bluuebunny/crossref_metadata_2025_split huggingface dataset:
BetaAlign: a deep learning approach for multiple sequence alignment
Authors: Dotan Edo , Wygoda Elya , Ecker Noa , Alburquerque Michael , Avram Oren , Belinkov Yonatan , Pupko Tal 
Published: March 2024

AbstractThe multiple sequence alignment (MSA) problem is a fundamental pillar in bioinformatics, comparative genomics, and phylogenetics. Here we characterize and improve BetaAlign, the first deep learning aligner, which substantially deviates from conventional algorithms of alignment computation. BetaAlign draws on natural language processing (NLP) techniques and trains transformers to map a set of unaligned biological sequences to an MSA. We show that our approach is highly accurate, comparable and sometimes better than state-of-the-art alignment tools. We characterize the performance of BetaAlign and the effect of various aspects on accuracy; for example, the size of the training data, the effect of different transformer architectures, and the effect of learning on a subspace of indel-model parameters (subspace learning). We also introduce a new technique that leads to improved performance compared to our previous approach. Our findings further uncover the potential of NLP-based approaches for sequence alignment, highlighting that AI-based methodologies can substantially challenge classic tasks in phylogenomics and bioinformatics.
Fat body lipogenic capacity in honey bee workers is affected by age, social role, and dietary protein
Authors: Scofield Sebastian , Amdam Gro. V. 
Published: March 2024

AbstractAll organisms need to balance processes that consume energy against those that produce energy. With an increase in biological complexity over evolutionary time, regulation of this balance has become much more complex, resulting in specialization of metabolic tasks between organelles, cells, organs, and in the case of eusocial organisms, between the individuals who comprise the ‘superorganism.’ Exemplifying this, nurse honey bees maintain high abdominal lipids, while foragers have very low lipid stores, likely contributing to efficient performance of their social role, and thus to colony fitness. The proximate mechanisms responsible for these metabolic differences remain poorly understood. Here, we investigated the effects of age, age class, and dietary macronutrients on the abdominal activity of fatty acid synthase (FAS), the enzyme responsible forde novosynthesis of fatty acids. We found that FAS activity declines as bees age past peak nursing age. Feeding both nurses and foragers carbohydrates increased FAS activity compared with starved bee, but, whether fed or starved, nurses had much higher FAS activity than similarly treated foragers, implicating reduced lipid synthesis as one component of foragers’ low lipid stores. Finally, we used artificial diets with different amounts of protein and fat to precociously induce low, forager-like FAS activity levels in nurse-age bees deprived of protein. We speculate that reduced protein appetite and consumption during the nurse-forager transition is responsible for suppressed lipid synthesis in foragers.Summary statementHoney bee workers show reduced fat synthesis capacity as they age and leave the nest to forage. Young bees deprived of protein have low, forager-like fat synthesis capacity.
A domain-swapped CaMKII conformation facilitates linker-mediated allosteric regulation
Authors: Nguyen Bao V. , Özden Can , Dong Kairong , Torres-Ocampo Ana P. , Dziedzic Noelle , Flaherty Daniel , Huang Jian , Sankura Saketh , Abromson Nikki Lyn , Tomchick Diana R. , Chen Jianhan , Garman Scott C , Stratton Margaret M 
Published: March 2024

ABSTRACTCa2+signaling plays a key role in physiological processes such as memory formation and cardiac function. Ca2+/calmodulin-dependent protein kinase II (CaMKII) is the primary kinase that responds to Ca2+inputs in these cells. There are four CaMKII paralogs in mammals which are alternatively spliced in the variable linker region to create upwards of 70 different variants. In this study, we systematically studied different linker regions and determined that the position of charged residues within the linker region modulates the Ca2+/CaM sensitivity of the holoenzyme. We present an X-ray crystal structure of full-length CaMKIIδ that shows a domain-swapped conformation of the subunits within the dodecameric holoenzyme. In this structure, the kinase domain of one subunit is docked onto the hub domain of a different subunit, providing an additional interface within the holoenzyme. Mutations at the equatorial and lateral interfaces revealed that the kinase-hub interaction dissociates as the hub-hub interfaces are disturbed, which led alterations in the stoichiometry of CaMKII holoenzyme and Ca2+/CaM sensitivity. Molecular dynamics simulations of linker-containing domain-swapped and non-domain-swapped CaMKIIs reveal that the domain-swapped configuration facilitates an interaction between the calmodulin binding domain and the variable linker region, such that dynamic electrostatic forces between charges on these segments can modulate the equilibrium between the compact and extended conformational states of the holoenzyme. Small angle X-ray scattering data confirms that a negatively charged linker CaMKII holoenzyme adopts a more compact conformation compared to a positively charged linker. These data support a model where patches of charged linker residues interact with the calmodulin binding domain to allosterically regulate sensitivity to Ca2+/CaM. Our findings provide a new framework for understanding CaMKII structure and allosteric regulation by the variable linker region in Ca2+-sensitive cells.
Muscle-resident mesenchymal progenitors sense and repair peripheral nerve injury via the GDNF-BDNF axis
Authors: Yoo Kyusang , Jo Young-Woo , Yoo Takwon , Hann Sang-Hyeon , Park Inkuk , Kim Yea-Eun , Kim Ye Lynne , Rhee Joonwoo , Song In-Wook , Kim Ji-Hoon , Baek Daehyun , Kong Young-Yun 
Published: March 2024

AbstractFibro-adipogenic progenitors (FAPs) are muscle-resident mesenchymal progenitors that can contribute to muscle tissue homeostasis and regeneration, as well as postnatal maturation and lifelong maintenance of the neuromuscular system. Recently, traumatic injury to the peripheral nerve was shown to activate FAPs, suggesting that FAPs can respond to nerve injury. However, questions of how FAPs can sense the anatomically distant peripheral nerve injury and whether FAPs can directly contribute to nerve regeneration remained unanswered. Here, utilizing single-cell transcriptomics and mouse models, we discovered that a subset of FAPs expressing GDNF receptorsRetandGfra1can respond to peripheral nerve injury by sensing GDNF secreted by Schwann cells. Upon GDNF sensing, this subset becomes activated and expressesBdnf. FAP-specific inactivation ofBdnf(Prrx1Cre;Bdnffl/fl) resulted in delayed nerve regeneration owing to defective remyelination, indicating that GDNF-sensing FAPs play an important role in the remyelination process during peripheral nerve regeneration. In aged mice, significantly reducedBdnfexpression in FAPs was observed upon nerve injury, suggesting the clinical relevance of FAP-derived BDNF in the age-related delays in nerve regeneration. Collectively, our study revealed the previously unidentified role of FAPs in peripheral nerve regeneration, and the molecular mechanism behind FAPs’ response to peripheral nerve injury.
The regulatory architecture of the primed pluripotent cell state
Authors: Li Bo I. , Alvarez Mariano J. , Zhao Hui , Chirathivat Napon , Califano Andrea , Shen Michael M. 
Published: March 2024

SummaryAlthough numerous studies have focused on defining transcriptional cell states in normal and disease contexts, the gene regulatory architecture that governs and defines specific mammalian cell states remains poorly understood. Here we present an integrative computational and experimental systems biology approach to elucidate the regulatory architecture of a conserved cell state of critical importance in development and stem cell biology, namely primed state pluripotency. We have used an unbiased approach to analyze protein activity profiles from mouse epiblast stem cells (EpiSCs), leading to identification and experimental confirmation of 132 transcription factors that are master regulators (MRs) of primed state pluripotency. These MRs include known as well as novel factors, many of which were further validated for their role in lineage-specific differentiation using CRISPR-mediated functional assays. To assemble a comprehensive regulatory network, we silenced each of the 132 MRs to assess their effects on the other MRs and their transcriptional targets, yielding a network of 1,273 MR→MR interactions. Network architecture analyses revealed four functionally distinct MR modules (communities), largely independent of lineage-specific differentiation, and identified key Speaker and Mediator MRs based on their hierarchical rank and centrality in mediating information flow in the pluripotent cell. Taken together, our findings elucidate the de-centralized logic of a “communal interaction” model in which the balanced activities of four MR communities maintain pluripotency, and define the primed pluripotent cell state in terms of its transcriptional regulatory network.
Longitudinal analysis of Flower-dependent cell competition fitness markers inDrosophila melanogaster
Authors: Marques-Reis Mariana , Hauert Barbara , Moreno Eduardo 
Published: March 2024

AbstractCell competition is a conserved phenomenon spanning from arthropods to humans. It involves the elimination of viable yet suboptimal “loser” cells when juxtaposed with their fitter “winner” counterparts. This process has received increased attention for its implications in cancer initiation and progression, neurodegeneration, and ageing.This study investigates the presence of the loser fitness fingerprint Flower LoseB (Fwe LB) and the fitness checkpoint Azot in the optic lobes over a period of 28 days. Notably, the absence of Azot is conventionally linked to the accumulation of loser cells over time. However, our investigation reveals that this accumulation is not perpetual and, intriguingly, Azot is not required for loser cell elimination in this context. Furthermore, we estimate that fewer than 50% of Fwe LB-expressing cells also express Azot and undergo apoptosis. Remarkably, our calculations also demonstrate that over 50% of cells undergoing apoptosis at any given time point are positive for the loser markers Fwe LB and Azot.This comprehensive analysis of fitness marker dynamics over a 28-day timeframe sheds new light on the intricate mechanisms governing Flower-dependent cell competition.
RNase L-induced bodies sequester subgenomic flavivirus RNAs and re-establish host RNA decay
Authors: Watkins J. Monty , Burke James M. 
Published: March 2024

SUMMARYSubgenomic flavivirus RNAs (sfRNAs) are structured RNA elements encoded in the 3’-UTR of flaviviruses that promote viral infection by inhibiting cellular RNA decay machinery. Herein, we analyze the production of sfRNAs using single-molecule RNA fluorescencein situhybridization (smRNA-FISH) and super-resolution microscopy during West Nile virus, Zika virus, or Dengue virus serotype 2 infection. We show that sfRNAs are initially localized diffusely in the cytosol or in processing bodies (P-bodies). However, upon activation of the host antiviral endoribonuclease, Ribonuclease L (RNase L), nearly all sfRNAs re-localize to antiviral biological condensates known as RNase L-induced bodies (RLBs). RLB-mediated sequestration of sfRNAs reduces sfRNA association with RNA decay machinery in P-bodies, which coincides with increased viral RNA decay. These findings establish a role of RLBs in promoting viral RNA decay, demonstrating the complex host-pathogen interactions at the level of RNA decay and biological condensation.HighlightsSingle-molecule imaging of sfRNA production and localizationsfRNAs localize to RNase L-induced bodiesRNase L-induced bodies sequester sfRNAs away from P-bodiesSequestration of sfRNAs by RNase L-induced bodies enhances decay of viral genomes
The Evolutionary Origins and Ancestral Features of Septins
Authors: Delic Samed , Shuman Brent , Lee Shoken , Bahmanyar Shirin , Momany Michelle , Onishi Masayuki 
Published: March 2024

ABSTRACTSeptins are a family of membrane-associated cytoskeletal GTPases that play crucial roles in various cellular processes, such as cell division, phagocytosis, and organelle fission. Despite their importance, the evolutionary origins and ancestral function of septins remain unclear. In opisthokonts, septins form five distinct groups of orthologs, with subunits from multiple groups assembling into heteropolymers, thus supporting their diverse molecular functions. Recent studies have revealed that septins are also conserved in algae and protists, indicating an ancient origin from the last eukaryotic common ancestor. However, the phylogenetic relationships among septins across eukaryotes remained unclear. Here, we expanded the list of non-opisthokont septins, including previously unrecognized septins from rhodophyte red algae and glaucophyte algae. Constructing a rooted phylogenetic tree of 254 total septins, we observed a bifurcation between the major non-opisthokont and opisthokont septin clades. Within the non-opisthokont septins, we identified three major subclades: Group 6 representing chlorophyte green algae (6A mostly for species with single septins, 6B for species with multiple septins), Group 7 representing algae in chlorophytes, heterokonts, haptophytes, chrysophytes, and rhodophytes, and Group 8 representing ciliates. Glaucophyte and some ciliate septins formed orphan lineages in-between all other septins and the outgroup. Combining ancestral-sequence reconstruction and AlphaFold predictions, we tracked the structural evolution of septins across eukaryotes. In the GTPase domain, we identified a conserved GAP-like arginine finger within the G-interface of at least one septin in most algal and ciliate species. This residue is required for homodimerization of the singleChlamydomonasseptin, and its loss coincided with septin duplication events in various lineages. The loss of the arginine finger is often accompanied by the emergence of the α0 helix, a known NC-interface interaction motif, potentially signifying the diversification of septin-septin interaction mechanisms from homo-dimerization to hetero-oligomerization. Lastly, we found amphipathic helices in all septin groups, suggesting that curvature-sensing is an ancestral trait of septin proteins. Coiled-coil domains were also broadly distributed, while transmembrane domains were found in some septins in Group 6A and 7. In summary, this study advances our understanding of septin distribution and phylogenetic groupings, shedding light on their ancestral features, potential function, and early evolution.
Heart failure admission characteristics in women with a history of sexual or physical abuse: a case-control study
Authors: Chan Alicia , Cosh Suzanne M. , Horowitz John , Tully Phillip J. 
Published: March 2024

ABSTRACTIntroductionAn emerging body of epidemiological evidence links a history of exposure to sexual and physical abuse or assault with an increased risk of developing cardiovascular disease. Understanding adverse physical health outcomes including heart failure (HF) in persons exposed to sexual and physical abuse is of particular importance to help improve multidisciplinary approaches to mental and physical wellbeing, including cardiovascular management, among vulnerable populations.MethodsThis case-control study was performed at a tertiary hospital in metropolitan South Australia. At index HF admission 12 consecutive female patients with exposure to sexual and physical abuse or assault were identified from the trauma module of a structured psychiatric interview. Index admission data were classified into HF phenotype and aetiology using the criteria and definitions of the European Society of Cardiology. The presentation profile at index HF admission was compared to 12 gender and age-matched comparators.ResultsThe clinical characteristics at index admission showed that most patients presented with pulmonary rales, peripheral oedema, and pulmonary congestion (67-75%), with diuretics the most common intervention (75%). By comparison to the non-exposed group, we observed differences between groups in HF severity determined by New York Heart Association class, diastolic blood pressure (BP), and heart rate (HR) but not systolic BP, saturation of peripheral oxygen (Sp02) or HF phenotypes. There were no differences in troponin, creatinine, sodium, admission use of inotropes, vasodilators or diuretics, post-traumatic stress disorder or comorbidities between the exposed patients and age-matched female controls.ConclusionWomen with a history of experiencing sexual and physical abuse or assault presented with a unique HF admission profile characterised by lower BP and HR. The findings support previous work suggesting that persons experiencing sexual and physical abuse or assault have blunted cardiovascular reactivity to stressors such as hospital admission.
Unbiased metagenomic detection of RNA viruses for rapid identification of viral pathogens in clinical samples
Authors: Kappell Anthony D. , Scholes Amanda N. , Scholz Matthew B. , Keplinger Nicolette C. , Allen Leah W. , Murray Matthew C. , Ternus Krista L. , Hewitt F. Curtis 
Published: March 2024

AbstractUnbiased long read sequencing approaches for clinical metagenomic sample analysis holds enormous potential for pathogen detection, including improved detection of unknown, novel or emerging viruses. However, the rapid rate of development in nanopore sequencing and library preparation methods complicates the process of selecting a standardized method for unbiased RNA virus detection. Here, we evaluate multiple sequencing approaches to identify a workflow with sufficient sensitivity, limits of detection, and throughput for potential utilization in a clinical laboratory setting. Four separate library preparation methods for the Oxford Nanopore Technologies MinION sequencer are compared, including direct RNA, direct cDNA, rapid cDNA, and double stranded cDNA. We also establish that depletion of host RNA is not required and can be deleterious for viral RNA detection in some instances when using samples in viral transport media (VTM) or plasma. Using unbiased whole genome amplification following reverse transcription, we achieve limits of detection on the order of 1.95E03 GE/mL of Venezuelan Equine Encephalitis Virus (VEEV) spiked in human plasma. We also report initial detection of 5.43E06 GE/mL of coronavirus 229E spiked into VTM samples containing human background RNA which are expected to decrease significantly during upcoming testing. These metrics were achieved within a 6-plex multiplex reaction, illustrating the potential to increase throughput and decrease costs for relevant sample analysis. Data analysis was performed using EPI2ME Labs framework and open access tools that are readily accessible to most clinical laboratories. Taken together, this work describes an optimized method for unbiased nanopore sequencing and analysis of RNA viruses present in two common clinical matrices.
Validation of an unbiased metagenomic detection assay for RNA viruses in viral transport media and plasma
Authors: Kappell Anthony D. , Schulte Kathleen Q. , Scheuermann Elizabeth A. , Scholz Matthew B. , Keplinger Nicolette C. , Scholes Amanda N. , Wolt Taylor A. , June Viviana M. , Schulte Cole J. , Allen Leah W. , Ternus Krista L. , Hewitt F. Curtis 
Published: March 2024

AbstractUnbiased long read sequencing holds enormous potential for the detection of pathogen sequences in clinical samples. However, the untargeted nature of these methods precludes conventional PCR approaches, and the metagenomic content of each sample increases the challenge of bioinformatic analysis. Here, we evaluate a previously described novel workflow for unbiased RNA virus sequence identification in a series of contrived and real-world samples. The novel multiplex library preparation workflow was developed for the Oxford Nanopore Technologies (ONT) MinIONTMsequencer using reverse transcription, whole genome amplification, and ONT’s Ligation Sequencing Kit with Native Barcode Expansion. The workflow includes spiked MS2 Phage as an internal positive control and generates an 8-plex library with 6 samples, a negative control and agfptranscript positive control. Targeted and untargeted data analysis was performed using the EPI2ME Labs framework and open access tools that are readily accessible to most clinical laboratories. Contrived samples composed of common respiratory pathogens (Influenza A, Respiratory Syncytial Virus and Human Coronavirus 229E) in viral transport media (VTM) and bloodborne pathogens (Zika Virus, Hepatitis A Virus, Yellow Fever Virus and Chikungunya Virus) in human plasma were used to establish the limits of detection for this assay. We also evaluated the diagnostic accuracy of the assay using remnant clinical samples and found that it showed 100% specificity and 62.9% clinical sensitivity. More studies are needed to further evaluate pathogen detection and better position thresholds for detection and non-detection in various clinical sample metagenomic mixtures.
Prescribing of antipsychotics for people diagnosed with severe mental illness in UK primary care: A 20-year investigation of who receives treatment, with which agents, and at what doses
Authors: Richards-Belle Alvin , Launders Naomi , Hardoon Sarah , Man Kenneth K.C. , Bramon Elvira , Osborn David P.J. , Hayes Joseph F. 
Published: March 2024

ABSTRACTBackgroundContemporary data relating to antipsychotic prescribing in UK primary care for patients diagnosed with severe mental illness (SMI) are lacking.AimsTo describe contemporary patterns of antipsychotic prescribing in UK primary care for patients diagnosed with SMI.MethodsCohort study of patients with an SMI diagnosis (i.e., schizophrenia, bipolar disorder, other non-organic psychoses) first recorded in primary care between 2000-2017 derived from Clinical Practice Research Datalink. Patients were considered exposed to antipsychotics if prescribed at least one antipsychotic in primary care between 2000-2019. We compared characteristics of patients prescribed and not prescribed antipsychotics; calculated annual prevalence rates for antipsychotic prescribing; and computed average daily antipsychotic doses stratified by patient characteristics.ResultsOf 309,378 patients first diagnosed with an SMI in primary care between 2000-2017, 212,618 (68.7%) were prescribed an antipsychotic between 2000-2019. Antipsychotic prescribing prevalence was 426 (95% CI, 420-433) per 1,000 patients in the year 2000, reaching a peak of 550 (547-553) in 2016, decreasing to 470 (468-473) in 2019. The proportion prescribed antipsychotics was higher amongst patients diagnosed with schizophrenia (81.0%) than with bipolar disorder (64.6%) and other non-organic psychoses (65.7%). Olanzapine, quetiapine, risperidone, and aripiprazole accounted for 78.8% of all prescriptions. Higher mean olanzapine equivalent total daily doses were prescribed to patients with the following characteristics: schizophrenia diagnosis, ethnic minority status, male sex, younger age, and greater deprivation.ConclusionsAntipsychotic prescribing is dominated by olanzapine, quetiapine, risperidone, and aripiprazole. Two thirds of patients with diagnosed SMI were prescribed antipsychotics in primary care, but this proportion varied according to SMI diagnosis. There were disparities in both receipt and dose of antipsychotics across subgroups - further efforts are needed to understand why certain groups are prescribed higher doses and whether they require dose optimisation to minimise side effects.