bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antarctic photosynthesis: energy transfer and charge separation in the diatomChaetoceros Simplex
Authors: Lee Shu En , van de Poll Willem , Chukhutsina Volha 
Published: January 2025

AbstractThe polar oceanic environment poses extreme challenges to photosynthetic organisms, which have evolved atypical strategies to maintain efficient photosynthesis in cold temperatures. Here, the psychrophilic diatomChaetoceros simplex (C. simplex)is studiedin vivoin the dark-adapted state using steady-state and time-resolved fluorescence methods. Our results show that all fucoxanthin chlorophyll a/c protein (FCP) antenna transfer energy to photosystem I (PSI) or photosystem II (PSII), with no detached FCPs. PSI exhibits no fluorescence of ‘red’ forms of chlorophyll (chl) beyond 700 nm in both 279 K and 77 K conditions. Despite this, it apparently has a long decay time of ∼85 ps indicating the presence of a large core-antenna supercomplex. PSII has an average lifetime of ∼500ps in open state (QAoxidized) and ∼1220 ps in closed state (QAreduced). PSII of C. simplex has kinetics that are slightly slower than temperate diatoms, suggesting slightly larger antenna. In addition, fucoxanthin (fx) molecules of FCP that absorb in the 500 - 550 nm range (fx-red) transfer more energy to PSII than fx that absorb in the blue range (fx-blue, 462 nm max absorption). A subpopulation of red-shifted, aggregated FCPs are detected at 77 K, that are active in energy transfer uphill at 279 K. Overall, our results indicate relatively larger antenna of PSI and PSII and an absence of red chls in PSI of cold-adapted species, compared to temperate species.
Atomistic Mechanism of Non-Canonical Voltage Gating in TREK K2PChannels
Authors: Aldakul Yessenbek K. , Schewe Marcus , Diez Carlos C. , Hwang Songhwan , Baukrowitz Thomas , Sun Han 
Published: January 2025

AbstractTwo-pore-domain K+(K2P) channels are essential regulators of cellular excitability and respond to various external stimuli that also include membrane potential for most K2Pchannels. Voltage gating is particularly pronounced in members of the TREK/TRAAK subfamily. This voltage sensitivity was surprising, as K2Pchannels lack a classical voltage sensing domain. Prior studies have attributed this non-canonical voltage sensing mechanism to the unique ion-flux gating properties of the K2Pselectivity filter (SF), where inward currents induce fast inactivation, while depolarization activates the SF. Here, we performed large-scale molecular dynamics (MD) simulations across various voltages to gain an atomistic understanding of ion-flux gating in TREK channels. Our analysis revealed an asymmetric stability difference in the SF, enabling water influx into the filter due to conformational flexibility on the extracellular side. Inward flux inactivation occurs when water entry halts ion permeation, followed by the unbinding of three K+ions, consistent with gating charge analysis. Additionally, MD simulations of TREK-2 mutants and the TWIK-1 channel, which exhibited increased SF flexibility, showed augmented SF water occupancy, aligning with their electrophysiological phenotypes. Key experimental evidence of this mechanism was provided by electrophysiology measurements, which showed that high extracellular sucrose slowed ion-flux inactivation by reducing water entry into the SF. These findings uncover the atomistic mechanism of voltage gating in TREK K2Pchannels and pave the way for exploring non-canonical voltage gating mechanisms in other ion channels.
Engineering Infrared Light Detection in Blind Human Retina Using Ultrasensitive Human TRPV1 Channels
Authors: Chevalier Morgan , Fadel Firas , Májer Tímea , Magda Dániel Péter , Gerendás Lili , Kilin Ferenc , Nagy Zoltán Zsolt , Szabó Arnold , Roska Botond , Testa-Silva Guilherme 
Published: January 2025

SummaryEngineering infrared light sensitivity in the blind human retina could restore visual function in patients with regional retinal degeneration. However, current approaches are complex and contain non-human biological components. Using rational protein design we engineered human TRPV1 channels (Δ786-840) with temperature sensitivity shifted from 45 to 41°C that enabled near-infrared light- induced heat activation of mammalian cells at close to physiological temperatures. When expressed in ganglion cells of human retinal explants, Δ786-840 TRPV1 generated robust spiking responses to brief near-infrared light-induced temperature transients. Additionally, increasing intensity of radiation evoked graded responses correlating with increasing firing frequencies. Unlike previous approaches that used non-human TRPV1 channels, which risk immune reactions and a multicomponent system that poses barriers to clinical implementation, this single component human-derived approach eliminates immunogenicity concerns, addressing a major challenge to clinical translation, and allow gene delivery using adeno-associated viral vectors.
VE-cadherin RGD motifs are dispensable for cell-cell junctions, endothelial barrier function and leukocyte extravasation
Authors: Schoon Rianne M. , van der Meer Werner J. , van Stalborch Anne-Marieke D. , van Buul Jaap D. , Huveneers Stephan 
Published: January 2025

AbstractVE-cadherin is a key transmembrane protein in endothelial cell-cell junctions, essential for maintaining vascular integrity and regulating selective leukocyte extravasation into inflamed tissue. The extracellular domain of human VE-cadherin contains two arginine-glycine-aspartate (RGD) motifs, which are known integrin-binding sites, particularly for integrins in the β1, β3, and β5 families. In this study, we examined the functional relevance of these RGD motifs by generating VE-cadherin variants with the RGD sequences mutated to non-functional RGE. Immunofluorescence analysis showed that the VE-cadherin[D238E], VE-cadherin[D301E], and double-mutant VE-cadherin[D238/301E] variants formed stable cell-cell junctions, comparable to wild-type VE-cadherin. Additionally, electric cell-substrate impedance sensing (ECIS) confirmed that endothelial cells expressing each VE-cadherin RGD>RGE variant maintained efficient barrier function. Moreover, leukocyte transmigration assays demonstrated that the RGD>RGE mutations did not affect leukocyte-endothelial interactions during transmigration. In summary, our findings indicate that the VE-cadherin RGD motifs are not essential for endothelial junction formation or leukocyte transmigration.
Rapid “recycling” of logical algorithm representations in fronto-parietal reasoning systems following computer programming instructions
Authors: Liu Yun-Fei , Bedny Marina 
Published: January 2025

AbstractProgramming is a cornerstone of modern society, yet its cognitive and neural basis remains poorly understood. In this study, we test the hypothesis that programming “recycles” pre-existing neural mechanisms and representations in fronto-parietal reasoning networks. Using fMRI, we scanned programming-naïve undergraduates (n=22) before (PRE) and after (POST) an introductory Python course. During the PRE scan, participants viewed pseudocode (plain English descriptions of algorithms), and during the POST scan, they read Python code. We found that a left-lateralized fronto-parietal network, previously implicated in programming experts, distinguished between “for” loops and “if” conditionals across both pseudocode and Python code. Representational similarity analysis revealed consistent representations of algorithms across formats (code/pseudocode) and learning stages. Furthermore, such representations encode abstract meanings rather than superficial features. Our findings demonstrate that programming not only recycles pre-existing neural resources evolved for logical reasoning, but the recycling takes place rapidly with only a single semester of training.
Modeling human limb skeletal development using human pluripotent stem cell-derived skeletal assembloids
Authors: Takao Tomoka , Osone Tatsunori , Sato Kohei , Yamada Daisuke , Fujisawa Yuki , Hagiwara Masaya , Nakata Eiji , Ozaki Toshifumi , Toguchida Junya , Takarada Takeshi 
Published: January 2025

SUMMARYDespite recent advances in pluripotent stem cell-based approaches to induce skeletal cells, recapitulating human limb skeletal development in terms of structure and longitudinally oriented growth remains an unresolved challenge. Here, we report a method to differentiate human pluripotent stem cells into region-specific skeletal organoids harboring GDF5+PRG4+interzone/articular chondrocyte progenitors (IZ/ACPs) and SP7+growth plate chondrocytes (GPCs) via PRRX1+limb-bud mesenchymal cells. Comparative analysis demonstrated marked similarities of IZ/ACP and GPC organoids to the human embryonic limb, and graft fate and regenerative capacityin vivowere further characterized. We also mimicked the limb skeletal developmental process in a spatially structured manner by vertically positioning two IZ/ACP organoids at both ends of a GPC organoid to generate a human skeletal assembloid. Notably, this human skeletal assembloid recapitulated endochondral ossification with longitudinal skeletal growth upon transplantation. In summary, our study provides a novel research platform for human limb skeletal development and disease.
Inherent instability of simple DNA repeats shapes an evolutionarily stable distribution of repeat lengths
Authors: McGinty Ryan J. , Balick Daniel J. , Mirkin Sergei M. , Sunyaev Shamil R. 
Published: January 2025

AbstractUsing the Telomere-to-Telomere reference, we assembled the distribution of simple repeat lengths present in the human genome. Analyzing over two hundred mammalian genomes, we found remarkable consistency in the shape of the distribution across evolutionary epochs. All observed genomes harbor an excess of long repeats, which are prone to developing into repeat expansion disorders. We measured mutation rates for repeat length instability, quantitatively modeled the per-generation action of mutations, and observed the corresponding long-term behavior shaping the repeat length distribution. We found that short repetitive sequences appear to be a straightforward consequence of random substitution. Evolving largely independently, longer repeats (10+ nucleotides) emerge and persist in a rapidly mutating dynamic balance between expansion, contraction and interruption. These mutational processes, collectively, are sufficient to explain the abundance of long repeats, without invoking natural selection. Our analysis constrains properties of molecular mechanisms responsible for maintaining genome fidelity that underlie repeat instability.
Genome-wide CRISPR knockout screening with viral replicons for identification of host factors involved in viral replication
Authors: Cheng Karen W. , Bhave Madhura , Markhard Andrew , Peng Duo , Bhatt Karan D. , Travisano Katherine , Medicielo Josette V. , Lembirik Sanae , Njoya Leila , Anantpadma Manu , Kuhn Jens H. , Puschnik Andreas S. , Kistler Amy 
Published: January 2025

AbstractPooled CRISPR knockout (KO) screens using live viruses are a proven and valuable approach for identifying essential host factors acting across viral life cycles. Here we describe the development of a pooled genome-wide CRISPR KO screening approach using stable viral replicon cell lines to specifically identify host factors essential for viral replication. Virus replicons are non-infectious, therefore enabling the study of highly virulent viruses under standard biosafety level 2 containment. We developed a stable fluorescent dengue virus type 2 (DENV-2) replicon cell line to perform a pooled genome-wide FACS-based CRISPR KO screen. This benchmark DENV-2 replicon screen successfully identified host genes previously known to be required for viral DENV-2 replication (e.g., endoplasmic reticulum membrane complex and oligosaccharyltransferase complex components) and confirmed two additional genes (DOHH and ZFP36L2) involved in replication that have not been recovered in prior live virus screens. We applied this replicon screening approach to two highly divergent viruses: chikungunya virus (CHIKV), a positive-sense RNA virus that replicates at the plasma membrane, and Ebola virus (EBOV), a negative-sense RNA virus that replicates in cytoplasmic inclusion bodies. The CHIKV replicon screen identified two genes known to be required for replication (G3BP1 and G3BP2) and several additional, novel genes (CLEC4G, CSDE1, GOLGA7, HNF1A, and PCBD1). We verified two of them (CSDE1 and GOLGA7) in live CHIKV replication assays. A distinct set of genes (EHMT1, EHMT2, and USP7) were recovered in the EBOV replicon screen and were further confirmed using independent transient transfection assays. Thus, viral replicon-based screens provide a useful approach that can be extended to viruses of diverse taxa to identify host pathways essential for viral replication and to uncover potential novel targets for host-directed medical countermeasures.
Neural mechanisms of object prioritization in vision
Authors: Grignolio Damiano , Meyyappan Sreenivasan , Geng Joy , Mangun George R. , Hickey Clayton 
Published: January 2025

AbstractSelective attention is widely thought to be sensitive to visual objects. This is commonly demonstrated in cueing studies, which show that when attention is deployed to a known target location that happens to fall on a visual object, responses to targets that unexpectedly appear at other locations on that object are faster and more accurate, as if the object in its entirety has been visually prioritized. However, this notion has recently been challenged by results suggesting that putative object-based effects may reflect the influence of hemifield anisotropies in attentional deployment, or of unacknowledged influences of perceptual complexity and visual clutter. Studies employing measures of behaviour provide limited opportunity to address these challenges. Here, we used EEG to directly measure the influence of task-irrelevant objects on the deployment of visual attention. We had participants complete a simple visual cueing task involving identification of a target that appeared at either a cued location or elsewhere. Throughout each experimental trial, displays contained task-irrelevant rectangle stimuli that could be oriented horizontally or vertically. We derived two cue-elicited indices of attentional deployment–lateralized alpha oscillations and the ADAN component of the event-related potential–and found that these were sensitive to the otherwise irrelevant orientation of the rectangles. Our results demonstrate that the allocation of visual attention is influenced by objects boundaries, supporting models of object-based attentional prioritization.
N6-methyladenosine and the NEXT complex direct Xist RNA turnover and X inactivation dynamics
Authors: Wei Guifeng , Coker Heather , Rodermund Lisa , Almeida Mafalda , Roach Holly L. , Nesterova Tatyana B. , Brockdorff Neil 
Published: January 2025

AbstractX chromosome inactivation (XCI) in mammals is orchestrated by the non-coding RNA Xist which together with specific interacting proteins, functionsin cisto silence an entire X chromosome. Defined sites on Xist RNA carry theN6-methyladenosine (m6A) modification, and perturbation of the m6A writer complex has been found to abrogate Xist-mediated gene-silencing. However, the relative contribution of m6A and its mechanism of action remain unclear. Here we investigate the role of m6A in XCI by applying rapid degron-mediated depletion of METTL3, the catalytic subunit of the m6A writer complex, an approach that minimises indirect effects due to transcriptome-wide depletion of m6A. We find that acute loss of METTL3/m6A accelerates Xist-mediated gene silencing, and that this correlates with increased levels and stability of Xist transcripts. We show that Xist RNA turnover is mediated by the nuclear exosome targeting (NEXT) complex but is independent of the principal nuclear m6A reader protein YTHDC1. Our findings demonstrate that the primary function of m6A on Xist RNA is to promote Xist RNA turnover which in turn regulates XCI dynamics.
Design of SARS-CoV-2 RBD Immunogens to Focus Immune Responses Towards Conserved Coronavirus Epitopes
Authors: Harris Caitlin , Kapingidza A. Brenda , San James E. , Christopher Jayani , Gavitt Tyler , Rhodes Brianna , Janowska Katarzyna , O’Donnell Christopher , Lindenberger Jared , Huang Xiao , Sammour Salam , Berry Madison , Barr Maggie , Parks Rob , Newman Amanda , Overton Mary , Oguin Thomas , Acharya Priyamvada , Haynes Barton F. , Saunders Kevin O. , Wiehe Kevin , Azoitei Mihai L. 
Published: January 2025

AbstractSARS-CoV-2 continues to evolve, with new variants emerging that evade pre-existing immunity and limit the efficacy of existing vaccines. One approach towards developing superior, variant-proof vaccines is to engineer immunogens that preferentially elicit antibodies with broad cross-reactivity against SARS-CoV-2 and its variants by targeting conserved epitopes on spike. The inner and outer faces of the Receptor Binding Domain (RBD) are two such conserved regions targeted by antibodies that recognize diverse human and animal coronaviruses. To promote the elicitation of such antibodies by vaccination, we engineered “resurfaced” RBD immunogens that contained mutations at exposed RBD residues outside the target epitopes. In the context of pre-existing immunity, these vaccine candidates aim to disfavor the elicitation of strain-specific antibodies against the immunodominant Receptor Binding Motif (RBM) while boosting the induction of inner and outer face antibodies. The engineered resurfaced RBD immunogens were stable, lacked binding to monoclonal antibodies with limited breadth, and maintained strong interactions with target broadly neutralizing antibodies. When used as vaccines, they limited humoral responses against the RBM as intended. Multimerization on nanoparticles further increased the immunogenicity of the resurfaced RBDs immunogens, thus supporting resurfacing as a promising immunogen design approach to rationally shift natural immune responses to develop more protective vaccines.
Molecular and structural basis of a subfamily of PrfH rescuing both the damaged and intact ribosomes stalled in translation
Authors: Tian Yannan , Li Qingrong , Fatma Shirin , Jiang Junyi , Jin Hong , Zeng Fuxing , Huang Raven H. 
Published: January 2025

AbstractIn bacteria, spontaneous mRNAs degradation and ribotoxin-induced RNA damage are two main biological events that lead to the stall of protein translation. The ubiquitous trans-translation system as well as several alternative rescue factors (Arfs) are responsible for rescuing the stalled ribosomes caused by truncated mRNAs that lack the stop codons. To date, protein release factor homolog (PrfH) is the only factor known to rescue the stalled ribosome damaged by ribotoxins. Here we show that a subfamily of PrfH, exemplified by PrfH fromCapnocytophaga gingivalis(CgPrfH), rescues both types of stalled ribosomes described above. Ourin vitrobiochemical assays demonstrate thatCgPrfH hydrolyzes the peptides attached to P-site tRNAs when in complex with both the damaged and intact ribosomes. Two cryo-EM structures ofCgPrfH in complex with the damaged and intact 70S ribosomes revealed thatCgPrfH employs two different regions of the protein to recognize two different stalled ribosomes to orient the GGQ motif for peptide hydrolysis. Thus, using a combination of bioinformatic, biochemical, and structural characterization described here, we have uncovered a family of ribosome rescue factors that possesses dual activities to resolve two distinct stalled protein translation in bacteria.
Subcontinental Genetic Diversity in theAll of UsResearch Program: Implications for Biomedical Research
Authors: Gouveia Mateus H. , Meeks Karlijn A. C. , Borda Victor , Leal Thiago P. , Kehdy Fernanda S. G. , Mogire Reagan , Doumatey Ayo P. , Tarazona-Santos Eduardo , Kittles Rick A. , Mata Ignacio F. , O’Connor Timothy D. , Adeyemo Adebowale A. , Shriner Daniel , Rotimi Charles N. 
Published: January 2025

ABSTRACTTheAll of UsResearch Program (All of Us) seeks to accelerate biomedical research and address the underrepresentation of minorities by recruiting over one million ethnically diverse participants across the United States. A key question is how self-identification with discrete, predefined race and ethnicity categories compares to genetic diversity at continental and subcontinental levels. To contextualize the genetic diversity inAll of Us, we analyzed ∼2 million common variants from 230,016 unrelated whole genomes using classical population genetics methods, alongside reference panels such as the 1000 Genomes Project, Human Genome Diversity Project, and Simons Genome Diversity Project. Our analysis reveals that participants within self-identified race and ethnicity groups exhibit a gradient of genetic diversity rather than discrete clusters. The distributions of continental and subcontinental ancestries show considerable variation within race and ethnicity, both nationally and across states, reflecting the historical impacts of U.S. colonization, the transatlantic slave trade, and recent migrations.All of Ussamples filled most gaps along the top five principal components of genetic diversity in current global reference panels. Notably, “Hispanic or Latino” participants spanned much of the three-way (African, Native American, and European) admixture spectrum. Ancestry was significantly associated with body mass index (BMI) and height, even after adjusting for socio-environmental covariates. In particular, West-Central and East African ancestries showed opposite associations with BMI. This study emphasizes the importance of assessing subcontinental ancestries, as the continental approach is insufficient to control for confounding in genetic association studies.
scMILD: Single-cell Multiple Instance Learning for Sample Classification and Associated Subpopulation Discovery
Authors: Jeong Kyeonghun , Choi Jinwook , Kim Kwangsoo 
Published: January 2025

AbstractSingle-cell transcriptomics enables the study of cellular heterogeneity, but current unsupervised strategies make it challenging to associate individual cells with sample conditions. We propose scMILD, a weakly supervised learning framework based on Multiple Instance Learning, which leverages sample-level labels to identify condition-associated cell subpopulations. scMILD employs a dual-branch architecture to perform sample-level classification and cell-level representation learning simultaneously. We validated the model’s reliable identification of condition-associated cells using controlled simulation studies with CRISPR-perturbed cells. Evaluated on diverse single-cell RNA-seq datasets, including Lupus, COVID-19, and Ulcerative Colitis, scMILD consistently outperformed state-of-the-art models and identified condition-specific cell subpopulations consistent with the original studies’ findings. This demonstrates scMILD’s potential for exploring cellular heterogeneity underlying various biological conditions and its applicability in different disease contexts.Key MessagesscMILD: A novel weakly supervised framework for single-cell transcriptomicsDual-branch architecture enables sample classification and cell subpopulation identificationOutperforms state-of-the-art models across diverse single-cell RNA-seq datasetsIdentifies biologically relevant condition-associated cell subpopulationsBridges the gap between sample-level phenotypes and cellular heterogeneity