bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating gene conversion tract length and rate from PacBio HiFi data
Authors: Charmouh Anders Poulsen , Sørud Peter Porsborg , Hansen Lasse Thorup , Besenbacher Søren , Winge Sofia Boeg , Almstrup Kristian , Hobolth Asger , Bataillon Thomas , Schierup Mikkel Heide 
Published: July 2024

AbstractGene conversions are broadly defined as the transfer of genetic material from a ‘donor’ to an ‘acceptor’ sequence and can happen both in meiosis and mitosis. They are a subset of non-crossover events and, like crossover events, gene conversion can generate new combinations of alleles and counteract mutation load by reverting germline mutations through GC-biased gene conversion. Estimating gene conversion rate and the distribution of gene conversion tract lengths remains challenging. We present a new method for estimating tract length, rate and detection probability of non-crossover events directly in HiFi PacBio long read data. The method can be used to make inference from sequencing of gametes from a single individual. The method is unbiased even under low single nucleotide variant (SNV) densities and does not necessitate any demographic or evolutionary assumptions. We test the accuracy and robustness of our method using simulated datasets where we vary length of tracts, number of tracts, the genomic SNV density and levels of correlation between SNV density and NCO event position. Our simulations show that under low SNV densities, like those found in humans, only a minute fraction (∼2%) of NCO events are expected to become visible as gene conversions by moving at least one SNV. We finally illustrate our method by applying it to PacBio sequencing data from human sperm.
Algal growth and morphogenesis-promoting factors released by cold-adapted bacteria contribute to the resilience and morphogenesis of the seaweedUlva(Chlorophyta) in Antarctica (Potter Cove)
Authors: Ghaderiardakani Fatemeh , Ulrich Johann F. , Barth Emanuel , Quartino Maria Liliana , Wichard Thomas 
Published: July 2024

AbstractMacroalgae are found in a variety of marine vegetation ecosystems around the world, contributing significantly to global net primary production. In particular, the sea lettuce species, i.e., members of the genusUlva(Chlorophyta), are located in many ecological niches and are characterized by excellent adaptability to environmental changes but depend on essential associated bacteria, which release algal growth and morphogenesis-promoting-factors (AGMPFs). Our work investigated the hypothesis that bacteria need to be stress-adapted to provide sufficient amounts of AGMPFs for the growth and morphogenesis ofUlvathroughout its life cycle, even under severe environmental conditions.Our study thus aimed to understand which bacteria contribute to overcoming a variety of stressors in polar regions. Green macroalgae were collected from Potter Cove, King George Island (Isla 25 de Mayo), Antarctica, to study the associated microbiome and, subsequently, to identify AGMPFs releasing bacteria. Therefore, microbiome analysis was combined with morphogenetic bioassays and chemical analysis, identifying bacteria essential for algal growth under Antarctic conditions. Hereby, axenic cultures of a MediterraneanUlva compressa(cultivarUlva mutabilis), previously developed as a model system for bacteria-induced algal growth and morphogenesis, were inoculated with freshly isolated and cultivable Antarctic bacteria to determine their morphogenetic activity.The exploratory microbiome investigation identified numerous cold-adapted AGMPF-producing bacteria. Unlike the reference bacterial strains isolated from the Mediterranean Sea, the cold-adapted isolatesMaribactersp. BPC-D8 andSulfitobactersp. BPC-C4, released sufficient amounts of AGMPFs, such as thallusin, necessary for algal morphogenesis even at 2°C. Our results illustrate the role of chemical mediators provided by bacteria in cross-kingdom interactions under cold conditions within aquatic systems. The newly isolated bacteria will enable further functional studies to understand the resilience of the holobiontUlvaand might applied in algal aquaculture even under adverse conditions. The study highlights the importance of ecophysiological assays in microbiome analysis.
Maternal diet alters offspring’s early life host-microbiota communication through goblet cells, resulting in long-lasting diseases susceptibility
Authors: Delaroque Clara , Bonazzi Erica , Huillet Marine , Ellero-Simatos Sandrine , Hao Fuhua , Patterson Andrew , Chassaing Benoit 
Published: July 2024

AbstractA crucial early-life developmental phase regulates microbiome settling while establishing critical and long-lasting immune and metabolic processes. During this period, the influence of select components of maternal diet on offspring microbiota and health remains largely unknown. To investigate the potential transgenerational impact of maternal exposure to microbiota-disrupting factors, dams were subjected prior breeding to dietary emulsifiers, known to directly perturb the microbiota. Such maternal exposure induced early-life microbiota alterations in offspring which associated with long-lasting susceptibility to diet-induced obesity and intestinal inflammation. These detrimental effects were entirely prevented by early-life microbiota normalization through cross-fostering procedures. Mechanistically, maternal emulsifier exposure induces strong offspring’s impairment in goblet cells-mediated host-microbiota communication which is central in driving the observed long-lasting deleterious effects. To conclude, this study underscores the central role played by maternal intake of microbiota-disrupting agents on the next generation’s microbiota, with long lasting consequences for intestinal and metabolic health.
Bayesian inference in arm posture perception
Authors: Peviani Valeria C. , Joosten Manon G.A. , Miller Luke E. , Medendorp W. Pieter 
Published: July 2024

AbstractTo configure our limbs in space the brain must compute their position based on sensory information provided by mechanoreceptors in the skin, muscles, and joints. Because this information is corrupted by noise, the brain is thought to process it probabilistically, and integrate it with prior belief about arm posture, following Bayes’ rule. Here, we combined computational modeling with behavioral experimentation to test this hypothesis. The model conceives the perception of arm posture as the combination of a probabilistic kinematic chain composed by the shoulder, elbow, and wrist angles, compromised with additive Gaussian noise, with a Gaussian prior about these joint angles. We tested whether the model explains errors in a VR-based posture-matching task better than a model that assumes a uniform prior. Human participants (N=20) were required to align their unseen right arm to a target posture, presented as a visual configuration of the arm in the horizontal plane. Results show idiosyncratic biases in how participants matched their unseen arm to the target posture. We used maximum likelihood estimation to fit the Bayesian model to these observations and retrieve key parameters including the prior means and its variance-covariance structure. The Bayesian model including a Gaussian prior explained the response biases and variance much better than a model with a uniform prior. The prior varied across participants, consistent with the idiosyncrasies in arm posture perception, and in alignment with previous behavioral research. Our work clarifies the biases in arm posture perception within a new perspective on the nature of proprioceptive computations.New & NoteworthyWe modeled the perception of arm posture as a Bayesian computation. A VR posture-matching task was used to empirically test this Bayesian model. The Bayesian model including a non-uniform postural prior well explained individual participants’ biases in arm posture perception.
Human-specific lncRNA TMEM9B-AS1 is downregulated in skeletal muscle of individuals with type 2 diabetes and regulates ribosomal biogenesis
Authors: Sen Ilke , Smith Jonathon A B , Caria Elena , Savikj Mladen , Lian Kristian , Ellefsen Stian , Zierath Juleen R , Krook Anna 
Published: July 2024

AbstractLong non-coding RNAs (lncRNAs) are important regulators of skeletal muscle physiology, with altered expression noted in several human diseases including type 2 diabetes. Here we report TMEM9B-AS1, a previously uncharacterized lncRNA, is downregulated in skeletal muscle of men with type 2 diabetes. Silencing of TMEM9B-AS1 in primary human myotubes attenuated protein synthesis, concomitant with reduced phosphorylation of ribosomal protein S6, a downstream target of ERK and mTOR pathways. Moreover, we provide evidence that TMEM9B-AS1 plays a pivotal role in the regulation of ribosomal biogenesis by facilitating mRNA stabilization of the transcription factor MYC through a direct physical interaction with the RNA-binding protein IGF2BP1. Disrupted ribosomal biogenesis resulting from TMEM9B-AS1 silencing is linked reduced skeletal muscle mass in type 2 diabetes, elucidating molecular mechanisms contributing to skeletal muscle loss in metabolic disease.
Cell crowding activates pro-invasive mechanotransduction pathway in high-grade DCIS via TRPV4 inhibition and cell volume reduction
Authors: Bu Xiangning , Ashby Nathanael , Vitali Teresa , Lee Sulgi , Gottumukkala Ananya , Yun Kangsun , Tabbara Sana , Latham Patricia , Teal Christine , Chung Inhee 
Published: July 2024

AbstractCell crowding is a common microenvironmental factor influencing various disease processes, but its role in promoting cell invasiveness remains unclear. This study investigates the biomechanical changes induced by cell crowding, focusing on pro-invasive cell volume reduction in ductal carcinoma in situ (DCIS). Crowding specifically enhanced invasiveness in high-grade DCIS cells through significant volume reduction compared to hyperplasia-mimicking or normal cells. Mass spectrometry revealed that crowding selectively relocated ion channels, including TRPV4, to the plasma membrane in high-grade DCIS cells. TRPV4 inhibition triggered by crowding decreased intracellular calcium levels, reduced cell volume, and increased invasion and motility. During this process, TRPV4 membrane relocation primed the channel for later activation, compensating for calcium loss. Analyses of patient-derived breast cancer tissues confirmed that plasma membrane- associated TRPV4 is specific to high-grade DCIS and indicates the presence of a pro-invasive cell volume reduction mechanotransduction pathway. Hyperosmotic conditions and pharmacologic TRPV4 inhibition mimicked crowding-induced effects, while TRPV4 activation reversed them. Silencing TRPV4 diminished mechanotransduction in high-grade DCIS cells, reducing calcium depletion, volume reduction, and motility. This study uncovers a novel pro-invasive mechanotransduction pathway driven by cell crowding and identifies TRPV4 as a potential biomarker for predicting invasion risk in DCIS patients.
Structural Characterization of DNA Binding Domain of Essential Mammalian Protein TTF 1
Authors: Singh Gajender , Bhopale Abhinetra Jagdish , Khatri Saloni , Prakash Prashant , Kumar Rajnish , Singh Sukh Mahendra , Singh Samarendra Kumar 
Published: July 2024

AbstractTranscription termination factor 1 (TTF1), being multifunctional in nature, is involved in a wide range of critical processes that make it essential for survival of the mammalian cells. TTF1 protein comprises three functional domains: the N-terminal (regulatory/inhibitory) domain, trans-activation domain, and C-terminal domain. The Myb domain is responsible for DNA-binding function of this protein and spans 550 to 732 amino acids (183 residues long). Despite the essential role of TTF1 in multiple cellular processes, there is no physical structure available to date. Purification of the functional full-length protein has been unsuccessful so far. Hence, we moved forward towards characterizing the Myb domain of this essential protein. We first constructed a three-dimensional model of the Myb domain using Robetta server and determined its stability through MD simulation in an explicit solvent. To validate the model, upon codon optimization we cloned this domain into a bacterial expression vector. The protein was then purified to homogeneity and its DNA-binding activity was checked by electro-mobility shift assay. We then proceeded to CD spectroscopy and Raman spectroscopy for secondary structure characterization. The results validated the computational model, concluding that this domain is predominantly helical in nature. The confidence built by this study now pushes us to move ahead in order to solve the atomic structure of this critical domain by crystallography or NMR spectroscopy, which in turn will decipher the exact mechanism by which this essential protein engages DNA to cater to various functions.
Dynamics and Regulatory Roles of RNA m6A Methylation in Unbalanced Genomes
Authors: Zhang Shuai , Wang Ruixue , Luo Kun , Gu Shipeng , Liu Xinyu , Wang Junhan , Zhang Ludan , Sun Lin 
Published: July 2024

AbstractN6-methyladenosine (m6A) in eukaryotic RNA is an epigenetic modification that is critical for RNA metabolism, gene expression regulation, and the development of organisms. Aberrant expression of m6A components appears in a variety of human diseases. RNA m6A modification in Drosophila has proven to be involved in sex determination regulated by Sxl and may affect X chromosome expression through the MSL complex. The dosage-related effects under the condition of genomic imbalance (i.e., aneuploidy) are related to various epigenetic regulatory mechanisms. Here, we investigated the roles of RNA m6A modification in unbalanced genomes using aneuploid Drosophila. The results showed that the expression of m6A components changed significantly under genomic imbalance, and affected the abundance and genome-wide distribution of m6A, which may be related to the developmental abnormalities of aneuploids. The relationships between methylation status and classical dosage effect, dosage compensation, and inverse dosage effect were also studied. In addition, we demonstrated that RNA m6A methylation may affect dosage-dependent gene regulation through dosage-sensitive modifiers, alternative splicing, the MSL complex, and other processes. More interestingly, there seems to be a closely relationship between MSL complex and RNA m6A modification. It is found that ectopically overexpressed MSL complex, especially the levels of H4K16Ac through MOF could influence the expression levels of m6A modification and genomic imbalance may be involved in this interaction. We found that m6A could affect the levels of H4K16Ac through MOF, a component of the MSL complex, and that genomic imbalance may be involved in this interaction. Altogether, our work reveals the dynamic and regulatory role of RNA m6A modification in unbalanced genomes, and may shed new light on the mechanisms of aneuploidy-related developmental abnormalities and diseases.
Nanotiming: telomere-to-telomere DNA replication timing profiling by nanopore sequencing
Authors: Theulot Bertrand , Tourancheau Alan , Simonin Chavignier Emma , Jean Etienne , Arbona Jean-Michel , Audit Benjamin , Hyrien Olivier , Lacroix Laurent , Le Tallec Benoît 
Published: July 2024

ABSTRACTCurrent temporal studies of DNA replication are either low-resolution or require complex cell synchronisation and/or sorting procedures. Here we introduce Nanotiming, a nanopore sequencing-based method producing high-resolution, telomere-to-telomere replication timing (RT) profiles of eukaryotic genomes by interrogating changes in intracellular dTTP concentration during S phase through competition with its analogue bromodeoxyuridine triphosphate (BrdUTP) for incorporation into replicating DNA. Nanotiming solely demands the labelling of asynchronously growing cells with an innocuous dose of BrdU during one doubling time followed by BrdU quantification along nanopore reads. We demonstrate in yeastS. cerevisiaethat Nanotiming precisely reproduces RT profiles generated by reference methods in wild-type and mutant cells inactivated for known RT determinants, for one-tenth of the cost. Nanotiming is simple, accurate, inexpensive, amenable to large-scale analyses, and is capable of unveiling RT at individual telomeres, revealing that Rif1 iconic telomere regulator directly delays the replication only of telomeres with specific subtelomeric elements.
N-acetyl-transferases required for iron uptake and aminoglycoside resistance promote virulence lipid production inM. marinum
Authors: Jones Bradley S. , Pareek Vikram , Hu Daniel D. , Weaver Simon D. , Syska Camille , Galfano Grace , Champion Matthew M. , Champion Patricia A. 
Published: July 2024

AbstractPhagosomal lysis is a key aspect of mycobacterial infection of host macrophages. Acetylation is a protein modification mediated enzymatically by N-acetyltransferases (NATs) that impacts bacterial pathogenesis and physiology. To identify NATs required for lytic activity, we leveragedMycobacterium marinum,a nontubercular pathogen and an established model forM. tuberculosis. M. marinumhemolysis is a proxy for phagolytic activity. We generatedM. marinumstrains with deletions in conserved NAT genes and screened for hemolytic activity. Several conserved lysine acetyltransferases (KATs) contributed to hemolysis. Hemolysis is mediated by the ESX-1 secretion system and by phthiocerol dimycocerosate (PDIM), a virulence lipid. For several strains, the hemolytic activity was restored by the addition of second copy of the ESX-1 locus. Using thin-layer chromatography (TLC), we found a single NAT required for PDIM and phenolic glycolipid (PGL) production. MbtK is a conserved KAT required for mycobactin siderophore synthesis and virulence. Mycobactin J exogenously complemented PDIM/PGL production in the ΔmbtKstrain. The ΔmbtK M. marinumstrain was attenuated in macrophage andGalleria mellonellainfection models. Constitutive expression of eithereisorpapA5,which encode a KAT required for aminoglycoside resistance and a PDIM/PGL biosynthetic enzyme, rescued PDIM/PGL production and virulence of the ΔmbtKstrain. Eis N-terminally acetylated PapA5in vitro, supporting a mechanism for restored lipid production. Overall, our study establishes connections between the MbtK and Eis NATs, and between iron uptake and PDIM and PGL synthesis inM. marinum. Our findings underscore the multifunctional nature of mycobacterial NATs and their connection to key virulence pathways.Significance StatementAcetylation is a modification of protein N-termini, lysine residues, antibiotics and lipids. Many of the enzymes that promote acetylation belong to the GNAT family of proteins.M. marinumis a well-established as a model to understand howM. tuberculosiscauses tuberculosis. In this study we sought to identify conserved GNAT proteins required for early stages of mycobacterial infection. UsingM. marinum,we determined that several GNAT proteins are required for the lytic activity ofM. marinum.We uncovered previously unknown connections between acetyl-transferases required for iron uptake and antimicrobial resistance, and the production of the unique mycobacterial lipids, PDIM and PGLOur data support that acetyl-transferases from the GNAT family are interconnected, and have activities beyond those previously reported.
Structural details of helix-mediated TDP-43 C-terminal domain multimerization
Authors: Rizuan Azamat , Shenoy Jayakrishna , Mohanty Priyesh , dos Passos Patricia M. S. , Mercado Ortiz José F. , Bai Leanna , Viswanathan Renjith , Wang Szu-Huan , Johnson Victoria , Mamede Lohany D. , Ayala Yuna M. , Ghirlando Rodolfo , Mittal Jeetain , Fawzi Nicolas L. 
Published: July 2024

AbstractThe primarily disordered C-terminal domain (CTD) of TAR DNA binding protein-43 (TDP-43), a key nuclear protein in RNA metabolism, forms neuronal inclusions in several neurodegenerative diseases. A conserved region (CR, spanning residues 319-341) in CTD forms transient helix-helix contacts important for its higher-order oligomerization and function that are disrupted by ALS-associated mutations. However, the structural details of CR assembly and the explanation for several ALS-associated variants’ impact on phase separation and function remain unclear due to challenges in analyzing the dynamic association of TDP-43 CTD using traditional structural biology approaches. By employing an integrative approach, combining biophysical experiments, biochemical assays, AlphaFold2-Multimer (AF2-Multimer), and atomistic simulations, we generated structural models of helical oligomerization of TDP-43 CR. Using NMR, we first established that the native state of TDP-43 CR under physiological conditions is α-helical. Next, alanine scanning mutagenesis revealed that while hydrophobic residues in the CR are important for CR assembly, phase separation and TDP-43 nuclear retention function, polar residues down regulate these processes. Finally, pairing AF2-Multimer modeling with AAMD simulations indicated that dynamic, oligomeric assemblies of TDP-43 that are stabilized by a methionine-rich core with specific contributions from a tryptophan/leucine pair. In conclusion, our results advance the structural understanding of the mechanisms driving TDP-43 function and provide a window into the initial stages of its conversion into pathogenic aggregates.
CBP/p300 lysine acetyltransferases inhibit HIV-1 expression in latently infected T-cells
Authors: Horvath Riley M. , Sadowski Ivan 
Published: July 2024

AbstractHIV-1 latency is regulated by chromatin modifying enzymes, and histone deacetylase inhibitors (HDACi) were previously found to reactivate provirus expression. We report that inhibitors of CBP/p300 acetyltransferases also cause reversal of latency in T-cells. CBP/p300 inhibitors synergize with mechanistically diverse latency reversing agents to cause HIV-1 reactivation. In contrast, inhibition of CBP/p300 impaired the latency reversal by the HDACi SAHA, indicating that CBP/p300 contribute to acetylation on the HIV-1 LTR associated with HDACi-mediated latency reversal. CBP/p300 inhibition caused loss of H3K27ac and H3K4me3 from the LTR, but did not affect association of the inhibitor protein BRD4. Furthermore, inhibition of the additional lysine acetyl transferases PCAF/GCN5 or KAT6A/KAT6B also caused reversal of latency, suggesting that protein acetylation has an inhibitory effect on HIV-1 expression. Collectively, these observations indicate that transcription from the HIV-1 LTR is controlled both positively and negatively by protein acetylation, likely including both histone and non-histone regulatory targets.