bluuebunny/crossref_metadata_2025 huggingface dataset:
Variation in diel timing in great tits is affected by the timing of their social mate
Authors: Strauß Aurelia F. T. , Tomotani Barbara M. , Visser Marcel E. , Helm Barbara
Published: August 2024

Diel rhythms are driven by genetic and environmental components. These rhythms are mediated by the circadian clock, and entail rhythmicity of various physiological and behavioural traits. Although individuals show to some extent repeatable timing (i.e., chronotype), there is ample variation of diel timing observed within and between individuals of the same species. Here, we investigated various environmental factors, including timing of the social partner, that could explain day-to-day variation within individuals. Synchronisation with the social partner during provisioning timing could increase breeding success, and decrease extrapair paternity opportunities for females during the fertile period in case of consistent timing across the breeding stages. Therefore, we also investigated fitness consequences of between-individual variation. We first assessed the magnitude of between- and within-individual variation in the timing of nest visits by great tits (Parus major). We monitored nest visits of males and females in 37 broods during chick provisioning in 2020 and 2021. Next, we explored the responsiveness of the diel timing to environmental variables, specifically comparing abiotic and social factors. The onset of nest visits varied significantly with day within the breeding season, rainfall and the diel timing of the breeding partner but not with night temperature. In response to the partner’s onset, females responded stronger compared to males. By contrast, offset was generally more variable within individuals and less variation was explained by the environmental variables. Both males and females delayed their activity offset with the progressing season and females also had a later onset with more daytime rainfall. Further, the reproductive output and extrapair paternity were independent of parental chronotype and their synchronisation within pairs. It is possible that consistency of chronotypes is less important for reproductive success than the ability to plastically respond to changing environmental conditions. Thus, the next step could be to investigate potential individual differences in plasticity which could be even linked to specific chronotypes. This information might be crucial to predict how species can cope with unpredictable environmental conditions.
LAT encodes T cell activation pathway balance
Authors: Rubin Adam J. , Dao Tyler T. , Schueppert Amelia V. , Regev Aviv , Shalek Alex K.
Published: August 2024

Immune cells transduce environmental stimuli into responses essential for host health via complex signaling cascades. T cells, in particular, leverage their unique T cell receptors (TCRs) to detect specific Human Leukocyte Antigen (HLA)-presented peptides. TCR activation is then relayed via linker for activation of T cells (LAT), a TCR-proximal disordered adapter protein, which organizes protein partners and mediates the propagation of signals down diverse pathways including NFAT and AP-1. Here, we studied how balanced downstream pathway activation is encoded in the amino acid sequence of LAT. To comprehensively profile the sequence-function relationship of LAT, we developed a pooled, single-cell, high-content screening approach in which a large series of mutants in the LAT protein were analyzed to characterize their effects on T cell activation. Measuring epigenetic, transcriptomic, and cell surface protein dynamics of single cells harboring distinct LAT mutants, we found functional regions spanning over 40% of the LAT amino acid sequence. Conserved sequence motifs for protein interactions along with charge distribution are critical sequence features, and contribute to interpretation of human genetic variation in LAT. While mutant defect severity spans from moderate to complete loss of function, nearly all defective mutants, irrespective of their position in LAT, confer balanced defects across all downstream pathways. To understand the molecular basis for this observation, we performed proximal protein labeling which demonstrated that disruption of LAT interaction with a single partner protein indirectly disrupts other partner interactions, likely through the dual roles of these proteins as effectors of downstream pathways and bridging factors between LAT molecules. Overall, we report widely distributed functional regions throughout a disordered adapter and a precise physical organization of LAT and interacting molecules which constrains signaling outputs. More broadly, we describe an approach for interrogating sequence-function relationships for proteins with complex activities across regulatory layers of the cell.
Cell cycle re-entry in the agingDrosophilabrain
Authors: Damschroder Deena , Sun Jenny , McDonald Katherine O. , Buttitta Laura
Published: August 2024

The brain is an organ comprised mostly of long-lived, quiescent cells that perform vital functions throughout an animal’s life. Due to the brain’s limited regenerative ability, these long-lived cells must engage unique mechanisms to cope with accumulated damage over time. We have shown that a subset of differentiated neuronal and glial cells in the fruit fly brain become polyploid during adulthood. Cell cycle re-entry in the brain has previously been associated with neurodegeneration, but there may be a more complex relationship between polyploidy and cell fitness in the brain. Here, we examine how known lifespan modifiers influence the accumulation of polyploidy in the aging fly brain. Flies aged at a low temperature, or with a low protein diet, accumulate polyploid cells in the brain more slowly than expected if this phenotype were solely regulated by lifespan mechanisms. Despite the slower accumulation of polyploid cells, animals under conditions that extend lifespan eventually reach similar levels of polyploidy in the brain as controls. Our work suggests known lifespan modifiers can influence the timing of cell cycle re-entry in the adult brain, indicating there is a flexible window of cell cycle plasticity in the aging brain.
Genomic signatures and demographic history of the widespread and critically endangered yellow-breasted bunting
Authors: Chen Guoling , Sin Simon Yung Wa
Published: August 2024

Population declines may have long-term genetic consequences, including genetic erosion and inbreeding depression, which could affect species’ evolutionary potential and increase their risk of extinction. Small populations are more vulnerable to genetic threats than common species, but even species with large populations can also be at risk of extinction. The yellow-breasted bunting (Emberiza aureola) is a common and widespread songbird in the northern Palearctic regions, but its population has drastically declined by around 90% throughout the past 30 years, leading to an upgrade of its conservation status to critically endangered. In this study, we identified three populations within this species using whole-genome resequencing data, but the genetic differentiation between populations was shallow. These populations underwent similar population fluctuations but differed in the extent of population decline, resulting in lower genetic diversity and more homozygous deleterious mutations in a population comprising individuals on islands. The ancient demographic history was mainly associated with the climate, while recent population declines are likely due to human activities. Our results suggest that the yellow-breasted bunting population before the recent population collapse faced relatively low genetic threats and had high evolutionary potential. However, we should be vigilant about the genetic threats faced by this species as our sampling time occurred at the onset of its recent global population collapse. This study provides valuable genetic information for appropriate conservation management of the yellow-breasted bunting and sheds light on the extinction risks and genetic consequences common species face.
The landscape of cellular clearance systems across human tissues and cell types is shaped by tissue-specific proteome needs
Authors: Vinogradov Ekaterina , Ravkaie Lior , Edri Bar , Jubran Juman , Ben-Zvi Anat , Yeger-Lotem Esti
Published: August 2024

Protein clearance is fundamental to proteome health. In eukaryotes, it is carried by two highly conserved proteolytic systems, the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway (ALP). Despite their pivotal role, the basal organization of the human protein clearance systems across tissues and cell types remains uncharacterized. Here, we interrogated this organization using diverse omics datasets. Relative to other protein-coding genes, UPS and ALP genes were more widely expressed, encoded more housekeeping proteins, and were more essential for growth, in accordance with their fundamental roles. Most of the UPS and ALP genes were nevertheless differentially expressed across tissues, and their tissue-specific upregulation was associated with tissue-specific functions, phenotypes, and disease susceptibility. The small subset of UPS and ALP genes that was stably expressed across tissues was more highly and widely expressed and more essential for growth than other UPS and ALP genes, suggesting that it acts as a core. Lastly, we compared protein clearance to other branches of the proteostasis network. Protein clearance and folding were closely coordinated across tissues, yet both were less pivotal than protein synthesis. Taken together, we propose that the proteostasis network is organized hierarchically and is tailored to the proteome needs. This organization could contribute to and illuminate tissue-selective phenotypes.
The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites
Authors: Lo Joelle , Vaeth Katherine F. , Bhardwaj Gurprit , Mukherjee Neelanjan , Russ Holger A. , Moore Jeffrey K. , Taliaferro J. Matthew
Published: August 2024

RNA molecules are localized to subcellular regions through interactions between localization-regulatory cis-elements and trans-acting RNA binding proteins (RBPs). However, the identities of RNAs whose localization is regulated by a specific RBP as well as the impacts of that RNA localization on cell function have generally remained unknown. Here, we demonstrate that the RBP HNRNPA2B1 acts to keep specific RNAs out of neuronal projections. Using subcellular fractionation, high-throughput sequencing, and single molecule RNA FISH, we find that hundreds of RNAs demonstrate markedly increased abundance in neurites in HNRNPA2B1 knockout cells. These RNAs often encode motor proteins and are enriched for known HNRNPA2B1 binding sites and motifs in their 3′ UTRs. The speed and processivity of microtubule-based transport is impaired in these cells, specifically in their neurites. HNRNPA2B1 point mutations that increase its cytoplasmic abundance relative to wildtype lead to stronger suppression of RNA mislocalization defects than seen with wildtype HNRNPA2B1. We further find that the subcellular localizations of HNRNPA2B1 target RNAs are sensitive to perturbations of RNA decay machinery, suggesting that it is HNRNPA2B1’s known role in regulating RNA stability that may explain these observations. These findings establish HNRNPA2B1 as a negative regulator of neurite RNA abundance and link the subcellular activities of motor proteins with the subcellular abundance of the RNAs that encode them.
Dynamic modeling of EEG responses to natural speech reveals earlier processing of predictable words
Authors: Dou Jin , Anderson Andrew J. , White Aaron S. , Norman-Haignere Samuel V. , Lalor Edmund C.
Published: August 2024

In recent years, it has become clear that EEG indexes the comprehension of natural, narrative speech. One particularly compelling demonstration of this fact can be seen by regressing EEG responses to speech against measures of how individual words in that speech linguistically relate to their preceding context. This approach produces a so-called temporal response function that displays a centro-parietal negativity reminiscent of the classic N400 component of the event-related potential. One shortcoming of previous implementations of this approach is that they have typically assumed a linear, time-invariant relationship between the linguistic speech features and the EEG responses. In other words, the analysis typically assumes that the response has the same shape and timing for every word – and only varies (linearly) in terms of its amplitude. In the present work, we relax this assumption under the hypothesis that responses to individual words may be processed more rapidly when they are predictable. Specifically, we introduce a framework wherein the standard linear temporal response function can be modulated in terms of its amplitude, latency, and temporal scale based on the expectedness of the current and prior words. We use the proposed approach to model EEG recorded from a set of participants who listened to an audiobook narrated by a single talker, and a separate set of participants who attended to one of two concurrently presented audiobooks. We show that expected words are processed faster – evoking lower amplitude N400-like responses with earlier peaks – and that this effect is driven both by the word’s own predictability and the predictability of the immediately preceding word. Additional analysis suggests that this finding is not simply explained based on how quickly words can be disambiguated from their phonetic neighbors. As such, our study demonstrates that the timing and amplitude of brain responses to words in natural speech depend on their predictability. By accounting for these effects, our framework also improves the accuracy with which neural responses to natural speech can be modeled.
Peptide therapeutic leads for multi-target inhibition of inflammatory cytokines in Inflammatory Bowel Disease - computational design and in-vitro validation
Authors: Tsaban Tomer , Kariv-Attias Gali , Khramushin Alisa , Gover Ofer , Hayouka Zvi , Schueler-Furman Ora , Schwartz Betty
Published: August 2024

Inflammatory Bowel Disease (IBD) are chronic and recurrent inflammatory disorders affecting the gastrointestinal tract, characterized by the involvement of numerous pro-inflammatory cytokines. These conditions profoundly impact both immune system dynamics and intestinal tissue integrity. Current therapeutic approaches predominantly rely on monoclonal antibodies, and frequently encounter limitations such as non-responsiveness, loss of efficacy over time, immunogenicity, adverse effects, and substantial cost. Consequently, there is a critical need for novel, targeted anti-inflammatory strategies. We present the computational structure guided design of peptidic inhibitors aimed at attenuating the activity of pivotal pro-inflammatory cytokines implicated in IBD pathogenesis, namely TNFα, IL-1β, and IL-6. These peptides were engineered to disrupt specific cytokine - receptor interactions, to block the release of pro-inflammatory cytokines. We structurally characterized key features in the studied interactions and used these to guide two computational design strategies, one based on the identification of dominant segments using our PeptiDerive approach, and one based on complementing fragments detected using our PatchMAN protocol. The designed peptides were synthesized and their efficacy was validated on Caco-2 intestinal epithelial cells and THP-1 macrophages, representative of the epithelial and immunological alterations typical of active IBD. The majority of the novel peptides effectively suppressed release of pro-inflammatory cytokines by both macrophages and intestinal epithelial cells, thereby reducing the risk of inflammation. This study underscores the efficacy of a rational design approach rooted in structural insights into inflammatory signaling complexes. Our findings demonstrate the potential of targeting key cytokines and receptor interaction with designed peptides as a promising therapeutic avenue for managing IBD and other inflammatory disorders.
A diverse landscape of FGFR alterations and co-mutations defines novel therapeutic strategies in pediatric low-grade gliomas
Authors: Morin Eric , Apfelbaum April A. , Sturm Dominik , Ayoub Georges , DiGiacomo Jeromy , Bahadur Sher , Chandarana Bhavyaa , Power Phoebe C. , Cusick Margaret M. , Novikov Dana , Jones Robert , Vogelzang Jayne , Bossi Connor C. , Malinowski Seth , Jeang John , Collins Jared , Oh Sehee , Jeon Hyesung , Cameron Amy , Rechter Patrick , Deleon Angela , Murugesan Karthikeyan , Montesion Meagan , Albacker Lee A. , Ramkissoon Shakti H. , Tilburg Cornelis M. , Hardin Emily C. , Sievers Philipp , Sahm Felix , Yeo Kee Kiat , Rosenberg Tom , Chi Susan , Wright Karen , Hébert Steve , Peck Sydney , Picca Alberto , Larouche Valérie , Renzi Samuele , Bale Tejus , Smith Amy A. , Touat Mehdi , Jabado Nada , Fischer Eric S. , Eck Michael J. , Baird Lissa , Witt Olaf , Kleinman Claudia , Nguyen Quang-De , Alexandrescu Sanda , Jones David T.W. , Ligon Keith L. , Bandopadhayay Pratiti
Published: August 2024

Alterations in Fibroblast growth factor receptor (FGFR)-family proteins frequently occur as oncogenes in many cancers, including a subset of pediatric gliomas. Here, we performed a genomic analysis of 11,635 gliomas across ages and found that 4.5% of all gliomas harbor FGFR alterations including structural variants (SV) and single nucleotide variants (SNV), with an incidence of almost 10% in pediatric gliomas. FGFR family members are differentially enriched by age, tumor grade, and histological subtype, with FGFR1-alterations associated with glioneuronal histologies and pediatric low-grade gliomas. Across development, we findFGFR1expression in both neuronal and glial precursors, whileFGFR3expression is largely restricted to astrocytic lineages. Leveraging novel isogenic model systems, we confirm FGFR1 alterations to be sufficient to activate MAPK and mTOR signaling, drive gliomagenesis, activate neuronal transcriptional programs and exhibit sensitivity to MAPK pathway inhibitors, including pan-FGFR inhibitors. Models driven by FGFR1 SVs exhibited different patterns of sensitivity compared to those driven by SNVs. Finally, we performed a retrospective analysis of clinical responses in children diagnosed with FGFR-driven gliomas and found that targeted MAPK or FGFR-inhibition with currently available inhibitors is largely associated with stability of disease. This study provides key insights into the biology of FGFR1-altered gliomas, therapeutic strategies to target them and associated challenges that still need to be overcome.
Synovial Transcriptome Profiling for Predicting Biological Treatment Response in Rheumatoid Arthritis: A Feasibility study
Authors: d’Ailly P.N. , Schäffers O.J.M. , Deugd C. , Versnel M.A. , van de Werken H.J.G. , Bindels E.M.J. , Tas S.W. , Gribnau J. , Schep N.W.L. , Bisoendial R.J.
Published: August 2024

Introduction

Disease-Modifying Anti-Rheumatic Drug (DMARD) treatment fails to achieve clinical remission in a substantial proportion of patients with rheumatoid arthritis (RA). Patient-derived synovial tissue (ST)-signatures, thought to determine this heterogeneity of treatment responses, can be studied by single-cell RNA sequencing (scRNA-seq).

Study aims

The first aim was to obtain viable ST from RA patients using wrist arthroscopy. The second aim was to identify patient-specific transcriptome signatures from the ST omics data that relate to clinical course and treatment responses in RA.

Methods

Radiocarpal and midcarpal synovectomy was performed using a standard set-up wrist arthroscopy. Single-cell suspensions of ST from affected wrists of two RA patients and a control subject were processed on the 10X Genomics Chromium Platform. Seurat was used for downstream analysis.

Results

In two RA patients and one non-inflammatory control, ST was successfully removed during wrist arthroscopy. No surgical complications occurred. For the RA patients and control, 17,176 and 7,884 high-quality cells were analyzed, respectively. Apart from enrichment of cell compartments in RA, including those of B- and plasma cells, T cell populations, NK cells, and macrophages, we observed interpatient variability that may influence the relationship between RA synovial signature and clinical phenotype, potentially also affecting treatment response and outcome. In-depth analysis of the prevailing cell-type abundance phenotype (CTAP) in the RA patients, as described previously, provided insights into the extent to which these CTAPs may be used to predict treatment responses.

Conclusion

In this feasibility study, we demonstrated that wrist arthroscopy successfully retrieves ST with good tissue viability, which may provide informative and high-quality transcriptomic data for predicting therapy response at an individual level.
Post-processing and weighted combination of infectious disease nowcasts
Authors: Amaral André Victor Ribeiro , Wolffram Daniel , Moraga Paula , Bracher Johannes
Published: August 2024

In infectious disease surveillance, incidence data are frequently subject to reporting delays and retrospective corrections, making it hard to assess current trends in real time. A variety of probabilistic nowcasting methods have been suggested to correct for the resulting biases. Building upon a recent comparison of eight of these methods in an application to COVID-19 hospitalization data from Germany, the objective of this paper is twofold. Firstly, we investigate how nowcasts from different models can be improved using statistical post-processing methods as employed, e.g., in weather forecasting. Secondly, we assess the potential of weighted ensemble nowcasts, i.e., weighted combinations of different probabilistic nowcasts. These are a natural extension of unweighted nowcast ensembles, which have previously been found to outperform most individual models. Both in post-processing and ensemble building, specific challenges arise from the fact that data are constantly revised, hindering the use of standard approaches. We find that post-processing can improve the individual performance of almost all considered models both in terms of evaluation scores and forecast interval coverage. Improving upon the performance of unweighted ensemble nowcasts via weighting schemes, on the other hand, poses a substantial challenge. Across an array of approaches, we find modest improvement in scores for some and decreased performance for most, with overall more favorable results for simple methods. In terms of forecast interval coverage, however, our methods lead to rather consistent improvements over the unweighted ensembles.
Estimating the undetected burden of infections and the likelihood of strain persistence of drug-resistantNeisseria gonorrhoeae
Authors: Oliveira Roster Kirstin I. , Rönn Minttu M. , Elder Heather , Gift Thomas L. , Roosevelt Kathleen A. , Salomon Joshua A. , Hsu Katherine K. , Grad Yonatan H.
Published: August 2024

Antimicrobial resistance (AMR) is a serious public health threat.Neisseria gonorrhoeaehas developed resistance to all antibiotics recommended for treatment and reports of reduced susceptibility to ceftriaxone, the last-line treatment, are increasing. Since many asymptomatic infections remain undiagnosed and most diagnosed infections do not undergo antibiotic susceptibility testing, surveillance systems may underestimate the number of ceftriaxone non-susceptible infections. There is an urgent need for better interpretation and use of surveillance data to estimate the prevalence of resistance. In this modeling study, we simulated the spread of a new strain of ceftriaxone non-susceptible gonorrhea in a population of men who have sex with men as well as heterosexual men and women. We compared scenarios with varying strain characteristics and surveillance capacity. For each scenario, we estimated (i) the number of undetected infections by the time the non-susceptible strain was discovered and (ii) the likelihood of strain persistence in the absence of newly reported cases. Upon detection of one ceftriaxone non-susceptible isolate, the undetected disease burden was an estimated 5.4 infections with substantial uncertainty (0-18 infections, 95% uncertainty interval). In the absence of additional reports of ceftriaxone non-susceptible infections over the subsequent 180 days, the estimate declined to 2.5 infections with a narrower uncertainty interval (0-10 infections). The likelihood of ongoing transmission also declined from 66% (26-86%) at first detection to 2% (0-10%) after 180 days. Enhanced monitoring of the magnitude and trends of AMR is a key priority to reduce the burden of resistance and extend the useful lifespan of last-line antibiotics.
Integrating a host transcriptomic biomarker with a large language model for diagnosis of lower respiratory tract infection
Authors: Van Phan Hoang , Spottiswoode Natasha , Lydon Emily C. , Chu Victoria T. , Cuesta Adolfo , Kazberouk Alexander D. , Richmond Natalie L. , Calfee Carolyn S. , Langelier Charles R.
Published: August 2024

Lower respiratory tract infections (LRTIs) are a leading cause of mortality worldwide. Despite this, diagnosing LRTI remains challenging, particularly in the intensive care unit, where non-infectious respiratory conditions can present with similar features. Here, we tested a new method for LRTI diagnosis that combines the transcriptomic biomarkerFABP4with assessment of text from the electronic medical record (EMR) using the large language model Generative Pre-trained Transformer 4 (GPT-4). We evaluated this methodology in a prospective cohort of critically ill adults with acute respiratory failure, in which we measured pulmonaryFABP4expression and identified patients with LRTI or non-infectious conditions using retrospective adjudication. A diagnostic classifier combiningFABP4and GPT-4 achieved an area under the receiver operator curve (AUC) of 0.92 ± 0.06 by five-fold cross validation (CV), outperforming classifiers based onFABP4expression alone (AUC 0.83) or GPT-4 alone (AUC 0.84). At the Youden’s index within each CV fold, the combined classifier achieved a mean sensitivity of 92% ± 7%, specificity of 90% ± 17% and accuracy of 91% +/- 8%. Taken together, our findings suggest that combining a host transcriptional biomarker with interpretation of EMR data using artificial intelligence is a promising new approach to infectious disease diagnosis.
Blood DNA methylation levels of the oxytocin promoter predict conversion from mild cognitive impairment to dementia in females within a clinical cohort of cognitive complaints
Authors: Koulousakis Philippos , Reijnders Rick , Ramakers Inez , Verhey Frans , Vanmierlo Tim , van den Hove Daniël L.A. , Riemens Renzo J.M.
Published: August 2024

Recent studies have highlighted the role of oxytocin (OXT) in Alzheimer’s disease (AD) dementia and demonstrated its potential as a therapeutic target to reverse cognitive impairment and mitigate AD pathology. Epigenetic dysregulation ofOXThas been identified in brain tissue from AD patients, and DNA methylation levels of the exact same locus in the blood of healthy aged individuals have shown predictive biomarker value for conversion to AD. Building on these insights, we investigated the DNA methylation status of theOXTpromoter in blood in a prospective cohort of consecutive patients from the BioBank Alzheimer Center Limburg (BBACL). This cohort included males and females suffering from subjective cognitive decline (SCD), mild cognitive impairment (MCI), and dementia. Our findings revealed that DNA methylation levels of theOXTpromoter at baseline predict the conversion from MCI to dementia in female participants. In addition to discovering differences in theOXTpromoter related to sex, we also observed alterations associated with aging, alcohol consumption, and smoking. Overall, our findings underscore the implications ofOXTand its DNA methylation changes in blood within the context of dementia.
Promising effects of duck vaccination against highly pathogenic avian influenza, France 2023-24
Authors: Guinat Claire , Fourtune Lisa , Lambert Sébastien , Martin Eva , Gerbier Guillaume , Jimenez Pellicer Andrea , Guérin Jean-Luc , Vergne Timothée
Published: August 2024

The ongoing panzootic of highly pathogenic avian influenza (HPAI) H5 clade 2.3.4.4b has caused widespread poultry mortality and raised concerns about zoonotic pandemics and wildlife conservation. France recently adopted a preventive vaccination strategy, vaccinating domestic ducks with inactivated and mRNA vaccines. This study evaluates the impact of this campaign on reducing HPAI H5 outbreaks. Using predictive modelling based on previous outbreak data, the expected number of outbreaks in 2023-24 without vaccination was significantly higher than the observed cases, indicating a 95.9% reduction attributable to vaccination. These findings suggest that vaccination effectively mitigated the HPAI H5 outbreak in France.
Structural and kinetic insights into tRNA promoter engagement by yeast general transcription factor TFIIIC
Authors: Seifert-Dávila Wolfram , Chaban Anastasiia , Baudin Florence , Girbig Mathias , Hauptmann Luis , Hoffmann Thomas , Duss Olivier , Eustermann Sebastian , Müller Christoph W.
Published: August 2024

Transcription of tRNA genes by RNA polymerase III requires the general transcription factor IIIC (TFIIIC), which recognizes intragenic A-box and B-box DNA motifs of type II gene promoters. However, the underlying mechanism has remained elusive, in part due to missing structural information for A-box recognition. In this study, we use single-particle cryo-EM and single-molecule FRET (smFRET) to reveal structural and real-time kinetic insights into how the 520 kDa yeast TFIIIC complex engages A- and B-box DNA motifs in the context of a tRNA gene promoter. Cryo-EM structures of τA and τB subcomplexes bound to the A- and B-box were obtained at 3.7 and 2.5 Å resolution, respectively, while cryo-EM single particle mapping determined the specific distance and relative orientation of the τA and τB subcomplexes revealing a fully engaged state of TFIIIC. smFRET experiments show that overall recruitment and residence times of TFIIIC on a tRNA gene are primarily governed by B-box recognition, while footprinting experiments suggest a key role of τA and the A-box in TFIIIB and Pol III recruitment following TFIIIC recognition of type II promoters.
GageTracker: a tool for dating gene age by micro- and macro-synteny with high speed and accuracy
Authors: Fang Chengchi , Dong Chuan , Wang Cheng , Xiong Fan , Lu Suxiang , Fang Wenyu , Li Tong , Gan Xiaoni , Yang Liandong , Zeng Honghui , He Shunping
Published: August 2024

With the advent of the Earth Genome Project, an increasing number of species' genomes presents exciting opportunities for exploring genetic and phenotypic diversity in organisms. Determining the origin time of genes facilitates the elucidation of crucial genetic mechanisms underlying significant biological evolutionary questions such as the transition from aquatic to terrestrial life, the emergence of mammals, the origin of humans, as well as the development of species- or lineage-specific traits. However, accurately determining the origin time of these genes in species separated by long evolutionary distances remains a major challenge in bioinformatics as these genes often undergo significant changes in their genome sequences, making it difficult to trace them back to their origin. Here, we proposed a new approach for dating gene age based on the micro- and macro-synteny algorithms. This approach employs the parallel computation of orthologous genome alignments across multiple species. Our method was integrated into the GageTracker (Gene Age Tracker) software, providing a fast and accurate way to trace gene age with minimal user input, available at https://github.com/RiversDong/GageTracker. Benchmarked against the simMammals dataset (Alignathon), GageTracker achieved the same high-quality genome alignments as the optimized LastZ aligner, but improved operation speed by 1.4-7 times. In a separate analysis of 12 Drosophila genomes, GageTracker efficiently assessed the ages of 23,720 genes (including ~13,965 protein-coding genes) in just ~22 hours with default parameters. When comparing with the GenTree database (recognized as the most comprehensive and accurate tool for evaluating gene age), GageTracker achieved an impressive ~94.4% accuracy and ~99% macro consistency in assessing the age of protein-coding genes. Moreover, for the ~5.6% conflicting genes, GageTracker displayed slightly higher support rates than GenTree, as evidenced by data from OrthoDB, FlyBase, and Ensembl ortholog databases. Notably, younger genes identified by GageTracker exhibited a preferential expression pattern in the testis, further reinforcing the reliability of GageTracker in accurately tracing gene age.
Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in post-transcriptional repression of starvation-induced pathways
Authors: Kumar Rakesh , Zhang Fan , Niphadkar Shreyas , Onu Chisom , Vijjamarri Anil Kumar , Greenberg Miriam L. , Laxman Sunil , Hinnebusch Alan G.
Published: August 2024

Degradation of many yeast mRNAs involves decapping by the Dcp1:Dcp2 complex. Previous studies on decapping activators Edc3 and Scd6 suggested their limited roles in mRNA decay. RNA-seq analysis of mutants lacking one or both proteins revealed that Scd6 and Edc3 have largely redundant activities in targeting numerous mRNAs for degradation that are masked in the single mutants. These transcripts also are frequently targeted by decapping activators Dhh1 and Pat1, and the collective evidence suggests that Scd6/Edc3 act interchangeably to recruit Dhh1 to Dcp2. Ribosome profiling shows that redundancy between Scd6 and Edc3 and their functional interactions with Dhh1 and Pat1 extend to translational repression of particular transcripts, including a cohort of poorly translated mRNAs displaying interdependent regulation by all four factors. Scd6/Edc3 also participate with Dhh1/Pat1 in post-transcriptional repression of proteins required for respiration and catabolism of alternative carbon sources, which are normally expressed only in limiting glucose. Simultaneously eliminating Scd6/Edc3 increases mitochondrial membrane potential and elevates metabolites of the tricarboxylic acid and glyoxylate cycles typically observed only during growth in low glucose. Thus, Scd6/Edc3 act redundantly, in parallel with Dhh1 and in cooperation with Pat1, to adjust gene expression to nutrient availability by controlling mRNA decapping and decay.
The transaminase-ω-amidase pathway is a redox switch in glutamine metabolism that generates α-ketoglutarate
Authors: Herrle Niklas , Malacarne Pedro F. , Warwick Timothy , Cabrera-Orefice Alfredo , Chen Yiheng , Gheisari Maedeh , Chatterjee Souradeep , Leisegang Matthias S. , Sarakpi Tamim , Wionski Sarah , Lopez Melina , Koch Ina , Keßler Marcus , Klein Sabine , Uschner Frank Erhard , Trebicka Jonel , Brunst Steffen , Proschak Ewgenij , Günther Stefan , Rosas-Lemus Mónica , Baumgarten Nina , Klatt Stephan , Speer Thimoteus , Wittig Ilka , Schulz Marcel H. , Richards J. Brent , Gilsbach Ralf , Denton Travis T. , Fleming Ingrid , Hannibal Luciana , Brandes Ralf P. , Rezende Flávia
Published: August 2024

Oxidative stress is caused by short-lived molecules and metabolic changes belong to the fastest cellular responses. Here we studied how the endothelial cell metabolome reacts to acute oxidative challenges (menadione or H2O2) to identify redox-sensitive metabolic enzymes. H2O2selectively increased α-ketoglutaramate (αKGM), a largely uncharacterized metabolite produced by glutamine transamination and a yet unrecognized intermediate of endothelial glutamine catabolism. The enzyme nitrilase-like 2 ω-amidase (NIT2) converts αKGM to α-ketoglutarate (αKG). Reversible oxidation of specific cysteine in NIT2 by H2O2inhibited its catalytic activity. Furthermore, a variant in theNIT2gene that decreases its expression is associated with high plasma αKGM level in humans. Endothelial-specific knockout mice of NIT2 exhibited increased levels of αKGM and impaired angiogenesis. Knockout of NIT2 impaired endothelial cell proliferation and sprouting and induced senescence. In conclusion, we show that the glutamine transaminase-ω-amidase pathway is a metabolic switch in which NIT2 is the redox-sensitive enzyme. The pathway is modulated in humans and functionally important for endothelial glutamine metabolism.
Renal outcomes of combination therapy with sodium-glucose cotransporter 2 inhibitors plus renin-angiotensin system blockers in patients with type 2 diabetes mellitus: A population-based cohort study
Authors: Tsai Ming-Hsien , Chen Ming-chih , Huang Yen-Chun , Chang Wei-Shan , Hsiao Kai-Yuan , Liou Hung-Hsiang , Fang Yu-Wei
Published: August 2024

Background

Sodium-glucose cotransporter 2 inhibitors (SGLT2i) can benefit patients with type 2 diabetes mellitus by reducing hazardous renal outcomes. This study aimed to evaluate whether the combination of sodium-glucose cotransporter 2 inhibitors (SGLT2i) and conventional renin-angiotensin system blockers (RASB) provides a synergistic effect on renal outcomes in patients with type 2 diabetes mellitus, compared to the combination of RASB and dipeptidyl peptidase 4 inhibitors (DPP4i).

Methods

This is a retrospective cohort study. The study utilized data from the Taiwan National Health Insurance Research Database (NHIRD), including patients with type 2 diabetes mellitus enrolled between January 1, 2016, and December 31, 2016. Participants were divided into two groups: the case group (n = 3,622) receiving RASB plus SGLT2i and the comparison group (n = 3,622) receiving RASB plus DPP4i. The groups were matched 1:1 based on gender, age, and Charlson comorbidity index. Additionally, TriNetX was used for external validation.

Results

Prior to matching, unadjusted hazard ratios (HRs) showed significant differences favoring the SGLT2i group for chronic kidney disease (CKD) (HR: 0.66; 95% CI, 0.58–0.74), advanced kidney failure (HR: 0.64; 95% CI, 0.44–0.93), and initiation of long-term dialysis (HR: 0.61; 95% CI, 0.38–0.97). These differences remained significant post-matching: CKD (HR: 0.74; 95% CI, 0.65–0.84), advanced kidney failure (HR: 0.62; 95% CI, 0.42–0.92), and commencement of long-term dialysis (HR: 0.53; 95% CI, 0.32–0.87). The renal benefits of the combination therapy were consistently observed in the TriNetX dataset.

Limitations

NHIRD lacks key clinical factors (e.g., physical features, lab data), potential baseline disparities due to retrospective design, and limited generalizability beyond Taiwanese patients, despite TriNexT validation.

Conclusions

In patients with type 2 diabetes mellitus, combination therapy with SGLT2i and RASB yielded better renal outcomes.
SF3B1-mutant mis-splicing ofUBA1confers a targetable therapeutic vulnerability through UBA1 inhibition
Authors: Thier Jonas , Hofmann Sophia , Kirchhof Katharina M , Todisco Gabriele , Mortera-Blanco Teresa , Barbosa Indira , Björklund Ann-Charlotte , Deslauriers André G , Papaemmanuil Elli , Papapetrou Eirini P , Hellström-Lindberg Eva , Moura Pedro L , Lundin Vanessa
Published: August 2024

SF3B1mutation-driven myelodysplastic syndromes (MDS-SF3B1) arise due to somatic mutation in the splicing factorSF3B1gene.SF3B1mutations induce RNA mis-splicing and loss of expression of critical genes for erythropoiesis, leading to erythroid dysplasia and ultimately refractory anemia. The development of precision medicine approaches for MDS-SF3B1is hampered by the complexity of the mis-splicing landscape and its evaluation in disease-accurate model systems. To identify novel RNA mis-splicing events, isogenicSF3B1K700EandSF3B1WTiPSC lines from an MDS-SF3B1patient were differentiated into hematopoietic cellsin vitroand subjected to unsupervised splicing event analysis using full-length RNA sequencing data. This revealedSF3B1K700E-specific mis-splicing of ubiquitin-like modifier activating enzyme 1 (UBA1) transcripts, which encode the essential E1 protein at the apex of the ubiquitination cascade.UBA1mis-splicing (UBA1ms) preservedUBA1msmRNA but not protein expression. Consequently,UBA1msdiminished the pool of functional UBA1, sensitizingSF3B1K700Ecell lines to the small-molecule UBA1 inhibitor TAK-243. Finally, analysis of CD34+RNA sequencing data from an MDS patient cohort confirmed unique and ubiquitousUBA1msin MDS-SF3B1patients, without detection in other splicing factor-mutated MDS patients, or in healthy individuals. TAK-243 selectively targeted MDS-SF3B1primary CD34+cells and reduced mutant cell number in colony-forming unit studies. In contrast, normal hematopoietic progenitor cells were unaffected. Altogether, we here defineUBA1msas a novel therapeutic vulnerability inSF3B1-mutant cells, introducing UBA1 inhibition as a potential avenue for future MDS-SF3B1treatments.
Gain-of-function study reveals the pleiotropic roles of serine protease HtrA inBorrelia burgdorferi
Authors: Zhang Kai , Sze Ching Wooen , Zhao Hang , Liu Jun , Li Chunhao
Published: August 2024

High-temperature requirement protease A (HtrA) is a family of serine proteases degrading misfolded and damaged proteins that are toxic to bacteria. The Lyme disease agentBorrelia burgdorferiencodes a single HtrA (BbHtrA). Previous studies have shown that BbHtrA is a key virulence determinant ofB. burgdorferias a deletion mutant ofhtrA(ΔhtrA) fails to establish infection in mice. However, previous complementation could only restore protein expression but not infectivity in mice. In this report, we first identify the native promoter of BbHtrA which allows us to construct a fully complementedΔhtrAstrain. Follow up promoter activity analysis reveals that BbHtrA is likely dually regulated by the house keeping sigma factor RpoD and the alternative sigma factor RpoS. TheΔhtrAmutant exhibits growth defect upon entering the mid-log to stationary phase especially at high temperatures. Microscopic analysis further demonstrates that the absence ofhtrAinduces extensive cell death. Additionally, theΔhtrAmutant has defects in cell locomotion as the expression of several key chemotaxis proteins are significantly downregulated. Cryo-electron tomography imaging ofhtrAmutant further reveals that deletion ofhtrAdisrupts flagellar homeostasis. The failure ofΔhtrAto establish an infection in mice is likely due to repressed expression of BosR and RpoS at the transcriptional level which ultimately causes dysregulation of the RpoS-induced virulence factors. Collectively, we conclude that the expression ofhtrAis finely tuned which is critical for its pleiotropic roles in the regulation of motility, stress response, and virulence gene expression inB. burgdorferi.

IMPORTANCE

Lyme borreliosis is the most commonly reported vector-borne illnesses in the United States, which is caused byBorrelia burgdorferi.As the enzootic pathogen alternates between the tick vector and mammalian hosts, adaptation to drastically different growth milieu is imperative to its survival. Hence, robust alteration of gene expression and proper quality control on protein synthesis and turnover are pivotal for its fitness. The family of HtrA serine proteases is mainly responsible for the maintenance of protein homeostasis particularly under stressful conditions. The significance of this report is to decode how BbHtrA contributes to the fitness ofB. burgdorferi. BbHtrA is essential for mammalian host infection but little is known about its regulatory mechanism as well as its contribution to the virulence ofB. burgdorferi. By deciphering the regulatory elements involved in the expression of BbHtrA, we are one step closer to comprehending its significance in the pathophysiology ofB. burgdorferi.
The influence of sleep disruption on learning and memory in fish
Authors: Sowersby W. , Kobayahsi T. , Awata S. , Sogawa S. , Kohda M.
Published: August 2024

Sleep is ubiquitous across animal taxa. Strong evolutionary pressures have conserved sleep over the evolutionary history of animals, yet our understanding of the functions of sleep still largely derives from mammals and select laboratory models. Sleep is considered to play an important role in mental processes, including learning and memory consolidation, but how widespread this relationship occurs across taxa remains unclear. Here, we test the impact of sleep disruption on the ability of the cleaner fish(Labroides dimidiatus)to both learn and then remember a novel cognitive task. We found a significant negative relationship between sleep disruption and the ability to learn a food reward choice system. Specifically, we found that fish in a disturbed sleep treatment took significantly longer and made more incorrect decisions when finding the food reward, compared to individuals in a non-disturbed/normal sleep treatment. In contrast, the differences between the two treatment groups were non-significant when fish where tasked with remembering the food reward several days later. Our results demonstrate a negative impact of sleep disruption on performance in a cognitive challenging task and that the effects were strongest when fish were first exposed to the challenge. Importantly, we show that the association between sleep and mental processes, such as learning, may be widespread across vertebrate taxa and potentially have an early origin in the evolutionary history of animals.
Effect of Wearing Glasses for Prevention of SARS-CoV-2 on Visits to Health Care Providers - Additional Results from a Randomized Controlled Trial
Authors: Elgersma Ingeborg Hess , Elstrøm Petter , Hemkens Lars G. , Helleve Arnfinn , Kacelnik Oliver , Fretheim Atle
Published: August 2024

We previously published results of a pragmatic randomized trial with 3717 participants in Norway that assessed the effect of wearing glasses on the risk of being infected with SARS-CoV-2 and other respiratory infections. Here we present unpublished findings on pre-specified secondary endpoints relying on routinely collected data from Norwegian health registries: Visits to health care providers for any cause (within 21 days), for respiratory symptoms (day 3-28), and for injuries (within 21 days).

1469 participants (39.5%) visited a health care provider for any cause at least once. There was no statistically significant difference between groups, with 39.9.% of participants wearing glasses versus 39.1% in the control group received primary or specialist care (absolute risk difference 0.76%; 95% CI, -2.4% to 3.9%; relative risk 1.02; 95% CI, 0.94 to 1.10).

Similarly, there was no statistically significant difference in visits due to respiratory symptoms (326 participants; 9.1% versus 8.4%; absolute risk difference 0.71%; 95% CI, -1.1% to 2.5%; relative risk 1.08; 95% CI, 0.88 to 1.33).

There were 3 participants having visited primary or specialist care and having an injury registered in a registry for injuries, the difference between groups not statistically significant. The difference between participants in the proportion of visits for injury related diagnoses was nominally statistically significant (1.3% versus 0.7%; absolute risk difference 0.7%; 95% CI, 0.01% to 1.3%; relative risk 1.94; 95% CI, 1.01 to 3.89).

The study underscores the potential of utilizing registry-based outcomes for randomized evaluations of public health measures for infection control.