bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing the impact of whole genome duplication on gene expression and regulation during arachnid development
Authors: Aase-Remedios Madeleine E. , Leite Daniel J. , Janssen Ralf , McGregor Alistair P.
Published: December 2024

Whole genome duplication (WGD) generates new genetic material that can contribute to the evolution of the regulation of developmental processes and phenotypic diversification. A WGD occurred in an ancestor of arachnopulmonates (spiders, scorpions, and their relatives), which provides an important independent comparison to WGDs in other animal lineages like those in vertebrates and horseshoe crabs. After WGD, arachnopulmonates retained many duplicated copies (ohnologues) of developmental genes including clusters of homeobox genes, many of which have been inferred to have undergone subfunctionalisation. However, there has been little systematic analysis of gene regulatory sequences and comparison of the expression of ohnologues versus their single-copy orthologues between arachnids. Here we compare the regions of accessible chromatin and gene expression of ohnologues and single-copy genes during three embryonic stages between an arachnopulmonate arachnid, the spiderParasteatoda tepidariorum, and a non-arachnopulmonate arachnid, the harvestmanPhalangium opilio. We found that the expression of each spider ohnologue was lower than their single-copy orthologues in the harvestman providing evidence for subfunctionalisation. However, this was not reflected in a reduction in peaks of accessible chromatin because both spider ohnologues and single-copy genes had more peaks than the harvestman genes. We also found peaks of open chromatin that increased in the late stage associated with activation of genes expressed later during embryogenesis in both species. Taken together, our study provides the first genome-wide comparison of gene regulatory sequences and gene expression in arachnids and thus provides new insights into the impact of the arachnopulmonate WGD.

Significance statement

The comparison of independent WGD events is essential to understanding their evolutionary outcomes. Here we examine gene expression and chromatin accessibility during the development of two arachnids, one of which underwent an ancient WGD. Our data provide the first direct comparison of the regulation of ohnologues and single-copy genes in arachnids.
Standardized methods for rearing a moth larva,Manduca sexta, in a laboratory setting
Authors: Spencer Emma K. , Miller Craig R. , Bull James
Published: December 2024

The larval tobacco hornworm,Manduca sexta, has been used in a laboratory setting for physiological studies and for pathogen virulence studies. This moth offers a much larger size than the commonly used wax moth (Galleria mellonella), and it can thus be used for a greater variety of assays, such as repeated sampling of the same individual, growth measurements, and tissue sampling. Yet their occasional use in research has led to a minimally documented set of rearing methods. To facilitate further adoption of this insect model, we expanded on previously reported protocols and developed our own rearing methods, which we report here. Our protocol requires little specialized equipment, with a cost less than $100/month for the feeding and maintenance of a laboratory colony of about five hundred larvae of differing instar phases. The low cost generalized equipment and supplies, and the simplification of the standardized protocols allows for an easy entry point for rearing tobacco hornworm populations. We also describe a few methods that are relevant to the uses of these organisms as infection models.
Syngap1 and the development of murine neocortical progenitor cells
Authors: Barão Soraia , Hong Ingie , Müller Ulrich , Huganir Richard L.
Published: December 2024

SYNGAP1 is a major regulator of synaptic plasticity through its interaction with synaptic scaffold proteins and modulation of Ras and Rap GTPase signaling pathways.SYNGAP1mutations in humans are often associated with intellectual disability, epilepsy, and autism spectrum disorder.Syngap1heterozygous loss-of-function results in impaired LTP, premature maturation of dendritic spines, learning disabilities and seizures in mice. More recently, SYNGAP1 was shown to influence cortical neurogenesis and the proliferation of progenitors in human organoids. Here, we show that the absence or haploinsufficiency ofSyngap1does not influence the properties of neocortical progenitors and their cellular output in mice. This discrepancy highlights potential species-specific or methodological differences and raises important questions about the broader applicability of SYNGAP1’s role in neurogenesis.
Defining the molecular impacts of Humalite application on field-grown wheat (Triticum aestivumL.) using quantitative proteomics
Authors: Grubb Lauren E. , Talasila Mohana , Gorim Linda Y. , Uhrig R. Glen
Published: December 2024

Increasing global food production demands have resulted in increased fertilizer usage, causing detrimental environmental impacts. Biostimulants, such as humic substances, are currently being applied as a strategy to increase plant nutrient-use efficiency and minimize environmental impacts within cropping systems. Humalite is a unique, naturally occurring coal-like substance found in deposits across southern Alberta. These deposits contain exceptionally high ratios of humic acids (>70%) and micronutrients due to their unique freshwater depositional environment. Humalite has begun to be applied to fields based on scientific data suggesting positive impacts on crop growth, yield and nutrient usage; however, little is known about the underlying molecular mechanisms of Humalite. Here, we report a quantitative proteomics approach to identify systems-level molecular changes induced by the addition of different Humalite application rates in field-grown wheat (Triticum aestivumL.) under three urea fertilizer application rates. In particular, we see wide-ranging abundance changes in proteins associated with several metabolic pathways and growth-related biological processes that suggest how Humalite modulates the plant molecular landscape. Overall, our results provide new, functional information that will help better inform agricultural producers on optimal biostimulant and fertilizer usage.
The impact of subunit type, alternative splicing, and auxiliary proteins on AMPA receptor trafficking
Authors: Couch Tyler , McCullock Tyler W. , MacLean David M.
Published: December 2024

AMPA receptors underlie fast excitatory synaptic transmission in the mammalian nervous system and are critical for the expression of synaptic plasticity. Four genes encode the AMPA subunits, each subject to RNA editing and alternative splicing at multiple positions. In addition, each tetrameric AMPA receptor can harbor up to four auxiliary proteins, of which there are multiple types. Subunit type, alternative splicing, and auxiliary proteins are all known to affect AMPA receptor gating and trafficking. However, determining which factors dominate AMPA receptor trafficking requires high throughput assessment of trafficking across multiple conditions. Here, we deploy two such methods to assess the relative contribution of AMPA subunit type (GluA1 versus GluA2), alternative splicing (flip versus flop), and various transmembrane AMPA receptor regulatory proteins (TARPs) to AMPA receptor trafficking. We find that subunit type is the most important factor, with GluA2 showing much better surface expression than GluA1, and alternative splicing plays a secondary role, with flip subunits consistently outperforming flop variants in surface expression across all conditions. Type 1 TARPs (γ2-4 and γ8) enhance surface trafficking, while Type 2 TARPs (γ5 and γ7) reduced surface expression, although we could not detect differences within each type. These data will be a helpful resource in comparing surface expression across a variety of AMPA receptor compositions. Our assays will also enable high throughput assessment of novel disease-associated mutations, chimeras, and auxiliary and chaperone proteins.
Heterologous immunization strategy developed broadly reactive human monoclonal antibodies against the BK virus
Authors: Duty J. Andrew , Kraus Thomas , Kumar Madhu , Tortorella Nicolo A. , Jimoh Tajudeen O. , Pastrana Diana V. , Buck Christopher B. , Moran Thomas , Tortorella Domenico
Published: December 2024

BK polyomavirus (BKV) causes polyomavirus-associated nephropathy (PyVAN) and polyomavirus-associated hemorrhagic cystitis (PyVHC) following kidney transplantation and allogeneic hematopoietic stem cell transplantation (HST). BKV strains fall into four distinct genotypes (BKV-I, -II, -III, and -IV) with more than 80% of individuals are seropositive against BKV-I genotype, while the seroprevalence of the other four genotypes is lower. PyVAN and PyVHC occurs in immunosuppressed (e.g. transplant recipients) or immunomodulated (e.g. pregnant women) individuals. In the case of transplant patients, the sole treatment is to reduce immunosuppression, which increases the chance of graft failure. Multiple investigations have shown that polyclonal antibodies have a role in preventing or treating BKV-mediated sickness, implying that a broadly reactive monoclonal antibody (mAb) regimen targeting BKV could be used to limit virus propagation in varied patient populations. Thus, we utilized a heterologous immunization strategy using BKV genotype I-IV major capsid protein VP1 DNA in transgenic VelocImmune@ mice to generate broadly reactive anti-BKV antibodies. Hybridoma clones from the immunized mice were screened using high-throughput binding assays against VP1 of the various BK genotypes. The binding clones were then assessed for neutralization of BKV pseudoviruses consisting of the VP1 protein of the BKV-I, -II, -III, or -IV genotypes. Overall, the screening identified more than 170 genotype-specific mAbs, as well as 15 broadly cross-neutralizing mAbs against BKV-I, -II, -III, and - IV PsVs. The unique panel of broadly neutralizing mAbs could be utilized prophylactically or therapeutically to prevent or treat BKV-induced illnesses.
Associations of Cardiovascular-Kidney-Metabolic syndrome with premature mortality and life expectancies in US adults: a cohort study
Authors: Lei Lubi , Li Jingkuo , Wang Wei , Yu Yanwu , Pu Boxuan , Peng Yue , Zhang Lihua , Guo Yuanlin
Published: December 2024

Background

The American Heart Association recently updated the Cardiovascular-Kidney-Metabolic (CKM) Health advisory, proposing a new framework for defining, staging, and predicting CKM risk. However, the prevalence and adverse effects of CKM stages remain insufficiently characterized.

Methods

We analyzed data from the National Health and Nutrition Examination Survey (NHANES) (1999–2018), including 18,350 US adults aged 20– 79 years. CKM syndrome encompasses subclinical or clinical cardiovascular disease (CVD), chronic kidney disease (CKD), and metabolic risk factors. Participants were categorized into four CKM stages based on clinical severity. We assessed associations of CKM stages with mortality risk and life expectancy.

Results

Only 12.9% of participants were classified as CKM stage 0. The prevalence of CKM stages 1, 2, 3, and 4 was 23.1%, 53.6%, 3.6%, and 6.7%, respectively. Compared to CKM stage 0, individuals in stage 4 had a markedly higher risk of all-cause mortality (HR: 4.30, 95% CI: 2.95– 6.26) and lost 15.5 (12.5–19.8) years of life at age 50. Sex and racial/ethnic disparities were also observed.

Conclusions

Higher CKM stages were strongly associated with increased mortality and reduced life expectancy. Our findings underscore the urgent need for enhanced CKM health management, social support, and policy interventions.

Key Messages

What is already known on this topic

Metabolic disorders, chronic kidney disease, and cardiovascular diseases are significantly associated with premature mortality. By taking into account the overlaps between cardiovascular-kidney-metabolic (CKM) syndrome, it is possible to improve risk stratification and employ an integrated approach to multimorbidity management.

What this study adds?

Only 12.6% of individuals had no CKM conditions, whereas approximately 50% of individuals had CKM stage 2, encompassing metabolic disorders, chronic kidney disease, or a combination of both.

The estimated life expectancy of individuals with CKM stage 4 was 15.5 years lower than that of individuals with CKM stage 0 at the age of 50.

How this study might affect research, practice or policy?

Our results indicate that the CKM condition is prevalent among US adults. We advocate the implementation of the new staging system for the prevention and treatment of CKM syndrome.

Life expectancy is reduced in adults who have a combination of metabolic risk factors, chronic kidney disease, or cardiovascular disease. We highlight the importance of incorporating a people-centered approach that includes the development of social support and policy, the integration of CKM health multidisciplinary management, and the enhancement of obesity management.
Attitudes towards deprescribing in patients with multimorbidity and polypharmacy in primary care
Authors: Shantsila Eduard , Woodall Alan , Mair Frances S , Abuzour Aseel S , Bollegala Danushka , Cant Harriet , Clegg Andrew , Gabbay Mark , Griffiths Alan , Hama Layik , Harmsworth-King James , Jones Benedict , Leeming Gary , Lo Emma , Maskell Simon , O’Connell Maurice , Popoola Olusegun , Relton Samuel , Aslam Asra , Ruddle Roy A , Schofield Pieta , Sperrin Matthew , Van Staa Tjeerd , Wilson Samantha , Buchan Iain , Walker Lauren E
Published: December 2024

Background

Population ageing has led to an increase in multimorbidity and polypharmacy. Some medications may need to be stopped, but patient attitudes towards deprescribing are poorly understood. This study explores attitudes towards (de)prescribing in patients with multimorbidity in the UK primary care.

Methods

Patients with multimorbidity were invited to complete the Revised Patients’ Attitudes Towards Deprescribing (rPATD) Questionnaire using an Evergreen Life’s Personal Health Record App (Manchester, UK). The responses were linked to electronic health records. Anonymised data were analysed in a trusted research environment (University of Liverpool) for group comparisons and using multivariable logistic regression to identify factors associated with satisfaction with current medications.

Results

A total 1,019 patients participated in the study (n=365 aged <65, 30% males; n=654 ≥65, 57% males). Most patients were satisfied with their current medications (74% aged <65, 70% aged ≥65) but were willing to stop one or more of their regular medicines if their doctor said it was possible (82%, 68% accordingly). Polypharmacy, use of antihypertensive drugs, and antidepressants were associated with patient-reported burden in taking medicines. Frailty did not influence patient deprescribing attitudes. Patients who were satisfied with current medications had fewer medications. Independent predictors of satisfaction with current medications were higher total involvement and appropriateness scores, and lower total burden score.

Conclusions

Most patients with multimorbidity would consider stopping some of their medications, even when they are generally satisfied with the treatments they received. Frailty status does not imply willingness to stop medications. Clinicians should discuss medication deprescribing for shared decision.
Qualitative Evaluation of the Work Lifestyle-integrated Functional Exercise Program for Older Employees (wLiFE55+) from Participants’ Perspectives
Authors: Pfister Diana , Ritter Yvonne , Steckhan Greta M. , Voelter-Mahlknecht Susanne , Weber Britta , Augustin Sankt , Ellegast Rolf , Augustin Sankt , Gruber Markus , Schwenk Michael
Published: December 2024

Background

The rise in older employees and physical inactivity necessitates targeted health and exercise promotion approaches. Physical training has positive health effects; however, traditional offerings are often underutilized due to time constraints or lack of motivation. The wLiFE55+ program offers a promising approach by integrating neuromotor, strength, and physical activity activities into daily routines with minimal time commitment. There is a high demand for workplace physical activity intervention (WPAI) with sustainable implementation. This study evaluated the wLiFE55+ program, designed for employees aged 55+, focusing on (1) participants’ perspectives on its components and (2) gathering insights for further development.

Methods

The wLiFE55+ program was piloted in a four-week study with a pre-post design. Participants attended four personal trainer sessions and integrated neuromotor, strength, and physical activities into their daily routines. Two focus groups (n=8) were conducted post-program. Half of the focus group participants (mean age 58.5 years, SD = 3.1) were female (5 full-time, 3 part-time), with low to moderate physical activity levels at work and varying functional performance. Audio recordings were transcribed and analyzed using deductive qualitative content analysis. Participants’ statements were categorized into predefined categories, creating a structured analysis system. Three main categories were applied to the transcripts.

Results

The focus groups demonstrated a balanced distribution of speech contributions, with an average participation rate of 12.5% per participant. In total, 313 statements were categorized into three main areas: “Overall Program” (59), “Program Content” (137), and “Behavioral Change” (117). Participant feedback highlighted requests for more practice time, targeted communication, and precise feedback about progress (“Overall Program”). Personal trainer support and tailoring of activities were evaluated positively (“Program Content”). High motivation existed at the start of the study but challenges in executing the program at the workplace were reported (“Behavioral Change”).

Conclusion

Overall, the wLiFE55+ program was well-received as a workplace physical activity intervention (WPAI), particularly for the support provided by personal trainers, the activities included, and participants’ progress. The wLiFE55+ program has shown potential as a WPAI, and areas for improvement were identified, such as more communication, digitizing the documentation process, and simplifying activity planning.
Modeling Insights into Potential Mechanisms of Opioid-Induced Respiratory Depression within Medullary and Pontine Networks
Authors: Olsen Wendy L. , Hayes John A. , Shuman Dale , Morris Kendall F. , Bolser Donald C.
Published: December 2024

The opioid epidemic is a pervasive health issue and continues to have a drastic impact on the United States. This is primarily because opioids cause respiratory suppression and the leading cause of death in opioid overdose is respiratory failure (i.e., opioid-induced respiratory depression, OIRD). Opioid administration can affect the frequency and magnitude of inspiratory motor drive by activating µ-opioid receptors that are located throughout the respiratory control network in the brainstem. This can significantly affect ventilation and blunt CO2responsiveness, but the precise neural mechanisms that suppress breathing are not fully understood. Previous research has suggested that opioids affect medullary and pontine inspiratory neuron activity by disrupting upstream elements within this circuit.

Inspiratory neurons within this network exhibit synchrony consistent with shared excitation from other neuron populations and recurrent mechanisms. One possible target for opioid suppression of inspiratory drive are excitatory synapses. Reduced excitability of these synaptic elements may result in disfacilitation and reduced synchrony among inspiratory neurons. Downstream effects of disfacilitation may result in abnormal output from phrenic motoneurons resulting in distressed breathing. We tested the plausibility of this hypothesis with a computational model of the respiratory network by targeting the synaptic excitability in fictive medullary and pontine populations. The synaptic conductances were systematically decreased while monitoring the overall respiratory motor pattern and aggregate firing rates of subsets of cell populations. Simulations suggest that highly selective, rather than generalized, actions of opioids on synapses within the inspiratory network may account for different observed breathing mechanics.
Post-transcriptional modifications on tRNA fragments confer functional changes to high-density lipoproteins in atherosclerosis
Authors: Semler Elizabeth M. , Michell Danielle L. , Kingsley Philip J. , Massick Clark , Ramirez Marisol A. , Castleberry Mark A. , Doran Amanda C. , Carr John J. , Marnett Lawrence J. , Sheng Quanhu , Linton MacRae F. , Vickers Kasey C.
Published: December 2024

Epitranscriptomic modifications on RNA play critical roles in stability, processing, and function, partly by influencing interactions with RNA-binding proteins and receptors. The role of post-transcriptional RNA modifications on cell-free non-coding small RNA (sRNA) remains poorly understood in disease contexts. High-density lipoproteins (HDL), which transport sRNAs, can lose their beneficial properties in atherosclerosis cardiovascular disease (ASCVD). We hypothesize that changes to regulatory modifications on HDL-sRNAs contribute to this dysfunction. To assess changes in HDL-sRNA modification status, HDL-derived RNA from healthy subjects and those with atherosclerotic lesion development were analyzed using LC-MS/MS and AlkB-facilitated RNA (de)Methylation Sequencing. ASVD-HDL showed an enrichment in modified nucleosides including m1A tRNA-derived sRNAs (tDRs), particularly tDR-ArgACG-1. Functional studies revealed that ASCVD-HDL induced cell adhesion genes, including TMEM123, in primary macrophages. Recombinant HDL loaded with m1A-tDR-ArgACG-1 induced immune signaling, and similarly upregulated TMEM123. These findings suggest HDL-delivered-m1A-tDR-ArgACG-1 act on adhesion genes and immune pathways, promoting macrophage activation.
Local Gradients of Functional Connectivity Enable Precise Fingerprinting of Infant Brains During Dynamic Development
Authors: Yuan Xinrui , Cheng Jiale , Hu Dan , Wu Zhengwang , Wang Li , Lin Weili , Li Gang
Published: December 2024

Brain functional connectivity patterns exhibit distinctive, individualized characteristics capable of distinguishing one individual from others, like fingerprint. Accurate and reliable depiction of individualized functional connectivity patterns during infancy is crucial for advancing our understanding of individual uniqueness and variability of the intrinsic functional architecture during dynamic early brain development, as well as its role in neurodevelopmental disorders. However, the highly dynamic and rapidly developing nature of the infant brain presents significant challenges in capturing robust and stable functional fingerprint, resulting in low accuracy in individual identification over ages during infancy using functional connectivity. Conventional methods rely on brain parcellations for computing inter-regional functional connections, which are sensitive to the chosen parcellation scheme and completely ignore important fine-grained, spatially detailed patterns in functional connectivity that encodes developmentally-invariant, subject-specific features critical for functional fingerprinting. To solve these issues, for the first time, we propose a novel method to leverage the high-resolution, vertex-level local gradient map of functional connectivity from resting-state functional MRI, which captures sharp changes and subject-specific rich information of functional connectivity patterns, to explore infant functional fingerprint. Leveraging a longitudinal dataset comprising 591 high-resolution resting-state functional MRI scans from 103 infants, our method demonstrates superior performance in infant individual identification across ages. Our method has unprecedentedly achieved 99% individual identification rates across three age-varied sub-datasets, with consistent and robust identification rates across different phase encoding directions, significantly outperforming atlas-based approaches with only around 70% accuracy. Further vertex-wise uniqueness and differential power analyses highlighted the discriminative identifiability of higher-order functional networks. Additionally, the local gradient-based functional fingerprints demonstrated reliable predictive capabilities for cognitive performance during infancy. These findings suggest the existence of unique individualized functional fingerprints during infancy and underscore the potential of local gradients of functional connectivity in capturing neurobiologically meaningful and fine-grained features of individualized characteristics for advancing normal and abnormal early brain development.
Cell type transcriptional identities are maintained in culturedex vivohuman brain tissue
Authors: McGinnis JP , Ortiz-Guzman Joshua , Mallannagari Sai , Guevara Maria Camila , Belfort Benjamin D. W. , Bao Suyang , Srivastava Snigdha , Morkas Maria , Ji Emily , Katlowitz Kalman A. , Addison Angela , Tantry Evelyne K. , Blessing Melissa M. , Mohila Carrie A. , Gadgil Nisha , McClugage Samuel G. , Bauer David F. , Whitehead William E. , Aldave Guillermo , Tanweer Omar , Jaleel Naser , Jalali Ali , Patel Akash J. , Sheth Sameer A. , Weiner Howard L. , Gopinath Shankar , Rao Ganesh , Harmanci Akdes Serin , Curry Daniel , Arenkiel Benjamin R.
Published: December 2024

It is becoming more broadly accepted that human-based models are needed to better understand the complexities of the human nervous system and its diseases. The recently developed human brain organotypic culture model is one highly promising model that requires the involvement of neurosurgeons and neurosurgical patients. Studies have investigated the electrophysiological properties of neurons in suchex vivohuman tissues, but the maintenance of other cell types within explanted brain remains largely unknown. Here, using single-nucleus RNA sequencing, we systematically evaluate the transcriptional identities of the various cell types found in six patient samples after fourteen days in culture (83,501 nuclei from day 0 samples and 45,738 nuclei from day 14 samples). We used two pediatric temporal lobectomy samples, an adult frontal cortex sample, two IDH wild-type glioblastoma samples, and one medulloblastoma sample. We found remarkably high correlations of day 14 transcriptional identities to day 0 tissue, especially in tumor cells (r = 0.90 to 0.93), though microglia (r = 0.86), oligodendrocytes (r = 0.80), pericytes (r = 0.77), endothelial cells (r = 0.78), and fibroblasts (r = 0.76) showed strong preservation of their transcriptional profiles as well. Astrocytes and excitatory neurons showed more moderate preservation (r = 0.66 and 0.47, respectively). Because the main difficulty with organotypic brain cultures is the acquisition of human tissue, which is readily available to neurosurgeons, this model is easily accessible to neurosurgeon-scientists and neurosurgeons affiliated with research laboratories. Broad uptake of this more representative model should prompt advances in our understanding of many uniquely human diseases, lead to more reliable clinical trial performance, and ultimately yield better therapies for our patients.
A deep learning method for predicting interactions for intrinsically disordered regions of proteins
Authors: Majila Kartik , Ullanat Varun , Viswanath Shruthi
Published: December 2024

Intrinsically disordered proteins or regions (IDPs/IDRs) adopt diverse binding modes with different partners, ranging from ordered to multivalent to fuzzy conformations in the bound state. Characterizing IDR interfaces is challenging experimentally and computationally. Alphafold-multimer and Alphafold3, the state-of-the-art structure prediction methods, are less accurate at predicting IDR binding sites at their benchmarked confidence cutoffs. Their performance improves upon lowering the confidence cutoffs. Here, we developed Disobind, a deep-learning method that predicts inter-protein contact maps and interface residues for an IDR and a partner protein, given their sequences. It outperforms AlphaFold-multimer and AlphaFold3 at multiple confidence cutoffs. Combining the Disobind and AlphaFold-multimer predictions further improves the performance. In contrast to most current methods, Disobind considers the context of the binding partner and does not depend on structures and multiple sequence alignments. Its predictions can be used to localize IDRs in integrative structures of large assemblies and characterize and modulate IDR-mediated interactions.
The TUTase URT1 regulates the transcriptome of seeds and their primary dormancy
Authors: Peter Jackson , Roignant Jeanne , Sacharowski Sebastian , Ubrig Elodie , Lefèvre Benjamin , Swiezewski Szymon , Gagliardi Dominique , Zuber Hélène
Published: December 2024

RNA uridylation is a pervasive mechanism that regulates the degradation of eukaryotic mRNAs. In Arabidopsis, uridylation influences mRNA decay both by favoring 5’ to 3’ degradation and by preventing excessive deadenylation. Yet, the significance of mRNA uridylation during plant development remains largely unknown. Here, we adapted FLEP-seq2, a method based on nanopore sequencing, to generate a comprehensive inventory of mRNA uridylation events in different Arabidopsis tissues. We also evaluated the respective contribution of the two known Arabidopsis uridylyltransferases, URT1 and HESO1, in mRNA uridylation. Our transcriptome-wide analysis showed that, URT1 is the main enzyme responsible for mRNA uridylation, in all analyzed tissues, while HESO1 can marginally uridylate mRNAs. Importantly, our results revealed the singularity of mRNA uridylation pattern in seeds and the dual function of URT1-dependent uridylation in shaping the transcriptome during seed maturation. We propose that during seed maturation, URT1-dependent uridylation promotes the elimination of unnecessary translation-associated mRNAs, by facilitating their degradation, while also promoting the accumulation of mRNAs associated with the maturation program, by hindering their deadenylation. In line with its important function in shaping the seed transcriptome, our study also identifies URT1 as a novel regulator of seed dormancy. Overall, our study reveals the biological relevance of mRNA uridylation during seed maturation.
Tonic sound-evoked motility of cochlear outer hair cells in mice with impaired mechanotransduction
Authors: Dewey James B.
Published: December 2024

Cochlear outer hair cells (OHCs) transduce sound-induced vibrations of their stereociliary bundles into receptor potentials that drive changes in cell length. While fast, phasic OHC length changes are thought to underlie an amplification process required for sensitive hearing, OHCs also exhibit large tonic length changes. The origins and functional significance of this tonic motility are unclear. Here,in vivocochlear vibration measurements reveal tonic, sound-induced OHC motility in mice with stereociliary defects that impair mechanotransduction and eliminate cochlear amplification. Tonic motility in impaired mice was physiologically vulnerable but weakly related to any residual phasic motility, possibly suggesting a dissociation between the underlying mechanisms. Nevertheless, a simple model demonstrates how tonic responses in both normal and impaired mice can result from asymmetric mechanotransduction currents and be large even when phasic motility is undetectable. Tonic OHC responses are therefore not unique to sensitive ears, though their potential functional role remains uncertain.
Distinct Microbiomes Underlie Divergent Responses of Methane Emissions from Diverse Wetland soils to Oxygen Shifts
Authors: Reji Linta , Duan Jianshu , Myneni Satish , Zhang Xinning
Published: December 2024

Hydrological shifts in wetlands, a globally important methane (CH4) source, are critical constraints on CH4emissions and carbon-climate feedbacks. A limited understanding of how hydrologically driven oxygen (O2) variability affects microbial CH4cycling in diverse wetlands makes wetland CH4emissions uncertain. Transient O2exposure significantly stimulated anoxic CH4production in incubations ofSphagnumpeat from a temperate bog by enriching for polyphenol oxidizers and polysaccharide degraders, enhancing substrate flow toward methanogenesis under subsequent anoxic conditions. To assess whether shifts in soil microbiome structure and function operate similarly across wetland types, here we examined the sensitivity of different wetland soils to transient oxygenation. In slurry incubations ofSphagnumpeat from a minerotrophic fen, and sediments from a freshwater marsh and saltmarsh, we examined temporal shifts in microbiomes coupled with geochemical characterization of slurries and incubation headspaces. Oxygenation did not affect microbiome structure and anoxic CH4production in mineral-rich fen-origin peat and freshwater marsh soils. Key taxa linked to O2-stimulated CH4production in the bog-origin peat were notably rare in the fen-origin peat, supporting microbiome structure as a primary determinant of wetland response to O2shifts. In contrast to freshwater wetland experiments, saltmarsh geochemistry—particularly pH—and microbiome structure were persistently and significantly altered post-oxygenation, albeit with no significant impact on greenhouse gas emissions. These divergent responses suggest wetlands may be differentially resilient to O2fluctuations. With climate change driving greater O2variability in wetlands, our results inform mechanisms of wetland resiliency and highlight microbiome structure as a potential resiliency biomarker.
Quantitative Characterization and Prediction of the Binding Determinants and Immune Escape Hotspots for Groups of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling of the SARS-CoV-2 Spike Complexes with Antibodies
Authors: Alshahrani Mohammed , Parikh Vedant , Foley Brandon , Raisinghani Nishank , Verkhivker Gennady
Published: December 2024

The growing body of experimental and computational studies suggested that the cross-neutralization antibody activity against Omicron variants may be driven by balance and tradeoff of multiple energetic factors and interaction contributions of the evolving escape hotspots involved in antigenic drift and convergent evolution. However, the dynamic and energetic details quantifying the balance and contribution of these factors, particularly the balancing nature of specific interactions formed by antibodies with the epitope residues remain scarcely characterized. In this study, we performed molecular dynamics simulations, ensemble-based deep mutational scanning of SARS-CoV-2 spike residues and binding free energy computations for two distinct groups of broadly neutralizing antibodies : E1 group (BD55-3152, BD55-3546 and BD5-5840) and F3 group (BD55-3372, BD55-4637 and BD55-5514). Using these approaches, we examine the energetic determinants by which broadly potent antibodies can largely evade immune resistance. Our analysis revealed the emergence of a small number of immune escape positions for E1 group antibodies that correspond to R346 and K444 positions in which the strong van der Waals and interactions act synchronously leading to the large binding contribution. According to our results, E1 and F3 groups of Abs effectively exploit binding hotspot clusters of hydrophobic sites critical for spike functions along with selective complementary targeting of positively charged sites that are important for ACE2 binding. Together with targeting conserved epitopes, these groups of antibodies can lead to the expanded neutralization breadth and resilience to antigenic shift associated with viral evolution. The results of this study and the energetic analysis demonstrate excellent qualitative agreement between the predicted binding hotspots and critical mutations with respect to the latest experiments on average antibody escape scores. We argue that E1 and F3 groups of antibodies targeting binding epitopes may leverage strong hydrophobic interactions with the binding epitope hotspots critical for the spike stability and ACE2 binding, while escape mutations tend to emerge in sites associated with synergistically strong hydrophobic and electrostatic interactions.
Simpler predictive models provide higher accuracy for ovarian cancer detection
Authors: Wood Derrick E. , Roy Joseph , Ballew Bari J.
Published: December 2024

Ovarian cancer remains a danger to women’s health, and accurate screening tests would likely increase survival. Two established protein biomarkers, CA125 and HE4, have been shown to work well in isolation, but achieve even higher accuracy when combined using logistic regression (LR). We show here that this LR-based combination of protein concentrations achieves high accuracy when distinguishing healthy samples from cancer samples (AUC = 0.99) and benign masses from cancer (AUC = 0.86). This approach exhibits superior performance on an external validation cohort compared to a more complex method, which was published with the dataset we use here and tested on the same data. While our method only uses proteins, the more complex method also uses features derived from cell-free DNA (cfDNA). We show that many of that method’s cfDNA features are affected by confounding technical variation, which impacts the previously reported results. Our results are in line with the principle that simpler machine learning models will tend to exhibit better generalizability on new data.
To Peck or Not To Peck: The influence of early-life social environment on response inhibition and impulsive aggression in Japanese quails
Authors: Vernouillet Alizée , Willcox Kathryn , Allaert Reinoud , Dewulf Anneleen , Zhang Wen , Troisi Camille A. , Knoch Sophia , Martel An , Lens Luc , Verbruggen Frederick
Published: December 2024

1

Deficits in response inhibition (i.e., the ability to suppress inappropriate responses) may contribute to increased impulsive aggression (i.e., unplanned behaviors that harm others). Since early-life environment might influence the development of response inhibition, it could also indirectly affect impulsive aggression. However, this relationship has rarely been directly examined. Here, we investigated whether response inhibition is associated with impulsive aggression and whether this relationship explains the effects of early-life social environments on impulsive aggression in Japanese quails (Coturnix japonica). Quails (n= 120) were raised in two social conditions: Small groups of five birds or Large groups of 15 birds. Response inhibition was assessed using the Barrier and Cylinder tasks, while impulsive aggression was measured in two contexts - within a group of five familiar individuals and in a dyad with an unfamiliar individual. We found that some aspects of response inhibition were related to impulsive aggression. Furthermore, quails reared in small groups showed significantly poorer response inhibition than those reared in large groups. Yet, impulsive aggression did not significantly differ between the two conditions. These findings suggest that, while impulsive aggression is partly related to response inhibition, other factors mitigate the effects of early social environments on its expression.
ThePorphyromonas gingivalislipid A 1-phosphatase LpxE has unique features and requires a functional type IX secretion system for its activity
Authors: Wang Sunjun , Liu Yichao , Zhang Beichang , Aduse-Opoku Joseph , Buccafusca Roberto , Mastroianni Giulia , Machado Pedro , Roberts Mark A. J. , Curtis Michael A. , Garnett James A.
Published: December 2024

Porphyromonas gingivalisis a Gram-negative bacterium that plays a central role in the development of periodontal disease. It uses a type IX secretion system (T9SS) to export a range of virulence factors to the bacterial surface where they are attached to A-LPS, one of the two forms of lipopolysaccharide (LPS) produced inP. gingivalis, and then packaged into outer membrane vesicles (OMVs). We previously showed that 1-P dephosphorylation of the lipid A component of LPS is regulated by the T9SS outer membrane protein (OMP) PorV, and this is linked to membrane destabilisation and OMV blebbing/formation. In this study we aimed to extend this and investigate the role of other T9SS OMPs in OMV biogenesis. We examined gingipain activity, gingipain secretion, A-LPS production, OMV morphology, and lipid A structure inP. gingivalisW50 and T9SS OMP mutant strains, and our results support an essential role for these proteins in type IX secretion. In addition, we produced a lipid A 1-phosphatase (ΔlpxE) mutant and show that all T9SS OMPs are required for LpxE activity and correct vesicle formation. LpxE has a unique C-terminal extension, and we propose that a cargo protein exported by the T9SS can directly/indirectly interact with this and regulate LpxE activity. This study provides insight into a new mechanism that links type IX cargo sorting with OMV blebbing, which may also be present in other Bacteroidota that colonise the gut and oral cavity.
Parental rejection is associated with intergenerational inheritance of reduced survival, altered behaviours and miRNAs in Owl Monkeys
Authors: Farinha Jayde , Clausi Marroquin Mirtha , Pardo Chambi Fabian O , Sanchez Nofre , Boot James , Mein Charles A , Yip Ping , Paredes Ursula M
Published: December 2024

Introduction: Intergenerational inheritance of stress is the transmission of acquired exposures down to the next generation. Complete parental rejection of newborns in captive primate colonies is considered a severe form of early life stress and widespread across globe. Intergenerational effects associated with parental rejection are uncharacterised but could have significant impact on progeny, affecting their welfare. Methods: We investigated intergenerational inheritance of rejection in a species where parental rejections occurs spontaneously in captivity (Aotus nancymaae), and its effects across 2 generations. We analysed demographic records (n=1389), observed stress and affiliative behaviours (n=65, 10 families, 2 generations), and profiled miRNAs expression in blood (48 from 10 families, 2 generations). Results: Rejected individuals showed significantly reduced lifespan, and a lower probability of reaching reproductive age and increased rates of clinic visits throughout life. Remarkably, well-reared descendants of rejected animals showed a similar reduction in surviving to reproductive age and lifespan as seen in their parents. Behavioural analysis revealed persistent alterations in stress reactivity and social behaviour, with rejected adults showing significant increase in fear aggression and reduced infant care, and infants showing reduced locomotion and biting, but also positive stress coping. Blood miRNA analysis revealed no significant differences between rejected and controls, but rejected female offspring, showed a significant upregulation of mml-miR-30a-5p an miRNA upregulated in the plasma of humans who after exposure to early life stress, suffer from behavioural disorders. Discussion: Our findings demonstrate that parental rejection is associated intergenerational effects on stress and affiliative behaviours, reduced survival, and miRNA expression, suggesting intergenerational inheritance of stress. This report contributing to understanding developmental origins of ill health and mortality in captive primates.
Characterisation of transgenic lines labelling reticulospinal neurons in larval zebrafish
Authors: Collins Elena MD , Silva Pedro TM , Ostrovsky Aaron D , Renninger Sabine L , Tomás Ana R , Diez del Corral Ruth , Orger Michael B
Published: December 2024

From lamprey to monkeys, the organization of the descending control of locomotion is conserved across vertebrates. Reticulospinal neurons (RSNs) form a bottleneck for descending commands, receiving innervation from diencephalic and mesencephalic locomotor centres and providing locomotor drive to spinal motor circuits. Given their optical accessibility in early development, larval zebrafish offer a unique opportunity to study reticulospinal circuitry. In fish, RSNs are a small, highly stereotyped, uniquely identifiable group of large neurons spanning from the midbrain to the medulla. Classically labelled by tracer dye injections into the spinal cord, recent advances in genetic tools have facilitated the targeted expression of transgenes in diverse brainstem neurons of larval zebrafish. Here, we provide a comparative characterization of four existing and three newly established transgenic lines in larval zebrafish. We determine which identified neurons are consistently labelled and offer projection-specific genetic access to subpopulations of RSNs. We showcase transgenic lines that label most or all RSNs (nefma, adcyap1bccu96Et) or subsets of RSNs, including ipsilateral (vsx2, calcaccu75Et), contralateral (pcp4accu97Tg) or all (tiam2ay264Et) components of the Mauthner array, or midbrain-only RSNs (s1171tEt). In addition to RSNs, selected transgenic lines (nefma, s1171tEt, calcaccu75Et) labelled other potential neurons of interest in the brainstem. For those, we performedin situhybridisation to show expression patterns of several excitatory and inhibitory neurotransmitters at larval stages as well as glutamatergic expression patterns in juvenile fish. We provide an overview of transgene expression in the brainstem of larval zebrafish that serves to lay a foundation for future studies in the supraspinal control of locomotion.
Yersinia pestisactively inhibits the production of extracellular vesicles by human neutrophils
Authors: Sheneman Katelyn R. , Cummins Timothy D. , Merchant Michael L. , Hood Joshua L. , Uriarte Silvia M. , Lawrenz Matthew B.
Published: December 2024

Yersinia pestisis the etiologic agent of the plague. A hallmark of plague is subversion of the host immune response by disrupting host signaling pathways required for inflammation. This non-inflammatory environment permits bacterial colonization and has been shown to be essential for disease manifestation. Previous work has shown thatY. pestisinhibits phagocytosis and degranulation by neutrophils. Manipulation of these key vesicular trafficking pathways suggests thatY. pestisinfluences EV secretion, cargo selection, trafficking, and/or maturation. Our goal was to define the EV population produced by neutrophils in response toY. pestisand determine how these vesicles might influence inflammation. Toward these goals, EVs were isolated from human neutrophils infected withY. pestisor a mutant lacking bacterial effector proteins known to manipulate host cell signaling. Mass spectrometry data revealed that cargoes packaged in EVs isolated from mutant infected cells were enriched with antimicrobials and cytotoxic proteins, contents which differed from uninfected andY. pestisinfected cells. Further, EVs produced in response toY. pestislacked inflammatory properties observed in those isolated from neutrophils responding to the mutant. Together, these data demonstrate thatY. pestisactively inhibits the production of antimicrobial EVs produced by neutrophils, likely contributing to immune evasion.