bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuratede novotranscription unit annotation from run-on and sequencing data
Authors: Munn Paul R. , Chia Jay , Danko Charles G. 
Published: February 2025

ABSTRACTFunctional element annotations are critical tools used to provide insight into the molecular processes governing cell development, differentiation, and disease. Run-on and sequencing assays measure the production of nascent RNAs and can provide an effective data source for discovering functional elements. However, the accurate inference of functional elements from run-on sequencing data remains an open problem because the signal is noisy and challenging to model. Here we investigated computational approaches that convert run-on and sequencing data into annotations representing transcription units, including genes and non-coding RNAs. We developed a convolutional neural network, calledconvolutional discovery ofgeneanatomy usingPRO-seq (CGAP), trained to identify different anatomical features of a transcription unit, which were then stitched together into transcript annotations using a hidden Markov model (HMM). Comparison with existing methods showed a significant performance improvement using our novel CGAP-HMM approach. We developed a voting system that ensembles the top three annotation strategies, resulting in large and significant improvements in transcription unit annotation accuracy over the best performing individual method. Finally, we also report a conditional generative adversarial network (cGAN) as a generative approach to transcription unit annotation that shows promise for further development. Collectively our work provides novel tools forde novotranscription unit annotation from run-on and sequencing data that are accurate enough to be useful in many applications.
Multiple Xpa In vivo crystallization routes in HEK 293 human cells
Authors: Leymarie O. , Skobelkina A. , Montaville P. , Brewee C. , Isabet T. , Chauvet H. , Pereiro E. , Chavas L. , Jamme F. 
Published: February 2025

AbstractPhase changes of macromolecules in living cells gained recently a major interest in cell biology as liquid liquid phase separation or liquid solid phase transition phenomenon being observed in increasing number of biological or pathological processes. Comprehensive characterization of these phases remains challenging and requires new methodological approaches for their complete description across spatial and temporal scales. We propose a combination of imaging methods applied to a model system and report thein vivocrystallization pathways of a macromolecule from its solution to crystalline states at the cell population level down to the meso scale. Combining various live fluorescence based techniques and a high resolution cryo imaging technique within unaltered cryopreserved cells, we could described the unexpectedly wide landscape of thein vivocrystalline states of the fluorescent coral derived protein xpa, gain information of crystal growth dynamicsin cellulo, and provide hypothesis of the crystal nucleation requirements of this stochastic process.
Mapping the dimerization specificity of bZIP transcription factors in bread wheat
Authors: Kaur Raminder , Sharma Nishtha , Jain Prateek , Verma Mamta , Apkari Ashish , Rishi Vikas 
Published: February 2025

AbstractDimerization plays a pivotal role in target-binding interactions among various transcription factors (TFs), including bZIPs, bHLHs, MYBs, and zinc finger TFs. The bZIP family is defined by an α-helix class of TFs containing a basic region that binds to the major groove of double-stranded DNA (dsDNA), followed by a leucine zipper motif that mediates dimerization through coiled-coil structures, forming homo- or heterodimers. In polyploid bread wheat (Triticum aestivumcv.), bZIPs and their homeologs interact through the dimerization motifs to form specific bZIP pairs with distinct regulatory functions. The dimerization pattern of bZIPs is critical for gene regulation, however, the mechanisms underlying their specificity remain poorly understood. Here, we focus on the dimerization specificity of coiled-coil α- helical bZIP proteins in bread wheat, highlighting the leucine zipper region as a key dimerization motif. We identified 265 bZIPs containing the bZIP motif, following dimerization criteria established in humans,Drosophila, andArabidopsisbased on the presence of specific amino acids at the ’a’, ’d’, ’e’, and ’g’ positions in heptads. Eight key bZIP TFs were cloned, expressed, and purified for the structural analysis. This study not only provides the dimerization trend exhibited by bZIPs during thermal stability analysis but also provides the reversibility pattern followed by the thermal denaturation exposure at 85°C. Our study also points towards that how amino acid substitutions and the length of the leucine zipper influence the formation of coiled-coil structures among bZIP homeologs of polyploid wheat. Overall, the study advances our understanding of the role of leucine zippers, in determining the specificity and stability of bZIP dimers, which in turn governs DNA binding and gene regulation in plants.
Assembly and annotation ofSolanum dulcamaraandSolanum nigrumplant genomes, two nightshades with different susceptibilities toRalstonia solanacearum
Authors: Ortega Sara Franco , James Sally , Gilbert Lesley , Hogg Karen , Stevens Harry , Daff Jason , Friman Ville-Petri , Harper Andrea L. 
Published: February 2025

AbstractTo understand why close wild plant relatives of crops, such asSolanum dulcamara, are resistant toRalstonia solanacearumwe need genetic resources to perform comparative studies and identify key genes and pathways. Wede-novoassembled and annotated the genome of resistantS. dulcamaraand susceptibleSolanum nigrumplants using a hybrid approach including Oxford Nanopore Technologies and Illumina sequencing. Comparative genomic analysis was then performed to find differences between the genome ofS. dulcamaraand other susceptible Solanaceous species including potato, tomato, aubergine, andS. nigrumand one susceptible and one resistantS. americanumaccession. We identified genes associated with auxin-transport only inS. dulcamaraand a collection of pattern recognition receptors (PRRs) was identified in orthogroups only found in plant species with resistant/tolerant phenotype, suggesting novel plant receptors in these accessions that may improve recognition of pathogen-associated molecular patterns (PAMPs) associated withR. solanacearum. We also identified differences in methylation frequency across the gene bodies in both species, which may be associated with epigenetic regulation of resistance. Future work should assess the functional role of these PRRs during bacterial wilt development to determine if they could offer potential novel targets for breeding improved wilt resistance.
Understanding of ATP-lid conformational dynamics in the N-terminal domain of Hsp90 and its mutants by use of a computational biochemistry approach
Authors: Gohda Keigo 
Published: February 2025

ABSTRACTChaperone Hsp90 regulates the activation and maturation of various protein, and is an attractive target for drug discovery. In catalytic cycle of Hsp90, ATP hydrolysis is a key event that drives structural changes, including the interchange of the dimeric Hsp90 structure between open and closed forms. For ATP hydrolysis, ATP-lid closure in the ATP-binding site from the up- to down-conformation is an indispensable co-ordinated structural change. However, the atomistic mechanism underlying lid closure remains unclear. In this study, a computational biochemistry approach was applied to wild-type apo and ATP-complex structures, and the lid-mutants A107N and T101I ATP-complex, to understand lid closure.A total of 15-μs molecular dynamic simulation, including the equilibration and production phases, was conducted for every structure starting from the lid up-conformation, but no lid-closures were observed. However, a very early event, i.e.,a sign, of lid closure have been captured. In the simulations of wild-type and A107N ATP-complex structures, lid segment showed conformational fluctuations, and helix-7 (H7) segment in lid segment was unwound. This conformational instability of lid segment energetically weakened its interaction with facing region, suggesting the up-to-down transition was triggered by the instability of lid segment, particularly H7 segment. The interaction energy between lid segment and facing region was ranked in the order A107N > wild-type > T101I, which was correlated with experimental results such as the orders of ATP-hydrolytic activity and rapidity of conformational changes of lid segment, measured in ATP-spiking experiments by fluorescence resonance energy transfer method (i.e., A107N > wild-type > T101I).
Right atrial dilatation associates with conduction velocity, incidence of arrhythmias and clinical outcomes in pulmonary hypertension
Authors: Reddy S Ashwin , Middleton Jennifer T , De Bie Eckart MDD , Nethercott Sarah L , Polwarth Gary J , Bullock Katherine , Patel Kiran Hk , Bajaj Nikesh , Statton Ben K , Zahra Syeda Anum , Ehnesh Mahmoud , Roney Caroline H , Ng Fu Siong , Kiely David G , Swift Andrew J , Church Colin , Coghlan Gerry , Gräf Stefan , Lawrie Allan , Lordan James , Mackenzie Ross Robert V , Wilkins Martin R , Wort S John , Taboada Dolores , Bunclark Katherine , Cannon John E , Sheares Karen S , Pepke-Zaba Joanna ,   National Cohort Study of Idiopathic and Heritable PAH Collaboration,   UniPHy Clinical Trials Network, Martin Claire A , Rothman Alex MK , Toshner Mark R 
Published: February 2025

AbstractIntroductionThe mechanism, frequency and clinical impact of arrhythmias in pulmonary hypertension (PH) are unclear. We sought to clarify the electrophysiological mechanism in PH and correlate with arrhythmia incidence and clinical outcomes.MethodsInvasive (n=10) and non-invasive (n=30) electrophysiological mapping techniques determined myocardial conduction velocity, scar burden and atrioventricular (AV) nodal refractoriness, which were then related to cardiac structure and function.Implantable cardiac monitors (ICMs) were implanted into 80 patients with pulmonary arterial hypertension (PAH). Arrhythmia and clinical worsening episodes were prospectively assessed over 186 patient-years follow-up, and features associated with arrhythmia incidence were identified. Two cohorts encompassing all causes of PH (n=564 and n=3348) were interrogated to assess the relationship between defined arrhythmia risk variables and outcomes.ResultsRight atrial (RA) dilatation was associated with slower conduction velocity (R=0.52, p=0.01) and more prolonged AV nodal refractoriness (R=0.82, p=0.03). In the ICM study, 79 arrhythmia events were noted in 40% of participants. Only RA size was independently associated with significant arrhythmia (HR 1.03, 95% CI 1.01-1.06, p=0.01). Arrhythmia incidence associated with clinical worsening, and 20% of patients received ICM-uncovered targeted arrhythmia treatment. 69% of patients with treated arrhythmia were asymptomatic (median time-to-arrhythmia-detection 7 months). In both longitudinal PH cohorts, right atrial (RA) size was associated with worse survival independent of RA pressure and pulmonary vascular resistance.InterpretationThe dominant mechanism associated with disordered cardiac electrophysiology in pulmonary hypertension patients is RA enlargement. RA size was the only significant variable associated with longitudinal arrhythmias in PAH and in two large prospective cohorts with representative populations of all causes of pulmonary hypertension, RA size is predictive of outcomes independent of pulmonary vascular resistance. Randomised trials are needed to clarify if screening and treating arrhythmias in pulmonary hypertension improves outcomes.
Asynchronous viral spread of two unrelated viruses determines Lettuce Big Vein Disease symptom development
Authors: Schravesande Willem E. W. , de Heer Peter M. , Heilijgers Maurice , Verhage Adriaan , van den Burg Harrold A. 
Published: February 2025

AbstractLettuce big-vein disease (LBVD) is a major disease affecting lettuce cultivation worldwide. LBVD is caused by two unrelated negative-stranded RNA viruses, that is, Mirafiori lettuce big-vein virus (MiLBVV) and Lettuce big-vein associated virus (LBVaV) both vectored by the soilborne fungusOlpidium virulentus. Despite extensive research, a synergistic effect between the two viruses has not been observed, while both viruses individually have been suggested to be the causal agent for the disease. By performing lettuce reinfections using a large soil sample collection carrying LBVD infestedO. virulentusspores, the presence of LBVaV was consistently established in diseased lettuce heads, while MiLBVV infections were apparently less prevalent. Yet, aboveground infections with MiLBVV corresponded with strong disease symptoms. Strikingly, the spread of LBVaV from the root to shoot always preceded that of MiLBVV. The LBVaV systemic spread was highly synchronized between plants, while MiLBVV spread was always delayed and asynchronous. A pan-genome analysis revealed independent segment reassortments for both viruses indicative of mixed field infections over the sampled period. Yet, RNA segment abundance was highly conserved for both viruses between all re-infections, suggesting that segment abundance has a regulatory role for the two individual viruses, but that segment abundance is not impacted by the presence of the other two viruses. The pan-genome analysis also revealed different evolutionary rates of the viral ORFs suggesting that mutagenesis of certain ORFs compromises viral fitness and thus revealing a potential weak spot for both viruses.ImportanceLettuce big-vein disease (LBVD) is an important viral disease complex affecting lettuce cultivation worldwide. Here we reveal a synergistic interaction between the two principal associated segmented RNA viruses, Mirafiori lettuce big-vein virus (MiLBVV) and Lettuce big-vein associated virus (LBVaV). We show unequivocally that MiLBVV is the main virus responsible for severe disease symptoms in lettuce heads. Yet, MiLBVV root-to-shoot movement was in our conditions always preceded by LBVaV movement into the lettuce heads. Arguably, LBVaV thus facilitates the root-to-shoot movement of MiLBVV. Moreover, both viruses undergo segment reassortment increasing their genome plasticity and the reassortment events appeared to be independent events with mixed infections. Finally, we provide data that both viruses regulate gene expression via the copy number of their RNA segments, but that the genome formula does not change in dual infections. We thus provide evidence for a synergistic interaction needed for strong LBVD symptoms.
Atomistic modelling of lysophospholipids from the Campylobacter jejuni lipidome
Authors: Newman Kahlan E. , Brandner Astrid F. , Essex Jonathan W. , Khalid Syma 
Published: February 2025

AbstractLysophospholipids are an important class of lipids in both prokaryotic and eukaryotic organisms. These lipids typically constitute a very small proportion (<1%) of the bacterial lipidome, but can constitute 20-45% of theCampylobacter jejunilipidome under stress conditions. It is thus of importance to include these lipids in modelC. jejunimembrane simulations for an accurate representation of the lipidic complexity of these systems. Here, we present atomistic models for four lysophospholipids from theC. jejunilipidome, each derived from existing phospholipid models. Herein we use molecular dynamics simulations to evaluate the ability of these models to reproduce the expected micellar, hexagonal, and lamellar phases at varying levels of hydration. Mixtures of phospholipids and lysophospholipids emulating theC. jejunilipidome under ideal growth conditions were found to self-assemble into bilayers in solution. The properties of these mixed bilayers were compared to those containing only phospholipids: the presence of the selected lysophospholipids causes a subtle thinning of the bilayer and a reduction in area per lipid, but no significant change in lipid diffusion. We further test the mixed bilayer model running simulations in which a native inner membrane protein is embedded within the bilayer. Finally, we show that lysophospholipids facilitate the formation of pores in the membrane, with lysophospholipid-containing bilayers more susceptible to electroporation than those containing only phospholipids.
In vivo pulse-chase inC. elegansreveals intestinal histone turnover changes upon starvation
Authors: Borchers Christopher , Osburn Kara , Roh Hyun Cheol , Aoki Scott T. 
Published: February 2025

AbstractThe ability to study protein dynamics and function in the authentic context of a multicellular organism is paramount to better understand biological phenomena in animal health and disease. Pulse-chase of self-labeling fusion protein tags provide the opportunity to label proteins of interest and track those proteins over time. There are currently several challenges associated with performing in vivo protein pulse-chase in animals, such as cost, reproducibility, and accurate detection methods. TheC. elegansmodel organism has attributes that alleviate many of these challenges. This work tests the feasibility of applying the Halo modified enzyme (HaloTag) for in vivo protein pulse-chase inC. elegans. HaloTag intestinal histone reporters were created in the worm and used to demonstrate that reporter protein could be efficiently pulse-labeled by soaking animals in ligand. Labeled protein stability could be monitored over time by fluorescent confocal microscopy. Further investigation revealed reporter protein stability was dependent on the animal’s nutritional state. Chromatin Immunoprecipitation and sequencing (ChIP-seq) of the reporters showed incorporation in chromatin with little change hours into starvation, implying a lack of chromatin regulation at the time point tested. Collectively, this work presents a straightforward method to label and track proteins of interest inC. elegansthat can address a multitude of biological questions surrounding protein stability and dynamics in this animal model.
Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia
Authors: Madsen Cody S. , Kimbrel Jeffrey A. , Diep Patrick , Ricci Dante P. 
Published: February 2025

AbstractBiofertilizers are critical for sustainable agriculture since they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. Yet, to continue improving deployment, the persistence of designer biofertilizers within native soil consortia must be elucidated and enhanced. Here, we describe a high-throughput, modular, and automation-friendlyin vitroapproach to screen for biofertilizer organism persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. We profiled ∼1200 SynComs isolated from various soil sources and cultivated in divergent media types, and detected significant phylogenetic diversity (e.g., Shannon index > 4) and richness (Observed richness > 400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrate the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs where an engineered biofertilizer organism (i.e.Bacillus subtilis) persists. Additionally, our approach enables an analysis of the ecological impact ofB. subtilisinoculation on SynCom structure and profile alterations in community diversity and richness (or lack thereof) associated with the presence of a genetically modified model bacterium. Ultimately, this work establishes a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessing persistence and interaction of a specific organism of interest with native consortia.
TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination
Authors: Eickhoff Nils , Janetzko Janina , Padrão Nuno , Gregoricchio Sebastian , Siefert Joseph C. , Hoekman Liesbeth , Linder Simon , Bleijerveld Onno , Bergman Andries M. , Zwart Wilbert 
Published: February 2025

ABSTRACTThe Androgen Receptor (AR) is a ligand-dependent transcription factor that drives prostate cancer development and progression. Although, a detailed effect on AR biology has been described for a number of interacting proteins, many AR coregulators remain to be characterized in relation to their distinct impact on AR function. Here, we describe TRIM33 as a conserved AR-interactor across multiple prostate cancer cell lines. We observed that TRIM33 and AR share overall chromatin interaction profiles, in which TRIM33 is involved in downstream responsive transcriptomic output. In contrast to prior reports, we show that TRIM33 does not impact AR protein stability, but instead propose a model in which TRIM33 facilitates maximal AR activity by interfering with H2BK120 ubiquitination levels.
Selective manipulation of excitatory and inhibitory neurons in top-down and bottom-up visual pathways using ultrasound stimulation
Authors: Jo Yehhyun , Liang Xiaojia , Nguyen Hong Hanh , Choi Yeonseo , Bae Ga-Eun , Cho Yakdol , Woo Jiwan , Lee Hyunjoo Jenny 
Published: February 2025

AbstractIntroductionTechniques for precise manipulation of neurons in specific neural pathways are crucial for excitatory/inhibitory (E/I) balance and investigation of complex brain circuits. Low-intensity focused ultrasound stimulation (LIFUS) has emerged as a promising tool for noninvasive deep-brain targeting at high spatial resolution. However, there is a lack of studies that extensively investigate the modulation of top-down and bottom-up corticothalamic circuits via selective manipulation of excitatory and inhibitory neurons. Here, a comprehensive methodology using electrophysiological recording and c-Fos staining is employed to demonstrate pulse repetition frequency (PRF)-dependent E/I selectivity of ultrasound stimulation in the top-down and bottom-up corticothalamic pathways of the visual circuit in rodents.Materials and methodsUltrasound stimulation at various PRFs is applied to either the lateral posterior nucleus of the thalamus (LP) or the primary visual cortex (V1), and multi-channel single-unit activity is recorded from the V1 using a silicon probe.Results and conclusionOur results demonstrate that high frequency PRFs, particularly at 3 kHz and 1 kHz, are effective at activating the bidirectional corticothalamic visual pathway. In addition, brain region-specific PRFs modulate E/I cortical signals, corticothalamic projections, and synaptic neurotransmission, which is imperative for circuit-specific applications and behavioral studies.