bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chd4 remodels chromatin to control retinal cell type specification and lineage termination
Authors: Shah Sujay , Lourenço Fernandes José Alex , Medisetti Suma , Mattar Pierre 
Published: January 2025

AbstractDuring development, neural progenitor cells modify their output over time to produce different types of neurons and glia in chronological sequences. Previous studies have shown that epigenetic processes play a crucial role in regulating neural progenitor potential, but the underlying mechanisms are not well understood. Here, we hypothesized that nucleosome remodelling would regulate the competence transitions of retinal progenitors. We generated retina-specific conditional knockouts (cKOs) in the key nucleosome remodelling enzymeChd4.Chd4cKOs overproduced early-born retinal ganglion and amacrine cells. Postnatally, later-born rod photoreceptors were drastically underproduced. Concomitantly, progenitors failed to be exhausted at late phases of development and ultimately overproduced Müller glia. To determine how Chd4 regulates the genome, we used cut&run-seq to reveal Chd4 genome occupancy, and ATAC-seq experiments to visualize nucleosome remodelling. These data revealed that genome accessibility was significantly increased at ∼10,000 regulatory elements and ∼4,000 genes in theChd4cKO. Together, these results suggest that Chd4 restricts the genome to repress progenitor identity and promote rod photoreceptor production. Accordingly, multiplexed single-cell transcriptomics demonstrated that deletion ofChd4led to markedly divergent gene expression profiles. However, despite overproduction of early fates and underproduction of later-born rods, the perinatal transition between early and late progenitor competence was not altered as determined by birthdating experiments and transcriptomic signatures. Taken together, our data suggest that Chd4-dependent chromatin remodelling regulates cell fate specification, and is also required to terminate retinal neurogenesis, but that it does not regulate the progenitor competence windows that restrict early- vs. late-cell-type production.Key findings1)Chd4cKOs exhibit a strong shift in neurogenesis, with early-born neurons overproduced and late-born neurons underproduced.2)We present an epigenetic atlas that combines the occupancy of NuRD proteins such as Chd4 and Mbd3, with nucleosome remodelling data and transcriptomic correlates.3)We show that NuRD regulates the competence transition that terminates the retinal lineage but not earlier competence transitions, showing for the first time that the epigenetic mechanisms governing retinal competence transitions may vary.
Epithelial to Mesenchymal Transition in the Endometrium Mediated by HOXA10 drives Embryo Implantation
Authors: Ashary Nancy , Suresh Sanjana , Bhide Anshul , Shyamal Sharmishtha , Pranya N , Mishra Anuradha , Anuradha A , Hansda Shruti , Harshavardhan B V , Jolly Mohit Kumar , Modi Deepak 
Published: January 2025

AbstractEmbryo implantation requires the breaching of the endometrial luminal epithelium (LE) to facilitate invasion. In this study, we report that during implantation, endometrial LE cells undergo partial epithelial-to-mesenchymal transition (pEMT) specifically at the implantation sites. This pEMT in the LE is critical, as thein vivoknockdown of the EMT transcription factorTwist2 inhibits embryo implantation. Furthermore, we observed a reduction in the expression of the transcription factor HOXA10 in LE cells at the implantation sites. Interestingly, LE cells of HOXA10-hypomorphic mice and human endometrial epithelial cells (RL95-2) withHOXA10knockdown (HOXA10KD) also undergo pEMT and acquire a migratory phenotypein vitro, suggesting that the loss of HOXA10 drives pEMT in the endometrial epithelium. TheHOXA10KD cells have a higher pEMT score and differential expression of genes associated with cell migration and TGF-β signaling pathways. We also determined the genome-wide occupancy sites of HOXA10 in human endometrial epithelial cells and identified 1,246 direct targets that had significant roles in EMT. Collectively, our findings suggest that HOXA10 is required to maintain an epithelial state and its loss activates mesenchymal genes resulting in a pEMT phenotype. This adds HOXA10 as a member of the MET inducer team that engage in mutually inhibitory feedback loops directly or indirectly with EMT inducer team. In summary, our study establishes that pEMT in the LE as a critical step for embryo implantation and reveals that HOXA10 regulates this process.
The Q226L mutation can convert a highly pathogenic H5 2.3.4.4e virus to bind human-type receptors
Authors: Carrasco María Ríos , Lin Ting-Hui , Zhu Xueyong , García Alba Gabarroca , Uslu Elif , Liang Ruonan , Spruit Cindy M. , Richard Mathilde , Boons Geert-Jan , Wilson Ian A. , de Vries Robert P. 
Published: January 2025

AbstractH5Nx viruses continue to wreak havoc in avian and mammalian species worldwide. The virus distinguishes itself by the ability to replicate to high titers and transmit efficiently in a wide variety of hosts in diverse climatic environments. Fortunately, transmission to and between humans is scarce. Yet, if such an event were to occur, it could spark a pandemic as humans are immunologically naïve to H5 viruses. A significant determinant of transmission to and between humans is the ability of the influenza A virus hemagglutinin (HA) protein to shift from an avian-type to a human-type receptor specificity. Here, we demonstrate that a 2016 2.3.4.4e virus HA can convert to human-type receptor binding via a single Q226L mutation, in contrast to a cleavage-modified 2016 2.3.4.4b virus HA. Using glycan arrays, x-ray structural analyses, tissue- and direct glycan binding, we show that L133aΔ and 227Q are vital for this phenotype. Thus, whereas the 2.3.4.4e virus HA only needs a single amino acid mutation, the modified 2.3.4.4b HA was not easily converted to human-type receptor specificity.
Chemoproteomic Profiling ofC. albicansfor Characterization of Anti-fungal Kinase Inhibitors
Authors: Shirley David J. , Nandakumar Meganathan , Cabrera Aurora , Yiu Bonnie , Puumala Emily , Liu Zhongle , Robbins Nicole , Whitesell Luke , Smith Jeffrey L. , Lyons Scott P. , Mordant Angie L. , Herring Laura E. , Graves Lee M. , Couñago Rafael M. , Drewry David H. , Cowen Leah E. , Willson Timothy M. 
Published: January 2025

ABSTRACTCandida albicansis a growing health concern as the leading causal agent of systemic candidiasis, a life-threatening fungal infection with a mortality rate of ∼40% despite best available therapy. Yck2, a fungal casein kinase 1 (CK1) family member, is the cellular target of inhibitors YK-I-02 (YK) and MN-I-157 (MN). Here, multiplexed inhibitor beads paired with mass spectrometry (MIB/MS) employing ATP-competitive kinase inhibitors were used to define the selectivity of these Yck2 inhibitors across the globalC. albicansproteome. The MIB matrix captured 89% of the known and predictedC. albicansprotein kinases present in cell lysate. In MIB/MS competition assays, YK and MN demonstrated exquisite selectivity across theC. albicansfungal kinome with target engagement of only three CK1 homologs (Yck2, Yck22, and Hrr25) and a homolog of human p38α (Hog1). Additional chemoproteomics using a custom MN-kinobead identified only one additionalC. albicansprotein, confirming its remarkable fungal proteome-wide selectivity. To identify new Yck2 inhibitors with selectivity over Hog1, thirteen human CK1 kinase inhibitors were profiled for fungal kinase-binding activity using MIB/MS competition assays and in-cell NanoBRET target engagement assays. A new chemotype of family-selective Yck2 inhibitors with antifungal activity was identified. Together, these findings expand the application of MIB/MS proteomic profiling for non-human kinomes and demonstrate its utility in the discovery and development of selective inhibitors of fungal kinases with potential antimicrobial activity.GRAPHICAL ABSTRACT
Single-molecule assay reveals the impact of composition, RNA duplex, and inhibitors on the binding dynamics of SARS-CoV-2 polymerase complex
Authors: Lovell Terri C. , Dewling Heidi A. F. , Li Cynthia X. , Lee Hery W. , Gordon Calvin J. , Kocincova Dana , Badmalia Maulik D. , Tchesnokov Egor P. , Götte Matthias , Cosa Gonzalo 
Published: January 2025

AbstractThe genome replication of SARS-CoV-2, the causative agent of COVID-19, involves a multi-subunit replication complex consisting of non-structural proteins (nsps) 12, 7 and 8. While the structure of this complex is known, the dynamic behavior of the subunits interacting with RNA is missing. Here we report a single-molecule protein-induced fluorescence enhancement (SM-PIFE) assay to monitor binding dynamics between the reconstituted or co-expressed replication complex and RNA. Increasing binding times were observed, in this order, with nsp7 (none) nsp8 and nsp12, in nsp8-nsp12 mixtures and in reconstituted mixtures bearing all three proteins. Unstable, transient, and stable binding modes were recorded in the latter case, indicating that complexation is dynamic, and the correct conformation must be achieved before stable RNA binding can occur. Notably, the co-expressed protein yields mostly stable binding even at low concentrations, while the reconstituted proteins exhibit unstable binding indicating inefficient complexation with reduced protein. The SM-PIFE assay distinguishes inhibitors that impact protein binding from those that prevent replication, as demonstrated with suramin and remdesivir, respectively. The data reveals a correlation between binding lifetime/affinity, and protein activity, and underscores differences between co-expressed vs reconstituted mixtures, suggesting the existence of trapped conformations that may not evolve to productive binding.
A post-assembly conformational change makes the SARS-CoV-2 polymerase elongation-competent
Authors: Klein Misha , Das Arnab , Bera Subhas C. , Anderson Thomas K. , Kocincova Dana , Lee Hery W. , Wang Bing , Papini Flavia S. , Marecki John C. , Arnold Jamie J. , Cameron Craig E. , Raney Kevin D. , Artsimovitch Irina , Götte Mathias , Kirchdoerfer Robert N. , Depken Martin , Dulin David 
Published: January 2025

AbstractCoronaviruses (CoV) encode sixteen non-structural proteins (nsps), most of which form the replication-transcription complex (RTC). The RTC contains a core composed of one nsp12 RNA-dependent RNA polymerase (RdRp), two nsp8s and one nsp7. The core RTC recruits other nsps to synthesize all viral RNAs within the infected cell. While essential for viral replication, the mechanism by which the core RTC assembles into a processive polymerase remains poorly understood. We show that the core RTC preferentially assembles by first having nsp12-polymerase bind to the RNA template, followed by the subsequent association of nsp7 and nsp8. Once assembled on the RNA template, the core RTC requires hundreds of seconds to undergo a conformational change that enables processive elongation. In the absence of RNA, the (apo-)RTC requires several hours to adopt its elongation-competent conformation. We propose that this obligatory activation step facilitates the recruitment of additional nsp’s essential for efficient viral RNA synthesis and may represent a promising target for therapeutic interventions.
Infectome analysis of bat kidneys from Yunnan province, China, reveals close relatives of Hendra-Nipah viruses and prevalent bacterial and eukaryotic pathogens
Authors: Kuang Guopeng , Yang Tian , Yang Weihong , Wang Jing , Pan Hong , Pan Yuanfei , Gou Qin-yu , Wu Wei-chen , Wang Juan , Yang Lifeng , Han Xi , Chen Yao-qing , Eden John-Sebastian , Holmes Edward C. , Shi Mang , Feng Yun 
Published: January 2025

AbstractBats are natural reservoirs for a wide range of microorganisms, including many notable zoonotic pathogens. However, the infectome of bat kidneys remains poorly understood. To address this gap, we performed meta-transcriptomic sequencing on kidney tissues from 142 bats, spanning ten species sampled at five locations in Yunnan province, China. This analysis identified 22 viral species, including 20 novel viruses, two of which represented newly discovered henipaviruses closely related to the highly pathogenic Hendra and Nipah viruses. These henipaviruses were found in the kidneys of bats inhabiting an orchard near villages, raising concerns about potential fruit contamination via bat urine and transmission risks to livestock or humans. Additionally, we identified a novel protozoan parasite, tentatively namedKlossiella yunnanensis, along with two highly abundant bacterial species, one of which is a newly discovered species—Flavobacterium yunnanensis. These findings broaden our understanding of the bat kidney infectome, underscore critical zoonotic threats, and highlight the need for comprehensive, full-spectrum microbial analyses of previously understudied organs to better assess spillover risks from bat populations.
Monocarboxylate transporter 2 is required for the maintenance of myelin and axonal integrity by oligodendrocytes
Authors: Izagirre-Urizar Leire , Mora-Huerta Luna , Soler-Saez Irene , Morales-Gallel Raquel , Ulloa-Navas Maria-Jose , Chara Juan-Carlos , Calovi Stefano , Deboux Cyrille , Merino-Cacho Laura , Netzahualcoyotzi Citlalli , Domercq Maria , Zugaza José L. , Pellerin Luc , Garcia-Garcia Francisco , Garcia-Verdugo Jose-Manuel , Matute Carlos , Nait-Oumesmar Brahim , Tepavcevic Vanja 
Published: January 2025

ABSTRACTNeurodegenerative pathologies including multiple sclerosis (MS) are consistently associated with energy deficit in the central nervous system (CNS). This might directly impact myelinating oligodendrocytes as these are particularly vulnerable to metabolic insults. Importantly, oligodendroglial dysfunction and myelin alterations occur in most, if not all neurodegenerative diseases, and are associated with axonal pathology/loss. Thus, elucidating metabolic mechanisms required for oligodendroglial myelin maintenance and axonal support might be crucial to identify therapeutic targets to achieve neuroprotection. While monocarboxylates are important energy fuels for the CNS, their role in myelinating oligodendrocyte function remains unclear. Here we show that, just like neurons, myelinating oligodendrocytes express high affinity monocarboxylate transporter 2 (MCT2) both in mice and humans, which is downregulated in progressive MS. While deletion of MCT2 in mouse oligodendrocytes did not affect the survival of these cells, it resulted in downregulation of lipid synthesis-associated enzymes and failure of myelin maintenance. Moreover, axonal upregulation of lactate dehydrogenase A concomitant with axonal damage was observed but could be alleviated by ketogenic diet. We conclude that oligodendroglial MCT2 is required for myelin maintenance and axonal support, which becomes altered in progressive MS, but may be compensated for by specific metabolic therapies.Graphical abstract
Recreating coronary vascularization and sympathetic innervation of myocardium on a human pluripotent stem cell-derived heart organoid
Authors: Branco Mariana A. , Nunes Mafalda Marques , Rayagra Ana Luísa , Tenreiro Miguel F. , Cabral Joaquim M.S. , Diogo Maria Margarida 
Published: January 2025

SUMMARYCoronary vascularization and sympathetic innervation of the myocardium is a concomitant event during embryonic heart development and both systems are crucial to ensure normal adult heart function. Here we describe a self-organized hiPSC-derived heart organoid that recreates both the coronary vascular plexus and the sympathetic neuronal network of the ventricle myocardium, with a physiologically relevant in-vivo-like structural organization and function. Through modulation of PDGF-β and VEGF signalling pathways, we attained a heart organoid that incorporates 1) an external epicardial layer (mesothelium) of DACH1, NR2F2 and WT1 positive cells, 2) a sub-epicardial space from where a functional primary coronary vascular plexus of CD31+/DACH1+cells emerge, 3) a compact myocardial region adjacent to the epicardium, enriched in proliferative cardiomyocytes and ECM deposition, and 4) a sympathetic neuronal network that controls heart organoid contraction. Therefore, the human heart organoid described herein, is a unique model to study new regenerative medicine-based approaches to restore innervation and promote re-vascularization in adult heart after ischemic events and to perform adult and developmental cardiotoxicity studies.
Developmental axon diameter growth of central nervous system axons does not depend on ensheathment or myelination by oligodendrocytes
Authors: Bin Jenea M , Emberley Katie , Buscham Tobias J , Eichel-Vogel Maria A , Doan Ryan A , Steyer Anna M , Nolan Matthew F , Möbius Wiebke , Monk Kelly R , Werner Hauke B , Emery Ben , Lyons David A 
Published: January 2025

SUMMARYMyelination facilitates the rapid conduction of action potentials along axons. In the central nervous system (CNS), myelinated axons vary over 100-fold in diameter, with conduction speed scaling linearly with increasing diameter. Axon diameter and myelination are closely interlinked, with axon diameter exerting a strong influence on myelination. Conversely, myelinating Schwann cells in the peripheral nervous system can both positively and negatively affect axon diameter. However, whether axon diameter is regulated by CNS oligodendrocytes is less clear. Here, we investigated CNS axon diameter growth in the absence of myelin using mouse (Mbpshi/shiand Myrfconditional knockout) and zebrafish (olig2morpholino) models. We find that neither the ensheathment of axons, nor the formation of compact myelin are required for CNS axons to achieve appropriate and diverse diameters. This indicates that developmental CNS axon diameter growth is independent of myelination, and shows that myelinating cells of CNS and PNS differentially influence axonal morphology.
Resolving forebrain developmental organisation by analysis of differential growth patterns
Authors: Manning Elizabeth , Chinnaiya Kavitha , Furley Caitlyn , Kim Dong Won , Blackshaw Seth , Placzek Marysia , Place Elsie 
Published: January 2025

AbstractThe forebrain is the most complex region of the vertebrate CNS, and its developmental organisation is controversial. We fate-mapped the embryonic chick forebrain using lipophilic dyes and Cre-recombination lineage tracing, and built a 4D model of brain growth. We reveal modular patterns of anisotropic growth, ascribed to progenitor regions through multiplex HCR. Morphogenesis is dominated by directional growth towards the eye, more isometric expansion of the prethalamus and dorsal telencephalon, and anterior movement of ventral cells into the hypothalamus. Fate conversion experiments in chick and comparative gene expression analysis in chick and mouse support placement of the hypothalamus ventral to structures extending from the telencephalon up to and including the zona limitans intrathalamica (ZLI), with the dorsoventral axis becoming distorted at the base of the ZLI. Our findings challenge the widely accepted prosomere model of forebrain organisation, and we propose an alternative ‘tripartite hypothalamus’ model.
A zebrafish model of nicotinamide adenine dinucleotide (NAD+) deficiency-derived congenital disorders
Authors: Tsurho Visakuo , Gilliland Carla , Ensing Jessica , Vansickle Elizabeth , Lanning Nathan J. , Mark Paul R. , Grainger Stephanie 
Published: January 2025

AbstractCongenital NAD deficiency disorder (CNDD) is a multisystem condition in which cardiac, renal, vertebral, and limb anomalies are most common, but anomalies in all organ systems have been identified. Patients with this condition have biallelic pathogenic variants involving genes in the nicotinamide adenine dinucleotide (NAD+) synthesis pathway leading to decreased systemic NAD+levels. CNDD anomalies mimic the clinical features described in vertebral-anal-cardiac-tracheoesophageal fistula-renal-limb (VACTERL) association raising the possibility that CNDD and VACTERL association possess similar underlying causes. However, the mechanism by which NAD+deficiency causes CNDD developmental anomalies has not been determined, nor has NAD+deficiency been definitively linked to VACTERL association. Therefore, additional animal models amenable to detailed observation of embryonic development are needed to address the causes and progression of congenital anomalies in both CNDD and VACTERL association. Here, we describe a zebrafish model of NAD+disruption to begin to model CNDD and VACTERL association phenotypes, assessing developmental anomalies in real-time. Treatment of zebrafish embryos with 2-amino-1,3,4-thiadiazole (ATDA), a teratogen known to disrupt NAD+metabolism, resulted in neural tube, craniofacial, cardiac, and tail defects. These defects were rescued by the administration of nicotinamide (NAM) in a dose-dependent manner. Our work establishes zebrafish as a useful model for investigating the mechanistic causes and developmental dynamics of CNDD and VACTERL association. Further, as VACTERL association has been linked to teratogens, our zebrafish model provides a platform to assess these agents.One sentence summaryNAD(H) deficiency causes multiple congenital anomalies in zebrafish.
Uptake of Prochlorococcus-derived metabolites byAlteromonas macleodiiMIT1002 shows high levels of substrate specificity
Authors: Halloran Kathryn H. , Braakman Rogier , Coe Allison , Swarr Gretchen , Kido Soule Melissa C. , Chisholm Sallie W. , Kujawinski Elizabeth B. 
Published: January 2025

AbstractSeawater contains an abundance of small biomolecules, or metabolites, that are highly labile components of dissolved organic matter (DOM). Marine microbes interact by exchanging metabolites, thus shaping marine microbial ecology, DOM composition, and global carbon cycling. To better constrain one set of microbe-metabolite interactions, we cultured the marine gammaproteobacteriumAlteromonas macleodiiMIT1002 on a range of compounds excreted by a sympatric cyanobacterium,Prochlorococcus.Alteromonascould assimilate the branched chain amino acids leucine, isoleucine, and valine, as well as 3-methyl-2-oxobutanoic acid (a branched chain ketoacid intermediate of valine metabolism), but not thymidine, kynurenine, 4-hydroxybenzoic acid, or the other branched chain ketoacids. The assimilation of branched chain amino acids indicates thatAlteromonascan metabolically process each corresponding ketoacid, suggesting that transporter specificity underlies the observed substrate specificity for 3-methyl-2-oxobutanoic acid. These experiments show that even subtle changes in chemical structure can result in different microbial interactions and different fates for dissolved metabolites.Significance StatementMicrobial interactions with dissolved organic matter are important controls on the marine carbon cycle. Dissolved organic matter is often considered in bulk, which leaves the specificity and nature of these interactions poorly constrained. Here we show that microbe-molecule interactions can be highly specific, distinguishing between molecules that are structurally and biochemically similar. This implies that small changes in this pool of carbon could have large impacts for the overall system function, and that measuring this pool of carbon with molecular-level resolution is important to characterizing microbe-molecule interactions. We further explore the mechanism underlying the observed substrate specificity and suggest that it is caused by transporter selectivity, meaning the ability of these microbes to selectively uptake specific dissolved organic molecules.