@article {pmid38715571,
year = {2024},
author = {Murwani, R and Anggraeni, R and Setiawan, GNA and Astari, PD and Cahyani, NKD and Sibero, MT and Ambariyanto, A},
title = {Lactic Acid Bacteria Isolates and the Microbiome of Cincalok, Tempoyak, and Mandai: A Traditional Fermented Food from Kalimantan Island, Indonesia.},
journal = {International journal of food science},
volume = {2024},
number = {},
pages = {6589766},
pmid = {38715571},
issn = {2314-5765},
abstract = {Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food and feed products. This research is aimed at (1) obtaining and identifying LAB isolates and (2) studying the microbiome (bacterial diversity and abundance) of spontaneously-fermented traditional foods of Kalimantan Island, Cincalok, Tempoyak, and Mandai. To obtain LAB isolates, food samples were serially diluted and inoculated on MRS agar that contained 1% CaCO3 (MRSA). Isolates forming clear zones were purified and identified by DNA barcoding. The microbiome was studied using genomic-sequencing techniques and analysed for taxonomic composition. Seven pure isolates were obtained from Cincalok, two Tempoyak, and one Mandai. DNA barcoding revealed that the Cincalok seven isolates were Staphylococcus carnosus (strain HSP-S16), Tetragenococcus halophilus (FSB201), Corynebacterium phoceense, Vagococcus vulneris (SS1995), Enterococcus faecalis (S11-6), Pisciglobus halotolerans (C01), and Priestia filamentosa (P3.1); two from Tempoyak, Levilactobacillus brevis (E1D3BL1) and Lactiplantibacillus plantarum (UMCC-2996); and one from Mandai, Staphylococcus cohnii (XAAS.x13; non-LAB). The T. halophilus, E. faecalis, P. halotolerans, L. brevis, and L. plantarum belong to LAB. The P. halotolerans from Cincalok and non-LAB in these three fermented foods were the first documented report. The microbiome revealed the dominance of Firmicutes phyla in the fermented foods, with 93% in Cincalok, 89.94% in Tempoyak, and 60.32% in Mandai. On the genus level, Cincalok was dominated by Tetragenococcus 40.33%, Anaerococcus 23.29%, Vagococcus 9.27%, and Lactobacillus 6.84%. Meanwhile, Tempoyak was dominated only by Lactobacillus 89.94%. Mandai were dominated by Lactobacillus 31.97%, Proteus 17.14%, Aerococcus 16.85%, Mangrovibacter 15.15%, and Vagococcus 6.2%. However, Mandai's microbiome LAB was not culturable/isolated on MRSA. The plausibility is that those unculturable LAB require coculturing with other bacteria and additional media components to grow on MRSA. This study is the first report regarding the microbiome of Cincalok, Tempoyak, and Mandai, along with their culturable LAB isolates.},
}

@article {pmid38714853,
year = {2024},
author = {Lindenhofer, D and Haendeler, S and Esk, C and Littleboy, JB and Brunet Avalos, C and Naas, J and Pflug, FG and van de Ven, EGP and Reumann, D and Baffet, AD and von Haeseler, A and Knoblich, JA},
title = {Cerebral organoids display dynamic clonal growth and tunable tissue replenishment.},
journal = {Nature cell biology},
volume = {},
number = {},
pages = {},
pmid = {38714853},
issn = {1476-4679},
abstract = {During brain development, neural progenitors expand through symmetric divisions before giving rise to differentiating cell types via asymmetric divisions. Transition between those modes varies among individual neural stem cells, resulting in clones of different sizes. Imaging-based lineage tracing allows for lineage analysis at high cellular resolution but systematic approaches to analyse clonal behaviour of entire tissues are currently lacking. Here we implement whole-tissue lineage tracing by genomic DNA barcoding in 3D human cerebral organoids, to show that individual stem cell clones produce progeny on a vastly variable scale. By using stochastic modelling we find that variable lineage sizes arise because a subpopulation of lineages retains symmetrically dividing cells. We show that lineage sizes can adjust to tissue demands after growth perturbation via chemical ablation or genetic restriction of a subset of cells in chimeric organoids. Our data suggest that adaptive plasticity of stem cell populations ensures robustness of development in human brain organoids.},
}

@article {pmid38714828,
year = {2024},
author = {Sipiczki, M and Czentye, K and Kállai, Z},
title = {High intragenomic, intergenomic, and phenotypic diversity in pulcherrimin-producing Metschnikowia yeasts indicates a special mode of genome evolution.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10521},
pmid = {38714828},
issn = {2045-2322},
mesh = {*Metschnikowia/genetics ; *Genome, Fungal ; *Evolution, Molecular ; *Phylogeny ; Genetic Variation ; Phenotype ; DNA, Mitochondrial/genetics ; },
abstract = {In molecular systematics, the delimitation of yeast species is based on the notion that the barcode differences are smaller within species than between them. The most widely used barcodes are segments of the chromosomal repeats coding for ribosomal RNAs that are homogenised in yeasts. The analysis of these segments of the type strains of ten species recently merged in Metschnikowia pulcherrima and 37 new isolates demonstrated that this is not the case in this species. The intragenomic diversity significantly exceeded the threshold gaps used to differentiate related yeast species. Large segments of the D1/D2 domains were not diverse within the genomes and could therefore be used to determine the taxonomic affiliation of the isolates. The genome structures of the isolates were compared by RAPD and the RFLP of the mitochondrial DNA. Both patterns were highly heterogeneous. The sequence analysis of the PUL4 gene (a member of the PUL gene cluster involved in pulcherrimin production) revealed very high intragenomic differences, suggesting that the genomes may be chimerised. Three phenotypic traits related to the antimicrobial antagonism characteristic of the species were also highly diverse and prone to reversible segregation resembling epigenetic processes (silencing and reactivation of regulators) rather than mutations and back-mutations. These features make M. pulcherrima unique among yeasts and indicate that it evolves in a non-standard way.},
}

*Metschnikowia/genetics
*Genome, Fungal
*Evolution, Molecular
*Phylogeny
Genetic Variation
Phenotype
DNA, Mitochondrial/genetics

@article {pmid38712508,
year = {2024},
author = {Voorspoels, A and Gevers, J and Santermans, S and Akkan, N and Martens, K and Willems, K and Van Dorpe, P and Verhulst, AS},
title = {Design Principles of DNA-Barcodes for Nanopore-FET Readout, Based on Molecular Dynamics and TCAD Simulations.},
journal = {The journal of physical chemistry. A},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jpca.4c01772},
pmid = {38712508},
issn = {1520-5215},
abstract = {Nanopore field-effect transistor (NP-FET) devices hold great promise as sensitive single-molecule sensors, which provide CMOS-based on-chip readout and are also highly amenable to parallelization. A plethora of applications will therefore benefit from NP-FET technology, such as large-scale molecular analysis (e.g., proteomics). Due to its potential for parallelization, the NP-FET looks particularly well-suited for the high-throughput readout of DNA-based barcodes. However, to date, no study exists that unravels the bit-rate capabilities of NP-FET devices. In this paper, we design DNA-based barcodes by labeling a piece of double-stranded DNA with dumbbell-like DNA structures. We explore the impact of both the size of the dumbbells and their spacing on achievable bit-rates. The conformational fluctuations of this DNA-origami, as observed by molecular dynamics (MD) simulation, are accounted for when selecting label sizes. An experimentally informed 3D continuum nanofluidic-nanoelectronic device model subsequently predicts both the ionic current and FET signals. We present a barcode design for a conceptually generic NP-FET, with a 14 nm diameter pore, operating in conditions corresponding to experiments. By adjusting the spacing between the labels to half the length of the pore, we show that a bit-rate of 78 kbit·s[-1] is achievable. This lies well beyond the state-of-the-art of ≈40 kbit·s[-1], with significant headroom for further optimizations. We also highlight the advantages of NP-FET readout based on the larger signal size and sinusoidal signal shape.},
}

@article {pmid38712231,
year = {2024},
author = {Yang, L and Liu, F and Hahm, H and Okuda, T and Li, X and Zhang, Y and Kalyanaraman, V and Heitmeier, MR and Samineni, VK},
title = {Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.24.590975},
pmid = {38712231},
abstract = {Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain wide projections. However, investigating the spatial organization, transcriptional and epigenetic landscapes of brain wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.},
}

@article {pmid38709890,
year = {2024},
author = {Li, W and Miller, D and Liu, X and Tosi, L and Chkaiban, L and Mei, H and Hung, PH and Parekkadan, B and Sherlock, G and Levy, SF},
title = {Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae332},
pmid = {38709890},
issn = {1362-4962},
support = {R01HG011676/NH/NIH HHS/United States ; },
abstract = {Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45 000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.},
}

@article {pmid38709485,
year = {2024},
author = {Wang, S and Chi, WY and Au, G and Huang, CC and Yang, JM and Huang, CH},
title = {Reconstructing Signaling Networks Using Biosensor Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2800},
number = {},
pages = {189-202},
pmid = {38709485},
issn = {1940-6029},
mesh = {*Biosensing Techniques/methods ; *Signal Transduction ; Humans ; ErbB Receptors/metabolism/genetics ; },
abstract = {Understanding how signaling networks are regulated offers valuable insights into how cells and organisms react to internal and external stimuli and is crucial for developing novel strategies to treat diseases. To achieve this, it is necessary to delineate the intricate interactions between the nodes in the network, which can be accomplished by measuring the activities of individual nodes under perturbation conditions. To facilitate this, we have recently developed a biosensor barcoding technique that enables massively multiplexed tracking of numerous signaling activities in live cells using genetically encoded fluorescent biosensors. In this chapter, we detail how we employed this method to reconstruct the EGFR signaling network by systematically monitoring the activities of individual nodes under perturbations.},
}

*Biosensing Techniques/methods
*Signal Transduction
Humans
ErbB Receptors/metabolism/genetics

@article {pmid38705596,
year = {2024},
author = {Schulz, AR and Rademacher, J and Bockhorn, V and Mei, HE},
title = {Harmonized analysis of PBMC by mass cytometry.},
journal = {Methods in cell biology},
volume = {186},
number = {},
pages = {107-130},
doi = {10.1016/bs.mcb.2024.02.015},
pmid = {38705596},
issn = {0091-679X},
mesh = {Humans ; *Leukocytes, Mononuclear/cytology/immunology ; *Flow Cytometry/methods/standards ; Immunophenotyping/methods ; Single-Cell Analysis/methods ; },
abstract = {Mass cytometry permits the high dimensional analysis of cellular systems at single-cell resolution with high throughput in various areas of biomedical research. Here, we provide a state-of-the-art protocol for the analysis of human peripheral blood mononuclear cells (PBMC) by mass cytometry. We focus on the implementation of measures promoting the harmonization of large and complex studies to aid robustness and reproducibility of immune phenotyping data.},
}

Humans
*Leukocytes, Mononuclear/cytology/immunology
*Flow Cytometry/methods/standards
Immunophenotyping/methods
Single-Cell Analysis/methods

@article {pmid38705187,
year = {2024},
author = {Meier, R and Hartop, E and Pylatiuk, C and Srivathsan, A},
title = {Towards holistic insect monitoring: species discovery, description, identification and traits for all insects.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230120},
doi = {10.1098/rstb.2023.0120},
pmid = {38705187},
issn = {1471-2970},
mesh = {*Insecta/physiology/classification/genetics ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; },
abstract = {Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}

*Insecta/physiology/classification/genetics
Animals
*DNA Barcoding, Taxonomic/methods
Biodiversity

@article {pmid38705185,
year = {2024},
author = {Łukasik, P and Kolasa, MR},
title = {With a little help from my friends: the roles of microbial symbionts in insect populations and communities.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230122},
doi = {10.1098/rstb.2023.0122},
pmid = {38705185},
issn = {1471-2970},
mesh = {Animals ; *Insecta/microbiology/physiology ; *Symbiosis ; *Microbiota/physiology ; Biodiversity ; },
abstract = {To understand insect abundance, distribution and dynamics, we need to understand the relevant drivers of their populations and communities. While microbial symbionts are known to strongly affect many aspects of insect biology, we lack data on their effects on populations or community processes, or on insects' evolutionary responses at different timescales. How these effects change as the anthropogenic effects on ecosystems intensify is an area of intense research. Recent developments in sequencing and bioinformatics permit cost-effective microbial diversity surveys, tracking symbiont transmission, and identification of functions across insect populations and multi-species communities. In this review, we explore how different functional categories of symbionts can influence insect life-history traits, how these effects could affect insect populations and their interactions with other species, and how they may affect processes and patterns at the level of entire communities. We argue that insect-associated microbes should be considered important drivers of insect response and adaptation to environmental challenges and opportunities. We also outline the emerging approaches for surveying and characterizing insect-associated microbiota at population and community scales. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}

Animals
*Insecta/microbiology/physiology
*Symbiosis
*Microbiota/physiology
Biodiversity

@article {pmid38705177,
year = {2024},
author = {Li, Y and Devenish, C and Tosa, MI and Luo, M and Bell, DM and Lesmeister, DB and Greenfield, P and Pichler, M and Levi, T and Yu, DW},
title = {Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230123},
doi = {10.1098/rstb.2023.0123},
pmid = {38705177},
issn = {1471-2970},
mesh = {*Arthropods/classification ; *Biodiversity ; Animals ; *DNA, Environmental/analysis ; *Remote Sensing Technology/methods ; Forests ; Animal Distribution ; DNA Barcoding, Taxonomic/methods ; },
abstract = {Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into 'many-row (observation), many-column (species)' datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These 'novel community datasets' let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers using a deep neural net in a joint species distribution model. With this approach, we generate distribution maps for 76 arthropod species across a 225 km[2] temperate-zone forested landscape. We combine the maps to visualize the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this 'sideways biodiversity modelling' method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}

*Arthropods/classification
*Biodiversity
Animals
*DNA, Environmental/analysis
*Remote Sensing Technology/methods
Forests
Animal Distribution
DNA Barcoding, Taxonomic/methods

@article {pmid38705075,
year = {2024},
author = {Li, X and Liu, R and Zhang, N and Zhao, J and Zhou, Y and Zhou, Q and Gu, Z and Zhang, D},
title = {Carbon nanotubes integrated photonic barcodes in Herringbone Microfluidics for Multiplex Biomarker Quantification.},
journal = {Biosensors & bioelectronics},
volume = {258},
number = {},
pages = {116350},
doi = {10.1016/j.bios.2024.116350},
pmid = {38705075},
issn = {1873-4235},
abstract = {Early monitoring of cardiovascular disease (CVD) is crucial for its treatment and prognosis. Hence, highly specific and sensitive detection method is urgently needed. In this study, we propose a novel herringbone microfluid chip with aptamer functionalized core-shell photonic crystal (PhC) barcode integration for high throughput multiplex CVD detection. Based on the PhC derived from co-assembled carboxylated single-wall carbon nanotubes and silicon dioxide nanoparticles, we obtain core-shell PhC barcodes by hydrogel replicating and partially etching. These core-shell PhC barcodes not only retain the original structural colors coding element, but also fully expose a large number of carboxyl elements in the ore for the probe immobilization. We further combine the functionalized barcodes with herringbone groove microfluidic chip to elucidate its acceptability in testing clinical sample. It is demonstrated that the special design of microfluidic chip can significantly enhance fluid vortex resistance and contact frequency, improving the sample capture efficiency and detection sensitivity. These features indicate that our core-shell PhC barcodes-integrated herringbone microfluidic system possesses great potential for multiplex biomarker detection in clinical application.},
}

@article {pmid38705192,
year = {2024},
author = {van Klink, R},
title = {Delivering on a promise: futureproofing automated insect monitoring methods.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230105},
doi = {10.1098/rstb.2023.0105},
pmid = {38705192},
issn = {1471-2970},
mesh = {Animals ; *Insecta/physiology ; *Biodiversity ; Entomology/methods/instrumentation/trends ; Automation/methods ; },
abstract = {Due to rapid technological innovations, the automated monitoring of insect assemblages comes within reach. However, this continuous innovation endangers the methodological continuity needed for calculating reliable biodiversity trends in the future. Maintaining methodological continuity over prolonged periods of time is not trivial, since technology improves, reference libraries grow and both the hard- and software used now may no longer be available in the future. Moreover, because data on many species are collected at the same time, there will be no simple way of calibrating the outputs of old and new devices. To ensure that reliable long-term biodiversity trends can be calculated using the collected data, I make four recommendations: (1) Construct devices to last for decades, and have a five-year overlap period when devices are replaced. (2) Construct new devices to resemble the old ones, especially when some kind of attractant (e.g. light) is used. Keep extremely detailed metadata on collection, detection and identification methods, including attractants, to enable this. (3) Store the raw data (sounds, images, DNA extracts, radar/lidar detections) for future reprocessing with updated classification systems. (4) Enable forward and backward compatibility of the processed data, for example by in-silico data 'degradation' to match the older data quality. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}

Animals
*Insecta/physiology
*Biodiversity
Entomology/methods/instrumentation/trends
Automation/methods

@article {pmid38705180,
year = {2024},
author = {Li, R and Ratnasingham, S and Zarubiieva, I and Somervuo, P and Taylor, GW},
title = {PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230124},
doi = {10.1098/rstb.2023.0124},
pmid = {38705180},
issn = {1471-2970},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Algorithms ; Classification/methods ; Computer Graphics ; Animals ; },
abstract = {DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entries and missing taxa. PROTAX addresses these issues with a probabilistic approach to taxonomic classification, advancing on methods that rely solely on sequence similarity. It provides calibrated probabilistic assignments to a partially populated taxonomic hierarchy, accounting for taxa that lack references and incorrect taxonomic annotation. While effective on smaller scales, global application of PROTAX necessitates substantially larger reference libraries, a goal previously hindered by computational barriers. We introduce PROTAX-GPU, a scalable algorithm capable of leveraging the global Barcode of Life Data System (>14 million specimens) as a reference database. Using graphics processing units (GPU) to accelerate similarity and nearest-neighbour operations and the JAX library for Python integration, we achieve over a 1000 × speedup compared with the central processing unit (CPU)-based implementation without compromising PROTAX's key benefits. PROTAX-GPU marks a significant stride towards real-time DNA barcoding, enabling quicker and more efficient species identification in environmental assessments. This capability opens up new avenues for real-time monitoring and analysis of biodiversity, advancing our ability to understand and respond to ecological dynamics. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}

*DNA Barcoding, Taxonomic/methods
*Algorithms
Classification/methods
Computer Graphics
Animals

@article {pmid38703100,
year = {2024},
author = {Molero-Baltanás, R and Mitchell, A and Gaju-Ricart, M and Robla, J},
title = {Worldwide revision of synanthropic silverfish (Insecta: Zygentoma: Lepismatidae) combining morphological and molecular data.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {3},
pages = {},
doi = {10.1093/jisesa/ieae045},
pmid = {38703100},
issn = {1536-2442},
support = {//the Australian Museum Research Institute/ ; //University of Córdoba/ ; },
mesh = {Animals ; *Phylogeny ; *Insecta/genetics/anatomy & histology/classification ; Female ; Male ; Animal Distribution ; },
abstract = {Synanthropic silverfish are the best-known and most widely distributed insects of the order Zygentoma. However, there is a great gap in the knowledge and confusion about the geographic distribution and the diagnostic characteristics that allow their identification. In this work, we provide an exhaustive and deep analysis of the most common 9 synanthropic silverfish of the world, combining previously published and newly derived morphological and molecular data. Updated descriptions of Ctenolepisma calvum (Ritter, 1910) and Ctenolepisma (Sceletolepisma) villosum (Fabricius, 1775) are included, and morphological remarks, illustrations, and photographs of the remaining synanthropic species are provided to clarify their diagnosis and differentiation among them and from other free-living species. In addition, Ctenolepisma targionii (Grassi and Rovelli, 1889) is synonymized with C. villosum. A molecular phylogeny is presented based on the COI sequences of all the synanthropic species deposited in BOLD and GenBank, with 15 new sequences provided by this study. This has allowed us to detect and correct a series of identification errors based on the lack of morphological knowledge of several species. Moreover, 2 different lineages of Ctenolepisma longicaudatumEscherich, 1905 have also been detected. To help future studies, we also provide a taxonomic interpretation guide for the most important diagnostic characters of the order Zygentoma, as well as an identification key for all the Synanthropic studied species. Finally, an approximation of the global distribution of synanthropic silverfish is discussed. Several new records indicate that the expansion of these species, generally associated with the transport of goods and people, is still far from over.},
}

Animals
*Phylogeny
*Insecta/genetics/anatomy & histology/classification
Female
Male
Animal Distribution

@article {pmid38703052,
year = {2024},
author = {Burg, S and Ovaskainen, O and Furneaux, B and Ivanova, N and Abrahamyan, A and Niittynen, P and Somervuo, P and Abrego, N},
title = {Experimental evidence that root-associated fungi improve plant growth at high altitude.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17376},
doi = {10.1111/mec.17376},
pmid = {38703052},
issn = {1365-294X},
support = {101057437//H2020 European Research Council/ ; 101059492//H2020 European Research Council/ ; 856506//H2020 European Research Council/ ; 30865//Research Council of Finland/ ; 336212//Research Council of Finland/ ; 342374//Research Council of Finland/ ; 345110//Research Council of Finland/ ; 346492//Research Council of Finland/ ; },
abstract = {Unravelling how species communities change along environmental gradients requires a dual understanding: the direct responses of the species to their abiotic surroundings and the indirect variation of these responses through biotic interactions. Here, we focus on the interactive relationships between plants and their symbiotic root-associated fungi (RAF) along stressful abiotic gradients. We investigate whether variations in RAF community composition along altitudinal gradients influence plant growth at high altitudes, where both plants and fungi face harsher abiotic conditions. We established a translocation experiment between pairs of Bistorta vivipara populations across altitudinal gradients. To separate the impact of shifting fungal communities from the overall influence of changing abiotic conditions, we used a root barrier to prevent new colonization by RAF following translocation. To characterize the RAF communities, we applied DNA barcoding to the root samples. Through the utilization of joint species distribution modelling, we assessed the relationship between changes in plant functional traits resulting from experimental treatments and the corresponding changes in the RAF communities. Our findings indicate that RAF communities influence plant responses to stressful abiotic conditions. Plants translocated from low to high altitudes grew more when they were able to associate with the resident high-altitude RAF compared to those plants that were not allowed to associate with the resident RAF. We conclude that interactions with RAF impact how plants respond to stressful abiotic conditions. Our results provide experimental support that interactions with RAF improve plant stress tolerance to altitudinal stressors such as colder temperatures and less nutrient availability.},
}

@article {pmid38701091,
year = {2024},
author = {Aggarwal, S and Walker, FC and Weagley, JS and McCune, BT and Wu, X and Schriefer, LA and Makimaa, H and Lawrence, D and Sridhar, P and Baldridge, MT},
title = {Interferons and tuft cell numbers are bottlenecks for persistent murine norovirus infection.},
journal = {PLoS pathogens},
volume = {20},
number = {5},
pages = {e1011961},
doi = {10.1371/journal.ppat.1011961},
pmid = {38701091},
issn = {1553-7374},
abstract = {Noroviruses (NoVs) are a leading cause of viral gastroenteritis. Despite global clinical relevance, our understanding of how host factors, such as antiviral cytokines interferons (IFNs), modulate NoV population dynamics is limited. Murine NoV (MNoV) is a tractable in vivo model for the study of host regulation of NoV. A persistent strain of MNoV, CR6, establishes a reservoir in intestinal tuft cells for chronic viral shedding in stool. However, the influence of host innate immunity and permissive cell numbers on viral population dynamics is an open question. We generated a pool of 20 different barcoded viruses (CR6BC) by inserting 6-nucleotide barcodes at the 3' position of the NS4 gene and used this pool as our viral inoculum for in vivo infections of different mouse lines. We found that over the course of persistent CR6 infection, shed virus was predominantly colon-derived, and viral barcode richness decreased over time irrespective of host immune status, suggesting that persistent infection involves a series of reinfection events. In mice lacking the IFN-λ receptor, intestinal barcode richness was enhanced, correlating with increased viral intestinal replication. IL-4 treatment, which increases tuft cell numbers, also increased barcode richness, indicating the abundance of permissive tuft cells to be a bottleneck during CR6 infection. In mice lacking type I IFN signaling (Ifnar1-/-) or all IFN signaling (Stat1-/-), barcode diversity at extraintestinal sites was dramatically increased, implicating different IFNs as critical bottlenecks at specific tissue sites. Of interest, extraintestinal barcodes were overlapping but distinct from intestinal barcodes, indicating that disseminated virus represents a distinct viral population than that replicating in the intestine. Barcoded viruses are a valuable tool to explore the influence of host factors on viral diversity in the context of establishment and maintenance of infection as well as dissemination and have provided important insights into how NoV infection proceeds in immunocompetent and immunocompromised hosts.},
}

@article {pmid38699348,
year = {2024},
author = {Berleant, JD and Banal, JL and Rao, DK and Bathe, M},
title = {Scalable search of massively pooled nucleic acid samples enabled by a molecular database query language.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.12.24305660},
pmid = {38699348},
abstract = {The surge in nucleic acid analytics requires scalable storage and retrieval systems akin to electronic databases used to organize digital data. Such a system could transform disease diagnosis, ecological preservation, and molecular surveillance of biothreats. Current storage systems use individual containers for nucleic acid samples, requiring single-sample retrieval that falls short compared with digital databases that allow complex and combinatorial data retrieval on aggregated data. Here, we leverage protective microcapsules with combinatorial DNA labeling that enables arbitrary retrieval on pooled biosamples analogous to Structured Query Languages. Ninety-six encapsulated pooled mock SARS-CoV-2 genomic samples barcoded with patient metadata are used to demonstrate queries with simultaneous matches to sample collection date ranges, locations, and patient health statuses, illustrating how such flexible queries can be used to yield immunological or epidemiological insights. The approach applies to any biosample database labeled with orthogonal barcodes, enabling complex post-hoc analysis, for example, to study global biothreat epidemiology.},
}

@article {pmid38699326,
year = {2024},
author = {Zhuang, X and Vo, V and Moshi, MA and Dhede, K and Ghani, N and Akbar, S and Chang, CL and Young, AK and Buttery, E and Bendik, W and Zhang, H and Afzal, S and Moser, D and Cordes, D and Lockett, C and Gerrity, D and Kan, HY and Oh, EC},
title = {Early Detection of Novel SARS-CoV-2 Variants from Urban and Rural Wastewater through Genome Sequencing and Machine Learning.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.18.24306052},
pmid = {38699326},
abstract = {Genome sequencing from wastewater has emerged as an accurate and cost-effective tool for identifying SARS-CoV-2 variants. However, existing methods for analyzing wastewater sequencing data are not designed to detect novel variants that have not been characterized in humans. Here, we present an unsupervised learning approach that clusters co-varying and time-evolving mutation patterns leading to the identification of SARS-CoV-2 variants. To build our model, we sequenced 3,659 wastewater samples collected over a span of more than two years from urban and rural locations in Southern Nevada. We then developed a multivariate independent component analysis (ICA)-based pipeline to transform mutation frequencies into independent sources with co-varying and time-evolving patterns and compared variant predictions to >5,000 SARS-CoV-2 clinical genomes isolated from Nevadans. Using the source patterns as data-driven reference "barcodes", we demonstrated the model's accuracy by successfully detecting the Delta variant in late 2021, Omicron variants in 2022, and emerging recombinant XBB variants in 2023. Our approach revealed the spatial and temporal dynamics of variants in both urban and rural regions; achieved earlier detection of most variants compared to other computational tools; and uncovered unique co-varying mutation patterns not associated with any known variant. The multivariate nature of our pipeline boosts statistical power and can support accurate and early detection of SARS-CoV-2 variants. This feature offers a unique opportunity for novel variant and pathogen detection, even in the absence of clinical testing.},
}

@article {pmid38695131,
year = {2024},
author = {Ramos, SC and Culver, M},
title = {Integration of Indigenous Research Methodologies, Traditional Ecological Knowledge and molecular scatology in an assessment of mesocarnivore presence, diet and habitat use on Yurok Ancestral Lands.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e13963},
doi = {10.1111/1755-0998.13963},
pmid = {38695131},
issn = {1755-0998},
support = {2010-3-03//The University of Arizona/Sloan Indigenous Graduate Partnership Program/ ; 1906338//National Science Foundation/ ; },
abstract = {Partnerships between Tribes and researchers in wildlife monitoring and application of Traditional Ecological Knowledge (TEK) have taken a variety of forms, and some scholars have noted a need for culturally sensitive approaches. Guided by Indigenous Research Methodologies, this research is coupled with Yurok TEK, or hlkelonah 'ue-megetohl ('to take care of the earth'), enabling an applied, culturally sensitive approach in partnership with the Yurok Tribe. We present results from a molecular scatology study of wildlife within the ancestral territory of the Yurok Tribe. Scats were collected opportunistically on road transects. All samples (N = 132) were analysed via DNA barcoding and results matched to documented 'Oohl 'we-toh (Yurok language) names to determine the depositor species (N = 8). Though there were four focal mesocarnivore species in our study, only bobcat (Chmuuek; Lynx rufus) and gray fox (Wergers; Urocyon cinereoargenteus) were detected as depositor species. Post hoc analyses were conducted to explore distribution, habitat use and selection in a use-availability context, and food habits of these two species. We found almost complete separation of bobcat and gray fox use of transects, as well as indication of partitioning of vegetation cover types and food. We demonstrate an integrated framework of Western and Indigenous sciences that allows the Indigenous researcher to transcend structured academic disciplinary boundaries. Our approach can be modified for partnerships between Tribes, agencies, academics and students for wildlife monitoring in broader geographic regions in various research applications.},
}

@article {pmid38694266,
year = {2024},
author = {Ossowska, EA and Moncada, B and Lücking, R and Flakus, A and Rodriguez-Flakus, P and Olszewska, S and Kukwa, M},
title = {Additional new species and new records of the genus Sticta (lichenised Ascomycota, lobarioid Peltigeraceae) from Bolivia.},
journal = {MycoKeys},
volume = {105},
number = {},
pages = {21-47},
doi = {10.3897/mycokeys.105.120810},
pmid = {38694266},
issn = {1314-4049},
abstract = {Four species of the genus Sticta are described as new from Bolivia, based on morphological examination and phylogenetic analysis of the fungal ITS barcoding marker. Additionally, two species are reported as new to Bolivia (their identification confirmed by molecular data) and one previously reported species is confirmed by molecular data for the first time. Detailed morphological and anatomical descriptions are provided for all new species. Two of the new species, S.isidiolobulata Ossowska, B. Moncada, Lücking & Kukwa and S.madidiensis Ossowska, B. Moncada, Lücking & Kukwa belong to clade I, as defined in previous studies. In contrast, S.montepunkuensis Ossowska, B. Moncada, Lücking & Kukwa and S.macrolobata Ossowska, B. Moncada, Lücking & Kukwa, also described here as new to science, belong to clade III. Stictaisidiolobulata has an irregular to suborbicular thallus of medium size, with isidia developing into spathulate lobules, cyanobacterial photobiont and apothecia with entire to weakly-crenate margins. The large irregular thallus of the cyanobacteria-associated S.macrolobata has broad lobes, apothecia with verrucous to tomentose margins and cyphellae with raised margins, whereas S.madidiensis has a medium-sized, palmate to irregular thallus with a stipe, but without vegetative propagules and apothecia. Stictamontepunkuensis has large and irregular thalli with green algae as photobiont, apothecia with crenate to verrucous margins and urceolate cyphellae with a wide pore and a scabrid basal membrane. Two species, S.beauvoisii Delise and S.riparia Merc.-Díaz are reported as new to Bolivia (the latter also as new to South America) and belong to clade III. Stictatomentosa (Sw.) Ach., species confirmed from Bolivia by molecular data, belongs to clade II. Stictabeauvoisii is characterised by a smooth yellowish-brown upper surface with darker apices and abundant, marginal isidia and a brown lower surface with golden-chocolate brown primary tomentum and sparse, golden-brown rhizines. Stictariparia has a strongly branched thallus, with undulate lobes and abundant, marginal, palmate, grey to dark brown phyllidia and greyish-brown lower surface with the primary tomentum absent towards the margins. Stictatomentosa has palmate, bluish thalli with white cilia and abundant, submarginal apothecia and creamy-white lower surface with a sparse, white primary tomentum.},
}

@article {pmid38693183,
year = {2024},
author = {Moustafa, MAM and Mohamed, WMA and Chatanga, E and Nagib, D and Matsuno, K and Gofton, AW and Barker, SC and Nonaka, N and Nakao, R},
title = {Unraveling the phylogenetics of genetically closely related species, Haemaphysalis japonica and Haemaphysalis megaspinosa, using entire tick mitogenomes and microbiomes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9961},
pmid = {38693183},
issn = {2045-2322},
support = {16H06431//Japan Society for the Promotion of Science/ ; 19H03118//Japan Society for the Promotion of Science/ ; 19F19097//Japan Society for the Promotion of Science/ ; 20K21358//Japan Society for the Promotion of Science/ ; 20KK0151//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Phylogeny ; *Ixodidae/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Genome, Mitochondrial ; Genetic Variation ; },
abstract = {Ticks have a profound impact on public health. Haemaphysalis is one of the most widespread genera in Asia, including Japan. The taxonomy and genetic differentiation of Haemaphysalis spp. is challenging. For instance, previous studies struggled to distinguish Haemaphysalis japonica and Haemaphysalis megaspinosa due to the dearth of nucleotide sequence polymorphisms in widely used barcoding genes. The classification of H. japonica japonica and its related sub-species Haemaphysalis japonica douglasi or Haemaphysalis jezoensis is also confused due to their high morphological similarity and a lack of molecular data that support the current classification. We used mitogenomes and microbiomes of H. japonica and H. megaspinosa to gain deeper insights into the phylogenetic relationships and genetic divergence between two species. Phylogenetic analyses of concatenated nucleotide sequences of protein-coding genes and ribosomal DNA genes distinguished H. japonica and H. megaspinosa as monophyletic clades, with further subdivision within the H. japonica clade. The 16S rRNA and NAD5 genes were valuable markers for distinguishing H. japonica and H. megaspinosa. Population genetic structure analyses indicated that genetic variation within populations accounted for a large proportion of the total variation compared to variation between populations. Microbiome analyses revealed differences in alpha and beta diversity between H. japonica and H. megaspinosa: H. japonica had the higher diversity. Coxiella sp., a likely endosymbiont, was found in both Haemaphysalis species. The abundance profiles of likely endosymbionts, pathogens, and commensals differed between H. japonica and H. megaspinosa: H. megaspinosa was more diverse.},
}

Animals
*Phylogeny
*Ixodidae/microbiology/genetics
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
Genome, Mitochondrial
Genetic Variation

@article {pmid38690989,
year = {2024},
author = {Li, J and Li, M and Wuethrich, A and Guan, R and Zhao, L and Hu, C and Trau, M and Sun, Y},
title = {Molecular Stratification and Treatment Monitoring of Lung Cancer Using a Small Extracellular Vesicle-Activated Nanocavity Architecture.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.4c00558},
pmid = {38690989},
issn = {1520-6882},
abstract = {Development of molecular diagnostics for lung cancer stratification and monitoring is crucial for the rational planning and timely adjustment of treatments to improve clinical outcomes. In this regard, we propose a nanocavity architecture to sensitively profile the protein signature on small extracellular vesicles (sEVs) to enable accurate, noninvasive staging and treatment monitoring of lung cancer. The nanocavity architecture is formed by molecular recognition through the binding of sEVs with the nanobox-based core-shell surface-enhanced Raman scattering (SERS) barcodes and mirrorlike, asymmetric gold microelectrodes. By imposing an alternating current on the gold microelectrodes, a nanofluidic shear force was stimulated that supported the binding of sEVs and the efficient assembly of the nanoboxes. The binding of sEVs further induced a nanocavity between the nanobox and the gold microelectrode that significantly amplified the electromagnetic field to enable the simultaneous enhancement of Raman signals from four SERS barcodes and generate patient-specific molecular sEV signatures. Importantly, evaluated on a cohort of clinical samples (n = 76) on the nanocavity architecture, the acquired patient-specific sEV molecular signatures achieved accurate identification, stratification, and treatment monitoring of lung cancer patients, highlighting its potential for transition to clinical utility.},
}

@article {pmid38688969,
year = {2024},
author = {Blanc-Benigeri, A and Poirier, V and Narango, D and Elliott, KH and Frei, B},
title = {Diet of moulting Swainson's Thrushes (Catharus ustulatus) and Tennessee Warblers (Leiothlypis peregrina) at a stopover site during fall migration measured with fecal DNA metabarcoding.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9913},
pmid = {38688969},
issn = {2045-2322},
support = {#522431//Natural Sciences and Engineering Research Council of Canada-Undergraduate Student Research Award (NSERC USRA)/ ; #320544//Graduate Scholarship-Master's (CGS M) award, a Fonds de recherche du Québec-Nature et technologies (FRQNT)/ ; },
mesh = {Animals ; *Animal Migration/physiology ; *Songbirds/physiology ; *Diet ; *Feces/chemistry ; DNA Barcoding, Taxonomic/methods ; Seasons ; },
abstract = {Moult and migration are energetically demanding and require adequate nutrition. In some species, individuals may interrupt their fall migration to moult at discrete stopover locations outside of their breeding grounds (i.e., moult-migration) leading to competing nutritional demands for moult and migration. Here, we use DNA barcoding of fecal samples to compare the diet of moulting and actively migrating (post-moult) Swainson's Thrushes (Catharus ustulatus) and Tennessee Warblers (Leiothlypis peregrina) during their fall migration stopover at a large urban greenspace in Montreal, Canada. Diet differed according to moult status, species, and seasonality. Swainson's Thrushes had a broad diet with frequent detections of both insects and berry-producing shrubs; while detections in Tennessee Warblers' diets were mainly arthropods. For both species, more actively migrating individuals consumed fleshy-fruiting plants than moulting individuals. A higher proportion of moulting birds consumed arthropods compared to active migrants, due to either arthropod availability or a dietary preference for proteinaceous foods to grow feathers. Both species and moult classes consumed more native plants than non-native plants later in the season. We show the importance of managing urban greenspaces with native plants and diverse food sources that can provide for the different dietary needs of migratory birds.},
}

Animals
*Animal Migration/physiology
*Songbirds/physiology
*Diet
*Feces/chemistry
DNA Barcoding, Taxonomic/methods
Seasons

@article {pmid38684618,
year = {2024},
author = {Wang, X and Zhang, Z and Shi, Y and Man, J and Huang, Y and Zhang, X and Liu, S and He, G and An, K and Amu, L and Chen, W and Liu, Z and Wang, X and Wei, S},
title = {Population identification and genetic diversity analysis of Fritillaria ussuriensis (Fritillaria) based on chloroplast genes atpF and petB.},
journal = {Journal of applied genetics},
volume = {},
number = {},
pages = {},
pmid = {38684618},
issn = {2190-3883},
support = {20221156//study on breeding and cultivation technology of precision medicine Bupleurum bupleurum based on molecular anti-counterfeiting technology/ ; 2020110031009385//research project on molecular anti-counterfeiting technology of 4 precision medicinal materials such as Platycodon grandiflorus/ ; 2022YFC3501505//National Key Research and Development Program of China/ ; },
abstract = {The chloroplast genomes of five Fritillaria ussuriensis materials from different production areas were comparatively analyzed, atpF and petB were screened as specific DNA barcodes, and the population identification and genetic diversity of F. ussuriensis were analyzed based on them. The F. ussuriensis chloroplast genome showed a total length of 151 515-151 548 bp with a typical tetrad structure and encoded 130 genes. atpF and petB were used to amplify 183 samples from 13 populations, and they could identify 6 and 9 haplotypes, respectively. Joint analysis of the two sequences revealed 18 haplotypes, named H1-H18, with the most widely distributed and most abundant being H4. Ten haplotypes were unique for 7 populations that they could be used to distinguish from others. Haplotype diversity and nucleotide diversity were 0.99 and 2.09 × 10[-3], respectively, indicating the genetic diversity was relatively rich. The results of the intermediary adjacency network showed that H5 was the oldest haplotype, and stellate radiation was centered around it, indicating that population expansion occurred in genuine production areas. This study lays a theoretical foundation for the population identification, genetic evolution, and breed selection of F. ussuriensis.},
}

@article {pmid38683343,
year = {2024},
author = {Vences, M and Miralles, A and DeSalle, R},
title = {A Glossary of DNA Barcoding Terms.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {561-572},
pmid = {38683343},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Terminology as Topic ; DNA/genetics ; Humans ; },
abstract = {This chapter provides a reference glossary for the protocols in this volume. We have chosen only the very basic terms in the DNA barcode lexicon to include, and provide clear and concise definitions of these terms. We hope the reader finds this glossary useful.},
}

*DNA Barcoding, Taxonomic/methods
Terminology as Topic
DNA/genetics
Humans

@article {pmid38683342,
year = {2024},
author = {Williams, J and Nash, B and Ghiban, C and Khalfan, M and Hilgert, U and Lauter, S and Yang, CH and Micklos, DA},
title = {Analysis of DNA Barcodes Using DNA Subway.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {551-560},
pmid = {38683342},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Phylogeny ; DNA/genetics ; Workflow ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {DNA Subway makes bioinformatic analysis of DNA barcodes classroom friendly, eliminating the need for software installations or command line tools. Subway bundles research-grade bioinformatics software into workflows with an easy-to-use interface. This chapter covers DNA Subway's DNA barcoding analysis workflow (Blue Line) starting with one or more Sanger sequence reads. During analysis, users can view trace files and sequence quality, pair and align forward and reverse reads, create and trim consensus sequences, perform BLAST searches, select reference data, align multiple sequences, and compute phylogenetic trees. High-quality sequences with the required metadata can also be submitted as barcode sequences to NCBI GenBank.},
}

*DNA Barcoding, Taxonomic/methods
*Software
*Computational Biology/methods
Phylogeny
DNA/genetics
Workflow
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods

@article {pmid38683341,
year = {2024},
author = {Shumskaya, M},
title = {DNA Barcoding for an Undergraduate Class.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {537-550},
pmid = {38683341},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Students ; Universities ; DNA/genetics/analysis ; Humans ; Curriculum ; Polymerase Chain Reaction/methods ; },
abstract = {DNA technique is a topic mandatorily covered in a biology and biochemistry undergraduate curriculum. Inquiry-based pedagogy is proven to be the most effective way of learning, and DNA barcoding method allows to merge necessary-to-study experimental techniques such as DNA isolation and purification, PCR, and basic BLAST search into a two- or three-week inquiry-based student project. It also provides a research-based experience to the students, who, when organized in groups, can design their own DNA-barcoding project if they wish. Here, we describe how DNA barcoding can be offered in an undergraduate college or advanced high school settings. This chapter is intended to help college and high school instructors to include DNA barcoding in their classes.},
}

*DNA Barcoding, Taxonomic/methods
*Students
Universities
DNA/genetics/analysis
Humans
Curriculum
Polymerase Chain Reaction/methods

@article {pmid38683340,
year = {2024},
author = {Wright, L and Garbarino, J and Marizzi, C},
title = {Engaging Students and Teachers as Community Scientists in DNA Barcoding Initiatives.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {525-535},
pmid = {38683340},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Students ; Humans ; Curriculum ; Faculty ; },
abstract = {Historically, contributions to scientific knowledge have been perceived as something that only professional scientists have the ability to affect. This has led to the belief that scientific pursuits are done not by everyday people but by individuals who have no connection to the communities that their discoveries might impact. DNA barcoding initiatives have the potential to bridge this gap. Community leaders, students, teachers, and other community members can come together with engaged scientists to solve relevant issues that affect them. Over the last 20 years, DNA barcoding has been used successfully in a variety of educational contexts to incorporate original research into school curricula and informal outreach and education programs. DNA barcoding is especially suitable for educational settings because it is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and free and open-access online tools exist that allow participants to contribute high-quality data to international research efforts. DNA barcoding also offers a unique service-learning opportunity, where participants gain both knowledge and confidence in science. This is important because a growing body of evidence suggests that actively conducting research increases student and teacher engagement and retention of students in science. Here, we describe a framework and case studies in different educational settings that can be modeled and adapted to various educational contexts.},
}

*DNA Barcoding, Taxonomic/methods
*Students
Humans
Curriculum
Faculty

@article {pmid38683339,
year = {2024},
author = {Pepenella, S and Hackett, J and Fernandez-Marco, C and Petracca, J and Marizzi, C and Nash, B and Micklos, DA},
title = {A Rapid, Equipment-Free DNA Isolation Method for DNA Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {517-523},
pmid = {38683339},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA/isolation & purification/genetics ; DNA, Plant/genetics/isolation & purification ; Plants/genetics ; Chromatography/methods ; Lichens/genetics ; },
abstract = {This rapid, equipment-free DNA isolation procedure using chromatography paper is a simple method that can be performed in less than 30 min and requires no wet lab experience. With minimal expense, it offers an affordable alternative for anyone wanting to explore biodiversity. It also provides an excellent option for use in classrooms or other activities that are time limited. The method works best for plants or lichens, producing stable DNA on Whatman® chromatography paper at room temperature, which can be eluted as needed.},
}

*DNA Barcoding, Taxonomic/methods
DNA/isolation & purification/genetics
DNA, Plant/genetics/isolation & purification
Plants/genetics
Chromatography/methods
Lichens/genetics

@article {pmid38683338,
year = {2024},
author = {Wangh, LJ and Rice, JE and Sanchez, JA},
title = {Recent Applications of FastFish-ID.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {503-514},
pmid = {38683338},
issn = {1940-6029},
mesh = {Animals ; *Fishes ; *Sharks ; *DNA Barcoding, Taxonomic/methods ; Animal Fins ; },
abstract = {FastFish-ID via Closed-Tube barcoding is a portable platform for rapid and accurate identification of fish species that was conceived at Brandeis University, commercialized at Thermagenix, Inc., and further improved at Ecologenix, LLC (see Chap. 17 in this volume). This chapter focuses on the use of FastFish-ID for (1) identification of intraspecies variants, (2) quantitative use of FastFish-ID to measure the decay of fresh fish, and (3) use of FastFish-ID for the identification of dried and processed shark fins.},
}

Animals
*Fishes
*Sharks
*DNA Barcoding, Taxonomic/methods
Animal Fins

@article {pmid38683337,
year = {2024},
author = {Gwiazdowski, R},
title = {Principles for Constructing DNA Barcode Reference Libraries.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {491-502},
pmid = {38683337},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Gene Library ; Reference Standards ; DNA/genetics ; Humans ; },
abstract = {All DNA barcode methods rely on reference sequences linked to well-curated voucher specimens. Definitions for and locations of DNA barcode reference libraries are not standardized, and vary throughout the literature. Standardizing, and centralizing reference specimens would provide an unambiguous source, analogous to reference genomes, to reproduce identifications and improve a library. This chapter proposes a working definition of a DNA barcode reference library, consistent with DNA barcode data standards, along with principles and methods to consider when producing or using such a library. These methods allow explicit traceback to sequence-sources which elevate the value of voucher specimens, and create a potential for community curation.},
}

*DNA Barcoding, Taxonomic/methods
*Gene Library
Reference Standards
DNA/genetics
Humans

@article {pmid38683336,
year = {2024},
author = {O'Brien, TD and Blanco-Bercial, L and Questel, JM and Batta-Lona, PG and Bucklin, A},
title = {MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {475-489},
pmid = {38683336},
issn = {1940-6029},
mesh = {Animals ; *Aquatic Organisms/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Ecosystem ; Databases, Genetic ; Databases, Nucleic Acid ; },
abstract = {The MetaZooGene Atlas and Database (MZGdb; https://metazoogene.org/mzgdb/) is an open-access data and metadata portal synchronized with the NCBI GenBank and BOLD data repositories. The MZGdb includes sequences for genes used for the classification and identification of marine organisms based on DNA barcoding and metabarcoding. The focus of the MZGdb is biodiversity of marine ecosystems, including phytoplankton and microbes, zooplankton and invertebrates, fish, and other marine vertebrates (pinnipeds, cetaceans, and sea turtles). DNA sequences currently included are mitochondrial cytochrome oxidase I (COI), 12S, and 16S rRNA, and nuclear 18S and 28S rRNA. The MZGdb provides data and mapping tools for assembling and downloading compilations of reference sequence data that are specific to selected genes, taxonomic groups, and/or ocean regions. An additional feature of the MZGdb is the Atlas which summarizes data coverage and proportional completeness based on statistics of species with available sequences versus species commonly found in each ocean region.This chapter is a collaborative effort of the Scientific Committee for Ocean Research (SCOR) Working Group WG157: MetaZooGene: Toward a new global view of marine zooplankton biodiversity based on DNA metabarcoding and reference DNA sequence databases (https://metazoogene.org).},
}

Animals
*Aquatic Organisms/genetics/classification
*DNA Barcoding, Taxonomic/methods
*Biodiversity
Ecosystem
Databases, Genetic
Databases, Nucleic Acid

@article {pmid38683335,
year = {2024},
author = {Whitley, BS and Li, Z and Jones, L and de Vere, N},
title = {Mega-Barcoding Projects: Delivering National DNA Barcoding Initiatives for Plants.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {445-473},
pmid = {38683335},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Plants/genetics ; *DNA, Plant/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Gene Library ; },
abstract = {Plant DNA barcoding has a multitude of applications ranging from species detection and biomonitoring to investigating ecological networks and checking food quality. The ability to accurately identify species, using DNA barcoding, depends on the quality and comprehensiveness of the reference library that is used. This chapter describes how to create plant reference libraries using the rbcL, matK, and ITS2 DNA barcode regions. It covers the creation of species lists, the collection of specimens from the field and herbarium, DNA extraction, PCR amplification, and DNA sequencing. This methodology gives special attention to using samples from herbaria, as they represent important collections of easily accessible, taxonomically verified plant material.},
}

*DNA Barcoding, Taxonomic/methods
*Plants/genetics
*DNA, Plant/genetics
Polymerase Chain Reaction/methods
Sequence Analysis, DNA/methods
Gene Library

@article {pmid38683334,
year = {2024},
author = {Ratnasingham, S and Wei, C and Chan, D and Agda, J and Agda, J and Ballesteros-Mejia, L and Boutou, HA and El Bastami, ZM and Ma, E and Manjunath, R and Rea, D and Ho, C and Telfer, A and McKeowan, J and Rahulan, M and Steinke, C and Dorsheimer, J and Milton, M and Hebert, PDN},
title = {BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {403-441},
pmid = {38683334},
issn = {1940-6029},
mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; Software ; DNA/genetics ; },
abstract = {BOLD, the Barcode of Life Data System, supports the acquisition, storage, validation, analysis, and publication of DNA barcodes, activities requiring the integration of molecular, morphological, and distributional data. Its pivotal role in curating the reference library of DNA barcodes, coupled with its data management and analysis capabilities, makes it a central resource for biodiversity science. It enables rapid, accurate identification of specimens and also reveals patterns of genetic diversity and evolutionary relationships among taxa.Launched in 2005, BOLD has become an increasingly powerful tool for advancing the understanding of planetary biodiversity. It currently hosts 17 million specimen records and 14 million barcodes that provide coverage for more than a million species from every continent and ocean. The platform has the long-term goal of providing a consistent, accurate system for identifying all species of eukaryotes.BOLD's integrated analytical tools, full data lifecycle support, and secure collaboration framework distinguish it from other biodiversity platforms. BOLD v4 brought enhanced data management and analysis capabilities as well as novel functionality for data dissemination and publication. Its next version will include features to strengthen its utility to the research community, governments, industry, and society-at-large.},
}

*Biodiversity
*DNA Barcoding, Taxonomic/methods
*Computational Biology/methods
Software
DNA/genetics

@article {pmid38683333,
year = {2024},
author = {Damaso, N and Elwick, KE and Robertson, JM},
title = {Guidelines for the Analysis of DNA Barcoding/Metabarcoding Sequencing Data and Interpretation of Publicly Available Databases.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {391-402},
pmid = {38683333},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Databases, Nucleic Acid ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Databases, Genetic ; Software ; },
abstract = {This chapter describes procedures for the use of DNA sequence data to obtain and compare taxonomic identification using the public databases GenBank and Barcode of Life Data System (BOLD). The chapter begins by describing procedures used to prepare quality sequences for uploading into GenBank and BOLD. Next, steps used to query the DNA sequences against the public databases are described using GenBank BLAST and BOLD identification engines. Interpretation guidelines for the taxonomic identification assignments are presented. Finally, a procedure for evaluating the accuracy and reliability of sequences from GenBank and BOLD is provided.},
}

*DNA Barcoding, Taxonomic/methods
*Databases, Nucleic Acid
Computational Biology/methods
Sequence Analysis, DNA/methods
Databases, Genetic
Software

@article {pmid38683332,
year = {2024},
author = {Phillips, JD and Griswold, CK and Young, RG and Hubert, N and Hanner, RH},
title = {A Measure of the DNA Barcode Gap for Applied and Basic Research.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {375-390},
pmid = {38683332},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Coleoptera/genetics/classification ; DNA/genetics/analysis ; Species Specificity ; },
abstract = {DNA barcoding has largely established itself as a mainstay for rapid molecular taxonomic identification in both academic and applied research. The use of DNA barcoding as a molecular identification method depends on a "DNA barcode gap"-the separation between the maximum within-species difference and the minimum between-species difference. Previous work indicates the presence of a gap hinges on sampling effort for focal taxa and their close relatives. Furthermore, both theory and empirical work indicate a gap may not occur for related pairs of biological species. Here, we present a novel evaluation approach in the form of an easily calculated set of nonparametric metrics to quantify the extent of proportional overlap in inter- and intraspecific distributions of pairwise differences among target species and their conspecifics. The metrics are based on a simple count of the number of overlapping records for a species falling within the bounds of maximum intraspecific distance and minimum interspecific distance. Our approach takes advantage of the asymmetric directionality inherent in pairwise genetic distance distributions, which has not been previously done in the DNA barcoding literature. We apply the metrics to the predatory diving beetle genus Agabus as a case study because this group poses significant identification challenges due to its morphological uniformity despite both relative sampling ease and well-established taxonomy. Results herein show that target species and their nearest neighbor species were found to be tightly clustered and therefore difficult to distinguish. Such findings demonstrate that DNA barcoding can fail to fully resolve species in certain cases. Moving forward, we suggest the implementation of the proposed metrics be integrated into a common framework to be reported in any study that uses DNA barcoding for identification. In so doing, the importance of the DNA barcode gap and its components for the success of DNA-based identification using DNA barcodes can be better appreciated.},
}

*DNA Barcoding, Taxonomic/methods
Animals
Coleoptera/genetics/classification
DNA/genetics/analysis
Species Specificity

@article {pmid38683331,
year = {2024},
author = {Mahmoud, MAB},
title = {Classification of DNA Sequence Based on a Non-gradient Algorithm: Pseudoinverse Learners.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {359-373},
pmid = {38683331},
issn = {1940-6029},
mesh = {*Algorithms ; *Neural Networks, Computer ; DNA/genetics ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA/methods ; Humans ; Deep Learning ; },
abstract = {This chapter proposes a prototype-based classification approach for analyzing DNA barcodes that uses a spectral representation of DNA sequences and a non-gradient neural network. Biological sequences can be viewed as data components with higher non-fixed dimensions, which correspond to the length of the sequences. Through computational procedures such as one-hot encoding, numerical encoding plays an important role in DNA sequence evaluation (OHE). However, the OHE method has some disadvantages: (1) It does not add any details that could result in an additional predictive variable, and (2) if the variable has many classes, OHE significantly expands the feature space. To address these shortcomings, this chapter proposes a computationally efficient framework for classifying DNA sequences of living organisms in the image domain. A multilayer perceptron trained by a pseudoinverse learning autoencoder (PILAE) algorithm is used in the proposed strategy. The learning control parameters and the number of hidden layers do not have to be specified during the PILAE training process. As a result, the PILAE classifier outperforms other deep neural network (DNN) strategies such as the VGG-16 and Xception models.},
}

*Algorithms
*Neural Networks, Computer
DNA/genetics
Computational Biology/methods
DNA Barcoding, Taxonomic/methods
Sequence Analysis, DNA/methods
Humans
Deep Learning

@article {pmid38683330,
year = {2024},
author = {Bergmann, T},
title = {CAOS-R: Character-Based Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {347-357},
pmid = {38683330},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; },
abstract = {CAOS-Barcoding is a culmination of traditional taxonomy and modern DNA barcoding. CAOS identifies taxa by diagnostic characters as is done in traditional taxonomy and produces an identification matrix for taxon discrimination similar to DNA barcoding distance matrices. Here, I describe how to set up the CAOS-Barcoder and CAOS-Classifier software, which input data is needed, and how to interpret the output data. With the CAOS-Barcoder, single marker or concatenated data can be processed into diagnostic barcodes for taxon discrimination. The CAOS-Classifier can use the diagnostic barcodes for specimen identification.},
}

*DNA Barcoding, Taxonomic/methods
*Software

@article {pmid38683329,
year = {2024},
author = {Ramanan, V and Sarkar, IN},
title = {Characteristic Attribute Organization System (CAOS): Identifying Classification Rules Based on Phylogenetically Organized Sequences.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {335-345},
pmid = {38683329},
issn = {1940-6029},
mesh = {*Phylogeny ; *Software ; Computational Biology/methods ; Algorithms ; Sequence Alignment/methods ; },
abstract = {Classification is a technique that labels subjects based on the characteristics of the data. It often includes using prior learned information from preexisting data drawn from the same distribution or data type to make informed decisions per each given subject. The method presented here, the Characteristic Attribute Organization System (CAOS), uses a character-based approach to molecular sequence classification. Using a set of aligned sequences (either nucleotide or amino acid) and a maximum parsimony tree, CAOS will generate classification rules for the sequences based on tree structure and provide more interpretable results than other classification or sequence analysis protocols. The code is accessible at https://github.com/JuliaHealth/CAOS.jl/ .},
}

*Phylogeny
*Software
Computational Biology/methods
Algorithms
Sequence Alignment/methods

@article {pmid38683328,
year = {2024},
author = {Puillandre, N and Miralles, A and Brouillet, S and Fedosov, A and Fischell, F and Patmanidis, S and Vences, M},
title = {Species Delimitation and Exploration of Species Partitions with ASAP and LIMES.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {313-334},
pmid = {38683328},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Biodiversity ; Phylogeny ; Species Specificity ; Animals ; Genetic Speciation ; },
abstract = {DNA barcoding plays an important role in exploring undescribed biodiversity and is increasingly used to delimit lineages at the species level (see Chap. 4 by Miralles et al.). Although several approaches and programs have been developed to perform species delimitation from datasets of single-locus DNA sequences, such as DNA barcodes, most of these were not initially provided as user-friendly GUI-driven executables. In spite of their differences, most of these tools share the same goal, i.e., inferring de novo a partition of subsets, potentially each representing a distinct species. More recently, a proposed common exchange format for the resulting species partitions (SPART) has been implemented by several of these tools, paving the way toward developing an interoperable digital environment entirely dedicated to integrative and comparative species delimitation. In this chapter, we provide detailed protocols for the use of two bioinformatic tools, one for single locus molecular species delimitation (ASAP) and one for statistical comparison of species partitions resulting from any kind of species delimitation analyses (LIMES).},
}

*DNA Barcoding, Taxonomic/methods
*Software
*Computational Biology/methods
Biodiversity
Phylogeny
Species Specificity
Animals
Genetic Speciation

@article {pmid38683327,
year = {2024},
author = {Fedosov, A and Puillandre, N and Fischell, F and Patmanidis, S and Miralles, A and Vences, M},
title = {DNA Barcode-Based Species Diagnosis with MolD.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {297-311},
pmid = {38683327},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Phylogeny ; Biodiversity ; },
abstract = {Rapid biodiversity loss sets new requirements for taxonomic research, prompting updating some long-established practices to maximize timely documentation of species before they have gone extinct. One of the crucial procedures associated with the description of new taxa in Linnean taxonomy is assigning them a diagnosis, which is an account of the specific features of the taxon, differentiating it from already described species. Traditionally, diagnostic characters have been morphological, but especially in the case of morphologically cryptic species, molecular diagnoses become increasingly important. In this chapter, we provide detailed protocols for molecular taxon diagnosis with the bioinformatic tool MolD which is available as open-source Python code, command-line driven binary, GUI-driven executable for Windows and Mac, and Galaxy implementation. MolD identifies diagnostic combinations of nucleotides (DNCs) in addition to single (pure) diagnostic sites, enabling users to base DNA diagnoses on a minimal number of diagnostic sites necessary for reliable differentiation of taxa.},
}

*DNA Barcoding, Taxonomic/methods
*Software
*Computational Biology/methods
Phylogeny
Biodiversity

@article {pmid38683326,
year = {2024},
author = {Vences, M and Patmanidis, S and Fedosov, A and Miralles, A and Puillandre, N},
title = {iTaxoTools 1.0: Improved DNA Barcode Exploration with TaxI2.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {281-296},
pmid = {38683326},
issn = {1940-6029},
mesh = {*Software ; *DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; DNA/genetics ; },
abstract = {The overall availability of user-friendly software tools tailored to the analysis of DNA barcodes is limited. Several obvious functions such as detecting and visualizing the DNA barcode gap, the calculation of matrices of pairwise distances at the level of species, or the filtering and decontaminating of sets of sequences based on comparisons with reference databases can typically be carried out only by complex procedures that involve various programs and/or a substantial manual work of formatting. The iTaxoTools project aims at contributing user-friendly software solutions to improve the speed and quality of the workflow of alpha-taxonomy. In this chapter, we provide detailed protocols for the use of a substantially improved version of the tool TaxI2 for distance-based exploration of DNA barcodes. The program calculates genetic distances from prealigned data sets, or based on pairwise alignments, or with an alignment-free approach. Sequence and metadata input can be formatted as tab-delimited files and TaxI2 then computes tables, matrices and graphs of distances, and distance summary statistics within and between species and genera. TaxI2 also includes modes to compare a set of sequences against one or two reference data sets and output lists of best matches or filter data according to thresholds or reciprocal matches. Here, detailed step-by-step protocols are provided for the use of TaxI2, as well as for the interpretation of the program's output.},
}

*Software
*DNA Barcoding, Taxonomic/methods
Computational Biology/methods
DNA/genetics

@article {pmid38683325,
year = {2024},
author = {Sanchez, JA and Rice, JE and Wangh, LJ},
title = {Recent Advances in Closed-Tube Barcoding for FastFish-ID.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {267-278},
pmid = {38683325},
issn = {1940-6029},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; Seafood ; Polymerase Chain Reaction/methods ; DNA, Mitochondrial/genetics ; Fisheries ; },
abstract = {FastFish-ID for rapid and accurate identification of fish species was conceived at Brandeis University based on pioneering work on Closed-Tube Barcoding (Rice et al., Mitochondrial DNA Part A 27(2):1358-1363, 2016; Sirianni et al., Genome 59:1049-1061, 2016). FastFish-ID was subsequently validated and commercialized at Thermagenix, Inc. using a portable device and high-precision PCR (Naaum et al., Food Res Int 141:110035, 2021). The motivation for these efforts was the pressing need for a technology that could be widely used throughout the seafood supply chain to combat IUU Fishing (Helyar et al., PLOS ONE 9, 2014) and overfishing (FAO, State of the World Fisheries and Aquaculture 2018. http://www.fao.org/documents/card/en/c/I9540EN/ , 2018), along with seafood fraud and mislabeling (Watson et al., Fish Fish 17:585-595, 2015). These destructive practices are wasting fish stocks, frustrating attempts to achieve seafood sustainability, endangering oceanic ecosystems, and causing consumers billions of dollars each year (Porterfield et al., Oceana: February, 2022). During the past three Covid19 pandemic years, EcologeniX, LLC has taken over further development and optimization of FastFish-ID. The present chapter provides an overview of the improvements introduced throughout the FastFish-ID process.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Fishes/genetics/classification
Seafood
Polymerase Chain Reaction/methods
DNA, Mitochondrial/genetics
Fisheries

@article {pmid38683323,
year = {2024},
author = {Liu, R and Wang, Y and Yao, X and Liu, C},
title = {Generating 2D Barcode for DNA Barcode Sequences.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {239-246},
pmid = {38683323},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; DNA/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {DNA barcode sequence is a short DNA sequence representing a sample from a particular species. The commonly used DNA barcodes are at least 200 bps long. This large number of characters cannot be encoded in two-dimensional codes for sample recognition and tracking. In the present study, we described a method that can be used to compress the DNA sequences and then generate the corresponding QR code. With the large numbers of software and hardware, the QR code can be used efficiently for printing, labeling, and scanning.},
}

*DNA Barcoding, Taxonomic/methods
*Software
DNA/genetics
Sequence Analysis, DNA/methods

@article {pmid38683322,
year = {2024},
author = {Srivathsan, A and Meier, R},
title = {Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {223-238},
pmid = {38683322},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods/economics ; *Nanopore Sequencing/methods ; Cost-Benefit Analysis ; High-Throughput Nucleotide Sequencing/methods/economics ; Software ; Gene Library ; Sequence Analysis, DNA/methods/economics ; Workflow ; DNA/genetics ; },
abstract = {DNA barcodes are useful in biodiversity research, but sequencing barcodes with dye termination methods ("Sanger sequencing") has been so time-consuming and expensive that DNA barcodes are not as widely used as they should be. Fortunately, MinION sequencers from Oxford Nanopore Technologies have recently emerged as a cost-effective and efficient alternative for barcoding. MinION barcodes are now suitable for large-scale species discovery and enable specimen identification when the target species are represented in barcode databases. With a MinION, it is possible to obtain 10,000 barcodes from a single flow cell at a cost of less than 0.10 USD per specimen. Additionally, a Flongle flow cell can be used for small projects requiring up to 300 barcodes (0.50 USD per specimen). We here describe a cost-effective laboratory workflow for obtaining tagged amplicons, preparing ONT libraries, sequencing amplicon pools, and analyzing the MinION reads with the software ONTbarcoder. This workflow has been shown to yield highly accurate barcodes that are 99.99% identical to Sanger barcodes. Overall, we propose that the use of MinION for DNA barcoding is an attractive option for all researchers in need of a cost-effective and efficient solution for large-scale species discovery and specimen identification.},
}

*DNA Barcoding, Taxonomic/methods/economics
*Nanopore Sequencing/methods
Cost-Benefit Analysis
High-Throughput Nucleotide Sequencing/methods/economics
Software
Gene Library
Sequence Analysis, DNA/methods/economics
Workflow
DNA/genetics

@article {pmid38683321,
year = {2024},
author = {Ivanov, V and Lee, KM and Mutanen, M},
title = {ddRAD Sequencing and DNA Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {213-221},
pmid = {38683321},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Polymorphism, Single Nucleotide ; *Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; DNA/genetics ; Gene Library ; Humans ; },
abstract = {Double-digest restriction site-associated DNA sequencing is a library preparation protocol that enables capturing variable sites across the genome including single-nucleotide polymorphisms (SNPs). These SNPs can be utilized to gain evolutionary insights into patterns observed in DNA barcodes, to infer population structure and phylogenies, to detect gene flow and introgression, and to perform species delimitation analyses. The protocol includes chemically shearing genomic DNA with restriction enzymes, unique tagging, size selection, and amplification of the resulting DNA fragments. Here we provide a detailed description of each step of the protocol, as well as information on essential equipment and common issues encountered during laboratory work.},
}

*DNA Barcoding, Taxonomic/methods
*Polymorphism, Single Nucleotide
*Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
DNA/genetics
Gene Library
Humans

@article {pmid38683320,
year = {2024},
author = {Seth, S and Bhattacharya, A},
title = {DNA Barcodes Using a Dual Nanopore Device.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {197-211},
pmid = {38683320},
issn = {1940-6029},
mesh = {*Nanopores ; *DNA Barcoding, Taxonomic/methods ; *Algorithms ; DNA/chemistry/genetics ; },
abstract = {We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781-20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a 48500 2400 ≅ 24 base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258-5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different species.},
}

*Nanopores
*DNA Barcoding, Taxonomic/methods
*Algorithms
DNA/chemistry/genetics

@article {pmid38683319,
year = {2024},
author = {Sethi, S and Wijesinghe, KM and Dhakal, S},
title = {Single-Molecule FRET-Based Multiplexed Detection.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {183-195},
pmid = {38683319},
issn = {1940-6029},
mesh = {*Fluorescence Resonance Energy Transfer/methods ; *Single Molecule Imaging/methods ; *Fluorescent Dyes/chemistry ; Biosensing Techniques/methods ; Humans ; },
abstract = {Single-molecule multiplexed detection is a high-promise toolkit for the expanding field of biosensing and molecular diagnostics. Among many single-molecule techniques available today for biomarker sensing including fluorescence, force, electrochemical, spectroscopic, barcoding, and other techniques, fluorescence-based approaches are arguably the most widely used methods due to their high sensitivity, selectivity, and readily available fluorophore-labeling schemes for a wide variety of biomolecules. However, multiplexed imaging using fluorescence techniques has proven to be challenging due to the sophisticated labeling schemes often requiring multiple FRET (fluorescence resonance energy transfer) pairs and/or excitation sources, which lead to overlapping signals and complicate data analysis. Here, we describe a single-molecule FRET method that enables multiplexed analysis while still using only one FRET pair, and thus the described approach is a significant step forward from conventional FRET methods.},
}

*Fluorescence Resonance Energy Transfer/methods
*Single Molecule Imaging/methods
*Fluorescent Dyes/chemistry
Biosensing Techniques/methods
Humans

@article {pmid38683317,
year = {2024},
author = {Elwick, KE and Damaso, N and Robertson, JM},
title = {DNA Barcoding and Metabarcoding Protocols for Species Identification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {155-169},
pmid = {38683317},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; Animals ; *Plants/genetics ; Insecta/genetics/classification ; Fungi/genetics/classification ; Sequence Analysis, DNA/methods ; Gene Library ; DNA/genetics ; },
abstract = {The article presents the several steps to be performed on a plant, fungal, insect, or soil sample to obtain DNA sequences for DNA barcode analysis. The chapter begins with a description of sample preparation including procedures for cleaning and proceeds to DNA extraction with methods adapted for the specific type of sample. Next, DNA quantification is described so the proper amount is used for the amplification of the selected barcode regions. Information is provided for reaction mixes and amplification conditions for several referenced barcode primer pairs tuned for the individual sample of interest. This is followed by a description of procedures to access the success of amplification, cleanup, and quantification of the product ready for either Sanger sequencing or library preparation for massive parallel sequencing (MPS). Finally, procedures are provided for Sanger sequencing, library preparation, and MPS sequencing. The chapter provides several references of barcode regions for different sample types.},
}

*DNA Barcoding, Taxonomic/methods
*High-Throughput Nucleotide Sequencing/methods
Animals
*Plants/genetics
Insecta/genetics/classification
Fungi/genetics/classification
Sequence Analysis, DNA/methods
Gene Library
DNA/genetics

@article {pmid38683316,
year = {2024},
author = {David, A and Deepa Arul Priya, J and Gautam, A},
title = {DNA Sequencing Technologies and DNA Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {139-154},
pmid = {38683316},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Biodiversity ; DNA/genetics ; Animals ; },
abstract = {DNA barcodes are short, standardized DNA segments that geneticists can use to identify all living taxa. On the other hand, DNA barcoding identifies species by analyzing these specific regions against a DNA barcode reference library. In its initial years, DNA barcodes sequenced by Sanger's method were extensively used by taxonomists for the characterization and identification of species. But in recent years, DNA barcoding by next-generation sequencing (NGS) has found broader applications, such as quality control, biomonitoring of protected species, and biodiversity assessment. Technological advancements have also paved the way to metabarcoding, which has enabled massive parallel sequ.encing of complex bulk samples using high-throughput sequencing techniques. In future, DNA barcoding along with high-throughput techniques will show stupendous progress in taxonomic classification with reference to available sequence data.},
}

*DNA Barcoding, Taxonomic/methods
*High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Biodiversity
DNA/genetics
Animals

@article {pmid38683315,
year = {2024},
author = {Hyman, O and Cass, A and Enke, R and Storm, A and Nash, B},
title = {Cost-Effective DNA Extraction for DNA Barcoding Diverse Biological Samples.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {129-137},
pmid = {38683315},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *DNA/genetics/isolation & purification ; *Cost-Benefit Analysis ; Polymerase Chain Reaction/methods ; Plants/genetics ; },
abstract = {DNA barcoding employs standard molecular techniques (e.g., DNA extraction, PCR, and Sanger sequencing) to taxonomically identify biological samples. While DNA barcoding is a useful experimental workflow for in-class active learning exercises, extracting DNA from diverse sample types in a time and cost-effective manner can be challenging in a classroom setting. Here, we provide two time and cost-effective methods that have been used by novice students to successfully extract DNA from a variety of animal, fungal, algal, and plant tissues for DNA barcoding.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*DNA/genetics/isolation & purification
*Cost-Benefit Analysis
Polymerase Chain Reaction/methods
Plants/genetics

@article {pmid38683314,
year = {2024},
author = {Hackett, J and Pepenella, S and Marco, CF and Bodt, L and Grajales, LR and Petracca, J and Burke, J and Mayle, A and Nash, B and Micklos, DA},
title = {Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {119-127},
pmid = {38683314},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Electron Transport Complex IV/genetics ; *Polymerase Chain Reaction/methods ; Invertebrates/genetics/classification ; DNA/genetics/isolation & purification ; },
abstract = {Chelex-based DNA extractions are well suited for student DNA barcoding research because they are simple, safe, and inexpensive and can be performed without specialized laboratory equipment, allowing them to be performed in classrooms or at home. Extracted DNA is stable in Chelex solution for at least a week at ambient temperature, allowing collection of DNA samples from remote students. These extractions provide quality DNA for many taxa and are optimal for barcoding invertebrates, especially in combination with novel cytochrome c oxidase I (COI) primer cocktails and PCR cycling conditions.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Electron Transport Complex IV/genetics
*Polymerase Chain Reaction/methods
Invertebrates/genetics/classification
DNA/genetics/isolation & purification

@article {pmid38683313,
year = {2024},
author = {Brower, AVZ and DeSalle, R},
title = {DNA Barcodes in Taxonomic Descriptions.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {105-115},
pmid = {38683313},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Software ; DNA/genetics ; Animals ; Phylogeny ; },
abstract = {This chapter discusses methods for incorporating DNA barcode information into formal taxonomic descriptions. We first review what a formal description entails and then discuss previous attempts to incorporate barcode information into taxonomic descriptions. Several computer programs are listed that extract diagnostics from DNA barcode data. Finally, we examine a test case (Astraptes taxonomy).},
}

*DNA Barcoding, Taxonomic/methods
Software
DNA/genetics
Animals
Phylogeny

@article {pmid38683312,
year = {2024},
author = {Miralles, A and Puillandre, N and Vences, M},
title = {DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {77-104},
pmid = {38683312},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Classification/methods ; Phylogeny ; Animals ; Species Specificity ; },
abstract = {Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.},
}

*DNA Barcoding, Taxonomic/methods
Classification/methods
Phylogeny
Animals
Species Specificity

@article {pmid38683311,
year = {2024},
author = {Hubert, N and Phillips, JD and Hanner, RH},
title = {Delimiting Species with Single-Locus DNA Sequences.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {53-76},
pmid = {38683311},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Algorithms ; Software ; Biodiversity ; Sequence Analysis, DNA/methods ; Haplotypes/genetics ; },
abstract = {DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The "Materials" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.},
}

*DNA Barcoding, Taxonomic/methods
*Phylogeny
*Algorithms
Software
Biodiversity
Sequence Analysis, DNA/methods
Haplotypes/genetics

@article {pmid38683310,
year = {2024},
author = {Ahrens, D},
title = {Species Diagnosis and DNA Taxonomy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {33-52},
pmid = {38683310},
issn = {1940-6029},
mesh = {*DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Classification/methods ; Phylogeny ; Species Specificity ; },
abstract = {The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.},
}

*DNA/genetics
DNA Barcoding, Taxonomic/methods
Classification/methods
Phylogeny
Species Specificity

@article {pmid38683309,
year = {2024},
author = {Schindel, DE and Page, RMP},
title = {Creating Virtuous Cycles for DNA Barcoding: A Case Study in Science Innovation, Entrepreneurship, and Diplomacy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {7-32},
pmid = {38683309},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Entrepreneurship ; Humans ; Inventions ; },
abstract = {This chapter on the history of the DNA barcoding enterprise attempts to set the stage for the more scholarly contributions in this volume by addressing the following questions. How did the DNA barcoding enterprise begin? What were its goals, how did it develop, and to what degree are its goals being realized? We have taken a keen interest in the barcoding movement and its relationship to taxonomy, collections, and biodiversity informatics more broadly considered. This chapter integrates our two different perspectives on barcoding. DES was the Executive Secretary of the Consortium for the Barcode of Life from 2004 to 2017, with the mission to support the success of DNA barcoding without being directly involved in generating barcode data. RDMP viewed barcoding as an important entry into the landscape of biodiversity data, with many potential linkages to other components of that landscape. We also saw it as a critical step toward the era of international genomic research that was sure to follow. Like the Mercury Program that paved the way for lunar landings by the Apollo Program, we saw DNA barcoding as the proving grounds for the interdisciplinary and international cooperation that would be needed for success of whole-genome research.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
Entrepreneurship
Humans
Inventions

@article {pmid38681421,
year = {2024},
author = {Halue, G and Chieochanthanakij, R and Kittipanyaworakun, T and Passorn, P and Kaewboonsert, D and Tharavichitkul, T and Banjongjit, A and Kanjanabuch, T and Eiam-Ong, S},
title = {Peritonitis Caused by Various Species of Diaporthe in Peritoneal Dialysis Patients: A Plant Pathogen to Human Infection.},
journal = {Cureus},
volume = {16},
number = {3},
pages = {e57016},
pmid = {38681421},
issn = {2168-8184},
abstract = {Peritonitis caused by dematiaceous molds is uncommon but poses a significant threat to patients undergoing peritoneal dialysis (PD), leading to high mortality and morbidity. This report highlights three cases of peritonitis caused by three distinct species of Diaporthe (D. amygdali, D. eucalyptorum, and D. phaseolorum), initially unidentified through conventional culture methods. The nucleotide sequences of internal transcribed spacer regions (ITS), 18S nuclear ribosomal small subunit (SSU), and 28S nuclear ribosomal large subunit (LSU) of the ribosomal DNA gene correctly identified the isolates. Despite early catheter removal and administration of appropriate antifungal medications, all patients experienced fatal outcomes. DNA barcoding emerges as a valuable tool for accurately diagnosing species within the genus of pathogenic microbes, aiding in identifying the root causes of infections. It emphasizes the importance of strict adherence to aseptic techniques during PD exchanges to prevent peritonitis caused by plant-borne pathogens.},
}

@article {pmid38680524,
year = {2024},
author = {Kermek, D and Pischiutta, N and Hlebec, D and Sivec, I and Kučinić, M},
title = {Utilising public sequence databases to investigate genetic diversity of stoneflies in Medvednica Nature Park.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e121398},
pmid = {38680524},
issn = {1314-2828},
abstract = {In Medvednica Nature Park, near Croatia's capital Zagreb, urbanisation significantly impacts the fauna. Comprehensive field research has never been conducted in this area, despite the presence of diverse microhabitats and the discovery of several rare species previously unknown in the Croatian fauna. This study provides the Park with first insight into the genetic and morphological diversity of stoneflies, one of the most endangered groups of organisms. Phylogenetic reconstructions and species delineation methods revealed intraspecific haplotype variation in most species (e.g. Brachypteraseticornis, Isoperlagrammatica and Leuctrabraueri), except for Leuctraprima. Additionally, our study has identified isolated populations that merit further in-depth investigation concerning morphology, genetics and ecology.},
}

@article {pmid38678568,
year = {2024},
author = {Gallaccio, G and Wang, M and Schlickeiser, S and Kunkel, D and Böttcher, C and Fernández-Zapata, C},
title = {Protocol to characterize immune cell subpopulations in cerebrospinal fluid of patients with neuroinflammatory diseases using mass cytometry.},
journal = {STAR protocols},
volume = {5},
number = {2},
pages = {103038},
doi = {10.1016/j.xpro.2024.103038},
pmid = {38678568},
issn = {2666-1667},
abstract = {Phenotypic and compositional changes of immune cells in cerebrospinal fluid (CSF) can be used as biomarkers to help diagnose and track disease activity for neuroinflammatory and neurodegenerative diseases. Here, we present a workflow to perform high-dimensional immune profiling at single-cell resolution using cytometry by time-of-flight (CyTOF) on cells isolated from the CSF of patients with neuroinflammation. We describe steps for sample collection and preparation, barcoding to allow for multiplexing, and downstream data analysis using R. For complete details on the use and execution of this protocol, please refer to Fernández-Zapata et al.[1].},
}

@article {pmid38676334,
year = {2024},
author = {Rong, Q and Deng, Y and Chen, F and Yin, Z and Hu, L and Su, X and Zhou, D},
title = {Polymerase-Based Signal Delay for Temporally Regulating DNA Involved Reactions, Programming Dynamic Molecular Systems, and Biomimetic Sensing.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e2400142},
doi = {10.1002/smll.202400142},
pmid = {38676334},
issn = {1613-6829},
support = {32141003//National Natural Science Foundation of China/ ; },
abstract = {Complex temporal molecular signals play a pivotal role in the intricate biological pathways of living organisms, and cells exhibit the ability to transmit and receive information by intricately managing the temporal dynamics of their signaling molecules. Although biomimetic molecular networks are successfully engineered outside of cells, the capacity to precisely manipulate temporal behaviors remains limited. In this study, the catalysis activity of isothermal DNA polymerase (DNAP) through combined use of molecular dynamics simulation analysis and fluorescence assays is first characterized. DNAP-driven delay in signal strand release ranged from 10[0] to 10[2] min, which is achieved through new strategies including the introduction of primer overhangs, utilization of inhibitory reagents, and alteration of DNA template lengths. The results provide a deeper insight into the underlying mechanisms of temporal control DNAP-mediated primer extension and DNA strand displacement reactions. Then, the regulated DNAP catalysis reactions are applied in temporal modulation of downstream DNA-involved reactions, the establishment of dynamic molecular signals, and the generation of barcodes for multiplexed detection of target genes. The utility of DNAP-based signal delay as a dynamic DNA nanotechnology extends beyond theoretical concepts and achieves practical applications in the fields of cell-free synthetic biology and bionic sensing.},
}

@article {pmid38674379,
year = {2024},
author = {Zhang, S and Han, S and Bi, D and Yang, J and Ge, W and Ye, Y and Gao, J and Dai, C and Kan, X},
title = {Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective.},
journal = {Genes},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/genes15040444},
pmid = {38674379},
issn = {2073-4425},
support = {BK20211078//the Basic Research Program of Natural Science Foundation of Jiangsu Province of China/ ; NEL&MARA-003//the Opening Foundation of National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, and Key Laboratory of Heavy Metal Pollution Prevention & Control, Ministry of Agriculture and Rural Affairs/ ; },
mesh = {*Phylogeny ; *Sedum/genetics ; Genome, Plastid ; Evolution, Molecular ; Genetic Variation ; Codon Usage ; Genome, Plant ; Base Composition/genetics ; },
abstract = {Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on plastomes between Sedum species, intra-species studies are scarce. Here, we sequenced plastomes from three Sedum species (Sedum alfredii, Sedum plumbizincicola, and Sedum japonicum) to understand their evolutionary relationships and plastome structural evolution. Our analyses revealed minimal size and GC content variation across species. However, gene distribution at IR boundaries, repeat structures, and codon usage patterns showed diversity at both inter-specific and intra-specific levels. Notably, an rps19 gene expansion and a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving as markers for future studies. Phylogenetic analyses confirmed the non-monophyly of Sedum and divided the Acre clade into two groups. Individuals from the same species clustered together, with strong support for the relationships between S. alfredii, S. tricarpum, and S. plumbizincicola. Additionally, S. japonicum clearly affiliates with the Acre clade. This study provides valuable insights into both intra-specific and intra-generic plastome variation in Sedum, as well as overall plastome evolution within the genus.},
}

*Phylogeny
*Sedum/genetics
Genome, Plastid
Evolution, Molecular
Genetic Variation
Codon Usage
Genome, Plant
Base Composition/genetics

@article {pmid38674377,
year = {2024},
author = {Kan, J and Zhang, S and Wu, Z and Bi, D},
title = {Exploring Plastomic Resources in Sempervivum (Crassulaceae): Implications for Phylogenetics.},
journal = {Genes},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/genes15040441},
pmid = {38674377},
issn = {2073-4425},
support = {BK20211078//the Basic Research Program (Natural Science Foundation) of Jiangsu Province (Grant no. BK20211078)/ ; RCYX20200714114538196//the Science Technology and Innovation Commission of Shenzhen Municipality/ ; JCYJ20220818103212025//the Shenzhen Fundamental Research Program/ ; 2021QN02N792//the Guangdong Pearl River Talent Program/ ; },
mesh = {*Phylogeny ; *Plastids/genetics ; Codon Usage ; Genome, Plastid/genetics ; Evolution, Molecular ; },
abstract = {The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering insights into plant evolution, diversity, and conservation. As an important group of horticultural ornamentals in the Crassulaceae family, Sempervivum plants are known for their unique rosette-like structures and reproduction through offsets. Despite their popularity, the classification status of Sempervivum remains uncertain, with only a single plastome sequence currently available. Furthermore, codon usage bias (CUB) is a widespread phenomenon of the unbalanced usage of synonymous codons in the coding sequence (CDS). However, due to the limited available plastid data, there has been no research that focused on the CUB analysis among Sempervivum until now. To address these gaps, we sequenced and released the plastomes of seven species and one subspecies from Sempervivum, revealing several consistent patterns. These included a shared 110 bp extension of the rps19 gene, 14 hypervariable regions (HVRs) with distinct nucleotide diversity (π: 0.01173 to 0.02702), and evidence of selective pressures shaping codon usage. Notably, phylogenetic analysis robustly divided the monophyletic clade into two sections: Jovibarba and Sempervivum. In conclusion, this comprehensive plastomic resource provides valuable insights into Sempervivum evolution and offers potential molecular markers for DNA barcoding.},
}

*Phylogeny
*Plastids/genetics
Codon Usage
Genome, Plastid/genetics
Evolution, Molecular

@article {pmid38672767,
year = {2024},
author = {Vankova, L and Vanek, D},
title = {Capillary-Electrophoresis-Based Species Barcoding of Big Cats: CR-mtDNA-Length Polymorphism.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/life14040497},
pmid = {38672767},
issn = {2075-1729},
support = {VJ01010026//Ministry of Interior Czech Republic/ ; },
abstract = {This study aimed to provide an overview of the methodological approach used for the species determination of big cats. The molecular system described herein employs mitochondrial DNA control region (CR-mtDNA)-length polymorphism in combination with highly sensitive and precise capillary electrophoresis. We demonstrated that the described CR-mtDNA barcoding system can be utilized for species determination where the presence of biological material from big cats is expected or used as a confirmatory test alongside Sanger or massive parallel sequencing (MPS). We have also addressed the fact that species barcoding, when based on the analysis of mtDNA targets, can be biased by nuclear inserts of the mitochondrial genome (NUMTs). The CR-mtDNA barcoding system is suitable even for problematic and challenging samples, such as hair. CR-mtDNA-length polymorphisms can also distinguish hybrids from pure breeds.},
}

@article {pmid38671234,
year = {2024},
author = {Rios-Willars, E and Chirinos-Arias, MC},
title = {Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm.},
journal = {Planta},
volume = {259},
number = {6},
pages = {134},
pmid = {38671234},
issn = {1432-2048},
mesh = {*Microsatellite Repeats/genetics ; *DNA Barcoding, Taxonomic/methods ; *Algorithms ; *Magnoliopsida/genetics ; DNA, Plant/genetics ; },
abstract = {Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm. Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon's Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.},
}

*Microsatellite Repeats/genetics
*DNA Barcoding, Taxonomic/methods
*Algorithms
*Magnoliopsida/genetics
DNA, Plant/genetics

@article {pmid38670414,
year = {2024},
author = {Lattos, A and Makri, V and Papadopoulos, DK and Gourzioti, E and Pagonis, C and Georgoulis, I and Karagiannis, D and Theodorou, JA and Michaelidis, B and Giantsis, IA and Feidantsis, K},
title = {Molecular characterization of Lernathropus kroyeri from intensive aquaculture and pathophysiology of infested sea bass.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {109576},
doi = {10.1016/j.fsi.2024.109576},
pmid = {38670414},
issn = {1095-9947},
abstract = {The copepod Lernathropus kroyeri constitutes one of the major parasites for the Mediterranean aquaculture, infesting the sea bass Dicentrarchus labrax causing thus disruptions of growth performance and occasionally mortalities. Despite the large spread and the high frequency of this parasite in mariculture farms of Eastern Mediterranean, L. kroyeri genetic profile from aquaculture as well as the pathophysiological response of D. labrax have not been studied so far. Keeping this in mind, in the present study we investigated the L. kroyeri infestation on D. labrax from two farms in Greece, examining both healthy and heavy parasitized individuals. Assays included histopathology, phylogenetic reconstruction of the parasite and physiological response of the fish by the means of antioxidant, inflammatory metabolic and stress related gene expression analysis at both mRNA and protein levels. Genetic analysis indicated that L. kroyeri composes a monophyletic group, highly phylogenetically distant from other congeneric groups. Heavy infested D. labrax witnessed a significantly increased immune response that further led to oxidative stress and metabolic alterations. Overall, our results demonstrate the, seasonally independent, high infestation of this parasitic copepods, which continue to affect Mediterranean intensive aquaculture systems.},
}

@article {pmid38670101,
year = {2024},
author = {Holze, H and Talarmain, L and Fennell, KA and Lam, EY and Dawson, MA and Vassiliadis, D},
title = {Analysis of synthetic cellular barcodes in the genome and transcriptome with BARtab and bartools.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {100763},
doi = {10.1016/j.crmeth.2024.100763},
pmid = {38670101},
issn = {2667-2375},
abstract = {Cellular barcoding is a lineage-tracing methodology that couples heritable synthetic barcodes to high-throughput sequencing, enabling the accurate tracing of cell lineages across a range of biological contexts. Recent studies have extended these methods by incorporating lineage information into single-cell or spatial transcriptomics readouts. Leveraging the rich biological information within these datasets requires dedicated computational tools for dataset pre-processing and analysis. Here, we present BARtab, a portable and scalable Nextflow pipeline, and bartools, an open-source R package, designed to provide an integrated end-to-end cellular barcoding analysis toolkit. BARtab and bartools contain methods to simplify the extraction, quality control, analysis, and visualization of lineage barcodes from population-level, single-cell, and spatial transcriptomics experiments. We showcase the utility of our integrated BARtab and bartools workflow via the analysis of exemplar bulk, single-cell, and spatial transcriptomics experiments containing cellular barcoding information.},
}

@article {pmid38667952,
year = {2024},
author = {Guerra-Mateo, D and Cano-Lira, JF and Fernández-Bravo, A and Gené, J},
title = {Sunken Riches: Ascomycete Diversity in the Western Mediterranean Coast through Direct Plating and Flocculation, and Description of Four New Taxa.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {4},
pages = {},
pmid = {38667952},
issn = {2309-608X},
support = {PID2021-128068NB-100//Ministeri de Ciència Innovació i Universitats/ ; },
abstract = {The Mediterranean Sea stands out as a hotspot of biodiversity, whose fungal composition remains underexplored. Marine sediments represent the most diverse substrate; however, the challenge of recovering fungi in culture hinders the precise identification of this diversity. Concentration techniques like skimmed milk flocculation (SMF) could represent a suitable solution. Here, we compare the effectiveness in recovering filamentous ascomycetes of direct plating and SMF in combination with three culture media and two incubation temperatures, and we describe the fungal diversity detected in marine sediments. Sediments were collected at different depths on two beaches (Miracle and Arrabassada) on the Spanish western Mediterranean coast between 2021 and 2022. We recovered 362 strains, and after a morphological selection, 188 were identified primarily with the LSU and ITS barcodes, representing 54 genera and 94 species. Aspergillus, Penicillium, and Scedosporium were the most common genera, with different percentages of abundance between both beaches. Arrabassada Beach was more heterogeneous, with 42 genera representing 60 species (Miracle Beach, 28 genera and 54 species). Although most species were recovered with direct plating (70 species), 20 species were exclusively obtained using SMF as a sample pre-treatment, improving our ability to detect fungi in culture. In addition, we propose three new species in the genera Exophiala, Nigrocephalum, and Queenslandipenidiella, and a fourth representing the novel genus Schizochlamydosporiella. We concluded that SMF is a useful technique that, in combination with direct plating, including different culture media and incubation temperatures, improves the chance of recovering marine fungal communities in culture-dependent studies.},
}

@article {pmid38667369,
year = {2024},
author = {Aguado-Aranda, P and Ricarte, A and Nedeljković, Z and Hauser, M and Kelso, S and Sainz-Escudero, L and Skevington, JH and Marcos-García, MÁ},
title = {Unveiling the Mainland vs. Insular Variability of the Eumerus barbarus Species Group (Diptera: Syrphidae) in the Western Mediterranean Basin.},
journal = {Insects},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/insects15040239},
pmid = {38667369},
issn = {2075-4450},
support = {PRE2019-087508//Ministerio de Ciencia, Innovación y Universidades (Spain)/ ; PGC2018-095851-A-C65//Ministerio de Ciencia, Innovación y Universidades (Spain)/ ; IME 2022//Institut Menorquí d'Estudis (Spain)/ ; },
abstract = {Comprising nearly 300 described species, Eumerus Meigen, 1822, is one of the most speciose syrphid genera worldwide, and its taxonomic diversity is remarkable in the Mediterranean basin. The Eumerus barbarus (Coquebert, 1804) group consists of four species in the western Mediterranean. Although the phenotypic variability of this species group has been commented on in previous studies, it has never been contrasted with molecular data. In the present work, the morphological variation found in 300+ specimens of this species group from the western Mediterranean is explored and tested against the COI mitochondrial DNA (mtDNA). The highest phenotypic disparity was found in E. barbarus and Eumerus sulcitibius Rondani 1868. The integrative approach has not revealed cryptic diversity within the species E. barbarus but in E. sulcitibius. As a result, a new species close to E. sulcitibius was discovered, Eumerus sardus Aguado-Aranda, Ricarte & Hauser sp. n., from Sardinia, Italy. The new insular species is here described, illustrated, and discussed. A total of twenty-three haplotypes of COI mtDNA were identified amongst the analyzed Mediterranean specimens of E. barbarus, whereas two and five haplotypes were distinguished in the Iberian specimens of E. sulcitibius and Eumerus gibbosus van Steenis, Hauser & van Zuijen, 2017, respectively. Moreover, the first known barcodes of E. gibbosus and Eumerus schmideggeri van Steenis, Hauser & van Zuijen, 2017 were obtained, and the distribution ranges of all species are mapped. An updated dichotomous key to the males of the E. barbarus group from the western Mediterranean is provided.},
}

@article {pmid38667358,
year = {2024},
author = {Wang, L and Wu, H and He, W and Lai, G and Li, J and Liu, S and Zhou, Q},
title = {Diversity of Parasitoid Wasps and Comparison of Sampling Strategies in Rice Fields Using Metabarcoding.},
journal = {Insects},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/insects15040228},
pmid = {38667358},
issn = {2075-4450},
support = {2023KJ113//the Agricultural Science and Technology Innovative and Promotion Program of Guangdong Province/ ; },
abstract = {A comprehensive and precise evaluation of Arthropoda diversity in agricultural landscapes can enhance biological pest control strategies. We used Malaise traps and sweep nets to collect insects from three double-cropping paddy fields. DNA was extracted from the ethanol preservative of the Malaise traps and from tissue samples of selected parasitoid wasps. This was followed by amplification using DNA barcoding primers to prepare high-throughput sequencing libraries. We annotated a total of 4956 operational taxonomic units (OTUs), encompassing 174 genera and 32 families of parasitoid wasps. The ethanol filter method efficiently captured a wide range of information. However, the method has low resolution and may result in a reduced estimate of species abundance. Additional insect species were also identified in the parasitoid samples. This suggests that high throughput sequencing from adult parasitoid wasps can also detect host species, enabling a better understanding of host species and providing insights into food webs.},
}

@article {pmid38666586,
year = {2024},
author = {Wang, J and Zhang, T and Gao, Z and Wei, M and Jia, Y and Tong, X and Hu, F and Zhao, YS},
title = {Two-Dimensional Lanthanide Metal-Organic Framework Heterostructures for Noninvasively Photoresponsive High-Security Photonic Barcodes.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.4c02440},
pmid = {38666586},
issn = {1944-8252},
abstract = {Stimuli-responsive micro/nanoscale photonic barcodes show great capacity for encryption and anticounterfeiting technologies due to multiple authentications, yet their application is commonly restricted by invasive stimuli. Herein, we report noninvasive light-stimulated high-security photonic barcodes based on spatially assembled photoresponsive two-dimensional (2D) 1,3,5-benzenetribenzoate (BTB)@Ln-MOF host-guest heterostructures. The photoluminescence (PL) spectra information on BTB@Ln-MOF heterostructures could be precisely controlled by the different wavelengths of ultraviolet (UV) light trigger. By using the PL properties and 2D heterostructures as cryptographic primitives, spatially resolved smart photonic barcodes based on both spectral and graphical coding are realized in BTB@Ln-MOF host-guest materials. These results will pave an avenue for the development of smart stimuli-responsive photonic barcodes for anticounterfeiting applications.},
}

@article {pmid38665980,
year = {2023},
author = {Li, GS and Leal-Dutra, CA and Cuesta-Maté, A and Conlon, BH and Peereboom, N and Beemelmanns, C and Aanen, DK and Rosendahl, S and de Beer, ZW and Poulsen, M},
title = {Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution.},
journal = {Persoonia},
volume = {51},
number = {},
pages = {257-279},
doi = {10.3767/persoonia.2023.51.07},
pmid = {38665980},
issn = {0031-5850},
abstract = {The genus Podaxis was first described from India by Linnaeus in 1771, but several revisions of the genus have left the taxonomy unclear. Forty-four Podaxis species names and nine intraspecific varieties are currently accepted, but most fungarium specimens are labelled Podaxis pistillaris. Recent molecular analyses based on barcoding genes suggest that the genus comprises several species, but their status is largely unresolved. Here we obtained basidiospores and photographs from 166 fungarium specimens from around the world and generated a phylogeny based on rDNA internal transcribed spacer ITS1,5.8S and ITS2 (ITS), and a phylogenomic analysis of 3 839 BUSCO genes from low-coverage genomes for a subset of the specimens. Combining phylogenetics, phylogenomics, morphology, ecology, and geographical distribution, spanning 250 years of collections, we propose that the genus includes at least 16 unambiguous species. Based on 10 type specimens (holotype, paratype, and syntype), four recorded species were confirmed, P. carcinomalis, P. deflersii, P. emerici, and P. farlowii. Comparing phylogenetic analysis with described species, including morphology, ecology, and distribution, we resurrected P. termitophilus and designated neotypes, epitypes, or lectotypes for five previously described species, P. aegyptiacus, P. africana, P. beringamensis, P. calyptratus, and P. perraldieri. Lastly, based on phylogenies and morphology of type material, we synonymized three reported species, P. algericus, P. arabicus, and P. rugospora with P. pistillaris, and described five new species that we named P. desolatus, P. inyoensis, P. mareebaensis, P. namaquensis, and P. namibensis. Citation: Li GS, Leal-Dutra CA, Cuesta-Maté A, et al. 2023. Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution. Persoonia 51: 257-279. doi: 10.3767/persoonia.2023.51.07.},
}

@article {pmid38665977,
year = {2023},
author = {Crous, PW and Costa, MM and Kandemir, H and Vermaas, M and Vu, D and Zhao, L and Arumugam, E and Flakus, A and Jurjević, Ž and Kaliyaperumal, M and Mahadevakumar, S and Murugadoss, R and Shivas, RG and Tan, YP and Wingfield, MJ and Abell, SE and Marney, TS and Danteswari, C and Darmostuk, V and Denchev, CM and Denchev, TT and Etayo, J and Gené, J and Gunaseelan, S and Hubka, V and Illescas, T and Jansen, GM and Kezo, K and Kumar, S and Larsson, E and Mufeeda, KT and Piątek, M and Rodriguez-Flakus, P and Sarma, PVSRN and Stryjak-Bogacka, M and Torres-Garcia, D and Vauras, J and Acal, DA and Akulov, A and Alhudaib, K and Asif, M and Balashov, S and Baral, HO and Baturo-Cieśniewska, A and Begerow, D and Beja-Pereira, A and Bianchinotti, MV and Bilański, P and Chandranayaka, S and Chellappan, N and Cowan, DA and Custódio, FA and Czachura, P and Delgado, G and De Silva, NI and Dijksterhuis, J and Dueñas, M and Eisvand, P and Fachada, V and Fournier, J and Fritsche, Y and Fuljer, F and Ganga, KGG and Guerra, MP and Hansen, K and Hywel-Jones, N and Ismail, AM and Jacobs, CR and Jankowiak, R and Karich, A and Kemler, M and Kisło, K and Klofac, W and Krisai-Greilhuber, I and Latha, KPD and Lebeuf, R and Lopes, ME and Lumyong, S and Maciá-Vicente, JG and Maggs-Kölling, G and Magistà, D and Manimohan, P and Martín, MP and Mazur, E and Mehrabi-Koushki, M and Miller, AN and Mombert, A and Ossowska, EA and Patejuk, K and Pereira, OL and Piskorski, S and Plaza, M and Podile, AR and Polhorský, A and Pusz, W and Raza, M and Ruszkiewicz-Michalska, M and Saba, M and Sánchez, RM and Singh, R and Śliwa, L and Smith, ME and Stefenon, VM and Strasiftáková, D and Suwannarach, N and Szczepańska, K and Telleria, MT and Tennakoon, DS and Thines, M and Thorn, RG and Urbaniak, J and van der Vegte, M and Vasan, V and Vila-Viçosa, C and Voglmayr, H and Wrzosek, M and Zappelini, J and Groenewald, JZ},
title = {Fungal Planet description sheets: 1550-1613.},
journal = {Persoonia},
volume = {51},
number = {},
pages = {280-417},
doi = {10.3767/persoonia.2023.51.08},
pmid = {38665977},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Neocamarosporium halophilum in leaf spots of Atriplex undulata. Australia, Aschersonia merianiae on scale insect (Coccoidea), Curvularia huamulaniae isolated from air, Hevansia mainiae on dead spider, Ophiocordyceps poecilometigena on Poecilometis sp. Bolivia, Lecanora menthoides on sandstone, in open semi-desert montane areas, Sticta monlueckiorum corticolous in a forest, Trichonectria epimegalosporae on apothecia of corticolous Megalospora sulphurata var. sulphurata, Trichonectria puncteliae on the thallus of Punctelia borreri. Brazil, Catenomargarita pseudocercosporicola (incl. Catenomargarita gen. nov.) hyperparasitic on Pseudocercospora fijiensis on leaves of Musa acuminata, Tulasnella restingae on protocorms and roots of Epidendrum fulgens. Bulgaria, Anthracoidea umbrosae on Carex spp. Croatia, Hymenoscyphus radicis from surface-sterilised, asymptomatic roots of Microthlaspi erraticum, Orbilia multiserpentina on wood of decorticated branches of Quercus pubescens. France, Calosporella punctatispora on dead corticated twigs of Aceropalus. French West Indies (Martinique), Eutypella lechatii on dead corticated palm stem. Germany, Arrhenia alcalinophila on loamy soil. Iceland, Cistella blauvikensis on dead grass (Poaceae). India, Fulvifomes maritimus on living Peltophorum pterocarpum, Fulvifomes natarajanii on dead wood of Prosopis juliflora, Fulvifomes subazonatus on trunk of Azadirachta indica, Macrolepiota bharadwajii on moist soil near the forest, Narcissea delicata on decaying elephant dung, Paramyrothecium indicum on living leaves of Hibiscus hispidissimus, Trichoglossum syamviswanathii on moist soil near the base of a bamboo plantation. Iran, Vacuiphoma astragalicola from stem canker of Astragalus sarcocolla. Malaysia, Neoeriomycopsis fissistigmae (incl. Neoeriomycopsidaceae fam. nov.) on leaf spots on flower Fissistigma sp. Namibia, Exophiala lichenicola lichenicolous on Acarospora cf. luederitzensis. Netherlands, Entoloma occultatum on soil, Extremus caricis on dead leaves of Carex sp., Inocybe pseudomytiliodora on loamy soil. Norway, Inocybe guldeniae on calcareous soil, Inocybe rupestroides on gravelly soil. Pakistan, Hymenagaricus brunneodiscus on soil. Philippines, Ophiocordyceps philippinensis parasitic on Asilus sp. Poland, Hawksworthiomyces ciconiae isolated from Ciconia ciconia nest, Plectosphaerella vigrensis from leaf spots on Impatiens noli-tangere, Xenoramularia epitaxicola from sooty mould community on Taxus baccata. Portugal, Inocybe dagamae on clay soil. Saudi Arabia, Diaporthe jazanensis on branches of Coffea arabica. South Africa, Alternaria moraeae on dead leaves of Moraea sp., Bonitomyces buffels-kloofinus (incl. Bonitomyces gen. nov.) on dead twigs of unknown tree, Constrictochalara koukolii on living leaves of Itea rhamnoides colonised by a Meliola sp., Cylindromonium lichenophilum on Parmelina tiliacea, Gamszarella buffelskloofina (incl. Gamszarella gen. nov.) on dead insect, Isthmosporiella africana (incl. Isthmosporiella gen. nov.) on dead twigs of unknown tree, Nothoeucasphaeria buffelskloofina (incl. Nothoeucasphaeria gen. nov.), on dead twigs of unknown tree, Nothomicrothyrium beaucarneae (incl. Nothomicrothyrium gen. nov.) on dead leaves of Beaucarnea stricta, Paramycosphaerella proteae on living leaves of Protea caffra, Querciphoma foliicola on leaf litter, Rachicladosporium conostomii on dead twigs of Conostomium natalense var. glabrum, Rhamphoriopsis synnematosa on dead twig of unknown tree, Waltergamsia mpumalanga on dead leaves of unknown tree. Spain, Amanita fulvogrisea on limestone soil, in mixed forest, Amanita herculis in open Quercus forest, Vuilleminia beltraniae on Cistus symphytifolius. Sweden, Pachyella pulchella on decaying wood on sand-silt riverbank. Thailand, Deniquelata cassiae on dead stem of Cassia fistula, Stomiopeltis thailandica on dead twigs of Magnolia champaca. Ukraine, Circinaria podoliana on natural limestone outcrops, Neonematogonum carpinicola (incl. Neonematogonum gen. nov.) on dead branches of Carpinus betulus. USA, Exophiala wilsonii water from cooling tower, Hygrophorus aesculeticola on soil in mixed forest, and Neocelosporium aereum from air in a house attic. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Costa MM, Kandemir H, et al. 2023. Fungal Planet description sheets: 1550-1613. Persoonia 51: 280-417. doi: 10.3767/persoonia.2023.51.08.},
}

@article {pmid38665369,
year = {2024},
author = {Sun, W and Wei, Z and Gu, Y and Wang, T and Liu, B and Yan, Y},
title = {Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1328080},
doi = {10.3389/fpls.2024.1328080},
pmid = {38665369},
issn = {1664-462X},
abstract = {Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.},
}

@article {pmid38661214,
year = {2024},
author = {Ylagan, M and Xu, Q and Kowalski, J},
title = {TTSBBC: triplex target site biomarkers and barcodes in cancer.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae312},
pmid = {38661214},
issn = {1362-4962},
support = {//University of Texas Dell Medical School Research Funds/ ; },
abstract = {The technology of triplex-forming oligonucleotides (TFOs) provides an approach to manipulate genes at the DNA level. TFOs bind to specific sites on genomic DNA, creating a unique intermolecular triple-helix DNA structure through Hoogsteen hydrogen bonding. This targeting by TFOs is site-specific and the locations TFOs bind are referred to as TFO target sites (TTS). Triplexes have been observed to selectively influence gene expression, homologous recombination, mutations, protein binding, and DNA damage. These sites typically feature a poly-purine sequence in duplex DNA, and the characteristics of these TTS sequences greatly influence the formation of the triplex. We introduce TTSBBC, a novel analysis and visualization platform designed to explore features of TTS sequences to enable users to design and validate TTSs. The web server can be freely accessed at https://kowalski-labapps.dellmed.utexas.edu/TTSBBC/.},
}

@article {pmid38660246,
year = {2024},
author = {Lin, T and Liu, D and Guan, Z and Zhao, X and Li, S and Wang, X and Hou, R and Zheng, J and Cao, J and Shi, M},
title = {CRISPR screens in mechanism and target discovery for AML.},
journal = {Heliyon},
volume = {10},
number = {8},
pages = {e29382},
pmid = {38660246},
issn = {2405-8440},
abstract = {CRISPR-based screens have discovered novel functional genes involving in diverse tumor biology and elucidated the mechanisms of the cancer pathological states. Recently, with its randomness and unbiasedness, CRISPR screens have been used to discover effector genes with previously unknown roles for AML. Those novel targets are related to AML survival resembled cellular pathways mediating epigenetics, synthetic lethality, transcriptional regulation, mitochondrial and energy metabolism. Other genes that are crucial for pharmaceutical targeting and drug resistance have also been identified. With the rapid development of novel strategies, such as barcodes and multiplexed mosaic CRISPR perturbation, more potential therapeutic targets and mechanism in AML will be discovered. In this review, we present an overview of recent progresses in the development of CRISPR-based screens for the mechanism and target identification in AML and discuss the challenges and possible solutions in this rapidly growing field.},
}

@article {pmid38659825,
year = {2024},
author = {Simon, JJ and Fowler, DM and Maly, DJ},
title = {Multiplexed, multimodal profiling of the intracellular activity, interactions, and druggability of protein variants using LABEL-seq.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.19.590094},
pmid = {38659825},
abstract = {Multiplexed assays of variant effect are powerful tools for assessing the impact of protein sequence variation, but are limited to measuring a single protein property and often rely on indirect readouts of intracellular protein function. Here, we developed LAbeling with Barcodes and Enrichment for biochemicaL analysis by sequencing (LABEL-seq), a platform for the multimodal profiling of thousands of protein variants in cultured human cells. Multimodal measurement of ∼20,000 variant effects for ∼1,600 BRaf variants using LABEL-seq revealed that variation at positions that are frequently mutated in cancer had minimal effects on folding and intracellular abundance but could dramatically alter activity, protein-protein interactions, and druggability. Integrative analysis of our multimodal measurements identified networks of positions with similar roles in regulating BRaf's signaling properties and enabled predictive modeling of variant effects on complex processes such as cell proliferation and small molecule-promoted degradation. LABEL-seq provides a scalable approach for the direct measurement of multiple biochemical effects of protein variants in their native cellular context, yielding insight into protein function, disease mechanisms, and druggability.},
}

@article {pmid38656593,
year = {2024},
author = {Al-Sarar, AS and Abobakr, Y and Alzabib, AA and Saleh, AA},
title = {First Report on Banana Weevil, Cosmopolites sordidus (Germar 1823) (Coleoptera: Curculionidae), an Exotic Economically Important Pest from Saudi Arabia.},
journal = {Neotropical entomology},
volume = {},
number = {},
pages = {},
pmid = {38656593},
issn = {1678-8052},
support = {2-17-04-001-0040//National Plan for Science, Technology and Innovation/ ; },
abstract = {We report the first record of the occurrence of the banana weevil, Cosmopolites sordidus (Germar, 1823) (Coleoptera: Curculionidae), an economically important pest of bananas (Musa spp.), from Fifa Mountains in Saudi Arabia. Moreover, we recorded the first observation of damage caused to bananas by C. sordidus in a banana farm in Jazan Province, southwestern Saudi Arabia, in March 2022. Molecular characterization using DNA sequences of the mitochondrial COI gene confirmed the morphological identification of C. sordidus. This discovery is considered a warning notice to prevent the potential establishment and spread of this dangerous pest in the banana cultivation regions in Saudi Arabia. Therefore, it is recommended that detection and monitoring of banana weevil should be undertaken in Saudi banana farms in order to restrict the dissemination of this weevil to other banana cultivation areas.},
}

@article {pmid38656472,
year = {2024},
author = {Yuan, JM and Su, J and Zhang, ZH and Sun, B and Jiao, XL and Zhang, X and Zhai, YP and Chen, YJ},
title = {Initial study and phylogenetic analysis of hard ticks (Acari: Ixodidae) in Nantong, China along the route of avian migration.},
journal = {Experimental & applied acarology},
volume = {},
number = {},
pages = {},
pmid = {38656472},
issn = {1572-9702},
support = {MS2023092//Research Project Foundation of Nantong Health Commission/ ; MS2023092//Research Project Foundation of Nantong Health Commission/ ; MS2023092//Research Project Foundation of Nantong Health Commission/ ; MS2023092//Research Project Foundation of Nantong Health Commission/ ; MS2023092//Research Project Foundation of Nantong Health Commission/ ; MS2023092//Research Project Foundation of Nantong Health Commission/ ; MS2023092//Research Project Foundation of Nantong Health Commission/ ; MS2023092//Research Project Foundation of Nantong Health Commission/ ; },
abstract = {The growing concern about migratory birds potentially spreading ticks due to global warming has become a significant issue. The city of Nantong in this study is situated along the East Asia-Australasian Flyway (EAAF), with numerous wetlands serving as roosting sites for migratory birds. We conducted an investigation of hard ticks and determined the phylogenetic characteristics of tick species in this city. We utilized three different genes for our study: the mitochondrial cytochrome oxidase subunit 1 (COX1) gene, the second internal transcribed spacer (ITS2), and the mitochondrial small subunit rRNA (12 S rRNA) gene. The predominant tick species were Haemaphysalis flava (H. flava) and Haemaphysalis longicornis (H. longicornis). Additionally, specimens of Haemaphysalis campanulata (H. campanulata) and Rhipicephalus sanguineus (R. sanguineus) were collected. The H. flava specimens in this study showed a close genetic relationship with those from inland provinces of China, as well as South Korea and Japan. Furthermore, samples of H. longicornis exhibited a close genetic relationship with those from South Korea, Japan, Australia, and the USA, as well as specific provinces in China. Furthermore, R. sanguineus specimens captured in Nantong showed genetic similarities with specimens from Egypt, Nigeria, and Argentina.},
}

@article {pmid38656420,
year = {2024},
author = {Oyuntsetseg, D and Nyamgerel, N and Baasanmunkh, S and Oyuntsetseg, B and Urgamal, M and Yoon, JW and Bayarmaa, GA and Choi, HJ},
title = {The complete chloroplast genome and phylogentic results support the species position of Swertia banzragczii and Swertia marginata (Gentianaceae) in Mongolia.},
journal = {Botanical studies},
volume = {65},
number = {1},
pages = {11},
pmid = {38656420},
issn = {1817-406X},
support = {P2023-4591//National University of Mongolia/ ; KNA1-2-42, 22-2//Korea National Arboretum/ ; 2023R1A6C101B022//Korea Basic Science Institute/ ; },
abstract = {BACKGROUND: Swertia banzragczii and S. marginata are important medicinal species in Mongolia. However, their taxonomic positions and genetic backgrounds remain unknown. In this study, we explored the complete chloroplast genomes and DNA barcoding of these species and compared them with those of closely related species within the subgenus to determine their taxonomic positions and phylogenetic relationships.

RESULT: The chloroplast genomes of S. banzragczii and S. marginata encoded 114 genes, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among them, 16 genes contained a single intron, and 2 genes had two introns. Closely related species had a conserved genome structure and gene content. Only differences in genome length were noticed, which were caused by the expansion and contraction of the inverted repeat (IR) region and loss of exons in some genes. The trnH-GUG-psbA and trnD-GUC-trnY-GUA intergenic regions had high genetic diversity within Swertia plastomes. Overall, S. banzragczii and S. marginata are true species and belong to the subgenus Swertia.

CONCLUSIONS: These results provide valuable genetic and morphological information on rare and subendemic Swertia species in Mongolia, which can be used for further advanced studies on the Swertia genus.},
}

@article {pmid38655012,
year = {2024},
author = {Ståhls, G},
title = {Pelecocera (Pelecocera) tricincta and Pelecocera (Chamaesyrphus) caledonica (Diptera, Syrphidae) reared from Rhizopogon fungal host in Finland.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e118563},
pmid = {38655012},
issn = {1314-2828},
abstract = {MtDNA COI barcodes have frequently been used in identification to associate an unknown life stage in insects with a known species. This study reports the discovery of hoverfly larvae in the fungal fruit bodies of Rhizopogonluteolus Fr. & Nordholm, 1817 in Finland. The identity of the larvae was firstly resolved using mtDNA COI barcodes generated from the larvae and tree-based identification confirming the species Pelecocera (Pelecocera) tricincta Meigen, 1822 and Pelecocera (Chamaesyrphus) caledonica (Collin, 1940) (Diptera, Syrphidae). Obtained pupae were reared into adult flies and produced the same two species. The morphological features of these mycophagous larvae are compared with those of other fungus-feeding hoverfly species. This study confirms Rhizopogonluteolus as fungal host for these Pelecocera species in the Western Palaearctic Region.},
}

@article {pmid38655011,
year = {2024},
author = {Kim, S and Čkrkić, J and Tomanović, Ž and Sohn, JH and Lim, J and Kim, H},
title = {A new species of genus Monoctonus (Hymenoptera, Braconidae, Aphidiinae) from South Korea.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e119476},
pmid = {38655011},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Monoctonus Haliday, 1833 is a small group which consists of 24 species worldwide. In South Korea, Chang and Youn (1983) recorded one species, M.similis Starý & Schlinger, 1967, but the evidence for identification of this species is doubtful and further confirmation is required (personal communication with Prof. Jong-Cheol Paik).

NEW INFORMATION: An additional Monoctonus species is recorded as new to science from South Korea. Descriptions and illustrations of the new species -Monoctonuskoreanus sp. nov. - are provided, together with its mitochondrial cytochrome c oxidase subunit I (COI) data and phylogenetic position. A key to the female of the two species present in Korea is provided.},
}

@article {pmid38652658,
year = {2024},
author = {Cheng, YL and Banu, MA and Zhao, W and Rosenfeld, SS and Canoll, P and Sims, PA},
title = {Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma.},
journal = {Cell reports},
volume = {43},
number = {5},
pages = {114139},
doi = {10.1016/j.celrep.2024.114139},
pmid = {38652658},
issn = {2211-1247},
abstract = {Glioblastoma (GBM) is a deadly brain tumor, and the kinesin motor KIF11 is an attractive therapeutic target with roles in proliferation and invasion. Resistance to KIF11 inhibitors, which has mainly been studied in animal models, presents significant challenges. We use lineage-tracing barcodes and single-cell RNA sequencing to analyze resistance in patient-derived GBM neurospheres treated with ispinesib, a potent KIF11 inhibitor. Similar to GBM progression in patients, untreated cells lose their neural lineage identity and become mesenchymal, which is associated with poor prognosis. Conversely, cells subjected to long-term ispinesib treatment exhibit a proneural phenotype. We generate patient-derived xenografts and show that ispinesib-resistant cells form less aggressive tumors in vivo, even in the absence of drug. Moreover, treatment of human ex vivo GBM slices with ispinesib demonstrates phenotypic alignment with in vitro responses, underscoring the clinical relevance of our findings. Finally, using retrospective lineage tracing, we identify drugs that are synergistic with ispinesib.},
}

@article {pmid38646932,
year = {2024},
author = {Saranholi, BH and França, FM and Vogler, AP and Barlow, J and Vaz de Mello, FZ and Maldaner, ME and Carvalho, E and Gestich, CC and Howes, B and Banks-Leite, C and Galetti, PM},
title = {Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e13961},
doi = {10.1111/1755-0998.13961},
pmid = {38646932},
issn = {1755-0998},
support = {MR/X032949/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle 'samplers' and its universal applicability independently of the species traits of local beetle communities.},
}

@article {pmid38646006,
year = {2024},
author = {Banerjee, P and Dey, G and Maity, JP and Stewart, KA and Sharma, RK and Chan, MWY and Lee, K and Chen, CY},
title = {The unseen invaders: Tracking phylogeographic dynamics and genetic diversity of cryptic Pomacea canaliculata and P. maculata (Golden apple snails) across Taiwan.},
journal = {Ecology and evolution},
volume = {14},
number = {4},
pages = {e11268},
pmid = {38646006},
issn = {2045-7758},
abstract = {The cryptic invasion of golden apple snails (Pomacea canaliculata and P. maculata) in Taiwan has caused significant ecological and economical damage over the last few decades, however, their management remains difficult due to inadequate taxonomic identification, complex phylogeny, and limited population genetic information. We aim to understand the current distribution, putative population of origin, genetic diversity, and potential path of cryptic invasion of Pomacea canaliculata and P. maculata across Taiwan to aid in improved mitigation approaches. The present investigation conducted a nationwide survey with 254 samples collected from 41 locations in 14 counties or cities across Taiwan. We identified P. canaliculata and P. maculata based on mitochondrial COI and compared their genetic diversity across Taiwan, as well as other introduced and native countries (based on publicly available COI data) to understand the possible paths of invasion to Taiwan. Based on mitochondrial COI barcoding, sympatric and heterogeneous distributions of invasive P. canaliculata and P. maculata were noted. Our haplotype analysis and mismatch distribution results suggested multiple introductions of P. canaliculata in Taiwan was likely originated directly from Argentina, whereas P. maculata was probably introduced from a single, or a few, introduction event(s) from Argentina and Brazil. Our population genetic data further demonstrated a higher haplotype and genetic diversity for P. canaliculata and P. maculata in Taiwan compared to other introduced regions. Based on our current understanding, the establishment of P. canaliculata and P. maculata is alarming and widespread beyond geopolitical borders, requiring a concerted and expedited national and international invasive species mitigation program.},
}

@article {pmid38645306,
year = {2024},
author = {Lammertse, E and Li, S and Kendall, J and Kim, C and Morris, P and Ranade, N and Levy, D and Wigler, M and Brouzes, E},
title = {Magnetically functionalized hydrogels for high-throughput genomic applications.},
journal = {Advanced materials technologies},
volume = {9},
number = {2},
pages = {},
pmid = {38645306},
issn = {2365-709X},
abstract = {Single-cell genomics has revolutionized tissue analysis by revealing the genetic program of individual cells. The key aspect of the technology is the use of barcoded beads to unambiguously tag sequences originating from a single cell. The generation of unique barcodes on beads is mainly achieved by split-pooling methods, which are labor-intensive due to repeated washing steps. Towards the automation of the split-pooling method, we developed a simple method to magnetize hydrogel beads. We show that these hydrogel beads provide increased yields and washing efficiencies for purification procedures. They are also fully compatible with single-cell sequencing using the BAG-Seq workflow. Our work opens the automation of the split-pooling technique, which will improve single-cell genomic workflows.},
}

@article {pmid38643988,
year = {2024},
author = {Nathans, JF and Ayers, JL and Shendure, J and Simpson, CL},
title = {Genetic Tools for Cell Lineage Tracing and Profiling Developmental Trajectories in the Skin.},
journal = {The Journal of investigative dermatology},
volume = {144},
number = {5},
pages = {936-949},
doi = {10.1016/j.jid.2024.02.006},
pmid = {38643988},
issn = {1523-1747},
abstract = {The epidermis is the body's first line of protection against dehydration and pathogens, continually regenerating the outermost protective skin layers throughout life. During both embryonic development and wound healing, epidermal stem and progenitor cells must respond to external stimuli and insults to build, maintain, and repair the cutaneous barrier. Recent advances in CRISPR-based methods for cell lineage tracing have remarkably expanded the potential for experiments that track stem and progenitor cell proliferation and differentiation over the course of tissue and even organismal development. Additional tools for DNA-based recording of cellular signaling cues promise to deepen our understanding of the mechanisms driving normal skin morphogenesis and response to stressors as well as the dysregulation of cell proliferation and differentiation in skin diseases and cancer. In this review, we highlight cutting-edge methods for cell lineage tracing, including in organoids and model organisms, and explore how cutaneous biology researchers might leverage these techniques to elucidate the developmental programs that support the regenerative capacity and plasticity of the skin.},
}

@article {pmid38642645,
year = {2024},
author = {Alloun, W and Berkani, M and Shavandi, A and Beddiar, A and Pellegrini, M and Garzia, M and Lakhdari, D and Ganachari, SV and Aminabhavi, TM and Vasseghian, Y and Muddapur, U and Chaouche, NK},
title = {Harnessing artificial intelligence-driven approach for enhanced indole-3-acetic acid from the newly isolated Streptomyces rutgersensis AW08.},
journal = {Environmental research},
volume = {},
number = {},
pages = {118933},
doi = {10.1016/j.envres.2024.118933},
pmid = {38642645},
issn = {1096-0953},
abstract = {Indole-3-acetic acid (IAA) derived from Actinobacteria fermentations on agro-wastes constitutes a safer and low-cost alternative to synthetic IAA. This study aims to select a high IAA-producing Streptomyces-like strain isolated from Lake Oubeira sediments (El Kala, Algeria) for further investigations (i.e., 16S rRNA gene barcoding and process optimization). Subsequently, artificial intelligence-based approaches were employed to maximize IAA bioproduction on spent coffee grounds as high-value-added feedstock. The specificity was the novel application of the Limited-Memory Broyden-Fletcher-Goldfarb-Shanno Box (L-BFGS-B) optimization algorithm. The new strain AW08 was a significant producer of IAA (26.116 ± 0.61 μg/mL) and was identified as Streptomyces rutgersensis by 16S rRNA gene barcoding and phylogenetic inquiry. The empirical data involved the inoculation of AW08 in various cultural conditions according to a four-factor Box Behnken Design matrix (BBD) of Response surface methodology (RSM). The input parameters and regression equation extracted from the RSM-BBD were the basis for implementing and training the L-BFGS-B algorithm. Upon training the model, the optimal conditions suggested by the BBD and L-BFGS-B algorithm were, respectively, L-Trp (X1) = 0.58 %; 0.57 %; T° (X2) = 26.37 °C; 28.19 °C; pH (X3) = 7.75; 8.59; and carbon source (X4) = 30 %; 33.29 %, with the predicted response IAA (Y) =152.8; 169.18 μg/mL). Our findings emphasize the potential of the multifunctional S. rutgersensis AW08, isolated and reported for the first time in Algeria, as a robust producer of IAA. Validation investigations using the bioprocess parameters provided by the L-BFGS-B and the BBD-RSM models demonstrate the effectiveness of AI-driven optimization in maximizing IAA output by 5.43-fold and 4.2-fold, respectively. This study constitutes the first paper reporting a novel interdisciplinary approach and providing insights into biotechnological advancements. These results support for the first time a reasonable approach for valorizing spent coffee grounds as feedstock for sustainable and economic IAA production from S. rutgersensis AW08.},
}

@article {pmid38641660,
year = {2024},
author = {Reicher, A and Reiniš, J and Ciobanu, M and Růžička, P and Malik, M and Siklos, M and Kartysh, V and Tomek, T and Koren, A and Rendeiro, AF and Kubicek, S},
title = {Pooled multicolour tagging for visualizing subcellular protein dynamics.},
journal = {Nature cell biology},
volume = {},
number = {},
pages = {},
pmid = {38641660},
issn = {1476-4679},
support = {ERC-CoG-772437//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; LS21-01//Vienna Science and Technology Fund (Wiener Wissenschafts-, Forschungs- und Technologiefonds)/ ; },
abstract = {Imaging-based methods are widely used for studying the subcellular localization of proteins in living cells. While routine for individual proteins, global monitoring of protein dynamics following perturbation typically relies on arrayed panels of fluorescently tagged cell lines, limiting throughput and scalability. Here, we describe a strategy that combines high-throughput microscopy, computer vision and machine learning to detect perturbation-induced changes in multicolour tagged visual proteomics cell (vpCell) pools. We use genome-wide and cancer-focused intron-targeting sgRNA libraries to generate vpCell pools and a large, arrayed collection of clones each expressing two different endogenously tagged fluorescent proteins. Individual clones can be identified in vpCell pools by image analysis using the localization patterns and expression level of the tagged proteins as visual barcodes, enabling simultaneous live-cell monitoring of large sets of proteins. To demonstrate broad applicability and scale, we test the effects of antiproliferative compounds on a pool with cancer-related proteins, on which we identify widespread protein localization changes and new inhibitors of the nuclear import/export machinery. The time-resolved characterization of changes in subcellular localization and abundance of proteins upon perturbation in a pooled format highlights the power of the vpCell approach for drug discovery and mechanism-of-action studies.},
}

@article {pmid38637345,
year = {2024},
author = {Patil, GS and Pinto, N and Nath, R and Goswami, M},
title = {Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {528},
pmid = {38637345},
issn = {1573-4978},
support = {BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {BACKGROUND: Catfishes (order Siluriformes) are among the most diverse and widely distributed fish groups in the world. They are not only used for human consumption but are also a major part of the ornamental fish trade. Being a Biodiversity Hotspot, the North Eastern Region of India is home to a diverse population of ornamental fishes. Catfishes contain a humongous number of species; in this study, the authors have tried to elucidate the phylogenetic relationship of some important ornamental catfishes found in North East India using DNA barcodes.

METHODS AND RESULTS: In this study, we have tried to explore the phylogenetic history of 13 species (41 specimens) of ornamental catfishes spanning 12 genera and 9 families of Siluriformes using DNA barcoding. Pairwise genetic distances using Kimura 2-Parameter (K2P) were calculated at intra-specific and inter-specific levels. A Neighbor-Joining tree was constructed to understand the phylogenetic relationship among the nine different catfish families. All the specimens under this study clustered with their respective species under the same family and formed three sub-clades. However, Olyra longicaudata, belonging to the Bagridae family, did not cluster with other species from the same family. In this study, the authors have suggested a revision of the classification of O. longicaudata back to its original family, Olyridae.

CONCLUSIONS: In this study, the maximum intraspecific genetic distance of 0.03 and the minimum interspecific genetic distance of 0.14 were observed among the species. Therefore, it is evident that there is a barcoding gap among the species, which helped in the correct identification of the species. Thus, DNA barcoding helped complement the phenetic approach and also revealed a different phylogenetic relationship among the catfishes belonging to the Bagridae family.},
}

@article {pmid38635627,
year = {2024},
author = {Chevée, V and Hullahalli, K and Dailey, KG and Güereca, L and Zhang, C and Waldor, MK and Portnoy, DA},
title = {Temporal and spatial dynamics of Listeria monocytogenes central nervous system infection in mice.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {17},
pages = {e2320311121},
doi = {10.1073/pnas.2320311121},
pmid = {38635627},
issn = {1091-6490},
support = {R01 AI042347/AI/NIAID NIH HHS/United States ; },
abstract = {Listeria monocytogenes is a bacterial pathogen that can cause life-threatening central nervous system (CNS) infections. While mechanisms by which L. monocytogenes and other pathogens traffic to the brain have been studied, a quantitative understanding of the underlying dynamics of colonization and replication within the brain is still lacking. In this study, we used barcoded L. monocytogenes to quantify the bottlenecks and dissemination patterns that lead to cerebral infection. Following intravenous (IV) inoculation, multiple independent invasion events seeded all parts of the CNS from the blood, however, only one clone usually became dominant in the brain. Sequential IV inoculations and intracranial inoculations suggested that clones that had a temporal advantage (i.e., seeded the CNS first), rather than a spatial advantage (i.e., invaded a particular brain region), were the main drivers of clonal dominance. In a foodborne model of cerebral infection with immunocompromised mice, rare invasion events instead led to a highly infected yet monoclonal CNS. This restrictive bottleneck likely arose from pathogen transit into the blood, rather than directly from the blood to the brain. Collectively, our findings provide a detailed quantitative understanding of the L. monocytogenes population dynamics that lead to CNS infection and a framework for studying the dynamics of other cerebral infections.},
}

@article {pmid38634956,
year = {2024},
author = {Chakraborty, M and Kaur, J and Gunjan, and Kathpalia, M and Kaur, N},
title = {Clinical relevance of glycosylation in triple negative breast cancer: a review.},
journal = {Glycoconjugate journal},
volume = {},
number = {},
pages = {},
pmid = {38634956},
issn = {1573-4986},
abstract = {Glycosylation alterations in TNBC have significant implications for tumor behavior, diagnosis, prognosis, and therapeutic strategies. Dysregulated glycosylation affects cell adhesion, signaling, immune recognition, and response to therapy in TNBC. Different types of glycosylation, including N-linked glycosylation, O-linked glycosylation, glycosphingolipid glycosylation, mucin-type glycosylation, and sialylation, play distinct roles in TNBC. The "barcoding" method based on glycosylation sites of the membrane type mannose receptor (MR) shows promise in accurately distinguishing breast cancer subtypes, including TNBC. Alpha-L-fucosidase 1 (FUCA1) and Monocarboxylate transporter 4 (MCT4) have been identified as potential diagnostic and prognostic markers for TNBC. The glycosylation status of PD-L1 impacts the response to immune checkpoint blockade therapy in TNBC. Inhibiting fucosylation of B7H3 enhances immune responses and improves anti-tumor effects. Targeting glycosylated B7H4 and modulating estrogen metabolism through glycosylation-related mechanisms are potential therapeutic strategies for TNBC. Understanding the role of glycosylation in TNBC provides insights into disease mechanisms, diagnosis, and potential therapeutic targets. Further research in this field may lead to personalized treatment approaches and improved outcomes for TNBC patients.},
}

@article {pmid38633369,
year = {2024},
author = {Kang, S and Choi, P and Maile-Moskowitz, A and Brown, CL and Gonzalez, RA and Pruden, A and Vikesland, PJ},
title = {Highly Multiplexed Reverse-Transcription Loop-Mediated Isothermal Amplification and Nanopore Sequencing (LAMPore) for Wastewater-Based Surveillance.},
journal = {ACS ES&T water},
volume = {4},
number = {4},
pages = {1629-1636},
pmid = {38633369},
issn = {2690-0637},
abstract = {Wastewater-based surveillance (WBS) has gained attention as a strategy to monitor and provide an early warning for disease outbreaks. Here, we applied an isothermal gene amplification technique, reverse-transcription loop-mediated isothermal amplification (RT-LAMP), coupled with nanopore sequencing (LAMPore) as a means to detect SARS-CoV-2. Specifically, we combined barcoding using both an RT-LAMP primer and the nanopore rapid barcoding kit to achieve highly multiplexed detection of SARS-CoV-2 in wastewater. RT-LAMP targeting the SARS-CoV-2 N region was conducted on 96 reactions including wastewater RNA extracts and positive and no-target controls. The resulting amplicons were pooled and subjected to nanopore sequencing, followed by demultiplexing based on barcodes that differentiate the source of each SARS-CoV-2 N amplicon derived from the 96 RT-LAMP products. The criteria developed and applied to establish whether SARS-CoV-2 was detected by the LAMPore assay indicated high consistency with polymerase chain reaction-based detection of the SARS-CoV-2 N gene, with a sensitivity of 89% and a specificity of 83%. We further profiled sequence variations on the SARS-CoV-2 N amplicons, revealing a number of mutations on a sample collected after viral variants had emerged. The results demonstrate the potential of the LAMPore assay to facilitate WBS for SARS-CoV-2 and the emergence of viral variants in wastewater.},
}

@article {pmid38631624,
year = {2024},
author = {Hu, H and Liu, L and Wei, XY and Duan, JJ and Deng, JY and Pei, DS},
title = {Revolutionizing aquatic eco-environmental monitoring: Utilizing the RPA-Cas-FQ detection platform for zooplankton.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172414},
doi = {10.1016/j.scitotenv.2024.172414},
pmid = {38631624},
issn = {1879-1026},
abstract = {The integration of recombinase polymerase amplification (RPA) with CRISPR/Cas technology has revolutionized molecular diagnostics and pathogen detection due to its unparalleled sensitivity and trans-cleavage ability. However, its potential in the ecological and environmental monitoring scenarios for aquatic ecosystems remains largely unexplored, particularly in accurate qualitative/quantitative detection, and its actual performance in handling complex real environmental samples. Using zooplankton as a model, we have successfully optimized the RPA-CRISPR/Cas12a fluorescence detection platform (RPA-Cas-FQ), providing several crucial "technical tips". Our findings indicate the sensitivity of CRISPR/Cas12a alone is 5 × 10[9] copies/reaction, which can be dramatically increased to 5 copies/reaction when combined with RPA. The optimized RPA-Cas-FQ enables reliable qualitative and semi-quantitative detection within 50 min, and exhibits a good linear relationship between fluorescence intensity and DNA concentration (R[2] = 0.956-0.974***). Additionally, we developed a rapid and straightforward identification procedure for single zooplankton by incorporating heat-lysis and DNA-barcode techniques. We evaluated the platform's effectiveness using real environmental DNA (eDNA) samples from the Three Gorges Reservoir, confirming its practicality. The eDNA-RPA-Cas-FQ demonstrated strong consistency (Kappa = 0.43***) with eDNA-Metabarcoding in detecting species presence/absence in the reservoir. Furthermore, the two semi-quantitative eDNA quantification technologies showed a strong positive correlation (R[2] = 0.58-0.87***). This platform also has the potential to monitor environmental pollutants by selecting appropriate indicator species. The novel insights and methodologies presented in this study represent a significant advancement in meeting the complex needs of aquatic ecosystem protection and monitoring.},
}

@article {pmid38632506,
year = {2024},
author = {Alkathiry, HA and Alghamdi, SQ and Sinha, A and Margos, G and Stekolnikov, AA and Alagaili, AN and Darby, AC and Makepeace, BL and Khoo, JJ},
title = {Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {380},
pmid = {38632506},
issn = {1471-2164},
abstract = {BACKGROUND: Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear.

RESULTS: Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin.

CONCLUSIONS: P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.},
}

@article {pmid38629445,
year = {2024},
author = {Fiedler, S and Frenzel, F and Würth, C and Tavernaro, I and Grüne, M and Schweizer, S and Engel, A and Resch-Genger, U},
title = {Interlaboratory Comparison on Absolute Photoluminescence Quantum Yield Measurements of Solid Light Converting Phosphors with Three Commercial Integrating Sphere Setups.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.4c00372},
pmid = {38629445},
issn = {1520-6882},
abstract = {Scattering luminescent materials dispersed in liquid and solid matrices and luminescent powders are increasingly relevant for fundamental research and industry. Examples are luminescent nano- and microparticles and phosphors of different compositions in various matrices or incorporated into ceramics with applications in energy conversion, solid-state lighting, medical diagnostics, and security barcoding. The key parameter to characterize the performance of these materials is the photoluminescence/fluorescence quantum yield (Φf), i.e., the number of emitted photons per number of absorbed photons. To identify and quantify the sources of uncertainty of absolute measurements of Φf of scattering samples, the first interlaboratory comparison (ILC) of three laboratories from academia and industry was performed by following identical measurement protocols. Thereby, two types of commercial stand-alone integrating sphere setups with different illumination and detection geometries were utilized for measuring the Φf of transparent and scattering dye solutions and solid phosphors, namely, YAG:Ce optoceramics of varying surface roughness, used as converter materials for blue light emitting diodes. Special emphasis was dedicated to the influence of the measurement geometry, the optical properties of the blank utilized to determine the number of photons of the incident excitation light absorbed by the sample, and the sample-specific surface roughness. While the Φf values of the liquid samples matched between instruments, Φf measurements of the optoceramics with different blanks revealed substantial differences. The ILC results underline the importance of the measurement geometry, sample position, and blank for reliable Φf data of scattering the YAG:Ce optoceramics, with the blank's optical properties accounting for uncertainties exceeding 20%.},
}

@article {pmid38629305,
year = {2024},
author = {Fening, KO and Okyere, SO and Forchibe, EE and Layodé, BFR and Richmond, TE and Agboyi, LKBA and Afreh-Nuamah, K and Wamonje, FO},
title = {First report of Leucinodes africensis and Leucinodes laisalis on Solanum aethiopicum and Solanum melongena in farmer's fields in southern Ghana.},
journal = {Bulletin of entomological research},
volume = {},
number = {},
pages = {1-15},
doi = {10.1017/S0007485324000154},
pmid = {38629305},
issn = {1475-2670},
abstract = {The eggplant fruit and shoot borer (EFSB) is a devastating pest of eggplants (Solanum aethiopicum L. and Solanum melongena L.) in Ghana, causing significant economic losses. Although initially thought to be the Leucinodes orbonalis Guenee species found in Asia, recent European and Mediterranean Plant Protection Organization reports suggest its absence in Africa. However, eight Leucinodes species have been recently described in Africa, including two new species, Leucinodes africensis sp. n. and Leucinodes laisalis Walker, which were intercepted in eggplant fruits exported from Ghana to the United Kingdom. Despite the reported absence of L. orbonalis in Africa, it remains on the pest list of Ghana as a species known to attack eggplants. To accurately determine the identity of the EFSB complex occurring on eggplant in Southern Ghana, molecular and morphological taxonomic tools were employed, and adult male populations were monitored in on-farm conditions. Our results revealed the presence of two EFSB species, L. africensis and L. laisalis, in the shoot and fruits of eggplants, with L. africensis being the dominant species and widely distributed in Southern Ghana. Notably, L. africensis males were attracted to the pheromone lure of L. orbonalis despite the two species being biologically distinct. This study provides crucial information on correctly identifying the EFSB species attacking eggplants in Southern Ghana and has significant implications for developing management interventions against these pests and their effects on international eggplant trade.},
}

@article {pmid38621699,
year = {2024},
author = {Grisendi, A and Calzolari, M and Defilippo, F and Torri, D and Marzani, K and Dottori, M and Bonilauri, P and Maioli, G},
title = {MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION OF AMBLYOMMA SCUTATUM (ACARI: IXODIDAE) ACCIDENTALLY INTRODUCED IN ITALY.},
journal = {The Journal of parasitology},
volume = {110},
number = {2},
pages = {155-158},
doi = {10.1645/20-69},
pmid = {38621699},
issn = {1937-2345},
abstract = {Eight ticks were found in Comacchio (FE), Italy parasitizing a young black iguana (Ctenosaura similis) that had been accidentally transported in a commercial plant container from Costa Rica. Specimens were identified morphologically as Amblyomma scutatum and then confirmed by the barcoding of the mitochondrial cytochrome c oxidase subunit 1 gene. Amblyomma scutatum is a common tick known to infest reptiles in Central America, Mexico, and Venezuela, but not in Europe. In Italy, the possibility for this tick to become endemic is unlikely because of the absence of its principal hosts. Nevertheless, this finding confirms the high risk of introducing exotic species that is linked with global commerce and therefore the need for veterinary control of shipments.},
}

@article {pmid38621643,
year = {2024},
author = {Liu, Z and Zeng, H and Xiang, H and Deng, S and He, X},
title = {Achieving single-cell-resolution lineage tracing in zebrafish by continuous barcoding mutations during embryogenesis.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.04.004},
pmid = {38621643},
issn = {1673-8527},
abstract = {Unraveling the lineage relationships of all descendants from a zygote is fundamental to advancing our understanding of developmental and stem cell biology. However, existing cell barcoding technologies in zebrafish lack the resolution to capture the majority of cell divisions during embryogenesis. A recently developed method, SMALT, successfully reconstructed high-resolution cell phylogenetic trees for Drosophila melanogaster. Here, we implement the SMALT system in zebrafish, recording a median of 14 substitution mutations on a one-kilobase-pair barcoding sequence for one-day post-fertilization embryos. Leveraging this system, we reconstruct four cell lineage trees for zebrafish fin cells, encompassing both original and regenerated fin. Each tree consists of hundreds of internal nodes with a median bootstrap support of 99%. Analysis of the obtained cell lineage trees reveals that regenerated fin cells mainly originate from cells in the same part of the fins. Through multiple times sampling germ cells from the same individual, we confirm the stability of the germ cell pool and the early separation of germ cell and somatic cell progenitors. Our system offers the potential for reconstructing high-quality cell phylogenies across diverse tissues, providing valuable insights into development and disease in zebrafish.},
}