bluuebunny/crossref_metadata_2025_split huggingface dataset:
A metagenomics approach to identification of eukaryotes in metazoan-associated microbiomes
Authors: Crouch Audra L. , Monsey Laine , Ramos Cameron , Anderson Matthew Z. 
Published: November 2023

ABSTRACTBackgroundMicrobial eukaryotes are integral components of the microbiome where they shape community composition and ecological interactions. However, the abundance and diversity of eukaryotic species within the microbiome, the ‘eukaryome’, remains poorly defined. These deficiencies arise from unresolved technical limitations in recovering DNA from microbial eukaryotes due to their relatively low abundance in most samples and resilience to extraction. To overcome these limitations, we developed an extraction protocol that specifically targets recovery of eukaryotic microbes from microbiome samples and allows for metagenomics sequencing of eukaryotic species.MethodsMicrobes were seeded in synthetic stool prior to DNA extraction to mimic microbiome samples from the gastrointestinal tract. Assessment of cell disruption was performed using intracellular staining with the azo dye trypan blue or quantification of DNA recovery. A mock microbial community of five bacteria and five eukaryotes was built to test the effectiveness of the full protocol by seeding stool with defined numbers of cells from each species.ResultsMechanical disruption efficiently released DNA from bacterial, fungal, and protozoan species where standard microbiome DNA extraction kits did not. Optimization of the bead beating parameters lysed >95% of fungal cells within synthetic stool samples. In a mixed bacteria- eukaryote sample, eukaryotic DNA could be further enriched by targeting methylated DNA for destruction with methyl-specific restriction endonucleases. Application of this approach to a defined community of 10 different microbes, five eukaryotes and five bacteria, seeded in synthetic stool demonstrated the success of this strategy by enriching for eukaryotes approximately 72-fold and producing a eukaryote-dominated DNA pool.ConclusionsOverall, development of a microbiome sample protocol that includes DNA extraction and enrichment from eukaryotic species will facilitate exploration of the eukaryome and its impact on human health.
Single-Molecule Direct RNA Sequencing Reveals the Shaping of Epitranscriptome Across Multiple Species
Authors: Xie Ying-Yuan , Zhong Zhen-Dong , Chen Hong-Xuan , Qiu Yuan-Tao , Ren Ze-Hui , Lan Ye-Lin , Wu Fu , Kong Jin-Wen , Luo Ru-Jia , Zhang Delong , Liu Biao-Di , Shu Yang , Yin Feng , Wu Jian , Li Zigang , Zhang Zhang , Luo Guan-Zheng 
Published: November 2023

AbstractN6-methyladenosine (m6A) is an essential RNA modification that regulates gene expression and influences diverse cellular processes. Yet, fully characterizing its transcriptome-wide landscape and biogenesis mechanisms remains challenging. Traditional next-generation sequencing (NGS) methods rely on short-reads aggregation, overlooking the inherent heterogeneity of RNA transcripts. Third-generation sequencing (TGS) platforms offer direct RNA sequencing (DRS) at the resolution of individual RNA molecules, enabling simultaneous detection of RNA modifications and RNA processing events. In this study, we introduce SingleMod, a deep learning model tailored for precise m6A modification mapping on individual RNA molecules from DRS data. Applying SingleMod to human cell lines, we systematically dissect the transcriptome-wide m6A landscape at single-molecule and single-base resolution, characterizing m6A heterogeneity in RNA molecules from the same transcript and revealing that multiple m6A sites on an RNA molecule can cumulatively influence its splicing and stability. Through comparative analyses across eight diverse species, we quantitatively elucidate three distinct m6A distribution patterns that suggest divergent regulatory mechanisms. This study provides a novel framework for understanding the shaping of epitranscriptome in a single-molecule perspective.
Do aposematic species have larger range sizes? A case study with Neotropical poison frogs
Authors: Silveira Priscila , Sousa Fernanda Gonçalves de , Böning Philipp , Maciel Natan M. , Stropp Juliana , Lötters Stefan 
Published: November 2023

ABSTRACTAimAposematic animals, i.e. those that are defended and warn potential predators through signals, are suggested to have resource-gathering advantages against non-aposematic ones. We here explore this in a biogeographic frame expecting that aposematic species are better dispersers, which translates into larger geographic range size.LocationSouth America.TaxonPoison frogs (Amphibia; Aromobatidae and Dendrobatidae).MethodsWe use 43 toxic and 26 non-toxic poison frog species from the lowlands only as representatives of aposematic and non-aposematic study organisms, respectively. Realized and potential geographic ranges are calculated using minimum convex polygon and species distribution modelling methods, respectively. Accounting for species body size and phylogeny, we test if both range and aposematism are correlated using linear mixed models.ResultsAposematic and non-aposematic species do neither differ in realized nor in potential geographic range size. There was no effect of body size.Main conclusionsThe role of aposematism yet is not as clear as suggested and determinants of poison frog range sizes are multifaceted. A more integrative approach is needed using information of behaviour, predation risk, and reproductive biology to assess the role of aposematism on observed species distributions. Such data are not yet available for most species, neither poison frogs nor other aposematic animals.
Genetic causes and genomic consequences of breakdown of distyly inLinum trigynum
Authors: Gutiérrez-Valencia Juanita , Zervakis Panagiotis-Ioannis , Postel Zoé , Fracassetti Marco , Losvik Aleksandra , Mehrabi Sara , Bunikis Ignas , Soler Lucile , Hughes P. William , Désamoré Aurélie , Laenen Benjamin , Abdelaziz Mohamed , Pettersson Olga Vinnere , Arroyo Juan , Slotte Tanja 
Published: November 2023

AbstractDistyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility (SI). Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly inLinum trigynum, which is closely related to distylousLinum tenue.Building on a high-quality genome assembly, we show thatL. trigynumharbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles inL. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylousPrimulaandFagopyrum,L. trigynumharbors no fixed loss-of-function mutations in coding sequences ofS-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating theS-linkedLtWDR-44candidate gene for male SI and/or anther height could underlie homostyly and self-compatibility (SC) inL. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate thatL. trigynumis highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative toL. tenue. Our analyses shed light on the loss of distyly inL. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.
Mode III tear resistance ofBombyx morisilk cocoons
Authors: Rehman Ateeq Ur , Koutsos Vasileios , Alam Parvez 
Published: November 2023

ABSTRACTThis paper concerns the tear properties and behaviour ofBombyx morisilk cocoons. The tear resistance of cocoon layers is found to increase progressively from the innermost layer to the outermost layer. Importantly, the increase in tear strength correlates with increased porosity, which itself affects fibre mobility. We propose a microstructural mechanism for tear failure, which begins with fibre stretching and sliding, leading to fibre piling, and eventuating in fibre fracture. The direction of fracture is then deemed to be a function of the orientation of piled fibres, which is influenced by the presence of junctions where fibres cross at different angles and which may then acts as nucleating sites for fibre piling. The interfaces between cocoon wall layers inBombyx moricocoon walls account for 38% of the total wall tear strength. When comparing the tear energies and densities ofBombyx moricocoon walls against other materials, we find that theBombyx moricocoon walls exhibit a balanced trade-off between tear resistance and lightweightness.
Whole-body positive synchronization pattern of metabolic transcriptomes
Authors: Sussman Ehud Z. , Mor Dana , Somekh Judith 
Published: November 2023

AbstractUnderstanding the relationship between transcriptomes in the entire body is crucial for comprehending health and disease. To achieve this, we have developed a framework that allows us to measure the general coordination pattern of functionally similar transcriptomes at a whole-body scale. Our approach employs meta-network level analysis to determine the interconnectivity level of metabolic co-expression modules throughout the body as opposed to randomly selected modules. We utilize dimensionality reduction of co-expression modules, inter-tissue connectivity, and clique community analysis. We applied our methodology to 19 distinct human tissues obtained from the GTEx project and detected 40/52 metabolic co-expression modules out of 609/652 cross-tissue generated modules in Cohort 1 and 2 respectively. We detected that the ratio of positive to negative inter-tissue co-expression of metabolic modules was significantly higher than control. We further validated these results for an additional cohort. Moreover, to detect a global concurrent synchronization pattern we performed graph theoretical analysis, specifically a clique community analysis of metabolic transcriptomes showing a significantly larger inter-tissue metabolic transcriptome community that control with a significantly higher connectivity for each metabolic module within the community. Additionally, we performed gene-level validation of our results. In summary, our findings reveal a significant global synchronization pattern of metabolic modules throughout the body. Our framework can be further used for other type of transcriptomes and serve as a measure detecting change in this global coordination pattern across conditions.
Machine learning approaches identify immunologic signatures of total and intact HIV DNA during long-term antiretroviral therapy
Authors: Semenova Lesia , Wang Yingfan , Falcinelli Shane , Archin Nancie , Cooper-Volkheimer Alicia D , Margolis David M , Goonetilleke Nilu , Murdoch David M , Rudin Cynthia D , Browne Edward P 
Published: November 2023

AbstractUnderstanding the interplay between the HIV reservoir and the host immune system may yield insights into HIV persistence during antiretroviral therapy (ART) and inform strategies for a cure. Here, we applied machine learning approaches to cross-sectional high-parameter HIV reservoir and immunology data in order to characterize host-reservoir associations and generate new hypotheses about HIV reservoir biology. High-dimensional immunophenotyping, quantification of HIV-specific T cell responses, and measurement of genetically intact and total HIV proviral DNA frequencies were performed on peripheral blood samples from 115 people with HIV (PWH) on long-term ART. Analysis demonstrated that both intact and total proviral DNA frequencies were positively correlated with T cell activation and exhaustion. Years of ART and select bifunctional HIV-specific CD4 T cell responses were negatively correlated with the percentage of intact proviruses. A Leave-One-Covariate-Out (LOCO) inference approach identified specific HIV reservoir and clinical-demographic parameters, such as age and biological sex, that were particularly important in predicting immunophenotypes. Overall, immune parameters were more strongly associated with total HIV proviral frequencies than intact proviral frequencies. Uniquely, however, expression of the IL-7 receptor alpha chain (CD127) on CD4 T cells was more strongly correlated with the intact reservoir. Unsupervised dimension reduction analysis identified two main clusters of PWH with distinct immune and reservoir characteristics. Using reservoir correlates identified in these initial analyses, decision tree methods were employed to visualize relationships among multiple immune and clinical-demographic parameters and the HIV reservoir. Finally, using random splits of our data as training-test sets, machine learning algorithms predicted with approximately 70% accuracy whether a given participant had qualitatively high or low levels of total or intact HIV DNA. The techniques described here may be useful for assessing global patterns within the increasingly high-dimensional data used in HIV reservoir and other studies of complex biology.
Building a barrier: investigating the defensive role of induced trichome production in herbicide exposed plants
Authors: Johnson Nia M , Baucom Regina S 
Published: November 2023

SummaryInduced plant defense is commonly hypothesized to be an adaptive response to environmental heterogeneity reflecting phenotypic costs and benefits. While various studies have explored the adaptability of induced trichomes in response to biotic factors, we have limited understanding of whether induced trichomes can be an adaptive defense strategy in the presence of novel anthropogenic environmental stressors, such as herbicide exposure.Using annual invasive weed velvetleaf (Abutilon theophrasti), we explore whether induced trichome production contributes to herbicide resistance and determine its impact on growth and fitness in the presence and absence of glyphosate (active ingredient in “Roundup”).We observed trichome traits (proportion of polymorphs and density) and found a significant tradeoff between constitutive and inducible strategies for total trichome density. We identified positive correlations between induced total trichome density and herbicide resistance as well as induced branched trichomes and herbicide resistance. Additionally, our selection analysis revealed positive linear selection acting upon induced increase of total trichome production and correlative selection favoring high induced trichome production and intermediate growth.Overall, our study indicates that induced trichome production may evolve as an adaptive defense strategy in agroecosystems and identifies significant constraints impacting the evolution of induced trichome defense.
Microbiota of laboratory channel catfish skin mucosa and aquaria water exposed to chloramine-T trihydrate
Authors: Kittel Elliott , Crosby Tina , Kocurek Brandon , Ottesen Andrea , Gieseker Charles 
Published: November 2023

AbstractHere, we describe the skin mucosa microbiome of channel catfish (Ictalurus punctatus) before and after exposure to chloramine-T. We also describe the aquaria water microbiome after the post-treatment period. These data provide a unique baseline description of skin mucosa and aquaria water microbiome from catfish reared in research aquaria.DisclaimerThe views expressed in this announcement are those of the authors and do not necessarily reflect the official policy of the Department of Health and Human Services, the U.S. Food and Drug Administration, or the U.S. Government. Reference to any commercial materials, equipment, or process does not in any way constitute approval, endorsement, or recommendation by the Food and Drug Administration
Outbreak of Highly Pathogenic Avian Influenza Virus H5N1 in Seals in the St. Lawrence Estuary, Quebec, Canada
Authors: Lair Stéphane , Quesnel Louise , Berhane Yohannes , Delnatte Pauline , Embury-Hyatt Carissa , Nadeau Marie-Soleil , Lung Oliver , Ferrell Shannon T. , Michaud Robert 
Published: November 2023

AbstractWe describe an unusual mortality event caused by a highly pathogenic avian influenza virus (HPAI) H5N1 clade 2.3.4.4b involving harbor (Phoca vitulina) and grey (Halichoerus grypus) seals in the St. Lawrence Estuary, Quebec, Canada. Fifteen (56%) of the seals submitted for necropsy were considered to be fatally infected by H5N1 containing fully Eurasian (EA) or Eurasian/North American genome constellation.Concurrently, presence of large numbers of bird carcasses infected with H5N1 at haul-out sites most likely contributed to the spill-over of infection to the seals. Histologic changes included meningoencephalitis (100%), fibrinosuppurative alveolitis, and multi-organ acute necrotizing inflammation. This is the first report of fatal H5N1 infection in pinnipeds in Canada, raising concerns about the expanding host of this virus, potential for establishment of a marine mammal reservoir, and the public health risks associated with spillover to mammals.
Non-destructive X-ray tomography of brain tissue ultrastructure
Authors: Bosch Carles , Aidukas Tomas , Holler Mirko , Pacureanu Alexandra , Müller Elisabeth , Peddie Christopher J. , Zhang Yuxin , Cook Phil , Collinson Lucy , Bunk Oliver , Menzel Andreas , Guizar-Sicairos Manuel , Aeppli Gabriel , Diaz Ana , Wanner Adrian A. , Schaefer Andreas T. 
Published: November 2023

AbstractMaps of dense subcellular features in biological tissue are the key to understanding the structural basis of organ function. Electron microscopy provides the necessary resolution, yet - as electrons penetrate samples for only a few 100s of nm - requires physical sectioning or ablation, which strongly challenges anatomical investigations of entire organs such as mammalian brains. As demonstrated for the engineering and physical sciences, X-ray nanotomography represents a promising alternative for ultrastructural 3d imaging without physical sectioning1–15. Leveraging the high brilliance of 4th generation synchrotron X-ray sources, it has the potential to non-destructively image mm³-sized samples at ultrastructural resolution within a few days16. A fundamental barrier to application to the life sciences is that, when irradiated with high-intensity X-rays, biological samples deform and ultimately disintegrate, prohibiting reaching sufficient resolution. Here, we introduce a combination of engineering solutions which defeat this barrier for X-ray ptychography17, a coherent diffractive X-ray imaging technique. The solutions include a cryogenic sample stage with high stability, high-precision interferometric positioners and tailored non-rigid tomographic reconstruction algorithms18. Furthermore, adapting an epoxy resin developed for the nuclear and aerospace industry, we demonstrate radiation resistance to X-ray doses exceeding 1010Gy. The resulting sub-40 nm isotropic resolution makes it possible to densely resolve axon bundles, boutons, dendrites and reliably identify synapses without physical sectioning. Moreover, we validated the X-ray technique using the current gold standard, namely focused ion beam scanning electron microscopy (FIB-SEM)19,20to demonstrate intact ultrastructure in tissue volumes first imaged by X-rays. This unlocks the potential of X-ray tomography for high-resolution tissue imaging, coinciding with the transformative advancements of next-generation synchrotrons worldwide21.
Lesions to different regions of frontal cortex have dissociable effects on voluntary persistence
Authors: van Geen Camilla , Chen Yixin , Kazinka Rebecca , Vaidya Avinash R. , Kable Joseph W. , McGuire Joseph T. 
Published: November 2023

AbstractDeciding how long to keep waiting for uncertain future rewards is a complex problem. Previous research has shown that choosing to stop waiting results from an evaluative process that weighs the subjective value of the awaited reward against the opportunity cost of waiting. In functional neuroimaging data, activity in ventromedial prefrontal cortex (vmPFC) tracks the dynamics of this evaluation, while activation in the dorsomedial prefrontal cortex (dmPFC) and anterior insula (AI) ramps up before a decision to quit is made. Here, we provide causal evidence of the necessity of these brain regions for successful performance in a willingness-to-wait task.28 participants with frontal lobe lesions were tested on their ability to adaptively calibrate how long they waited for monetary rewards. We grouped the participants based on the location of their lesions, which were primarily in ventromedial, dorsomedial, or lateral parts of their prefrontal cortex (vmPFC, dmPFC, and lPFC, respectively), or in the anterior insula. We compared the performance of each subset of lesion participants to behavior in a control group without lesions (n=18). Finally, we fit a newly developed computational model to the data to glean a more mechanistic understanding of how lesions affect the cognitive processes underlying choice.We found that participants with lesions to the vmPFC waited less overall, while participants with lesions to the dmPFC and anterior insula were specifically impaired at calibrating their level of persistence to the environment. These behavioral effects were accounted for by systematic differences in parameter estimates from a computational model of task performance: while the vmPFC group showed reduced initial willingness to wait, lesions to the dmPFC/anterior insula were associated with slower learning from negative feedback.These findings corroborate the notion that failures of persistence can be driven by sophisticated cost-benefit analyses rather than lapses in self-control. They also support the functional specialization of different parts of the prefrontal cortex in service of voluntary persistence.