bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determining glycosyltransferase functional order via lethality due to accumulated O-antigen intermediates, exemplified withShigella flexneriO-antigen biosynthesis
Authors: Qin Jilong , Hong Yaoqin , Totsika Makrina 
Published: December 2023

AbstractThe O antigen (OAg) polysaccharide is one of the most diverse surface molecules of Gram-negative bacterial pathogens. The structural classification of OAg based on serological typing and sequence analysis is important in epidemiology and surveillance of outbreaks of bacterial infections. Despite the diverse chemical structures of OAg repeating units (RUs) described, the genetic basis of the assembly of these RUs remains poorly understood and represents a major limitation in our understanding of the gene functions in the polysaccharide biosynthesis. Here we describe a genetic approach to interrogate the functional order of glycosyltransferases (GTs). UsingShigella flexnerias a model, we established an initial glycosyltransferase (IT) controlled system to allocate the functional order of the subsequent GT in a two-fold manner. First by reporting the growth defects caused by the sequestration of UndP through disruption of late GTs, and second by comparing the molecular sizes of stalled OAg intermediates when each putative GT is disrupted. Using this approach, we demonstrate that for RfbF and RfbG, the GTs involved in the assembly ofS. flexneribackbone OAg RU, RfbG is responsible for both the committed step of OAg synthesis, as well as the third transferase for the second L-Rha. We also show that RfbF functions as the last GT to complete theS. flexneriOAg RU backbone. We propose that this simple and effective genetic approach can be also extended to define the functional order of enzymatic synthesis of other diverse polysaccharides produced both by Gram-negative and Gram-positive bacteria.ImportanceThe genetic basis of enzymatic assembly of structurally diverse OAg repeating units in Gram-negative pathogens is poorly understood, representing a major limitation in our understanding of gene functions for the synthesis of bacterial polysaccharides. We present a simple genetic approach to assigning glycosyltransferase (GT) functions and the order in which they act in the assembly of the OAg RU in their native background strain with reasonable confidence. We demonstrated with this approach the functional allocation of GTs forShigella flexneriO antigen assembly. This approach can be generally applied in interrogating GT functions encoded by other bacterial polysaccharides to advance our understanding of diverse gene functions in the biosynthesis of polysaccharides, key knowledge in advancing biosynthetic polysaccharide production.
Human Trophoblast Stem Cells Restrict Human Cytomegalovirus Replication
Authors: Rollman Tyler B. , Berkebile Zachary W. , Okae Hiroaki , Bardwell Vivian J. , Gearhart Micah D. , Bierle Craig J. 
Published: December 2023

AbstractPlacental infection plays a central role in the pathogenesis of congenital human cytomegalovirus (HCMV) infections and is a cause of fetal growth restriction and pregnancy loss. HCMV can replicate in some trophoblast cell types, but it remains unclear how the virus evades antiviral immunity in the placenta and how infection compromises placental development and function. Human trophoblast stem cells (TSCs) can be differentiated into extravillous trophoblasts (EVTs), syncytiotrophoblasts (STBs), and organoids, and this study assessed the utility of TSCs as a model of HCMV infection in the first trimester placenta. HCMV was found to non-productively infect TSCs, EVTs, and STBs. Immunofluorescence assays and flow cytometry experiments further revealed that infected TSCs frequently only express immediate early viral gene products. Similarly, RNA-sequencing found that viral gene expression in TSCs does not follow the kinetic patterns observed during lytic infection in fibroblasts. Canonical antiviral responses were largely not observed in HCMV-infected TSCs and TSC-derived trophoblasts. Rather, infection dysregulated factors involved in cell identity, differentiation, and WNT signaling. Thus, while HCMV does not replicate in TSCs, infection may perturb trophoblast differentiation in ways that could interfere with placental function.ImportancePlacental infection plays a central role in HCMV pathogenesis during pregnancy, but the species-specificity of HCMV and the limited availability and lifespan of primary trophoblasts have been persistent barriers to understanding how infection impacts this vital organ. Human TSCs represent a new approach to modeling viral infection early in placental development. This study reveals that TSCs, like other stem cell types, restrict HCMV replication. However, infection perturbs the expression of genes involved in differentiation and cell fate determination, pointing to a mechanism by which HCMV could cause placental injury.
A Novel Classification System for Prokaryotic DNA Methyltransferases Based on 3D Catalytic Domain Topology
Authors: Samokhina Maria , Alexeevski A. 
Published: December 2023

ABSTRACTProkaryotic DNA methyltransferases (MTases) are essential enzymes that play a crucial role in restriction-modification systems, preventing the degradation of self DNA by restriction enzymes. In addition, they contribute to the regulation of gene expression, DNA repair, DNA replication, and other processes.We propose a novel classification of prokaryotic MTases that addresses a longstanding deficiency in the previous classification scheme developed by Malone and Bujnicki. The latter classification, which grouped MTases into categories such as α, β, γ, etc., has been in use for over 20 years.Our approach involves identifying 6 classes of MTases based on the 3D topology of the catalytic domain. This was achieved by analyzing the available 3D structures and certain predicted 3D structures of MTases from the AlfaFold database. The catalytic domains of each class of MTase exhibit homology not only in structure but also in conserved motifs. To develop this classification algorithm, we utilized a set of MTases from the gold standard REBASE database.Our new classification system facilitates the recovery of MTase evolution and MTase annotations in both existing and new sequence data sets. This is particularly important for understanding the complex relationships between MTases and their roles in various biological processes.GRAPHICAL ABSTRACT
Collaborative metabolic curation of an emerging model marine bacterium,Alteromonas macleodiiATCC 27126
Authors: Sher Daniel , George Emma E. , Wietz Matthias , Gifford Scott , Zoccaratto Luca , Weissberg Osnat , Koedooder Coco , Waseem Bashir VK , Filho Marcelo Malisano Barreto , Mireles Raul , Malavin Stas , Naim Michal Liddor , Idan Tal , Shrivastava Vibhaw , Itelson Lynne , Sade Dagan , Hamoud Alhan Abu , Soussan Yara , Barak Noga , Karp Peter , Moore Lisa 
Published: December 2023

AbstractInferring the metabolic capabilities of an organism from its genome is a challenging process, relying on computationally-derived or manually curated metabolic networks. Manual curation can correct mistakes in the draft network and add missing reactions based on the literature, but requires significant expertise and is often the bottleneck for high-quality metabolic reconstructions. Here, we present a synopsis of a community curation workshop for the emerging model marine bacteriumAlteromonas macleodiiATCC 27126 and its genome database in BioCyc, focusing on pathways for utilizing organic carbon and nitrogen sources. Due to the scarcity of biochemical information or gene knock-outs, the curation process relied primarily on published growth phenotypes and bioinformatic analyses, including comparisons with relatedAlteromonasstrains. We report full pathways for the utilization of the algal polysaccharides alginate and pectin in contrast to inconclusive evidence for one carbon metabolism and mixed acid fermentation, in accordance with the lack of growth on methanol and formate. Pathways for amino acid degradation are ubiquitous acrossAlteromonas macleodiistrains, yet enzymes in the pathways for the degradation of threonine, tryptophan and tyrosine were not identified. Nucleotide degradation pathways are also partial in ATCC 27126. We postulate that demonstrated growth on nitrate as sole N source proceeds via a nitrate reductase pathway that is a hybrid of known pathways. Our evidence highlights the value of joint and interactive curation efforts, but also shows major knowledge gaps regardingAlteromonasmetabolism. The manually-curated metabolic reconstruction is available as a “Tier-2” database on BioCyc.ImportanceMetabolic reconstructions are vital for the systemic understanding of an organism’s ecology. Here, we report the outcome of a collaborative, interactive curation workshop to build a curated “metabolic encyclopedia” forAlteromonas macleodiiATCC 27126, a marine heterotrophic bacterium with widespread occurrence. Curating pathways for polysaccharide degradation, one-carbon metabolism, and others closed major knowledge gaps, and identified further avenues of research. Our study highlights how the combination of bioinformatic, genomic and physiological evidence can be harvested into a detailed metabolic model, but also identifies challenges if little experimental data is available for support. Overall, we show how an interactive get-together by a diverse group of scientists can advance the ecological understanding of emerging model bacteria, with relevance for the entire scientific community.
A protective and broadly binding antibody class engages the influenza virus hemagglutinin head at its stem interface
Authors: Simmons Holly C. , Finney Joel , Kotaki Ryutaro , Adachi Yu , Moseman Annie Park , Watanabe Akiko , Song Shengli , Robinson-McCarthy Lindsey R. , Le Sage Valerie , Kuraoka Masayuki , Moseman E. Ashley , Kelsoe Garnett , Takahashi Yoshimasa , McCarthy Kevin R. 
Published: December 2023

AbstractInfluenza infection and vaccination impart strain-specific immunity that protects against neither seasonal antigenic variants nor the next pandemic. However, antibodies directed to conserved sites can confer broad protection. Here we identify and characterize a class of human antibodies that engage a previously undescribed, conserved epitope on the influenza hemagglutinin (HA) protein. Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head-stem interface epitope are non-neutralizingin vitrobut protect against lethal influenza infection in mice. Antibody isotypes that direct clearance of infected cells enhance this protection. Head-stem interface antibodies bind to most influenza A serotypes and seasonal human variants, and are present at low frequencies in the memory B cell populations of multiple human donors. Vaccines designed to elicit these antibodies might contribute to “universal” influenza immunity.
Impact of histone deacetylase inhibition and arimoclomol on heat shock protein expression and disease biomarkers in primary culture models of familial ALS
Authors: Comaduran Mario Fernández , Minotti Sandra , Jacob-Tomas Suleima , Rizwan Javeria , Larochelle Nancy , Robitaille Richard , Sephton Chantelle F. , Vera M. , Nalbantoglu Josephine N. , Durham Heather D. 
Published: December 2023

ABSTRACTProtein misfolding and mislocalization are common themes in neurodegenerative disorders, including the motor neuron disease, amyotrophic lateral sclerosis (ALS). Maintaining proteostasis is a crosscutting therapeutic target, including upregulation of heat shock proteins (HSP) to increase chaperoning capacity. Motor neurons have a high threshold for upregulating stress inducible HSPA1A, but constitutively express high levels of HSPA8. This study compared expression of these HSPs in cultured motor neurons expressing three variants linked to familial ALS: TDP-43G348C, FUSR521Gor SOD1G93A. All variants were poor inducers ofHspa1a,and reduced levels ofHspa8mRNA and protein, indicating multiple compromises in chaperoning capacity. To promote HSP expression, cultures were treated with the putative HSP co-inducer, arimoclomol, class I histone deacetylase (HDAC) inhibitors to promote active chromatin for transcription, and the combination. Treatments had variable, often different effects on expression ofHspa1aandHspa8, depending on the ALS variant expressed, mRNA distribution (somata and dendrites), and biomarker of toxicity measured (histone acetylation, maintaining nuclear TDP-43 and the nBAF chromatin remodeling complex component Brg1, mitochondrial transport, FUS aggregation). Overall, HDAC inhibition alone was effective on more measures than arimoclomol. In the TDP-43 model, arimoclomol failed to induce HSPA1A or preserveHspa8mRNA, despite preserving nuclear TDP-43 and Brg1, indicating neuroprotective properties other than HSP induction. The data speak to the complexity of drug mechanisms against multiple biomarkers of ALS pathogenesis, as well as to the importance of HSPA8 for neuronal proteostasis in both somata and dendrites.
Determinants of cerebral blood flow and arterial transit time in healthy older adults
Authors: Feron Jack , Segaert Katrien , Rahman Foyzul , Fosstveit Sindre H , Joyce Kelsey E , Gilani Ahmed , Lohne-Seiler Hilde , Berntsen Sveinung , Mullinger Karen J , Lucas Samuel J E 
Published: December 2023

AbstractCerebral blood flow (CBF) and arterial transit time (ATT), markers of brain vascular health, worsen with age. The primary aim of this cross-sectional study was to identify modifiable determinants of CBF and ATT in healthy older adults (n=78, aged 60–81 yrs). Associations between cardiorespiratory fitness and CBF or ATT were of particular interest as the impact of cardiorespiratory fitness is not clear in existing literature. Secondly, this study assessed whether CBF or ATT relate to cognitive function in older adults. Results from multiple linear regressions found higher BMI was associated with lower global CBF (β=-0.35,P=0.008) and a longer global ATT (β=0.30, P=0.017), global ATT lengthened with increasing age (β=0.43,P=0.004), and higher cardiorespiratory fitness was associated with longer ATT in parietal (β=0.44,P=0.004) and occipital (β=0.45,P=0.003) regions. Global or regional CBF or ATT were not associated with processing speed, working memory, or attention. In conclusion, preventing excessive weight gain may help attenuate age-related declines in brain vascular health. ATT may be more sensitive to age-related decline than CBF, and therefore useful for early detection and management of cerebrovascular impairment. Finally, cardiorespiratory fitness appears to have little effect on CBF but may induce longer ATT in specific regions.
SYNAPTIC PLASTICITY IN THE INJURED BRAIN DEPENDS ON THE TEMPORAL PATTERN OF STIMULATION
Authors: Fischer Quentin S. , Kalikulov Djanenkhodja , Di Prisco Gonzalo Viana , Williams Carrie A. , Baldwin Philip R. , Friedlander Michael J. 
Published: December 2023

ABSTRACTNeurostimulation protocols are increasingly used as therapeutic interventions, including for brain injury. In addition to the direct activation of neurons, these stimulation protocols are also likely to have downstream effects on those neurons’ synaptic outputs. It is well known that alterations in the strength of synaptic connections (long-term potentiation, LTP; long-term depression, LTD) are sensitive to the frequency of stimulation used for induction, however little is known about the contribution of the temporal pattern of stimulation to the downstream synaptic plasticity that may be induced by neurostimulation in the injured brain. We explored interactions of the temporal pattern and frequency of neurostimulation in the normal cerebral cortex and after mild traumatic brain injury (mTBI), to inform therapies to strengthen or weaken neural circuits in injured brains, as well as to better understand the role of these factors in normal brain plasticity. Whole-cell (WC) patch-clamp recordings of evoked postsynaptic potentials (PSPs) in individual neurons, as well as field potential (FP) recordings, were made from layer 2/3 of visual cortex in response to stimulation of layer 4, in acute slices from control (naïve), sham operated, and mTBI rats. We compared synaptic plasticity induced by different stimulation protocols, each consisting of a specific frequency (1 Hz, 10 Hz, or 100 Hz), continuity (continuous or discontinuous), and temporal pattern (perfectly regular, slightly irregular, or highly irregular). At the individual neuron level, dramatic differences in plasticity outcome occurred when the highly irregular stimulation protocol was used at 1 Hz or 10 Hz, producing an overall LTD in controls and shams, but a robust overall LTP after mTBI. Consistent with the individual neuron results, the plasticity outcomes for simultaneous FP recordings were similar, indicative of our results generalizing to a larger scale synaptic network than can be sampled by individual WC recordings alone. In addition to the differences in plasticity outcome between control (naïve or sham) and injured brains, the dynamics of the changes in synaptic responses that developed during stimulation were predictive of the final plasticity outcome. Our results demonstrate that the temporal pattern of stimulation plays a role in the polarity and magnitude of synaptic plasticity induced in the cerebral cortex while highlighting differences between normal and injured brain responses. Moreover, these results may be useful for optimization of neurostimulation therapies to treat mTBI and other brain disorders, in addition to providing new insights into downstream plasticity signaling mechanisms in the normal brain.
TopoDiff: Improving Protein Backbone Generation with Topology-aware Latent Encoding
Authors: Zhang Yuyang , Ma Zinnia , Gong Haipeng 
Published: December 2023

AbstractThede novodesign of protein structures is an intriguing research topic in the field of protein engineering. Recent breakthroughs in diffusion-based generative models have demonstrated substantial promise in tackling this task, notably in the generation of diverse and realistic protein structures. While existing models predominantly focus on unconditional generation or fine-grained conditioning at the residue level, the holistic, top-down approaches to control the overall topological arrangements are still insufficiently explored. In response, we introduce TopoDiff, a diffusion-based framework augmented by a global-structure encoding module, which is capable of unsupervisedly learning a compact latent representation of natural protein topologies with interpretable characteristics and simultaneously harnessing this learned information for controllable protein structure generation. We also propose a novel metric specifically designed to assess the coverage of sampled proteins with respect to the natural protein space. In comparative analyses with existing models, our generative model not only demonstrates comparable performance on established metrics but also exhibits better coverage across the recognized topology landscape. In summary, TopoDiff emerges as a novel solution towards enhancing the controllability and comprehensiveness ofde novoprotein structure generation, presenting new possibilities for innovative applications in protein engineering and beyond.
Liver Protects Cytoarchitecture, Neuron Viability and Electrocortical Activity in Post-Cardiac Arrest Brain Injury
Authors: Guo Zhiyong , Yin Meixian , Sun Chengjun , Xu Guixing , Wang Tielong , Jia Zehua , Zhang Zhiheng , Zhu Caihui , Zheng Donghua , Wang Linhe , Huang Shanzhou , Liu Di , Zhang Yixi , Xie Rongxing , Gao Ningxin , Yu Ping , Zhan Liqiang , He Shujiao , Zhu Yifan , Li Yuexin , Nashan Björn , Andrea Schlegel , Xu Jin , Zhao Qiang , He Xiaoshun 
Published: December 2023

ABSTRACTBACKGROUNDBrain injury is the major reason for patient deaths in victims who survive after cardiac arrest. Clinical studies have shown that the presence of hypoxic hepatitis and pre-cardiac arrest liver disease is associated with increased mortality and inferior neurological recovery. However, how the liver might impact the pathogenesis of post-cardiac arrest is still unknown.METHODSAnin vivoglobal cerebral ischemia model was established to assess how simultaneous liver ischemia affected the recovery of brain ischemic injury. In addition, anex vivobrain normothermic machine perfusion (NMP) model was established to evaluate how addition of a functioning liver might impact the circulation, cytoarchitecture, neuron viability and electrocortical activity of the reperfused brain post-cardiac arrest.RESULTSIn thein vivomodel, we observed a larger infarct area in the frontal lobe, elevated tissue injury scores in the CA1 region, as well as increased intravascular immune cell adhesion in the reperfused brains with hepatic ischemia, compared to those without simultaneous hepatic ischemia. The results of theex vivomodel demonstrated that the addition of a functioning liver to the brain NMP circuit significantly reduced post-cardiac arrest brain injury, increased neuronal viability and improved electrocortical activity. Furthermore, we observed significant alterations in gene expressions and metabolites in the presence or absence of hepatic ischemia.CONCLUSIONSOur research highlights the crucial role of the liver in the pathogenesis of post-cardiac arrest brain injury. These findings shed lights on a cardio-pulmonary-hepatic brain resuscitation strategy for patients with cardiac arrest.
Pu.1/Spi1 dosage controls the turnover and maintenance of microglia in zebrafish and mammals
Authors: Wu Yi , Guo Weilin , Kuang Haoyue , Wu Xiaohai , Wang Yuexin , Zhao Shizheng , Wen Zilong , Yu Tao 
Published: December 2023

AbstractMicroglia are brain-resident macrophages playing pivotal roles in CNS development and homeostasis. Yet, the cellular and molecular basis governing microglia maintenance remain largely unknown. Here, via utilizing a visible conditional knockout allele ofpu.1gene (the master regulator for microglia/macrophage lineage development) to generate mosaic microglia populations in adult zebrafish, we show that whilepu.1-deficient microglia are immediate viable, they are less competitive and chronically eliminated through Tp53-mediated cell competition. Interestingly, when conditionally inactivating Pu.1 in adultspi-b(the paralogue of zebrafish Pu.1) null mutants, microglia are rapidly depleted via apoptosis, suggesting that Pu.1 and Spi-b regulate microglia maintenance in a dosage-dependent manner. The dosage-dependent regulation of microglia maintenance by PU.1 is evolutionarily conserved in mice, as shown by conditionally inactivating single and bothPu.1alleles in microglia respectively. Collectively, our study reveals the conserved cellular and molecular mechanisms controlling microglia turnover and maintenance in teleost and mammals.