bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pleomorphic effects of three small-molecule inhibitors on transcription elongation byMycobacterium tuberculosisRNA polymerase
Authors: Herrera-Asmat Omar , Tong Alexander B. , Lin Wenxia , Kong Tiantian , Del Valle Juan R , Guerra Daniel G. , Ebright Yon W. , Ebright Richard H. , Bustamante Carlos 
Published: February 2025

AbstractTheMycobacterium tuberculosisRNA polymerase (MtbRNAP) is the target of the first-line anti-tuberculosis inhibitor rifampin, however, the emergence of rifampin resistance necessitates the development of new antibiotics. Here, we communicate the first single-molecule characterization of MtbRNAP elongation and its inhibition by three diverse small-molecule inhibitors: N(α)-aroyl-N-aryl-phenylalaninamide (D-IX216), streptolydigin (Stl), and pseudouridimycin (PUM) using high-resolution optical tweezers. Compared toEscherichia coliRNA polymerase (EcoRNAP), MtbRNAP transcribes more slowly, has similar mechanical robustness, and only weakly recognizesE. colipause sequences. The three small-molecule inhibitors of MtbRNAP exhibit strikingly different effects on transcription elongation. In the presence of D-IX216, which inhibits RNAP active-center bridge-helix motions required for nucleotide addition, the enzyme exhibits transitions between slowly and super-slowly elongating inhibited states. Stl, which inhibits the RNAP trigger-loop motions also required for nucleotide addition, inhibits RNAP primarily by inducing pausing and backtracking. PUM, a nucleoside analog of UTP, in addition to acting as a competitive inhibitor, induces the formation of slowly elongating RNAP inhibited states. Our results indicate that the three classes of small-molecule inhibitors affect the enzyme in distinct ways and show that the combination of Stl and D-IX216, which both target the RNAP bridge helix, has a strong synergistic effect on the enzyme.
Diversity, abundance, and biogeography of CO2fixing microorganisms in peatlands
Authors: Le Geay Marie , Mayers Kyle , Sytiuk Anna , Dorrepaal Ellen , Küttim Martin , Lamentowicz Mariusz , Tuittila Eeva-Stiina , Lauga Béatrice , Jassey Vincent E.J. 
Published: February 2025

AbstractMicrobial communities play a crucial role in the carbon (C) dynamic of peatlands— a major terrestrial C reservoir. While heterotrophic microorganisms attracted much attention over the past decades due to their role in peatland greenhouse gases emissions, CO2fixing microorganisms (CFMs) remained particularly overlooked. Here, by leveraging metabarcoding and digital droplet PCR (ddPCR), we provide a comprehensive survey of CFM communities, including oxygenic phototrophs, chemoautotrophs and aerobic anoxygenic phototrophic bacteria (AAnPBs), in different peatland types. We demonstrate that CFMs are very abundant and diverse in peatlands, with on average 1021 CFMs contributing up to 40% of the total bacterial abundance. In particular, we show that oxygenic phototrophs (mostly Cyanophyceae and Palmophylloceae) are the most abundant CFMs, closely followed by chemoautotrophs (Proteobacteria) and AAnPBs (Vulcanimicrobiia). Using a joint-species distribution model, we further find that CFMs aggregate into six major clusters with different niche size. These clusters constitute the core and specific CFM microbiome. The core microbiome, which the occurrence is strongly influenced by temperature and nutrients, directly modulate the diversity and abundance of CFMs. Our findings highlight the importance of CFM diversity and abundance in peatlands, further reveal their complex structuration in link with environmental conditions and suggest that changes in environmental conditions could shift CFMs communities. These results are the foundation to better understand the role of CFMs for the peatland C cycle inputs.
Multi-protein silencing using WRAP-based nanoparticles: a proof of concept
Authors: Konate Karidia , Pezzati Irène , Redjatti Karima , Agnel Estelle , Vivès Eric , Faure Sandrine , de Santa Barbara Pascal , Boisguérin Prisca , Deshayes Sébastien 
Published: February 2025

ABSTRACTCancer remains the leading cause of death, with chemotherapy, radiotherapy, and surgical resection being the primary treatment methods. However, chemotherapy’s side effects, surgical limitations, and drug resistance present significant challenges. Small interfering RNA (siRNA) has emerged as a promising tool in cancer therapy due to its ability to silence disease-related genes selectively. Recent advancements in non-viral delivery systems, particularly cell-penetrating peptides (CPPs), have enhanced the efficacy of siRNA delivery. The use of siRNA as a therapeutic tool in cancer treatment has been reported. However, silencing only one target protein has only minor effects on tumor cell proliferation as previously shown for WRAP-based nanoparticles targeting cyclin-dependent kinase 4 (CDK4) in human glioblastoma cells. Here, we designed a more sophisticated approach to enhance therapeutic efficacy, encapsulating multiple siRNAs targeting CDK4, cyclin D1 (CD1), and Mcl-1 proteins. The siRNA cocktail, delivered via WRAP5 nanoparticles, effectively silenced these targets and reduced cell proliferation in human glioblastoma cells. Furthermore, the nanoparticles also demonstrated potential therapeutic impact in gastrointestinal stromal tumors (GIST), a rare cancer characterized by its tendency to resist standard treatments. This study highlights the versatility of WRAP5 nanoparticles as a platform for personalized cancer therapy, suggesting that siRNA delivery systems may be tailored to specific cancer types for more effective treatment strategies.
Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD and Amide15N(1H) NMR Relaxation
Authors: Lesovoy Dmitry , Roshchin Konstantin , Sala Benedetta Maria , Sandalova Tatyana , Achour Adnane , Agback Tatiana , Orekhov Vladislav , Agback Peter 
Published: February 2025

AbstractConformational heterogeneity is critical for protein function, but the validation of dynamic ensembles remains a challenge. In this study, we introduced an approach that integrates free MD simulations, using an AlphaFold-generated structure as the starting point, with experimental relaxation data to identify biologically relevant conformational ensembles. For the extracellular region ofStreptococcus pneumoniaePsrSp, we found that only certain segments of the MD long trajectory aligned well with experimental data. The defined ensembles revealed two regions with increased flexibility that play important functional roles.
Cryo-correlative light and electron tomography of dopaminergic axonal varicosities reveals non-synaptic modulation of cortico-striatal synapses
Authors: Lapios Paul , Anger Robin , Paget-Blanc Vincent , Marza Esther , Lučić Vladan , Fronzes Rémi , Herzog Etienne , Perrais David 
Published: February 2025

AbstractDopamine is an essential brain neuromodulator involved in reward and motor control. Dopaminergic (DA) neurons project to most brain areas, with particularly dense innervation in the striatum. DA varicosities bind to target striatal synapses and form dopamine hub synapses (DHS). However, the basic features of dopamine release sites are still largely unknown. Here we studied the ultrastructure of fluorescent DA and glutamatergic (GLU) synaptosomes isolated from the striatum of adult mice with cryo-correlative light and electron microscopy and cryo-electron tomography. We observed that DA synaptosomes display ∼10 times fewer vesicles than GLU ones. DA vesicles are bigger and less round. Vesicle organization at single nanometer scale indicates that most GLU synaptosomes have tethered and primed vesicles, indicative of a readily releasable pool, while only 39 % of DA synaptosomes have tethered vesicles, which appear not to be primed. In addition, GLU terminals contacted by DA terminals in DHS have more primed vesicles than others. While DA varicosities do not form genuine synapses, their adhesion to cortico-striatal synapses may convey a local regulation of synaptic release properties.
Navigational Frames of Reference as Critical Regulators of Hippocampal Interneuron Coding Properties
Authors: Bott Jean-Bastien , Penazzi Lorene , Al-Achkar Salodin , Cho Minyoung , Rivard Bruno , Lafreniere Etienne Gautier , Williams Sylvain 
Published: February 2025

AbstractEfficient spatial navigation relies on the hippocampus integrating local (proximal) and global (distal) cues, collectively called frames of reference, to guide behavior and support memory. Although these cues control the anchoring of principal cell fields, how these frames tune interneuron functions remains unknown. Traditionally, interneurons such as O-LM and VIP cells have been viewed primarily as speed encoders, although some also encode spatial information or respond to discrete stimuli. Using calcium imaging in freely behaving mice performing a new spatial learning task that differentiates between reference frames, we demonstrate that O-LM cells displayed a striking bimodal activity pattern, altering both their speed and spatial encoding properties. In contrast, VIP interneurons were largely unaffected by changes in the frame of reference, instead correlating with familiarization. Notably, linear decoding using speed scores revealed that only O-LM interneurons provide an accurate readout of the dominant reference frame, enabling prediction of the animal’s navigation strategy. These findings highlight that hippocampal interneurons can flexibly adapt their functions depending on cognitive factors such as the reference frames used to guide behavior.
FG-Nup Sequence Length Polydispersity Enhances Selectivity of NPC Translocation
Authors: Patel Manoj K , Panwar Ajay S 
Published: February 2025

ABSTRACTThe central channel of the nuclear pore complex (NPC) exhibits polydispersity in FG-nucleoporin (FG-Nup) sequence length, with longer FG-Nups on the periphery and shorter FG-Nups in the interior of the pore. The functional role of FG-Nup polydispersity in NPC transport was investigated using a minimal, coarse-grained model and Langevin dynamics simulations. The NPC was modelled as a cylindrical pore lined with a random copolymer brush composed of hydrophobic and hydrophilic segments, mimicking FG-Nups. The total number of hydrophobic segments corresponded to the fraction of FG-repeats,f, in the FG-Nups. The translocation of karyopherin-bound spherical cargo (12 nm spherical tracers) was simulated through two model NPCs; a homogeneous NPC (h-NPC) with uniform FG-Nup lengths and an inhomogeneous NPC (ih-NPC) featuring shorter FG-Nups in the middle and longer FG-Nups at the periphery. Theih-NPC demonstrated enhanced selectivity and significantly higher passage probabilities for karyopherin-bound tracers, with an increase of up to 90% compared toh-NPC. Analysis of binding contacts between tracers and FG-Nup hydrophobic segments revealed that tracer translocation was facilitated by a handover process between successive FG-Nups along the NPC length. The enhanced selectivity of theih-NPC was attributed to an increase in binding contacts of the tracer with the shorter FG-Nups in its middle region. These findings provide a biophysical basis for the evolutionary significance of FG-Nup polydispersity in selective NPC transport.
Experimental insights on the behaviour and development of Near Eastern Fire salamanders (Salamandra infraimmaculata) indicate general strategies to cope with aquatic predators
Authors: Reinhardt Timm , Küpfer Eliane , Segev Ori , Blaustein Leon , Tobias Krause E. , Steinfartz Sebastian 
Published: February 2025

AbstractFishes are key predators of amphibian larvae with often devastating consequences for their abundance and survival.In Israel, the Near Eastern Fire salamander (Salamandra infraimmaculata) reaches the southern limit of the geographic distribution of the whole genusand has tocope with xeric terrestrial habitats- and a scarcity of suitable sites for the deposition of larvaewith permanentsprings and streams arebeingrare. One such location is the Tel Dan National Park in the North of Israel, were, surprisingly salamander larvae and fishes coexist successfully in a system of larger and smaller streams. In three experiments we tested different anti-predator behaviour with salamanders from Tel Dan and other locations. We analysedwhether gravid females avoid the presence of fish when depositing their larvae; if the presence of fish impacts larval development and if salamander larvae show active hiding behaviour when confronted with fish cues. While females from Tel Dan showed a bet-hedging strategy in site selection irrespective of fish presence, larval developmental rate was reduced in the presence of fish probably due to a lower feeding activity. Lastly, larvae from different sites displayed hiding behaviour in the presence of fish, irrespective whether they naturally coexist with fish or not. We infer from our results and existing studies thatS. infraimmaculatahas general rather than site-specific adaptations to cope with the presence of fish. We conclude that the general adaptations are essential to sustain this species in a range of extreme habitats at the southern limit of the s distribution.
Mechanism of forced-copy-choice RNA recombination by enteroviral RNA-dependent RNA polymerases
Authors: Arnold Jamie J. , Martinez Alexandre , Jain Abha , Liu Xinran , Moustafa Ibrahim M. , Cameron Craig E. 
Published: February 2025

AbstractForced-copy-choice recombination occurs at the end of a template, differing from copy-choice recombination, which happens at internal positions. This mechanism may produce full-length genomes from fragments created by host antiviral responses. Previous studies from our laboratory demonstrated that poliovirus (PV) RNA-dependent RNA polymerase (RdRp) switches to an “acceptor” templatein vitrowhen initiated on a heteropolymeric RNA-primed “donor” template. Surprisingly, recombinants showed template switching from the 3’-end of the donor template. We have developed a primed-template system to study PV RdRp-catalyzed forced-copy-choice RNA recombination. PV RdRp adds a single, non-templated nucleotide to the 3’-end of a blunt-ended, double-stranded RNA product, forming a “plus-one” intermediate essential for template switching. Non-templated addition of CMP was favored over AMP and GMP (80:20:1); UMP addition was negligible. A single basepair between the plus-one intermediate and the 3’-end of the acceptor template was necessary and sufficient for template switching, which could occur without RdRp dissociation. Formation of the plus-one intermediate was rate limiting for template switching. PV RdRp also utilized synthetic, preformed intermediates, including those with UMP 3’-overhangs. Reactions showed up to five consecutive template-switching events, consistent with a repair function for this form of recombination. PV RdRp may exclude UMP during forced-copy-choice RNA recombination to preclude creation of nonsense mutations during RNA fragment assembly. Several other picornaviral RdRps were evaluated, and all were capable of RNA fragment assembly to some extent. Lastly, we propose a structure-based hypothesis for the PV RdRp-plus-one intermediate complex based on an elongating PV RdRp structure.
Drosophilaembryo cellularization is modulated by the viscoelastic dynamics of cortical-membrane interactions
Authors: Stark Kyle , Bonilla Quintana Mayte , Sokac Anna Marie , Rangamani Padmini 
Published: February 2025

1AbstractThe generation of an epithelial sheet transforms fruit fly embryos from a single syncytial cell directly into a tissue. For this to happen, the apical microvillus membrane is pulled between peripherally anchored nuclei in a process known as furrow invagination. Experimental measurements of furrow invagination velocities have shown that the rate of invagination undergoes slow-to-fast and fast-to-stalled velocity transitions during the formation of individual cells. The causes of such changes are due to multiple intersecting mechanisms and molecular components, including motor proteins, microtubules, and F-actin. In this work, we develop a continuum model to describe the dynamics of furrow invagination. Our model is constrained by previously published experimental data and considers the roles of cytoskeletal forces, cytoplasmic drag, motor protein forces, and membrane tension. We find that the viscous forces produced by the cytoskeleton sliding beneath the plasma membrane dictates furrow velocity. We propose that the slow phase is slow because there is a high density of microvilli, which increases the number of viscous contact points between the plasma membrane and the underlying cytoskeleton. This in turn, results in a higher resistance to furrow invagination. We predict that the fast phase may benefit from fewer cytoskeleton-to-plasma membrane contact points, thus reducing viscous forces and promoting the slow-to-fast switch. Then, we use perturbation and loss-of-function simulations to show that microvillus and sub-apical membrane reservoirs are vital to setting furrow invagination dynamics. This work demonstrates how coupling between the cytoskeleton, the plasma membrane, and distinct membrane reservoirs affects the plasticity and dynamics of cellularization.
DeepMM: Identify and correct Metagenome Misassemblies with deep learning
Authors: Ding Yi , Xiao Jin , Zou Bohao , Yang Chao , Zhang Lu 
Published: February 2025

AbstractAccurate metagenomic assemblies are essential for constructing reliable metagenome-assembled genomes (MAGs). However, the complexity of microbial genomes continues to pose challenges for accurate assembly. Current reference-free assembly evaluation tools primarily rely on hand-crafted features and suffer from poor generalization across different metagenomic data. To address these limitations, we propose DeepMM, a novel deep learning-based visual model de-signed for the identification and correction of metagenomic misassemblies. DeepMM transforms alignments between assemblies and reads into a multi-channel image for misassembly feature learning and applies contrastive learning to bring different views of misassemblies closer. Fur-thermore, DeepMM offers a fine-tuning process to match different sequencer data. Our results show that DeepMM outperforms state-of-the-art methods in identifying misassemblies, achieving the highest AUPRC score in five CAMI datasets. DeepMM provides accurate correction of misassemblies, significantly improving downstream binning results, increasing the number of near-complete MAGs from 905 to 1006 in a large real metagenomic sequencing dataset derived from a diarrhea-predominant Irritable Bowel Syndrome (IBS-D) cohort.
CCR2 recruits monocytes to the lung, while CX3CR1 modulates positioning of monocyte-derived CD11cposcells in the lymph node during pulmonary tuberculosis
Authors: Mohapatra Alexander , Howard Zachary , Ernst Joel D. 
Published: February 2025

ABSTRACTInfection byMycobacterium tuberculosis(Mtb) continues to cause more than 1 million deaths annually, due to pathogen persistence in lung macrophages and dendritic cells derived from blood monocytes. While accumulation of monocyte-derived cells in the Mtb-infected lung partially depends on the chemokine receptor CCR2, the other chemoattractant receptors regulating trafficking remain undefined. We used mice expressing knock-in/knockout reporter alleles ofCcr2andCx3cr1to interrogate their expression and function in monocyte-derived populations of the lungs and draining mediastinal lymph nodes during Mtb infection. CCR2 and CX3CR1 expression varied across monocyte-derived subsets stratified by cell surface Ly6C expression in both organs. We found that expression of CCR2 predicted dependence of monocyte-derived cells on the receptor for lung and lymph node accumulation. CCR2-deficient mice were also observed to have worsened lung and lymph node Mtb burden. While CX3CR1 deficiency, alone or in combination with CCR2 deficiency, did not affect cell frequencies or lung Mtb control, its absence was associated with altered positioning of monocyte-derived dendritic cells in mediastinal lymph nodes. We found that combined loss ofCcr2andCx3cr1also worsened Mtb control in the mediastinal lymph node, suggesting a rationale for the persistent expression of CX3CR1 among monocyte-derived cells in pulmonary tuberculosis.IMPORTANCEMycobacterium tuberculosisis the respiratory pathogen responsible for the deadliest infectious disease worldwide. Susceptible humans exhibit ineffective immune responses, in which infected phagocytes are not able to eliminate the pathogen. Since recruited monocyte-derived cells serve as reservoirs for persistent infection, understanding how these phagocytes accumulate in the lung and why they are unable to eliminate Mtb can inform development of therapies that can synergize with antimicrobials to achieve faster and more durable Mtb elimination. Monocyte-derived cells express the chemokine receptors CCR2 and CX3CR1, but the role of the latter in Mtb infection remains poorly defined. The significance of our study is in elucidating the roles of these receptors in the trafficking of monocyte-derived cells in the infected lung and mediastinal lymph node. These data shed light on the host response in tuberculosis and in other pulmonary infections.
ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata
Authors: Zheng Ping , Audain Enrique , Webel Henry , Dai Chengxin , Klein Joshua , Hitz Marc-Phillip , Sachsenberg Timo , Bai Mingze , Perez-Riverol Yasset 
Published: February 2025

AbstractIntensity-based absolute quantification (iBAQ) is essential in proteomics as it allows for the assessment of a protein’s absolute abundance in various samples or conditions. However, the computation of these values for increasingly large-scale and high-throughput experiments, such as those using DIA, TMT, or LFQ workflows, poses significant challenges in scalability and reproducibility. Here, we present ibaqpy (https://github.com/bigbio/ibaqpy), a Python package designed to compute iBAQ values efficiently for experiments of any scale. ibaqpy leverages the Sample and Data Relationship Format (SDRF) metadata standard to incorporate experimental metadata into the quantification workflow. This allows for automatic normalization and batch correction while accounting for key aspects of the experimental design, such as technical and biological replicates, fractionation strategies, and sample conditions. Designed for large-scale proteomics datasets, ibaqpy can also recompute iBAQ values for existing experiments when an SDRF is available. We showcased ibaqpy’s capabilities by reanalyzing 17 public proteomics datasets from ProteomeXchange, covering HeLa cell lines with 4,921 samples and 5,766 MS runs, quantifying a total of 11,014 proteins. In our reanalysis, ibaqpy is a key component in automating reproducible quantification, reducing manual effort and making quantitative proteomics more accessible while supporting FAIR principles for data reuse.