern Europe, and notably Italy, where cryptic species abound and specimen-based research is scanty. The state of mammalian taxonomic knowledge in Italy shows that Linnaean and Wallacean shortfalls are no means restricted to hyperdiverse, understudied tropics. They undermine our knowledge of temperate regions, with severe consequences for biodiversity conservation policies in Europe, where conservation assessments overlook significant endemic biodiversity. European mammalogy stands to benefit from an infusion of the tree-thinking philosophy that undergirds evolutionary theory and particularly phylogenetic methods systematics. Furthermore, it is important that taxonomic research be seen as a normal part of scientific advancement and of critical importance as the basis of a sound biodiversity conservation policy.

RevDate: 2024-02-04

Petrović K, Orzali L, Krsmanović S, et al (2024)

Genetic diversity and pathogenicity of the Fusarium species complex on soybean in Serbia.

Plant disease [Epub ahead of print].

Using morphological and cultural characteristics for identification, 36 Fusarium isolates were recovered from diseased roots, stems, and seeds of soybean from several localities throughout Vojvodina Province, Serbia, were identified as Fusarium spp. Based on molecular characterization, 12 Fusarium species were identified: F. acuminatum, F. avenaceum, F. commune, F. equiseti, F. graminearum, F. incarnatum, F. oxysporum, F. proliferatum, F. solani, F. sporotrichioides, F. subglutinans, and F. tricinctum. The EF-1α based-phylogeny grouped the isolates into 12 well-supported clades, but the polymorphisms among sequences in some clades suggested the use of the species complex concept: (1) FIESC - F. incarnatum and F. equiseti; (2) FOSC - F. oxysporum; (3) FSSC - F. solani; and (4) FAATSC - F. acuminatum, F. avenaceum and F. tricinctum. Pathogenicity tests showed that the most aggressive species causing soybean seed rot were F. sporotrichioides, F. graminearum, FIESC, and F. avenaceum. Furthermore, F. subglutinans, FSSC, and F. proliferatum, showed a high percentage of pathogenicity on soybean seeds (80-100%), while variability in pathogenicity occurred within isolates of F. tricinctum species has occurred variability in the virulence of different isolates. FOSC, F. commune and F. acuminatum had the lowest pathogenicity degree. To our knowledge, this is the first study of the characterization of Fusarium complex species on soybean in Serbia. This study provides valuable information about the structure composition of Fusarium complex species and pathogenicity that will be used in further research on soybean resistance to Fusarium-based diseases.

RevDate: 2024-02-03

Zhang N, Xue Z, Shi L, et al (2024)

Unveiling the Detailed Mechanism and Origins of Chemo-, Regio-, and Stereoselectivity of Rare-Earth Catalyzed Alternating Copolymerization of Polar and Nonpolar Olefins.

Inorganic chemistry [Epub ahead of print].

The direct copolymerization of polar and nonpolar olefins is of great interest and significance, as it is the most atom-economical and straightforward strategy for the synthesis of functional polyolefin materials. Despite considerable efforts, the precise control of monomer-sequence and their regio- and stereochemistry is full of challenges, and the related mechanistic origins are still in their infancy to date. Herein, the mechanistic studies on the model reaction of Sc-catalyzed co-syndiospecific alternating copolymerization of anisylpropylene (AP) and styrene were performed by DFT calculations. The results suggest that the subtle balance between electronic and steric factors plays an important role during monomer insertions, and a new amino-dissociated mechanism was proposed for AP insertion at chain initiation. AP insertion follows the 2,1-si-insertion pattern, which is mainly controlled by steric factors caused by the restricted MeO···Sc interaction. As for styrene insertion, it prefers the 2,1-re-insertion manner and its regio- and stereoselectivities are influenced by steric repulsions between the inserting styrene and the polymer chain or the ligand. More interestingly, it is found that the alternating monomer-sequence is mainly determined by the "steric matching" principle, which is quantitatively expressed by the buried volume of the metal center of the preinserted species. The concept of steric pocket has been successfully applied to explain the different performances of several catalysts and other alternating copolymerization reactions. The insightful mechanistic findings and the quantitative steric pocket model present here are expected to promote rational design of new rare-earth catalysts for developing regio-, stereo-, and sequence-controlled copolymerization of specific polar and nonpolar olefins.

RevDate: 2024-02-02

Campos LR, Trefflich S, Morais DA, et al (2024)

Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analysis.

Molecular biology and evolution pii:7596672 [Epub ahead of print].

Orthology information has been used for searching patterns in high-dimensional data, allowing transferring functional information between species. The key concept behind this strategy is that orthologous genes share ancestry to some extent. While reconstructing the history of a single gene is feasible with the existing computational resources, the reconstruction of entire biological systems remains challenging. Here we present Bridge, a new algorithm designed to infer the evolutionary root of orthologous genes in large-scale evolutionary analysis. The Bridge algorithm infers the evolutionary root of a given gene based on the distribution of its orthologs in a species tree. The Bridge algorithm is implemented in R and can be used either to assess genetic changes across the evolutionary history of orthologous groups or to infer the onset of specific traits in a biological system.

RevDate: 2024-02-01

Abad ZG, Burgess TI, Bourret T, et al (2023)

Phytophthora : taxonomic and phylogenetic revision of the genus.

Studies in mycology, 106:259-348.

Many members of the Oomycota genus Phytophthora cause economic and environmental impact diseases in nurseries, horticulture, forest, and natural ecosystems and many are of regulatory concern around the world. At present, there are 223 described species, including eight unculturable and three lost species. Twenty-eight species need to be redescribed or validated. A lectotype, epitype or neotype was selected for 20 species, and a redescription based on the morphological/molecular characters and phylogenetic placement is provided. In addition, the names of five species are validated: P. cajani, P. honggalleglyana (Synonym: P. hydropathica), P. megakarya, P. pisi and P. pseudopolonica for which morphology and phylogeny are given. Two species, P. ×multiformis and P. uniformis are presented as new combinations. Phytophthora palmivora is treated with a representative strain as both lecto- and epitypification are pending. This manuscript provides the updated multigene phylogeny and molecular toolbox with seven genes (ITS rDNA, β-tub, COI, EF1α, HSP90, L10, and YPT1) generated from the type specimens of 212 validly published, and culturable species (including nine hybrid taxa). The genome information of 23 types published to date is also included. Several aspects of the taxonomic revision and phylogenetic re-evaluation of the genus including species concepts, concept and position of the phylogenetic clades recognized within Phytophthora are discussed. Some of the contents of this manuscript, including factsheets for the 212 species, are associated with the "IDphy: molecular and morphological identification of Phytophthora based on the types" online resource (https://idtools.org/tools/1056/index.cfm). The first version of the IDphy online resource released to the public in September 2019 contained 161 species. In conjunction with this publication, we are updating the IDphy online resource to version 2 to include the 51 species recently described. The current status of the 223 described species is provided along with information on type specimens with details of the host (substrate), location, year of collection and publications. Additional information is provided regarding the ex-type culture(s) for the 212 valid culturable species and the diagnostic molecular toolbox with seven genes that includes the two metabarcoding genes (ITS and COI) that are important for Sanger sequencing and also very valuable Molecular Operational Taxonomic Units (MOTU) for second and third generation metabarcoding High-throughput sequencing (HTS) technologies. The IDphy online resource will continue to be updated annually to include new descriptions. This manuscript in conjunction with IDphy represents a monographic study and the most updated revision of the taxonomy and phylogeny of Phytophthora, widely considered one of the most important genera of plant pathogens. Taxonomic novelties: New species: Phytophthora cajani K.S. Amin, Baldev & F.J. Williams ex Abad, Phytophthora honggalleglyana Abad, Phytophthora megakarya Brasier & M.J. Griffin ex Abad, Phytophthora pisi Heyman ex Abad, Phytophthora pseudopolonica W.W. Li, W.X. Huai & W.X. Zhao ex Abad & Kasiborski; New combinations: Phytophthora ×multiformis (Brasier & S.A. Kirk) Abad, Phytophthora uniformis (Brasier & S.A. Kirk) Abad; Epitypifications (basionyms): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora inundata Brasier et al., Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Lectotypifications (basionym): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Neotypifications (basionym): Phloeophthora syringae Kleb., Phytophthora meadii McRae Citation: Abad ZG, Burgess TI, Bourret T, Bensch K, Cacciola S, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl JC, Verkleij G, Broders K, Schena L, Redford AJ (2023). Phytophthora: taxonomic and phylogenetic revision of the genus. Studies in Mycology 106: 259-348. doi: 10.3114/sim.2023.106.05.

RevDate: 2024-01-30

Horstmann M, Quarles CD, Happel S, et al (2024)

Quantification of [[99]Tc]TcO4[-] in urine by means of anion-exchange chromatography-aerosol desolvation nebulization-inductively coupled plasma-mass spectrometry.

Analytical and bioanalytical chemistry [Epub ahead of print].

To sensitively determine [99]Tc, a new method for internal quantification of its most common and stable species, [[99]Tc]Tc[Formula: see text], was developed. Anion-exchange chromatography (IC) was coupled to inductively coupled plasma-mass spectrometry (ICP-MS) and equipped with an aerosol desolvation system to provide enhanced detection power. Due to a lack of commercial Tc standards, an isotope dilution-like approach using a Ru spike and called isobaric dilution analysis (IBDA) was used for internal quantification of [99]Tc. This approach required knowledge of the sensitivities of [99]Ru and [99]Tc in ICP-MS. The latter was determined using an in-house prepared standard manufactured from decayed medical [99m]Tc-generator eluates. This standard was cleaned and preconcentrated using extraction chromatography with TEVA resin and quantified via total reflection X-ray fluorescence (TXRF) analysis. IC coupled to ICP-MS enabled to separate, detect and quantify [[99]Tc]Tc[Formula: see text] as most stable Tc species in complex environments, which was demonstrated in a proof of concept. We quantified this species in untreated and undiluted raw urine collected from a patient, who previously underwent scintigraphy with a [99m]Tc-tracer, and determined a concentration of 19.6 ± 0.5 ng L[-1]. The developed method has a high utility to characterize a range of Tc-based radiopharmaceuticals, to determine concentrations, purity, and degradation products in complex samples without the need to assess activity parameters of [99(m)]Tc.

RevDate: 2024-01-29

Angeler DG, HB Fried-Petersen (2024)

Parallels of quantum superposition in ecological models: from counterintuitive patterns to eco-evolutionary interpretations of cryptic species.

BMC ecology and evolution, 24(1):15.

BACKGROUND: Superposition, i.e. the ability of a particle (electron, photon) to occur in different states or positions simultaneously, is a hallmark in the subatomic world of quantum mechanics. Although counterintuitive at first sight, the quantum world has potential to inform macro-systems of people and nature. Using time series and spatial analysis of bird, phytoplankton and benthic invertebrate communities, this paper shows that superposition can occur analogously in redundancy analysis (RDA) frequently used by ecologists.

RESULTS: We show that within individual ecosystems single species can be associated simultaneously with different orthogonal axes in RDA models, which suggests that they operate in more than one niche spaces. We discuss this counterintuitive result in relation to the statistical and mathematical features of RDA and the recognized limitations with current traditional species concepts based on vegetative morphology.

CONCLUSION: We suggest that such "quantum weirdness" in the models is reconcilable with classical ecosystems logic when the focus of research shifts from morphological species to cryptic species that consist of genetically and ecologically differentiated subpopulations. We support our argument with theoretical discussions of eco-evolutionary interpretations that should become testable once suitable data are available.

RevDate: 2024-01-26

Saccò M, Mammola S, Altermatt F, et al (2024)

Groundwater is a hidden global keystone ecosystem.

Global change biology, 30(1):e17066.

Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.

RevDate: 2024-01-24

Cheng R, Luo A, Orr M, et al (2024)

Cryptic diversity begets challenges and opportunities in biodiversity research.

Integrative zoology [Epub ahead of print].

How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.

RevDate: 2024-01-23

Godarzi B, Chandler F, van der Linden A, et al (2024)

A species-independent lateral flow microarray immunoassay to detect WNV and USUV NS1-specific antibodies in serum.

One health (Amsterdam, Netherlands), 18:100668 pii:S2352-7714(23)00188-X.

Arboviruses such as West Nile Virus (WNV) and Usutu Virus (USUV) are emerging pathogens that circulate between mosquitoes and birds, occasionally spilling over into humans and horses. Current serological screening methods require access to a well-equipped laboratory and are not currently available for on-site analysis. As a proof of concept, we propose here a species-independent lateral flow microarray immunoassay (LMIA) able to quickly detect and distinguish between WNV Non-Structural 1 (NS1) and USUV NS1-specific antibodies. A double antigen approach was used to test sera collected from humans, horses, European jackdaws (Corvus monedula), and common blackbirds (Turdus merula). Optimization of the concentration of capture antigen spotted on the LMIA membrane and the amount of detection antigen conjugated to detector particles indicated that maximizing both parameters increased assay sensitivity. Upon screening of a larger serum panel, the optimized LMIA showed significantly higher spot intensity for a homologous binding event. Using a Receiver Operating Characteristics (ROC) curve, WNV NS1 LMIA results in humans, horses, and C. monedula showed good correlation when compared to "gold standard" WNV FRNT90. The most optimal derived sensitivity and specificity of the WNV NS1 LMIA relative to corresponding WNV FRNT90-confirmed sera were determined to be 96% and 86%, respectively. While further optimization is required, this study demonstrates the feasibility of developing a species-independent LMIA for on-site analysis of WNV, USUV, and other arboviruses. Such a tool would be useful for the on-site screening and monitoring of relevant species in more remote or low-income regions.

RevDate: 2024-01-18

Reschke K, Morozova OV, Dima B, et al (2022)

Phylogeny, taxonomy, and character evolution in Entoloma subgenus Nolanea.

Persoonia, 49:136-170.

Nolanea is a well-known and long-established subgenus of the genus Entoloma traditionally defined mainly by the mycenoid basidiocarps of the included species. Until now, revisions of this subgenus including molecular data exist only on a regional scale. In this study, the phylogeny of species of Nolanea is analysed based on multi-gene DNA sequences including data of specimens from all continents. New primers are designed for the mitochondrial small subunit and RPB2. The performance of the DNA loci in reconstructing the phylogeny in subg. Nolanea is evaluated. An ancestral state reconstruction is used to infer the character state evolution as well as the importance and reliability of morphological characters used to define subclades below subgeneric rank. Based on the results, seven sections are recognised in Nolanea: the sections Holoconiota, Infularia, Mammosa, Nolanea, Papillata, Staurospora, and the newly described sect. Elegantissima. A large phylogeny based on the fungal barcode rDNA ITS with numerous type sequences is used to evaluate current species concepts. Several names are revealed to be synonyms of older names. Four species new to science are described, namely E. altaicum, E. argillaceum, E. cornicolor, and E. incognitum. Lectotypes, epitypes or neotypes are designated for E. cetratum, E. clandestinum, E. conferendum, E. cuspidiferum, E. hebes, E. minutum, E. nitens, and E. rhodocylix. The re-evaluation of the limits of subg. Nolanea leads to an altered concept excluding species with distinct, lageniform cheilocystidia. The section Ameides is placed in subg. Leptonia. For several species formerly accommodated in Nolanea, but excluded now, viz., E. lepiotoides, E. rhombisporum, E. subelegans, and E. velenovskyi the taxonomic position remains unclear, because of the yet unresolved phylogeny of the whole genus Entoloma. Citation: Reschke K, Morozova OV, Dima B, et al. 2022. Phylogeny, taxonomy, and character evolution in Entoloma subgenus Nolanea. Persoonia 49: 136-170. https://doi.org/10.3767/persoonia.2022.49.04.

RevDate: 2024-01-17

Miller KB, Michat MC, N Ferreira (Jr) (2024)

Reclassification of Cybistrinae Sharp, 1880 in the Neotropical Region (Coleoptera, Adephaga, Dytiscidae), with description of new taxa.

ZooKeys, 1188:125-168.

The classification of the Neotropical Cybistrinae Sharp, 1880 (Coleoptera: Adephaga: Dytiscidae) is extensively revised based on a phylogenetic analysis of morphological features of the group. A new genus, Nilssondytesgen. nov. is described for a unique new species, Nilssondytesdiversussp. nov. from Venezuela. The New World genus, Megadytes Sharp, 1882, with several subgenera, was found to not be monophyletic. The type species of Megadytes, Dytiscuslatus Fabricius, 1801 and the species Cybisterparvus Trémouilles, 1984 were found to be monophyletic together, and phylogenetically more closely related to Cybister Curtis, 1827 than to other species assigned to Megadytes sensu stricto, which were found to also be monophyletic. The name Megadytes is here restricted to include only Megadyteslatus and Megadytesparvus. These two species assigned to this newly restricted genus concept are reviewed and diagnosed. A new genus, Metaxydytesgen. nov., is erected to include all the other species currently assigned to Megadytes sensu stricto. The current subgenus names assigned to Megadytes, Bifurcitus Brinck, 1945, Paramegadytes Trémouilles & Bachmann, 1980, and Trifurcitus Brinck, 1945, are elevated to genus rank since they are variously paraphyletic. The two species assigned to Cybister (Neocybister) Miller, Bergsten & Whiting, 2007, Cybister (Neocybister) festae Griffini, 1895, and Cybister (Neocybister) puncticollis (Brullé, 1837) re reviewed and diagnosed with the former redescribed and its type specimens considered for the first time since its description. Another evidently new species and possible new genus, Megadytes species, IR57 (Ribera et al. 2008), from Peru, is also characterized, but not formally treated because of lack of important data for the single, partial specimen. Diagnostic features are illustrated for the entire group.

RevDate: 2024-01-14

Hilburn BG, Janosik AM, CE Johnston (2023)

Incipient speciation in allopatric Etheostoma rupestre (Percidae: Etheostomatinae) lineages, with the description of three new subspecies.

Zootaxa, 5343(2):151-172.

In recent years, new species descriptions for the North American darters have proliferated. Most species concepts accepted by contemporary ichthyologists require that a valid species be both monophyletic and diagnoseable, yet many lineages exhibit modal or range differences in morphological characteristics without individuals being diagnosable. Such scenarios present difficulties with regards to proper taxonomic recognition of divergent lineages and often prohibit appropriate conservation action. Following the example of recent authors, we provide meristic, geometric morphometric, and pigmentation data to support the recognition of three subspecies of Etheostoma rupestre, a species endemic to the Mobile Basin. These morphological data cohere with previous genetic work for E. rupestre. The nominate subspecies Etheostoma rupetsre rupestre (Tsais Rock Darter) is endemic to the Tombigbee River and Black Warrior River watersheds in Alabama and Mississippi and is characterized by having lower numbers of lateral blotches, lower range and mean of lateral line scales, lower modal number of scales above the lateral line, and lower degrees of nape squamation than other subspecies. Etheostoma rupestre piersoni (Shamrock Darter), ssp. nov., is endemic to the Cahaba and Alabama River Watersheds in Alabama and is characterized by intermediate counts of lateral blotches and higher scale counts and nape squamation than E. r. rupestre. Etheostoma rupestre uphapeense (Jade Darter), ssp. nov., is restricted to several small, disjunct populations in the Coosa and Tallapoosa watersheds in Alabama, Georgia, and Tennessee. Etheostoma r. uphapeense is characterized by having a higher mean number of lateral blotches than both other subspecies and higher scale counts than E. r. rupestre. While E. r. rupestre and E. r. piersoni are widespread and abundant within their respective ranges, E. r. uphapeense has a disjunct range and is often uncommon where it occurs. Etheostoma r. uphapeense should be monitored where it occurs to discern population trends.

RevDate: 2024-01-14

Hoare RJB, Patrick BH, Buckley TR, et al (2023)

Wing pattern variation and DNA barcodes defy taxonomic splitting in the New Zealand Pimelea Looper Notoreas perornata (Walker) (Lepidoptera: Geometridae: Larentiinae): the importance of populations as conservation units.

Zootaxa, 5346(1):1-27.

The endemic Notoreas perornata (Walker, 1863) complex (Lepidoptera: Geometridae: Larentiinae) from the North Island and northern South Island of New Zealand is reviewed. Larvae feed on Pimelea spp. (Thymelaeaceae), frequently in highly fragmented and threatened shrubland habitats. Allopatric populations tend to differ in size and wing pattern characteristics, but not in genitalia; moreover extensive variation renders recognition of subspecies / allopatric species based on any species concept problematic. A mitochondrial DNA gene tree is not congruent with morphology and indicates rapid recent divergence that has not settled into diagnosable lineages. Based on our results, we synonymise Notoreas simplex Hudson, 1898 with N. perornata (Walker, 1863), and retain N. perornata as a single, highly diverse but monotypic species. All known populations are illustrated to display variation. For conservation purposes, we recommend the continued recognition within the species of 10 populations or groups of populations that appear to be on the way to diverging at subspecific level based on morphological and/or DNA data. The conservation status of all these populations is reviewed. One conservation unit, comprising the populations from Westland, has not been seen since 1998 and is feared possibly extinct.

RevDate: 2024-01-13

Martin JM, Leece AB, Baker SE, et al (2024)

A lineage perspective on hominin taxonomy and evolution.

Evolutionary anthropology [Epub ahead of print].

An uncritical reliance on the phylogenetic species concept has led paleoanthropologists to become increasingly typological in their delimitation of new species in the hominin fossil record. As a practical matter, this approach identifies species as diagnosably distinct groups of fossils that share a unique suite of morphological characters but, ontologically, a species is a metapopulation lineage segment that extends from initial divergence to eventual extinction or subsequent speciation. Working from first principles of species concept theory, it is clear that a reliance on morphological diagnosabilty will systematically overestimate species diversity in the fossil record; because morphology can evolve within a lineage segment, it follows that early and late populations of the same species can be diagnosably distinct from each other. We suggest that a combination of morphology and chronology provides a more robust test of the single-species null hypothesis than morphology alone.

RevDate: 2024-01-11

Cai ZY, NH Xia (2023)

A Novel Elucidation for Synflorescences of Chinese Bamboos.

Plants (Basel, Switzerland), 13(1):.

The objective of this work is to elucidate the flowering structures of Chinese bamboos applying the synflorescence concept. To keep in line with grasses, the bamboo synflorescence is defined as a whole culm or a whole branch terminating in an inflorescence. For the first time, the repetitive and fundamental unit of bamboo synflorescences is clearly identified and termed as the "basic flowering branch". The basic flowering branch could be considered as the most simplified synflorescence for a bamboo species. Applying the synflorescence concept, the pseudospikelet is interpreted as a sort of basic flowering branch rather than a spikelet. Consequently, the synflorescence development pattern is consistent throughout the whole family. This study also marks the first recognition of both pseudospikelets and true spikelet flowering branches within the same bamboo synflorescence, which is observed in the genera Brachystachyum, Semiarundinaria and Menstruocalamus.

RevDate: 2024-01-08

Torresani M, Rocchini D, Ceola G, et al (2024)

Grassland vertical height heterogeneity predicts flower and bee diversity: an UAV photogrammetric approach.

Scientific reports, 14(1):809.

The ecosystem services offered by pollinators are vital for supporting agriculture and ecosystem functioning, with bees standing out as especially valuable contributors among these insects. Threats such as habitat fragmentation, intensive agriculture, and climate change are contributing to the decline of natural bee populations. Remote sensing could be a useful tool to identify sites of high diversity before investing into more expensive field survey. In this study, the ability of Unoccupied Aerial Vehicles (UAV) images to estimate biodiversity at a local scale has been assessed while testing the concept of the Height Variation Hypothesis (HVH). This hypothesis states that the higher the vegetation height heterogeneity (HH) measured by remote sensing information, the higher the vegetation vertical complexity and the associated species diversity. In this study, the concept has been further developed to understand if vegetation HH can also be considered a proxy for bee diversity and abundance. We tested this approach in 30 grasslands in the South of the Netherlands, where an intensive field data campaign (collection of flower and bee diversity and abundance) was carried out in 2021, along with a UAV campaign (collection of true color-RGB-images at high spatial resolution). Canopy Height Models (CHM) of the grasslands were derived using the photogrammetry technique "Structure from Motion" (SfM) with horizontal resolution (spatial) of 10 cm, 25 cm, and 50 cm. The accuracy of the CHM derived from UAV photogrammetry was assessed by comparing them through linear regression against local CHM LiDAR (Light Detection and Ranging) data derived from an Airborne Laser Scanner campaign completed in 2020/2021, yielding an [Formula: see text] of 0.71. Subsequently, the HH assessed on the CHMs at the three spatial resolutions, using four different heterogeneity indices (Rao's Q, Coefficient of Variation, Berger-Parker index, and Simpson's D index), was correlated with the ground-based flower and bee diversity and bee abundance data. The Rao's Q index was the most effective heterogeneity index, reaching high correlations with the ground-based data (0.44 for flower diversity, 0.47 for bee diversity, and 0.34 for bee abundance). Interestingly, the correlations were not significantly influenced by the spatial resolution of the CHM derived from UAV photogrammetry. Our results suggest that vegetation height heterogeneity can be used as a proxy for large-scale, standardized, and cost-effective inference of flower diversity and habitat quality for bees.

RevDate: 2024-01-01

Cook CN, Redford KH, MW Schwartz (2023)

Species conservation in the era of genomic science.

Bioscience, 73(12):885-890 pii:biad098.

The exponential increase in the availability of genomic data, derived from sequencing thousands of loci or whole genomes, provides exciting new insights into the diversity of life. However, it can also challenge established species concepts and existing management regimes derived from these concepts. Genomic data can help inform decisions about how to manage genetic diversity, but policies that protect identified taxonomic entities can generate conflicting recommendations that create challenges for practitioners. We outline three dimensions of management concern that arise when facing new and potentially conflicting interpretations of genomic data: defining conservation entities, deciding how to manage diversity, and evaluating the risks and benefits of management actions. We highlight the often-underappreciated role of values in influencing management choices made by individuals, scientists, practitioners, the public, and other stakeholders. Such values influence choices through mechanisms such as the Rashomon effect, whereby management decisions are complicated by conflicting perceptions of the causes and consequences of the conservation problem. To illustrate how this might operate, we offer a hypothetical example of this effect for the interpretation of genomic data and its implications for conservation management. Such value-based decisions can be challenged by the rigidity of existing management regimes, making it difficult to achieve the necessary flexibility to match the changing biological understanding. We finish by recommending that both conservation geneticists and practitioners reflect on their respective values, responsibilities, and roles in building a more robust system of species management. This includes embracing the inclusion of stakeholders in decision-making because, as in many cases, there are not objectively defensible right or wrong decisions.

RevDate: 2023-12-28

Noble PJ, Seitz C, Lee SS, et al (2023)

Characterization of algal community composition and structure from the nearshore environment, Lake Tahoe (United States).

Frontiers in ecology and evolution, 10:1-16.

Periphyton assemblages from the nearshore environment of the west (California) side of Lake Tahoe, were analyzed to determine their taxonomic composition and community structure across habitats and seasons. Lake Tahoe is the second deepest lake in the US and an iconic oligotrophic subalpine lake with remarkable transparency. It has experienced offshore cultural eutrophication since the 1960s with observations of nuisance nearshore algal growth since the mid 2000s attributed to anthropogenic stressors. Samplings from November 2019-September 2020 provide useful snapshots against which older monitoring may be contextualized. A voucher flora, complete with descriptions, photo-documentation and referencing to species concepts employed, was created as a method of providing reproducible identification and enumeration of algal species, and more seamless reconciliation of detailed taxonomic data with future monitoring projects. The eulittoral zone (0-2 m) is seasonally dominated by elongate araphid (Synedra, Ulnaria) and stalked or entubed diatoms (Gomphonema, Cymbella, Encyonema). The sublittoral zone (>2 m) is dominated by a nitrogen-fixing Epithemia-cyanobacteria assemblage with less seasonal changes in dominance and composition that expanded to impinge on the 2 m depths of the eulittoral zone in the Fall. Sublittoral epipsammic samples, despite their proximity to rocks, had a very distinct diatom composition and high species dominance, similar to what was seen in the Fall eulittoral samples, with high numbers of Staurosirella chains and small biraphid diatoms. The deeper samples at 30 and 50 m contained high numbers of live Epithemia, and indicate a thriving sublittoral assemblage at these greater depths, but with less biomass. The 2019-20 data show many of the same diatom taxa observed in the 1970's and 1980's but with changes in species dominance. Notably, there was less of the green alga Mougeotia, when compared to the 1970's data, and a higher dominance by nitrogen fixing Epithemia in the sublittoral zone, persisting year-round. These new data show roughly double the algal species biodiversity that had been documented previously in the Lake Tahoe nearshore, and is largely attributed to the methods employed. Adopting these new methods in future monitoring efforts should improve harmonization of taxonomic data and help advance our knowledge of the contributions to nearshore cultural eutrophication.

RevDate: 2023-12-21

Harrington TC, Ferreira MA, Somasekhara YM, et al (2023)

An expanded concept of Ceratocystis manginecans and five new species in the Latin American Clade of Ceratocystis.

Mycologia [Epub ahead of print].

The genus Ceratocystis contains a number of emerging plant pathogens, mostly members of the Latin American Clade (LAC), in which there are several unresolved taxonomic controversies. Among the most important are Brazilian pathogens in the C. fimbriata complex, C. manginecans and C. eucalypticola. Representatives of C. manginecans and C. eucalypticola from India and China, respectively, were shown to be fully interfertile in laboratory matings, and hybrids between the putative species were identified on Punica in India. An Indian tester strain was sexually compatible with representatives of what has been considered C. fimbriata on numerous hosts across Brazil. In this revision of the LAC, the name C. fimbriata is restricted to the widely dispersed Ipomoea strain, and C. manginecans is recognized as a Brazilian species that is important on Mangifera, Eucalyptus, and many other crops. C. mangivora and C. mangicola are also considered synonyms of C. manginecans. Based on phylogenetics and mating studies, two other Brazilian species are recognized: C. atlantica, sp. nov., and C. alfenasii, sp. nov., each with wide host ranges. Three new Caribbean species are recognized based on phylogenetics and earlier inoculation studies: C. costaricensis, sp. nov., on Coffea, C. cubensis, sp. nov., on Spathodea, and C. xanthosomatis, sp. nov., on the vegetatively propagated aroids Xanthosoma and Syngonium. Some of the other Ceratocystis species were based primarily on unique internal transcribed spacer (ITS) rDNA sequences, but the unreliability of rDNA sequences was demonstrated when intraspecific crossing of isolates with differing ITS sequences generated single-ascospore progeny with intragenomic variation in ITS sequences and others with new ITS sequences. Species recognition in Ceratocystis should use phenotype, including intersterility tests, to help identify which lineages are species. Although some species remain under-studied, we recognize 16 species in the LAC, all believed to be native to Latin America, the Caribbean region, or eastern USA.

RevDate: 2023-12-17

Rodriguez Gutierrez G, Ortiz Perez A, S Palzer (2023)

Integrated, Selective, Simultaneous Multigas Sensing Based on Nondispersive Infrared Spectroscopy-Type Photoacoustic Spectroscopy.

ACS sensors [Epub ahead of print].

Most chemical sensing scenarios require the selective and simultaneous determination of the concentrations of multiple gas species. In order to enable large-scale monitoring, reliability, robustness, and the potential for integration and miniaturization are key parameters that next-generation sensing technologies must comply with. Due to their superior sensitivity and selectivity as compared to standard NDIR-type systems, photoacoustic NDIR-approaches offer a means for selective detection at much reduced system dimensions such that microintegration becomes feasible. This contribution presents an acoustic frequency multiplexing method to integrate sensing capabilities for the parallel analysis of multiple gases in a single device without loss in selectivity via sound frequency separation. The approach is demonstrated using mid-infrared light emitting diodes and a multigas photoacoustic detector to monitor some of the most important greenhouse gases: carbon dioxide and methane. The number of gas species the sensor concept is able to detect simultaneously can be expanded without increasing the size of the system or its complexity. Additionally, the results demonstrate that the integrated device features the same selectivity and sensitivity as the currently used single gas photoacoustic NDIR systems. Furthermore, the possibility of an extension to any number of gas species is argued.

RevDate: 2023-12-14

Zhu LR, Wang ZY, Luo JJ, et al (2023)

Mercury-Mediated Epitaxial Accumulation of Au Atoms for Stained Hydrogel-Improved On-Site Mercury Monitoring.

Analytical chemistry [Epub ahead of print].

Trivalent Au ions are easily reduced to be zerovalent atoms by coexisting reductant reagents, resulting in the subsequent accumulation of Au atoms and formation of plasmonic nanostructures. In the absence of stabilizers or presence of weak stabilizers, aggregative growth of Au nanoparticles (NPs) always occurs, and unregular multidimensional Au materials are consequently constructed. Herein, the addition of nanomole-level mercury ions can efficiently prevent the epitaxial accumulation of Au atoms, and separated Au NPs with mediated morphologies and superior plasmonic characteristics are obtained. Experimental results and theoretical simulation demonstrate the Hg-concentration-reliant formation of plasmonic nanostructures with their mediated sizes and shapes in the presence of weak reductants. Moreover, the sensitive plasmonic responses of reaction systems exhibit selectivity comparable to that of Hg species. As a concept of proof, polymeric carbon dots (CDs) were used as the initial reductant, and the reactions between trivalent Au and CDs were studies. Significantly, Hg atoms prevent the epitaxial accumulation of Au atoms, and plasmonic NPs with decreased sizes were in situ synthesized, corresponding to varied surface plasmonic resonance absorption performance of the CD-induced hybrids. Moreover, with the integration of sensing substrates of CD-doped hydrogels, superior response stabilities, analysis selectivity, and sensitivity of Hg[2+] ions were achieved on the basis of the mercury-mediated in situ chemical reactions between trivalent Au ions and reductant CDs. Consequently, a high-performance sensing strategy with the use of Au NP-staining hydrogels (nanostaining hydrogels) was exhibited. In addition to Hg sensing, the nanostaining hydrogels facilitated by doping of emerging materials and advanced chem/biostrategies can be developed as high-performance on-site monitoring routes to various pollutant species.

RevDate: 2023-12-09

Shentu J, Lu Y, Li Y, et al (2023)

Compact Combustion Mechanisms of Typical n-Alkanes Developed by the Minimized Reaction Network Method.

Molecules (Basel, Switzerland), 28(23): pii:molecules28237695.

The existing combustion kinetic modeling method which aims at developing phenomenological combustion mechanisms characterized by multiple reactions confronts several challenges, including the conflicts between computing resources and mechanism scales during numerical simulation, etc. In order to address these issues, the minimized reaction network method for complex combustion system modeling based on the principle of simultaneous chemical equilibrium is proposed, which is aimed to develop combustion mechanisms with minimal reaction steps under a limited number of species. The concept of mechanism resolution is proposed in this method, and the reaction network with minimal reaction steps under a given mechanism resolution is constructed so that the scale of mechanisms is compressed greatly. Meanwhile, distinguishing from other mechanisms, the reversible form of elementary reactions is adopted and the classical two-parameter (A, Ea) Arrhenius equation fits the rate constants. Typical n-alkanes including n-butane, n-heptane, n-octane, n-decane, n-dodecane and n-hexadecane were taken as examples to indicate the development process of mechanisms and systematic kinetic validations were carried out. Results show that this method leads to very compact mechanisms with satisfactory accuracy, and it eliminates the process of mechanism reduction and is beneficial for mechanism optimization. This method and the derived kinetic mechanisms are hoped to contribute to combustion engineering applications.

RevDate: 2023-12-05

Logan RK, Vaudo JJ, Wetherbee BM, et al (2023)

Seasonally mediated niche partitioning in a vertically compressed pelagic predator guild.

Proceedings. Biological sciences, 290(2012):20232291.

Niche partitioning among closely related, sympatric species is a fundamental concept in ecology, and its mechanisms are of broad interest for understanding ecosystem functioning and predicting the impacts of human-driven environmental change. However, identifying mechanisms by which top marine predators partition available resources has been especially challenging given the difficulty of quantifying resource use of large pelagic animals. In the eastern tropical Pacific (ETP), three large, highly mobile and ecologically similar pelagic predators (blue marlin (Makaira nigricans), black marlin (Istiompax indica) and sailfish (Istiophorus platypterus)) coexist in a vertically compressed habitat. To evaluate each species' ecological niche, we leveraged a decade of recreational fisheries data, multi-year satellite tracking with high-resolution dive data, and stable isotope analysis. Fishery interaction and telemetry-based three-dimensional seasonal utilization distributions suggested high spatial and temporal overlap among species; however, seasonal and diel variability in diving behaviour produced spatial partitioning, leading to low trophic overlap among species. Expanding oxygen minimum zones will reduce the available vertical habitat within predator guilds, likely leading to increases in interspecific competition. Thus, understanding the mechanisms of habitat partitioning among predators in the vertically compressed ETP can provide insight into how predators in other ocean regions may respond to vertically limited habitats.

RevDate: 2023-11-25

Li WJ, Li FF, Bai J, et al (2023)

Isolation and characterization of intestinal bacteria associated with cellulose degradation in grasshoppers (Orthoptera).

Journal of insect science (Online), 23(6):.

Insect gut bacteria play an essential role in the nutritional metabolism, growth, and development of insects. Grasshoppers (Orthoptera) are cellulose-rich plant-feeding pests. Although the biological potential of grasshopper gut microorganisms to assist cellulose decomposition is well established, microbial resources for efficient degradation of cellulose biomass are still scarce and need to be developed. In this study, we used selective media to isolate cellulose-degrading bacteria from the intestines of Atractomorpha sinensis, Trilophidia annulata, Sphingonotus mongolicus, and Calliptamus abbreviatus. Phylogenetic analysis based on the maximum likelihood method using 16S rDNA sequencing sequences to identify bacteria revealed the isolation of 11 strains belonging to 3 genera, including Klebsiella, Aeromonas, and Bacillus. The degradability of the isolates to cellulose was then determined by the DNS colorimetric method, and the results showed that Bacillus had the highest degradation rate. The elucidation of microbial cellulose degradation capacity in grasshoppers not only contributes to the understanding of multiple plant-insect-microbe interactions, but also provides a valuable microbial resource for solving the biomass conversion of cellulose species problem.

RevDate: 2023-11-21

Kuang X, Liu Y, Luo H, et al (2023)

Triggerable Prodrug Nanocoating Enables On-Demand Activation of Microbial and Small-Molecular Therapeutics for Combination Treatment.

Journal of the American Chemical Society [Epub ahead of print].

The synergy of living microbial and small-molecular therapeutics has been widely explored for treating a variety of diseases, while current combination strategies often suffer from low bioavailability, heterogeneous spatiotemporal distribution, and premature drug release. Here, the use of a triggerable prodrug nanocoating is reported to enable the on-demand activation of microbial and small-molecular therapeutics for combination treatment. As a proof-of-concept study, a reactive oxygen species-responsive aromatic thioacetal linker is employed to prepare cationic chitosan-drug conjugates, which can form a nanocoating on the surface of living bacteria via electrostatic interaction. Following administration, the wrapped bacteria can be prevented from in vivo insults by the shielding effect of the nanocoating and be co-delivered with the conjugated drug in a spatiotemporally synchronous manner. Upon reaching the lesion site, the upgraded reactive oxygen species trigger in situ cleavage of the thioacetal linker, resulting in the release of the conjugated drug and a linker-derived therapeutic cinnamaldehyde. Meanwhile, a charge reversal achieved by the generation of negatively charged thiolated chitosan induces the dissociation of the nanocoating, leading to synchronous release of the living bacteria. The adequate activation of the combined therapeutics at the lesion site exhibits superior synergistic treatment efficacy, as demonstrated by an in vivo assessment using a mouse model of colitis. This work presents an appealing approach to combine living microbial and small-molecular therapeutics for advanced therapy of diseases.

RevDate: 2023-11-20

Wang MZ, Wu J, Zhang SL, et al (2023)

Species delimitation in Amana (Liliaceae): transcriptomes battle with evolutionary complexity.

Cladistics : the international journal of the Willi Hennig Society [Epub ahead of print].

Species delimitation has long been a subject of controversy, and there are many alternative concepts and approaches used to define species in plants. The genus Amana (Liliaceae), known as "East Asian tulips" has a number of cryptic species and a huge genome size (1C = 21.48-57.35 pg). It also is intriguing how such a spring ephemeral genus thrives in subtropical areas. However, phylogenetic relationships and species delimitation within Amana are challenging. Here we included all species and 84 populations of Amana, which are collected throughout its distribution range. A variety of methods were used to clarify its species relationships based on a combination of morphological, ecological, genetic, evolutionary and phylogenetic species concepts. This evidence supports the recognition of at least 12 species in Amana. Moreover, we explored the complex evolutionary history within the genus and detected several historical hybridization and introgression events based on phylogenetic trees (transcriptomic and plastid), phylonetworks, admixture and ABBA-BABA analyses. Morphological traits have undergone parallel evolution in the genus. This spring ephemeral genus might have originated from a temperate region, yet finally thrives in subtropical areas, and three hypotheses about its adaptive evolution are proposed for future testing. In addition, we propose a new species, Amana polymorpha, from eastern Zhejiang Province, China. This research also demonstrates that molecular evidence at the genome level (such as transcriptomes) has greatly improved the accuracy and reasonability of species delimitation and taxon classification.

RevDate: 2023-11-14

Karnbrock SBH, M Alcarazo (2023)

Cooperation between p-Block Elements and Redox-Active Ligands: Stoichiometric and Catalytic Transformations.

Chemistry (Weinheim an der Bergstrasse, Germany) [Epub ahead of print].

The relevance acquired by redox-active ligands in modern catalysis stems from their facile delivery and acceptance of electrons, either to the metal they coordinate or directly to an incoming substrate that also binds the central metal. Doing that, they generate coordinated radicals and provide access to more than one spin state during the catalytic cycle. As consequence, the new reaction barriers get reduced when compared to similar processes that are restricted to a single spin surface. The principles that govern this genuine approach to catalyst design are well-established, and their implementation has allowed the development of synthetically useful catalytic transformations; however, the extension of the concept to species in which p-block elements take the role of central atoms remains largely underdeveloped. Through the discussion of the key achievements and recent progress, this Concept Article highlights this original approach to design (organo)catalysts, discloses the progress achieved, and also reveals the many shortcomings still existing in the field.

RevDate: 2023-11-14

Pezoa JE, Ramírez DA, Godoy CA, et al (2023)

A Spatial-Spectral Classification Method Based on Deep Learning for Controlling Pelagic Fish Landings in Chile.

Sensors (Basel, Switzerland), 23(21): pii:s23218909.

Fishing has provided mankind with a protein-rich source of food and labor, allowing for the development of an important industry, which has led to the overexploitation of most targeted fish species. The sustainable management of these natural resources requires effective control of fish landings and, therefore, an accurate calculation of fishing quotas. This work proposes a deep learning-based spatial-spectral method to classify five pelagic species of interest for the Chilean fishing industry, including the targeted Engraulis ringens, Merluccius gayi, and Strangomera bentincki and non-targeted Normanichthtys crockeri and Stromateus stellatus fish species. This proof-of-concept method is composed of two channels of a convolutional neural network (CNN) architecture that processes the Red-Green-Blue (RGB) images and the visible and near-infrared (VIS-NIR) reflectance spectra of each species. The classification results of the CNN model achieved over 94% in all performance metrics, outperforming other state-of-the-art techniques. These results support the potential use of the proposed method to automatically monitor fish landings and, therefore, ensure compliance with the established fishing quotas.

RevDate: 2023-11-08

Ferchiou S, Caza F, de Boissel PGJ, et al (2022)

Applying the concept of liquid biopsy to monitor the microbial biodiversity of marine coastal ecosystems.

ISME communications, 2(1):61.

Liquid biopsy (LB) is a concept that is rapidly gaining ground in the biomedical field. Its concept is largely based on the detection of circulating cell-free DNA (ccfDNA) fragments that are mostly released as small fragments following cell death in various tissues. A small percentage of these fragments are from foreign (nonself) tissues or organisms. In the present work, we applied this concept to mussels, a sentinel species known for its high filtration capacity of seawater. We exploited the capacity of mussels to be used as natural filters to capture environmental DNA fragments of different origins to provide information on the biodiversity of marine coastal ecosystems. Our results showed that hemolymph of mussels contains DNA fragments that varied considerably in size, ranging from 1 to 5 kb. Shotgun sequencing revealed that a significant amount of DNA fragments had a nonself microbial origin. Among these, we found DNA fragments derived from bacteria, archaea, and viruses, including viruses known to infect a variety of hosts that commonly populate coastal marine ecosystems. Taken together, our study shows that the concept of LB applied to mussels provides a rich and yet unexplored source of knowledge regarding the microbial biodiversity of a marine coastal ecosystem.

RevDate: 2023-11-04

Francischini DDS, MAZ Arruda (2023)

One-point calibration and matrix-matching concept for quantification of potentially toxic elements in wood by LA-ICP-MS.

Analytical and bioanalytical chemistry [Epub ahead of print].

The aim of this work is to evaluate two quantitative methods, based on the external calibration applied in laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analysis, known as (i) analytical curve and (ii) one-point calibration, using the concept of matrix matching to quantify three potentially toxic elements (PTEs) in wood samples. These can biologically register changes in the abiotic environment and be applied to monitoring climate change or environmental toxicity. In this case, standard sample preparation was evaluated to prepare the standard pellets using Pinus taeda species as a matrix-matching concept. Six pellets of P. taeda, with different Pb, Cd, and Ba concentrations, were prepared to build the analytical curve and one-point calibration strategies. The LA-ICP-MS parameters were optimised for [206]Pb, [208]Pb, [112]Cd, [114]Cd, [137]Ba, and [138]Ba isotope analysis in wood samples. The two calibration strategies provided 74-110% analytical recovery from certified reference materials and similar results to those obtained by ICP-MS through the acid digestion of environmental wood samples from São Paulo City (Brazil). This demonstrated the applicability of the one-point calibration strategy in quantifying PTEs in wood samples, which could be used with environmental analyses. Differences observed between the Ba isotope results obtained via LA-ICP-MS and ICP-MS quantification were related to sampling by LA-ICP-MS and the ICP-MS sample introduction, as well as to laser matrix and transport effects because of the difference between the wood species evaluated.

RevDate: 2023-11-02

Hübner J, Chemyreva VG, DG Notton (2023)

Taxonomic and nomenclatural notes on Geodiaprialongiceps Kieffer, 1911 (Hymenoptera, Diapriidae) and synonymy of the genus Geodiapria Kieffer, 1910.

ZooKeys, 1183:1-11.

This paper reviews the status of Geodiapria and its nominotypical and only included species G.longiceps. Geodiapria was previously understood to be very similar to, and doubtfully separated from the genus Basalys. We use integrative taxonomy (morphology, DNA-barcoding, phylogenetic tree building) to show that the valid name for what was G.longiceps Kieffer, 1911 is now Basalysrufocinctus (Kiefer, 1911) and that Geodiapria is consequently a junior synonym of Basalyssyn. nov. The following taxa are new synonyms of B.rufocinctus: Loxotropalongiceps Wasmann, 1909, syn. nov., G.longiceps Kieffer, 1911, syn. nov., L.rufosignata Kieffer, 1911, syn. nov. Basalysrufocinctus is newly reported from Corsica, Germany, Norway and Spain.

RevDate: 2023-10-28

Sakala J (2024)

Fossil Wood Analyses: Several Examples from Five Case Studies in the Area of Central and NW Bohemia, Czech Republic.

Methods in molecular biology (Clifton, N.J.), 2722:89-104.

In the area of the Central and NW Bohemia, Czech Republic, the fossil wood is quite abundant, found in different states of preservation and present from Paleozoic (Pennsylvanian), through Mesozoic (Upper Cretaceous), to Cenozoic (upper Eocene to lower Miocene). So, this small area is ideal to demonstrate various aspects of the fossil wood analyses, including anatomy (unifacial vs. bifacial cambium, formation of tyloses and its significance, early vs. late wood, unambiguity of scientific terminology, stem vs. root wood), taphonomy (completeness of fossil record, influence of environment on mode of preservation, influence of preservation on wood anatomy and preservation potential, discrepancy between the record of wood and other organs), systematics (stem vs. crown group, wide concept of fossil wood genera, "mosaic" species, wood of extinct plants), and palaeoclimatic reconstruction (definition of "wood type," subjective vs. objective methods). The majority of the studied woods were thin-sectioned following the standard techniques and observed with a compound light microscope.

RevDate: 2023-10-28

Chen P, Abeywickrama PD, Ji S, et al (2023)

Molecular Identification and Pathogenicity of Diaporthe eres and D. hongkongensis (Diaporthales, Ascomycota) Associated with Cherry Trunk Diseases in China.

Microorganisms, 11(10): pii:microorganisms11102400.

This study aimed to identify fungal species associated with trunk diseases of sweet cherries (Prunus avium) in several commercial cherry orchards in Beijing, Guizhou and Shandong provinces, China. In total, eighteen fungal strains that fitted well into the species concept of Diaporthe were isolated. Based on both morphological and multi-locus phylogenetic analyses of internal transcribed spacer region (ITS), beta-tubulin (tub-2), calmodulin (Cal) and translation elongation factor 1-α (tef1-α) sequencing data, fourteen isolates were identified as Diaporthe eres, while four isolates were classified as D. hongkongensis. Here, we report D. hongkongensis causing sweet cherry branch dieback disease and, further, we confirmed the host association of D. eres with sweet cherries in China. A pathogenicity assay revealed the ability of both D. eres and D. hongkongensis to cause shoot necrosis and stem lesions on Prunus avium cv. 'Brooks' (mean lesion lengths of 1.86 cm and 1.56 cm, respectively). The optimal temperature for the growth of both Diaporthe species was tested. The optimal growth temperature for D. hongkongensis was 30 °C, and the 25-28 °C temperatures were the most favorable for the growth of D. eres strains. This research advances the understanding of fungal trunk diseases in fruit crops, particularly gummosis and branch dieback disease in Chinese cherry orchards, and will aid growers in making decisions about cultural practices and disease management.

RevDate: 2023-10-27

Wang Y, Shi J, Wu Y, et al (2023)

Selection of Flagship Species and Their Use as Umbrellas in Bird Conservation: A Case Study in Lishui, Zhejiang Province, China.

Animals : an open access journal from MDPI, 13(11): pii:ani13111825.

The concept of flagship species is widely used in conservation biology. Flagship birds play a key role in raising conservation funds, increasing awareness of biodiversity conservation, and maintaining ecosystem services. This study selected flagship bird species in Lishui, Zhejiang Province, China, and assessed their conservation effectiveness and ability to serve as umbrella species. A regional bird survey program from 2019-2022 recorded 361 bird species in Lishui. This study constructed a framework of flagship species selection based on social, ecological, economic, and cultural criteria. The analytic hierarchy process-entropy weight method (AHP-EM) was used to rank the score of 361 bird species, and the MaxEnt model was used to analyze the suitable distribution areas of these species. Finally, 10 species, which covered the distribution sites of all 361 bird species, were selected as the flagship species of Lishui. The distribution areas covered all the nature reserves and the priority areas of biodiversity of Lishui, in which these 10 species can also serve as umbrella species to protect local biodiversity. The methodology and ideas in this study could provide insights into the application of conservation concepts at the local level, as well as suggest possible recommendations for local governments to select flagship species for conservation.

RevDate: 2023-10-21

Chen SP, Liu WT, Cheng FY, et al (2023)

Ozone containment through selective mitigation measures on precursors of volatile organic compounds.

The Science of the total environment pii:S0048-9697(23)06580-4 [Epub ahead of print].

Abatement of volatile organic compounds (VOCs) ozone reduction is usually carried out by reducing the total amount of VOCs without considering reactivity between different species. This study incorporates the concept of maximum incremental reactivity (MIR) and speciation profiles into the industrial emission inventory of Taiwan to target organic species from industrial sources with the greatest ozone formation potentials (OFPs). These high OFP sources/species are then mitigated to assess the O3 reduction amount (ΔO3) with Community Multiscale Air Quality (CMAQ) modeling under VOC-limited conditions. The objective is to minimize the number of target sources/species and their tonnage while achieving maximum O3 reduction. This approach is referred to as the Selective Precursor Mitigation (SPM). A case study of a high ozone episode (September 4-10, 2020) was chosen for illustration, during which a relatively stagnant atmospheric condition with minimal transboundary ozone occurred. A series of scenarios to target the highest OFP chemicals/industries for mitigation are compared for the achievable max. ΔO3, areas affected (area coverage), and reduction efficiency. For instance, by reducing the ten leading industry classes with the island's highest OFPs (OFPind), up to 19 % of max. 1-h ΔO3 can be expected. If, however, the same tonnage of VOCs as that of OFPind is distributed to all industries without considering the reactivity, called the overall mitigation (OM), comparable results to those of OFPind were found, but the number of sources needed to be managed with OM would increase by nearly three times (29,662 for OM vs. 11,981 for OFPind). Further reducing the management scale by only zooming in the ten highest OFP chemicals within the ten leading OFP industries (OFPsp) would result in relatively limited area coverage. Still, major ozone hot spots could be alleviated. Although the domain is set on the island of Taiwan, the SPM approach is universally applicable to other regions worldwide to gain the maximum ozone reduction effect at a minimized societal cost.

RevDate: 2023-10-20

Nordmann T, Wickenhagen S, Doležal M, et al (2023)

Bichromatic UV detection system for atomically-resolved imaging of ions.

The Review of scientific instruments, 94(6):.

We present a compact bichromatic imaging system, located outside of the vacuum chamber of a trapped ion apparatus that collects the fluorescence of 230.6 and 369.5 nm photons simultaneously on a shared electron-multiplying charge-coupled device (EMCCD) camera. The system contains two lens doublets, consisting of a sphere and an asphere. They provide a numerical aperture of 0.45 and 0.40 at 230.6 and 369.5 nm, respectively, and enable spatially resolved state detection with a large field of view of 300 μm for long 115In+/172Yb+ Coulomb crystals. Instead of diffraction-limited imaging for one wavelength, the focus in this system is on simultaneous single-ion resolved imaging of both species over a large field, with special attention to the deep UV wavelength (230.6 nm) and the low scattering rate of In+ ions. The introduced concept is applicable to other dual-species applications.

RevDate: 2023-10-18

Melekhin M, Potekhin A, Gentekaki E, et al (2023)

Paramecium (Oligohymenophorea, Ciliophora) diversity in Thailand sheds light on the genus biogeography and reveals new phylogenetic lineages.

The Journal of eukaryotic microbiology [Epub ahead of print].

Paramecium (Ciliophora, Oligohymenophorea) is a good model to study ciliate biogeography. Extensive sampling mainly in northern hemisphere has led to 16 valid morphological species description thus far. However, a majority of hard-to-reach regions, including South East Asia, are underinvestigated. Our study combined traditional morphological and molecular approaches to reveal the biodiversity of Paramecium in Thailand from more than 110 samples collected in 10 provinces. Representatives of seven morphological species were identified from our collection, including the rare species, such as P. gigas and P. jenningsi. Additionally, we detected five different sibling species of the P. aurelia complex, described a new cryptic species P. hiwatashii n. sp. phylogenetically related to P. caudatum, and discovered a potentially new genetic species of the P. bursaria species complex. We also documented a variety of bacterial cytoplasmic symbionts from at least nine monoclonal cultures of Paramecium.

RevDate: 2023-10-18

Ibarra-Chávez R, Haag AF, Dorado-Morales P, et al (2020)

Rebooting Synthetic Phage-Inducible Chromosomal Islands: One Method to Forge Them All.

Biodesign research, 2020:5783064.

Phage-inducible chromosomal islands (PICIs) are a widespread family of mobile genetic elements, which have an important role in bacterial pathogenesis. These elements mobilize among bacterial species at extremely high frequencies, representing an attractive tool for the delivery of synthetic genes. However, tools for their genetic manipulation are limited and timing consuming. Here, we have adapted a synthetic biology approach for rapidly editing of PICIs in Saccharomyces cerevisiae based on their ability to excise and integrate into the bacterial chromosome of their cognate host species. As proof of concept, we engineered several PICIs from Staphylococcus aureus and Escherichia coli and validated this methodology for the study of the biology of these elements by generating multiple and simultaneous mutations in different PICI genes. For biotechnological purposes, we also synthetically constructed PICIs as Trojan horses to deliver different CRISPR-Cas9 systems designed to either cure plasmids or eliminate cells carrying the targeted genes. Our results demonstrate that the strategy developed here can be employed universally to study PICIs and enable new approaches for diagnosis and treatment of bacterial diseases.

RevDate: 2023-10-16

Yong RQ, Martin SB, NJ Smit (2023)

A new species of Siphoderina Manter, 1934 (Digenea: Cryptogonimidae) infecting the Dory Snapper Lutjanus fulviflamma (Teleostei: Lutjanidae) from the east coast of South Africa.

Systematic parasitology [Epub ahead of print].

Parasitological assessment of marine fishes at Sodwana Bay in the iSimangaliso Marine Protected Area on the east coast of South Africa revealed a new species of cryptogonimid trematode infecting the pyloric caeca of the Dory Snapper, Lutjanus fulviflamma (Forsskål) (Lutjanidae). The new species is morphologically consistent with the concept of the large genus Siphoderina Manter, 1934; its phylogenetic position within this genus was validated through molecular sequencing of the ITS2 and partial 28S ribosomal DNA sub-regions. We name this species Siphoderina nana n. sp. and comment on the current state of understanding for this genus of cryptogonimids.

RevDate: 2023-10-16

Li F, Hou L, Liu W, et al (2023)

Carbon Vacancy-Enhanced Activity of Fe-N-C Single Atom Catalysts toward Luminol Chemiluminescence in the Absence of H2O2.

Analytical chemistry [Epub ahead of print].

The classic luminol-H2O2 chemiluminescence (CL) systems suffer from easy self-decomposition of H2O2 at room temperature, hindering the practical applications of the luminol-H2O2 CL system. In this work, unexpectedly, we found that the carbon vacancy-modified Fe-N-C single atom catalysts (VC-Fe-N-C SACs) can directly trigger a luminol solution to generate strong CL emission in the absence of H2O2. The Fe-based SACs were prepared through the conventional pyrolysis of zeolitic imidazolate frameworks. The massive carbon vacancies were readily introduced into Fe-N-C SACs through a tannic acid-etching process. Carbon vacancy significantly enhanced the catalytic activity of Fe-N-C SACs on the CL reaction of luminol-dissolved oxygen. The VC-Fe-N-C SACs performed a 13.4-fold CL enhancement compared with the classic luminol-Fe[2+] system. It was found that the introduction of a carbon vacancy could efficiently promote dissolved oxygen to convert to reactive oxygen species. As a proof of concept, the developed CL system was applied to detect alkaline phosphatase with a linear range of 0.005-1 U/L as well as a detection limit of 0.003 U/L. This work demonstrated that VC-Fe-N-C SAC is a highly efficient CL catalyst that can promote the analytic application of the luminol CL system.

RevDate: 2023-10-14

Boltenkov EV (2023)

Resolving the Puzzle of Iris maackii (Iridaceae): A Morphological Insight into Its Taxonomy.

Plants (Basel, Switzerland), 12(19): pii:plants12193349.

Since the early 20th century, Iris maackii (Iridaceae) has been considered a synonym of I. laevigata, a synonym of I. pseudacorus, or an accepted species. The current concept of I. maackii in the literature and databases is often applied to yellow-flowered plants with prominently veined rosette leaves, which are diagnostic features of I. pseudacorus growing in Northeast Asia. Therefore, the objective was to clarify the taxonomic identity of I. maackii. This study is based on a critical examination of the literature, on the observed morphological characters in the holotype of I. maackii, and on a morphological comparison of I. maackii with living plants of I. laevigata and I. pseudacorus. Additionally, a morphometric comparison of the seed characters was carried out to clarify the morphological distinction among I. maackii, I. laevigata, and I. pseudacorus. A careful study demonstrated that the rosette leaf texture and the morphology of the flowering stem, fruit, and seeds of I. maackii are identical to or within the variation range of I. laevigata. Thus, I. maackii is morphologically non-distinct from I. laevigata and should be recognized as a taxonomic synonym of the latter. An image of the holotype of I. maackii is provided along with detailed illustrations of I. laevigata and I. pseudacorus.

RevDate: 2023-10-11

Shukla I, Gaynor KM, Worm B, et al (2023)

The diversity of animals identified as keystone species.

Ecology and evolution, 13(10):e10561.

Although the keystone species concept was conceived of over 50 years ago, contemporary efforts to synthesize related literature have been limited. Our objective was to create a list of keystone animal species identified in the literature and to examine the variation in the traits of species and the ecosystem influences they elicit. We documented 230 species considered keystones. A clustering analysis classified them into five archetypes based on combinations of their taxonomic class, body size, trophic level, and role (consumers, modifiers, or prey). Although conservation and public perception of keystones primarily focuses on large vertebrate consumers, our analysis reveals that researchers have defined a wide diversity of keystone species, with large variation in associated ecosystem processes. Future research may confront ambiguity in the definition of keystone status, as well as clarify the type, abundance, and quality of data required to assign the term. Identifying keystones with increased rigor would not only enrich the literature but also inform intervention to safeguard threatened keystones and their associated influences on ecosystems.

RevDate: 2023-10-06

Carlisle JD, Keinath DA, Albeke SE, et al (2018)

Identifying Holes in the Greater Sage-Grouse Conservation Umbrella.

The Journal of wildlife management, 82(5):948-957.

The umbrella species concept, wherein multiple species are indirectly protected under the umbrella of a reserve created for one, is intended to enhance conservation efficiency. Although appealing in theory and common in practice, empirical tests of the concept have been scarce. We used a real-world, semi-protected reserve established to protect a high-profile umbrella species (greater sage-grouse [Centrocercus urophasianus]) to investigate 2 potential mechanisms underlying the concept's successful application: reserve size and species similarity. We estimated how much habitat protection the established reserve provided to 52 species of conservation concern associated with vegetation communities where greater sage-grouse occur. To illustrate the importance of reserve size, we compared the effectiveness of the established reserve to alternative greater sage-grouse reserves of various sizes and to simulated reserves of equal size but sited with no regard for greater sage-grouse. We further assessed whether key species' traits were associated with different levels of protection under the umbrella reserve. The established umbrella reserve protected 82% of the state's greater sage-grouse population and 0-63% of the habitat of the background species examined. The reserve outperformed equally sized, simulated reserves for only 12 of 52 background species. As expected, larger alternative reserves served as better umbrellas, but regardless of reserve size, not all species received equal protection. The established reserve was most effective at protecting the habitat of species that were most similar to the umbrella species (i.e., avian species, those highly associated with sagebrush plant communities, and those with widespread habitat). In contrast, the habitat of species with restricted distributions, particularly when combined with vegetation associations not closely matching the umbrella species, was not protected as well by the umbrella reserve. Such species require additional, targeted attention to achieve conservation objectives. Successful application of the umbrella species concept requires careful consideration of the characteristics of the umbrella species, the reserve delineated on its behalf, and the similarity of the umbrella species to its purported background species.

RevDate: 2023-10-06

Carlisle JD, Stewart DR, AD Chalfoun (2017)


Western North American naturalist, 77(4):450-463.

Conservation practitioners often rely on areas designed to protect species of greatest conservation priority to also conserve co-occurring species (i.e., the umbrella species concept). The extent to which vertebrate species may serve as suitable umbrellas for invertebrate species, however, has rarely been explored. Sage-grouse (Centrocercus spp.) have high conservation priority throughout much of the rangelands of western North America and are considered an umbrella species through which the conservation of entire rangeland ecosystems can be accomplished. Harvester ants are ecosystem engineers and play important roles in the maintenance and function of rangeland ecosystems. We compared indices of the abundance of western harvester ants (Pogonomyrmex occidentalis) and Greater Sage-Grouse (Centrocercus urophasianus) at 72 sites in central Wyoming, USA in 2012. The abundance of harvester ant mounds was best predicted by a regression model that included a combination of local habitat characteristics and the abundance of sage-grouse. When controlling for habitat-related factors, areas with higher abundances of sage-grouse pellets (an index of sage-grouse abundance and/or habitat use) had higher abundances of ant mounds than areas with lower abundances of sage-grouse pellets. The causal mechanism underlying this positive relationship between sage-grouse and ant mound abundance at the fine scale could be indirect (e.g., both species prefer similar environmental conditions) or direct (e.g., sage-grouse prefer areas with a high abundance of ant mounds because ants are an important prey item during certain life stages). We observed no relationship between a broad-scale index of breeding sage-grouse density and the abundance of ant mounds. We suspect that consideration of the non-breeding habitat of sage-grouse and finer-scale measures of sage-grouse abundance are critical to the utility of sage-grouse as an umbrella species for the conservation of harvester ants and their important role in rangeland ecosystems.

RevDate: 2023-10-05

Eggertson QA, Rintoul TL, CA Lévesque (2023)

Resolving the Globisporangium ultimum (Pythium ultimum) species complex.

Mycologia [Epub ahead of print].

The Globisporangium ultimum (formerly Pythium ultimum) species complex was previously composed of two morphological varieties: var. ultimum and var. sporangiiferum. Prior attempts to resolve this morphology-based species complex using molecular techniques have been inconclusive or conflicting. The increased availability of sequenced genomes and isolates identified as G. ultimum var. ultimum and var. sporangiiferum has allowed us to examine these relationships at a higher resolution and with a broader scope than previously possible. Using comparative genomics, we identified highly variable gene regions and designed primers for four new protein-coding genes for phylogenetics. These were then used alongside three known markers to generate a nuclear multigene genealogy of the species complex. From a collection of 163 isolates belonging to the target taxa, a subset of 29 was chosen to be included in this study (verified with nuclear rDNA internal transcribed spacer 1 [ITS1] and mitochondrial cytochrome c oxidase subunit 1 [cox1] sequences). Seventeen isolates of var. ultimum were selected to be representative of variations in genotype, morphology, and geographic collection location. The 12 isolates of var. sporangiiferum included all available specimens identified either morphologically (in previous studies) or through sequence similarity with ITS1 and cox1. Based on the fulfillment of reciprocal monophyly and observed genealogical concordance under the genealogical concordance phylogenetic species recognition, we determined that the Globisporangium ultimum species complex is composed of four genetically distinct species: Globisporangium ultimum, Globisporangium sporangiiferum, Globisporangium solveigiae, and Globisporangium bothae.

RevDate: 2023-09-30

Abachi H, Moallem M, Taghavi SM, et al (2023)

Garlic Bulb Decay and Soft Rot Caused by the Cross-Kingdom Pathogen Burkholderia gladioli.

Plant disease [Epub ahead of print].

In 2021, two Gram-negative bacterial strains were isolated from garlic (Allium sativum) bulbs showing decay and soft rot symptoms in central Iran. The bacterial strains were aggressively pathogenic on cactus, garlic, gladiolus, onion, potato, and saffron plants, and induced soft rot symptoms on carrot, cucumber, potato and radish discs. Furthermore, they were pathogenic on sporophore of cultivated and wild mushrooms. Phylogenetic analyses revealed that the bacterial strains belong to Burkholderia gladioli species. Garlic bulb rot caused by B. gladioli has rarely been reported in the literature. Historically, B. gladioli strains had been assigned to four pathovars i.e. B. gladioli pv. alliicola, B. gladioli pv. gladioli, B. gladioli pv. agaricicola, and B. gladioli pv. cocovenenans infecting onion, Gladiolus sp., mushrooms, and poisoning foods, respectively. Multilocus (i.e., 16S rRNA, atpD, gyrB, and lepA genes) sequence-based phylogenetic investigations including reference strains of B. gladioli pathovars showed that the two garlic strains belong to phylogenomic clade 2 of the species which includes the pathotype strain of B. gladioli pv. alliicola. Although the garlic strains were phylogenetically closely related to the B. gladioli pv. alliicola reference strains, they possessed pathogenicity characteristics that overlapped with three of the four historical pathovars including the ability to rot onion (pv. alliicola), gladiolus (pv. gladioli) and mushrooms (pv. agaricicola). Further, pathotype of each pathovar could infect the hosts of other pathovars, undermining the utility of pathovar concept in this species. Overall, using phenotypic pathovar-oriented assays to classify B. gladioli strains should be replaced by phylogenetic or phylogenomic analysis.

RevDate: 2023-09-28

Cortese-Krott MM (2023)

The Reactive Species Interactome in Red Blood Cells: Oxidants, Antioxidants, and Molecular Targets.

Antioxidants (Basel, Switzerland), 12(9): pii:antiox12091736.

Beyond their established role as oxygen carriers, red blood cells have recently been found to contribute to systemic NO and sulfide metabolism and act as potent circulating antioxidant cells. Emerging evidence indicates that reactive species derived from the metabolism of O2, NO, and H2S can interact with each other, potentially influencing common biological targets. These interactions have been encompassed in the concept of the reactive species interactome. This review explores the potential application of the concept of reactive species interactome to understand the redox physiology of RBCs. It specifically examines how reactive species are generated and detoxified, their interactions with each other, and their targets. Hemoglobin is a key player in the reactive species interactome within RBCs, given its abundance and fundamental role in O2/CO2 exchange, NO transport/metabolism, and sulfur species binding/production. Future research should focus on understanding how modulation of the reactive species interactome may regulate RBC biology, physiology, and their systemic effects.

RevDate: 2023-09-27

Jiménez-Gaona Y, Vivanco-Galván O, Cruz D, et al (2023)

Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota).

Journal of fungi (Basel, Switzerland), 9(9): pii:jof9090894.

BACKGROUND: The delimitation of species of Tulasnella has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels-showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as Tulasnella.

OBJECTIVES: The aim of this study is to test evolutionary relationships using a combination of alignment-based and alignment-free distance matrices as an alternative molecular tool to traditional methods, and to consider the secondary structures and CBCs from ITS2 (internal transcribed spacer) sequences for species delimitation in Tulasnella.

METHODOLOGY: Three phylogenetic approaches were plotted: (i) alignment-based, (ii) alignment-free, and (iii) a combination of both distance matrices using the DISTATIS and pvclust libraries from an R package. Finally, the secondary structure consensus was modeled by Mfold, and a CBC analysis was obtained to complement the species delimitation using 4Sale.

RESULTS AND CONCLUSIONS: The phylogenetic tree results showed delimited monophyletic clades in Tulasnella spp., where all 142 Tulasnella sequences were divided into two main clades A and B and assigned to seven species (T. asymmetrica, T. andina, T. eichleriana ECU6, T. eichleriana ECU4 T. pinicola, T. violea), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, T. albida belongs to type I; T. eichleriana, T. tomaculum, and T. violea belong to type II; and T. asymmetrica, T. andina, T. pinicola, and T. spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species.

RevDate: 2023-09-25

Wang Z, Kim W, Wang YW, et al (2023)

The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics.

Frontiers in fungal biology, 4:1214537.

Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.

RevDate: 2023-09-20

Biswas R, Batista Da Rocha C, Bennick RA, et al (2023)

Water-Soluble Fullerene Monoderivatives for Biomedical Applications.

ChemMedChem [Epub ahead of print].

Monoderivatives of fullerenes functionalized with hydrophilic groups make them water soluble, while preserving the hydrophobic fullerene cage. This class of molecules have intriguing biomedical applications, including drug delivery, photodynamic therapy (PDT), antiviral and antimicrobial activity and reactive oxygen species (ROS)-scavenging abilities. In this Concept we discuss the synthesis and biomedical applications of water-soluble fullerene monoderivatives and their biological behavior based on their structures.

RevDate: 2023-09-18

Pollmann M, Kuhn D, König C, et al (2023)

New species based on the biological species concept within the complex of Lariophagus distinguendus (Hymenoptera, Chalcidoidea, Pteromalidae), a parasitoid of household pests.

Ecology and evolution, 13(9):e10524.

The pteromalid parasitoid Lariophagus distinguendus (Foerster) belongs to the Hymenoptera, a megadiverse insect order with high cryptic diversity. It attacks stored product pest beetles in human storage facilities. Recently, it has been shown to consist of two separate species. To further study its cryptic diversity, strains were collected to compare their relatedness using barcoding and nuclear genes. Nuclear genes identified two clusters which agree with the known two species, whereas the barcode fragment determined an additional third Clade. Total reproductive isolation (RI) according to the biological species concept (BSC) was investigated in crossing experiments within and between clusters using representative strains. Sexual isolation exists between all studied pairs, increasing from slight to strong with genetic distance. Postzygotic barriers mostly affected hybrid males, pointing to Haldane's rule. Hybrid females were only affected by unidirectional Spiroplasma-induced cytoplasmic incompatibility and behavioural sterility, each in one specific strain combination. RI was virtually absent between strains separated by up to 2.8% COI difference, but strong or complete in three pairs from one Clade each, separated by at least 7.2%. Apparently, each of these clusters represents one separate species according to the BSC, highlighting cryptic diversity in direct vicinity to humans. In addition, these results challenge the recent 'turbo-taxonomy' practice of using 2% COI differences to delimitate species, especially within parasitic Hymenoptera. The gradual increase in number and strength of reproductive barriers between strains with increasing genetic distance also sheds light on the emergence of barriers during the speciation process in L. distinguendus.

RevDate: 2023-09-14

Fowers BJ, Novak LF, Kiknadze NC, et al (2023)

Is the concept of personality capacious enough to incorporate virtues?.

Frontiers in psychology, 14:1232637.

We will consider four answers to the question about whether the concept of personality is capacious enough to incorporate virtues. The simplest is that the concept of personality encompasses all individual variations in persons. It follows from this answer that virtues would, as individual differences, be incorporated into personality. Unfortunately, definitions of personality do not always invoke such capaciousness, and, in practice, most scholars limit their work to the Big Five or HEXACO models, which do not incorporate virtues. The second answer is that the concept of personality incorporates all trait or dimension level variations across persons, with some exceptions, such as intelligence, attachment style, and psychopathy. Following this definition, virtues, as traits, would be incorporated into such a broad definition of personality. Unfortunately, the boundaries for inclusion and exclusion into personality are fuzzy in this case, and there is no extant definition of personality that solves this problem. The third answer is that personality traits and virtue traits are similar, but distinct concepts. This article presents conceptual and empirical arguments for this similarity in seeing traits as a higher order concept that includes the species of personality and the species of virtue. The fourth answer is that personality and virtue are unrelated. This answer is dismissed because there are many studies that indicate that they are correlated, and few advocate such a clear differentiation. The conclusion is that, pending conceptual and empirical results indicating otherwise, the genus-species relationship seems most fitting where traits are a genus, and personality and virtue are each a species within that genus.

RevDate: 2023-09-11

Thomas GWC, Hughes JJ, Kumon T, et al (2023)

The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats.

bioRxiv : the preprint server for biology pii:2023.08.28.555178.

A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.

RevDate: 2023-09-08

Mercogliano R, D Dongo (2023)

Fish welfare during slaughter: the European Council Regulation 1099/09 application.

Italian journal of food safety, 12(3):10926.

The Treaty of Lisbon states that animals are sentient beings. Fish species show physiological differences from terrestrial animals and are slaughtered and killed in a very different context. Many existing commercial killing methods expose fish to extensive suffering over a prolonged period of time, and some of the slaughtering practices they experience can cause pain and distress. This study highlights the limited feasibility of European Council Regulation 1099/09 requirements on welfare when killing cephalopods and crustaceans. Sentience is the animal's capacity to have positive (comfort, excitement) and negative (pain, anxiety, distress, or harm) feelings. Considerable evidence is now showing that the major commercial fish species, including cephalopods and crustaceans, possess complex neurological substrates supporting pain sensitivity and conscious experiences. In the legislation applied to scientific procedures, the concept of sentience in these species is important. Therefore, it would be appropriate to acknowledge current scientific evidence and establish reference criteria for fish welfare. For the welfare of fish species during slaughter, European Council Regulation 1099/09 applicability is limited. Fish welfare during slaughter is more than just an ethical problem. According to the One-Health approach, food safety should also include the concept of sentience for fish welfare. Pending studies that dispel all doubt, the precautionary principle of European Council Regulation 178/04 remains valid and should be applied to fish welfare.

RevDate: 2023-09-07

Ansari L, Asgari B, Zare R, et al (2023)

Penicillium rhizophilum, a novel species in the section Exilicaulis isolated from the rhizosphere of sugarcane in Southwest Iran.

International journal of systematic and evolutionary microbiology, 73(9):.

During a survey of species diversity of Penicillium and Talaromyces in sugarcane (Saccharum officinarum) rhizosphere in the Khuzestan province of Iran [1], 195 strains were examined, from which 187 belonged to Penicillium (11 species) and eight to Talaromyces (one species). In the present study, three strains of Penicillium belonging to section Exilicaulis series Restricta, identified as P. restrictum by Ansari et al. [1], were subjected to a phylogenetic study. The multilocus phylogeny of partial β-tubulin, calmodulin and RNA polymerase II second largest subunit genes enabled the recognition of one new phylogenetic species that is here formally described as Penicillium rhizophilum sp. nov. This species is phylogenetically distinct in series Restricta, but it does not show significant morphological differences from other species previously classified in the series. Therefore, we here placed bias on the phylogenetic species concept. The holotype of Penicillium rhizophilum sp. nov. is IRAN 18169F and the ex-type culture is LA30[T] (=IRAN 4042C[T]=CBS 149737[T]).

RevDate: 2023-08-31

Sen A, Ansari A, Swain A, et al (2023)

Probing the Origins of Puzzling Reactivity in Fe/Mn-Oxo/Hydroxo Species toward C-H Bonds: A DFT and Ab Initio Perspective.

Inorganic chemistry [Epub ahead of print].

Activation of C-H bonds using an earth-abundant metal catalyst is one of the top challenges of chemistry, where high-valent Mn/Fe-oxo(hydroxo) biomimic species play an important role. There are several open questions related to the comparative oxidative abilities of these species, and a unifying concept that could accommodate various factors influencing reactivity is lacking. To shed light on these open questions, here, we have used a combination of density functional theory (DFT) (B3LYP-D3/def2-TZVP) and ab initio (CASSCF/NEVPT2) calculations to study a series of high-valent metal-oxo species [M[n+]H3buea(O/OH)] (M = Mn and Fe, n = II to V; H3buea = tris[(N'-tert-butylureaylato)-N-ethylene)]aminato towards the activation of dihydroanthracene (DHA). The H-bonding network in the ligand architecture influences the ground state-excited state gap and brings several excited states of the same spin multiplicity closer in energy, which triggers reactivity via one of those excited states, reducing the kinetic barriers for the C-H bond activation and rationalizing several puzzling reactivity trends observed in various high-valent Mn/Fe-oxo(hydroxo) species.

RevDate: 2023-08-28

Génin F, Rambeloarivony H, Silvestro D, et al (2023)

Ontogeny and phylogeny of mating behaviour: social heteroch rony in primates.

Theoretical biology forum, 116(1-2):15-50.

Based on the Recognition Concept of species, the specific-mate contact model posits that mating systems develop as combinations of two fundamental courtship strategies that we interpret here in terms of behavioural heterochrony: territorial mate-attraction evolved as an effect of peramorphosis whereas group-living mate-seeking evolved as an effect of paedomorphosis. We tested this hypothesis on primates in a phylogenetic and paleo-climatic context. Our results suggest that primate promiscuity (both males and females are mate-seekers) evolved with group-living from ancestral pair-living monogamy (both males and females are mate-attractors) in the Palaeogene, as the result of a slowdown in growth (neoteny) caused by increased environmental predictability. A secondary return to territorial monogamy probably evolved as the result of accelerated growth driven by seasonality (acceleration). Polygamy evolved in the Neogene during periods of forest fragmentation and environmental unpredictability. Small monogamous ancestors evolved seasonal polyandry (female attraction) as an effect of truncated development (progenesis). Large promiscuous, neotenic ancestors evolved non-seasonal polygyny (male attraction) as an effect of prolonged development (hypermorphosis) in males. We conclude that social heterochrony offers alternative explanations for the coevolution of life history and mating be-haviour; and we discuss the implications of our model for human social evolution.

RevDate: 2023-08-26

Xesfyngi Y, Georgoutsou-Spyridonos M, Tripathy A, et al (2023)

A High-Performance Antibacterial Nanostructured ZnO Microfluidic Device for Controlled Bacterial Lysis and DNA Release.

Antibiotics (Basel, Switzerland), 12(8): pii:antibiotics12081276.

In this work, the antibacterial properties of nanostructured zinc oxide (ZnO) surfaces are explored by incorporating them as walls in a simple-to-fabricate microchannel device. Bacterial cell lysis is demonstrated and quantified in such a device, which functions due to the action of its nanostructured ZnO surfaces in contact with the working fluid. To shed light on the mechanism responsible for lysis, E. coli bacteria were incubated in zinc and nanostructured ZnO substrates, as well as the here-investigated ZnO-based microfluidic devices. The unprecedented killing efficiency of E. coli in nanostructured ZnO microchannels, effective after a 15 min incubation, paves the way for the implementation of such microfluidic chips in the disinfection of bacteria-containing solutions. In addition, the DNA release was confirmed by off-chip PCR and UV absorption measurements. The results indicate that the present nanostructured ZnO-based microfluidic chip can, under light, achieve partial inactivation of the released bacterial DNA via reactive oxygen species-mediated oxidative damage. The present device concept can find broader applications in cases where the presence of DNA in a sample is not desirable. Furthermore, the present microchannel device enables, in the dark, efficient release of bacterial DNA for downstream genomic DNA analysis. The demonstrated potential of this antibacterial device for tailored dual functionality in light/dark conditions is the main novel contribution of the present work.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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The complex idea of “species” has evolved over time, yet its meaning is far from resolved. This comprehensive work takes a fresh look at an idea central to the field of biology by tracing its history from antiquity to today. John S. Wilkins explores the essentialist view, a staple of logic from Plato and Aristotle through the Middle Ages to fairly recent times, and considers the idea of species in natural history―a concept often connected to reproduction. Tracing “generative conceptions” of species back through Darwin to Epicurus, Wilkins provides a new perspective on the relationship between philosophical and biological approaches to this concept. He also reviews the array of current definitions. Species is a benchmark exploration and clarification of a concept fundamental to the past, present, and future of the natural sciences.

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

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