bluuebunny/crossref_metadata_2025_split huggingface dataset:
Upregulation of ATP Citrate Lyase Phosphorylation and Neutral Lipid Synthesis through Viral Growth Factor Signaling during Vaccinia Virus Infection
Authors: Pant Anil , Brahim Belhaouari Djamal , Dsouza Lara , Yang Zhilong 
Published: September 2023

AbstractLike all other viruses, poxviruses rely on host cells to provide metabolites and energy. Vaccinia virus (VACV), the prototype poxvirus, induces profound metabolic alterations in host cells. We previously showed that VACV infection increases the tricarboxylic acid (TCA) cycle intermediates, including citrate, that can be transported to the cytosol to be converted to acetyl-CoA forde novofatty acid biosynthesis. ATP citrate lyase (ACLY) is a pivotal enzyme converting citrate to acetyl-CoA. Here, we report that VACV infection stimulates the S455 phosphorylation of ACLY, a post-translational modification that stimulates ACLY activity. We demonstrate that the chemical and genetic inhibition of ACLY severely suppresses VACV replication. Remarkably, we found that virus growth factor (VGF)-induced signaling is essential for the VACV-mediated upregulation of ACLY phosphorylation. Furthermore, the upregulation of ACLY phosphorylation during VACV infection is dependent on the activation of the cellular Akt kinase that phosphorylates ACLY. Finally, we report that VGF-induced ACLY phosphorylation via the EGFR-Akt pathway is important for VACV stimulations of neutral lipid droplet synthesis. These findings identified a previously unknown way of rewiring cell metabolism by a virus and a novel function for VGF in the governance of virus-host interactions through the induction of a key enzyme at the crossroads of the TCA cycle and fatty acidde novobiosynthesis. Our study also provides a mechanism for the role played by VGF and its downstream signaling cascades in the modulation of lipid metabolism in VACV-infected cells.ImportanceATP citrate lyase is a key metabolic enzyme that sits at the crossroads of glucose, glutamine, and lipid metabolism. However, how virus infection affects this protein is unclear. Using chemical, genetic, and metabolic approaches we show that VACV, the prototype poxvirus, increases the phosphorylation of ACLY in primary human fibroblasts in a VGF-dependent manner. We further show that the VGF-EGFR-Akt signaling pathway is vital for VACV-induced lipid droplet synthesis. Our findings identified ACLY as a potential target for novel antiviral development against pathogenic poxviruses. Our study also expands the role of growth factor signaling in boosting VACV replication by targeting multiple metabolic pathways.
Application of CRISPR-Cas12a technology in zebrafish to simulate ß-globin gene (HBB) mutations
Authors: Shafique Farheen , Ali Shaukat , Balckburn Edward , ul Hassan Mahreen 
Published: September 2023

AbstractBackgroundThe human ß-globin (HBB) gene translated into the hemoglobin subunit beta (ß) of the hemoglobin protein. When mutated, it can lead to the blood disorder ß-thalassemia. Recently, the CRISPR-Cas12 technology has shown promising potential in treating different genetic abnormalities.ObjectivesThis study aimed to evaluate the feasibility of zebrafish hbbe1.1 gene editing via CRISPR-Cas12a gene-technology.MethodsIn current study, thalassemic mutations were replicated in zebrafish to improve gene editing. the embryonic hemoglobin genehbbe1.1was preferred over adult hemoglobinhbß-a1due to its early detection at larval stages. The CRISPR-Cas12 technology was utilised in combination with phosphorothioated “rescue template” (ssDNA L33P) to introduce base edits to the DNA sequence of zebrafish.ResultsThese experiments indeed resulted in the alteration of a single amino acid at the protein level. With the help of this genetic editing method, we were able to generate a novel zebrafish strain that carried specific amino acid alterations resembling the pathogenic mutations found in HBB for ß-thalassemia disease. However, in several cases additional indels or base alterations were observed.ConclusionOur findings suggests that MMEJ double stranded break repair mechanism causes more knock-in events and germline inheritance than HR-mediated events. Modifying the technique could improve results by reducing MMEJ frequency.
The atypical cadherin FAT1 is a novel regulator of STAT1, driving its pro-tumorigenic effect via the STAT1/PDCD4 axis in glioblastoma
Authors: Khan Md. Tipu , Malik Nargis , Jalota Akansha , Sharma Shaifali , Almas Mariyam , Luthra Kalpana , Suri Vaishali , Suri Ashish , Seth Pankaj , Chosdol Kunzang , Sinha Subrata 
Published: September 2023

AbstractFAT1 is an atypical cadherin that has been shown to act both as an oncogene and a tumour suppressor gene (TSG) in different tumor types. We have earlier shown that upregulated FAT1 acts as an oncogene in glial tumors by promoting pro-tumorigenic inflammation and EMT in primary human glioblastoma and in cell lines. One effect was through the suppression of the Tumor Suppressor Gene (TSG), Programmed Cell Death 4 (PDCD4). Here, we have studied how, in glioblastoma, upregulated FAT1 affects downstream events that control PDCD4 expression.In silicoanalysis of the PDCD4 promoter revealed multiple STAT1 binding sites. We also found a positive correlation in mRNA levels of STAT1 and FAT1 in the Glioblastoma databases, as well as in resected patient derived tumor samples by qPCR. Increased FAT1 as well as STAT1 were associated with poor prognosis in these data bases. In the glioblastoma cell lines LN229 and U87MG, FAT1 knockdown resulted in decreased STAT1 expression. Also, STAT1 knockdown resulted in increased PDCD4 expression, implying that STAT1 may mediate FAT1’s role in suppressing PDCD4. Further, ChIP experiments showed that STAT1 protein binds to the PDCD4 promoter and upon FAT1 knockdown, STAT1 binding to the PDCD4 promoter reduces. As for FAT1, STAT1 knockdown also reduces the expression of pro-inflammatory cytokines and EMT markers, also migration and invasion of glioma derived cell lines. This work identifies STAT1 as a novel downstream mediator of FAT1 which mediates its pro-tumorigenic action in suppressing the TSG, PDCD4.
Microfluidic interfaces for chronic bidirectional access to the brain
Authors: Marcigaglia Simone , De Plus Robin , Vandendriessche Charysse , Cuypers Marie-Lynn , Cools Jordi , Hoffman Luis Diego , Vandenbroucke Roosmarijn , Dewilde Maarten , Haesler Sebastian 
Published: September 2023

AbstractHere, we used micron-scale 3D printing to develop microfluidic interfaces which provide chronic fluidic access to the brain of preclinical research models. In mice, we show the delivery interface enables faster, more precise and physiologically less disruptive fluid injection. Moreover, we demonstrate the blood brain barrier (BBB) is intact after chronic implantation of the sampling interface and establish frequent, longitudinal sampling of CSF and biomarkers from the ventricle over long time periods of up to 200 days.
Microfibril-associated glycoprotein 4 forms octamers that mediate interactions with elastogenic proteins and cells
Authors: Wozny Michael R. , Nelea Valentin , Siddiqui Iram Fatima S. , Wanga Shaynah , de Waard Vivian , Strauss Mike , Reinhardt Dieter P. 
Published: September 2023

AbstractMicrofibrillar-associated protein 4 (MFAP4) is a 36-kDa extracellular glycoprotein with critical roles in human pathologies, including fibrosis in several organ systems, chronic obstructive pulmonary disease, and cardiovascular disorders. In elastic tissues such as arteries, lungs, and skin, MFAP4 associates with microfibrils and elastic fibres, which are the central extracellular fibres affected in thoracic aneurysms. MFAP4 directly interacts with elastogenic proteins, including fibrillin-1 and tropoelastin, and with cells via integrins. MFAP4 multimerisation represents a critical hallmark required for its physiological and pathological properties. However, molecular details and functional consequences of MFAP4 multimerisation are lacking.Here we present a cryo-electron microscopy structure of human MFAP4. In the presence of calcium, MFAP4 assembles as an octamer with D2 point group symmetry, where two sets of homodimers constitute the top and bottom halves of each octamer. Each of the homodimers is linked together by an inter-molecular disulfide bond. An engineered C34S missense mutation in MFAP4 prevented disulfide-bond formation between monomers, but the mutant formed octamers similar to wild type MFAP4. The atomic model, built into the 3.55 Å cryo-EM map, suggests that several salt-bridges are important for interactions within and between homodimers, while non-polar interactions are important for octamer halves to assemble. In the absence of calcium, MFAP4 dissociates into tetramers, representing the top/bottom halves of the octamers. Binding studies with elastogenic proteins, including fibrillin-1, tropoelastin, LTBP4, and small fibulins showed that MFAP4 has multiple surfaces for protein-protein interactions, which depend upon the higher-order assembly of MFAP4. While the disulfide-bond mediated by C34S contributes little to those protein interactions, it modulated cell interaction. When MFAP4 forms assemblies with fibrillin-1, it abrogates MFAP4 interactions with cells. Overall, the study provides detailed molecular structure-function relationships of MFAP4 interactions with elastogenic proteins and cells.
Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides
Authors: Tang Simon , Peel Emma , Belov Katherine , Hogg Carolyn J. , Farquharson Katherine A. 
Published: September 2023

ABSTRACTThe number of genome-level resources for non-model species continues to rapidly expand. However, frog species remain underrepresented, with up to 90% of frog genera having no genomic or transcriptomic data. Here, we assemble the first genomic and transcriptomic resources for the recently described southern stuttering frog (Mixophyes australis). The southern stuttering frog is ground-dwelling, inhabiting naturally vegetated riverbanks in south-eastern Australia. Using PacBio HiFi long-read sequencing and Hi-C scaffolding, we generated a high-quality genome assembly, with a scaffold N50 of 369.3 Mb and 95.1% of the genome contained in twelve scaffolds. Using this assembly, we identified the mitochondrial genome, and assembled six tissue-specific transcriptomes. We also bioinformatically characterised novel sequences of two families of antimicrobial peptides (AMPs) in the southern stuttering frog, the cathelicidins and β-defensins. While traditional peptidomic approaches to peptide discovery have typically identified one or two AMPs in a frog species from skin secretions, our bioinformatic approach discovered 12 cathelicidins and two β-defensins that were expressed in a range of tissues. We investigated the novelty of the peptides and found diverse predicted activities. Our bioinformatic approach highlights the benefits of multi-omics resources in peptide discovery and contributes valuable genomic resources in an under-represented taxon.
Chemical proteomic approach for in-depth glycosylation profiling of plasma carcinoembryonic antigen in cancer patients
Authors: Chen Jin , Yang Lijun , Li Chang , Zhang Luobin , Gao Weina , Xu Ruilian , Tian Ruijun 
Published: September 2023

AbstractCarcinoembryonic antigen (CEA) of human plasma is a biomarker of many cancer diseases, and its N-glycosylation accounts for 60% of molecular mass. It is highly desirable to characterize its glycoforms for providing additional dimension of features to increase its performance in prognosis and diagnosis of cancers. However, to systematically characterize its site-specific glycosylation is challenging due to its low abundance. Here, we developed a highly sensitive strategy for in-depth glycosylation profiling of plasma CEA through chemical proteomics combined with multi-enzymatic digestion. A trifunctional probe was utilized to generate covalent bond of plasma CEA and its antibody upon UV irradiation. As low as 1 ng/mL CEA in plasma could be captured and digested with trypsin and chymotrypsin for intact glycopeptide characterization. Twenty six out of 28 potential N-glycosylation sites were well identified, which were the most comprehensive N-glycosylation site characterization of CEA on intact glycopeptide level as far as we known. Importantly, this strategy was applied to the glycosylation analysis of plasma CEA in cancer patients. Differential site-specific glycoforms of plasma CEA were observed in patients with colorectal carcinomas (CRC) and lung cancer. The distributions of site-specific glycoforms were different as the progression of CRC, and most site-specific glycoforms were overexpressed in stage II of CRC. Overall, we established a highly sensitive chemical proteomic method to profile site-specific glycosylation of plasma CEA, which should generally applicable to other well-established cancer glycoprotein biomarkers for improving their cancer diagnosis and monitoring performance.In BriefA chemical proteomic approach for glycosylation profiling of proteins was established for glycosylation characterization of plasma CEA with low abundance. Although CEA has been widely used in diagnosis and prognosis of many cancers, it lacks specificity and sensitivity. We found that the glycosylation of CEA on intact glycopeptide level provided additional dimension of molecular features to improve the performance of CEA in cancer diagnosis and progression.HighlightsA chemical proteomic approach for glycosylation profiling of proteins with low abundanceGlycosylation identification of plasma CEA on intact glycopeptide level with high sensitivity and reproducibilityGlycosylation features of plasma CEA in cancer patients with CRC and lung cancer and in CRC patients at different progression stagesGraphical Abstract
A new multiplexed magnetic-capture - droplet digital PCR (ddPCR) tool for monitoring wildlife population health and pathogen surveillance
Authors: Tschritter Christina , de Groot Peter V. C. , Branigan Marsha , Dyck Markus , Sun Zhengxin , Lougheed Stephen C. 
Published: September 2023

AbstractAnthropogenic stressors are exacerbating the emergence and spread of pathogens worldwide. In regions like the Arctic where ecosystems are particularly susceptible, marked changes are predicted in regional diversity, intensity, and patterns of infectious diseases. To understand such rapidly changing host-pathogen dynamics and mitigate the impacts of novel pathogens, we need sensitive disease surveillance tools. We developed and validated a novel multiplexed, magnetic-capture and ddPCR tool for the surveillance of multiple pathogens in polar bears, a sentinel species that is considered susceptible to climate change and other stressors with a pan-Arctic distribution. Through sequence-specific magnetic capture, we concentrated five target template sequences from three zoonotic bacteria (Erysipelothrix rhusiopathiae,Francisella tularensis, andMycobacterium tuberculosiscomplex) and two parasitic (Toxoplasma gondiiandTrichinellaspp.) pathogens from large quantities (< 100 g) of host tissue. We then designed and validated two multiplexed probe-based ddPCR assays for the amplification and detection of the low concentration target DNA. Validations used 48 polar bear tissues (muscle and liver). We detected 14, 1, 3, 4, and 22 tissue positives forE. rhusiopathiae,F. tularensis,Mycobacterium tuberculosiscomplex,T. gondii, andTrichinellaspp., respectively. These multiplexed assays offer a rapid, specific tool for quantifying and monitoring the changing geographical and host distributions of pathogens relevant to human and animal health.
Spinal cord pathology in a Dravet Syndrome mouse model
Authors: Antinao Diaz Juan , Chilcott Ellie , Keegan Anna , Schorge Stephanie , Waddington Simon N , Karda Rajvinder 
Published: September 2023

AbstractSummaryObjectivesDravet syndrome is a severe epileptic encephalopathy that begins in early childhood. More than 80% of patients with Dravet syndrome exhibit a haploinsufficiency inSCN1A, which encodes the voltage-gated sodium ion channel NaV1.1. The epilepsy is believed be caused by specific deficit ofSCN1Ain inhibitory interneurons of the hippocampus. However, the aetiology of other symptoms including gait disturbances, ataxia, cardiac issues and dysautonomia is less clear.MethodsIn anScn1aknock-out (Scn1a-/-) mouse model which recapitulates clinical phenotypes, we assessed NaV1.1 and neuroinflammation throughout the central nervous system.ResultsConsistent with current understanding, wild-type expression of NaV1.1 transcript and protein were absent in knock-out mice in the prefrontal cortex, striatum, hippocampus, thalamus, and cerebellum. Increased GFAP was detected in the brain only in the hippocampus. Transcript and protein were detected in wild-type cervical, thoracic and lumbar spinal cord but not in knock-out mice. Unexpectedly, GFAP was increased in all three spinal regions. Therefore, we proceeded to perform transcriptomic analysis of cortex, hippocampus and spinal cord. Pathways associated with monooxygenase activity, fatty acid ligases and lactate transporters were highly dysregulated in the spinal cord.ConclusionThe existence and relevance of pathology of the spinal cord in Dravet syndrome has received scant attention. Our findings are consistent with some systemic symptoms of Dravet syndrome, with the benefits of treatments which may modulate the astrocyte-neuron lactate shuttle such as Stiripentol and ketogenic dietary regimes, and with the efficacy of intrathecal delivery of therapeutics.Key PointsDecrease of endogenousScn1aand NaV1.1 expression inScn1a-/-mice has a widespread impact on the gene expression profile in the spinal cord.Increased GFAP expression observed in the spinal cord ofScn1a-/-mice.Differentially expressed genes related to monooxygenase activity, fatty acid ligases and lactate transporters in cervical spinal cord ofScn1a-/-mice.
Sensory experience steers representational drift in mouse visual cortex
Authors: Bauer Joel , Lewin Uwe , Herbert Elizabeth , Gjorgjieva Julijana , Schoonover Carl , Fink Andrew , Rose Tobias , Bonhoeffer Tobias , Hübener Mark 
Published: September 2023

AbstractRepresentational drift – the gradual continuous change of neuronal representations – has been observed across many brain areas. It is unclear whether drift is caused by synaptic plasticity elicited by sensory experience, or by the intrinsic volatility of synapses. Here, using chronic two-photon calcium imaging in mouse primary visual cortex, we find that the preferred stimulus orientation of individual neurons slowly drifts over the course of weeks. By using cylinder lens goggles to limit visual experience to a narrow range of orientations, we show that the direction of drift, but not its magnitude, is biased by the statistics of visual input. A network model suggests that drift of preferred orientation largely results from synaptic volatility, which under normal visual conditions is counteracted by experience-driven Hebbian mechanisms, stabilizing preferred orientation. Under deprivation conditions these Hebbian mechanisms enable adaptation. Thus, Hebbian synaptic plasticity steers drift to match the statistics of the environment.
Regeneration of actin filament branches from the same Arp2/3 complex
Authors: Ghasemi Foad , Cao LuYan , Mladenov Miroslav , Guichard Bérengère , Way Michael , Jégou Antoine , Romet-Lemonne Guillaume 
Published: September 2023

AbstractBranched actin filaments are found in many key cellular structures. Branches are nucleated by the Arp2/3 complex activated by nucleation-promoting factor (NPF) proteins and bound to the side of pre-existing ‘mother’ filaments. Over time, branches dissociate from their mother filament, leading to network reorganization and turnover, but this mechanism is less understood. Here, using microfluidics and purified proteins, we examined the dissociation of individual branches under controlled biochemical and mechanical conditions. We observe that Arp2/3 remains bound to the mother filament after most debranching events, even when accelerated by force. Unexpectedly, this mother-remaining Arp2/3 readily nucleates a new actin filament branch, without being activated anew by an NPF: it simply needs to exchange its nucleotide and bind an actin monomer. The protein GMF, which accelerates debranching, prevents branch re-nucleation. Our results suggest that actin filament re-nucleation can provide a self-repair mechanism, helping branched networks to sustain mechanical stress in cells over extended periods of time.
eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis
Authors: Burnham Katie L. , Milind Nikhil , Lee Wanseon , Kwok Andrew J. , Cano-Gamez Eddie , Mi Yuxin , Geoghegan Cyndi G. ,   GAinS Investigators, McKechnie Stuart , Soranzo Nicole , Hinds Charles J. , Knight Julian C. , Davenport Emma E. 
Published: September 2023

AbstractSepsis is a clinical syndrome of life-threatening organ dysfunction caused by a dysregulated response to infection, for which disease heterogeneity is a major obstacle to developing targeted treatments. We have previously identified gene expression-based patient subgroups (Sepsis Response Signatures: SRS) informative for outcome and underlying pathophysiology. Here we aimed to investigate the role of genetic variation in determining the host transcriptomic response and to delineate regulatory networks underlying SRS. Using genotyping and RNA-seq data on 638 adult sepsis patients, we report 16,049 independent expression (eQTLs) and 32 co-expression module (modQTLs) quantitative trait loci in this disease context. We identified significant interactions between SRS and genotype for 1,578 SNP-gene pairs, and combined transcription factor (TF) binding site information (SNP2TFBS) and predicted regulon activity (DoRothEA) to identify candidate upstream regulators. These included HIF1A and CEBPB, which were associated with progenitor and immature neutrophil subsets respectively, further implicating glycolysis and emergency granulopoiesis in SRS1. Overall, these approaches identified putative mechanistic links between host genetic variation, cell subtypes, and the individual transcriptomic response to infection. Understanding the regulatory networks underlying patient heterogeneity provides additional information for developing immunomodulatory treatments and a personalised medicine approach to treating sepsis.