bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human hnRNPA1 reorganizes telomere-bound Replication Protein A
Authors: Granger Sophie L. , Sharma Richa , Kaushik Vikas , Razzaghi Mortezaali , Honda Masayoshi , Gaur Paras , Bhat Divya S. , Labenz Sabryn M. , Heinen Jenna E. , Williams Blaine A. , Tabei S. M. Ali , Wlodarski Marcin W. , Antony Edwin , Spies Maria 
Published: May 2023

AbstractHuman replication protein A (RPA) is a heterotrimeric ssDNA binding protein responsible for many aspects of cellular DNA metabolism. Dynamic interactions of the four RPA DNA binding domains (DBDs) with DNA control replacement of RPA by downstream proteins in various cellular metabolic pathways. RPA plays several important functions at telomeres where it binds to and melts telomeric G-quadruplexes, non-canonical DNA structures formed at the G-rich telomeric ssDNA overhangs. Here, we combine single-molecule total internal reflection fluorescence microscopy (smTIRFM) and mass photometry (MP) with biophysical and biochemical analyses to demonstrate that heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) specifically remodels RPA bound to telomeric ssDNA by dampening the RPA configurational dynamics and forming a ternary complex. Uniquely, among hnRNPA1 target RNAs, telomeric repeat-containing RNA (TERRA) is selectively capable of releasing hnRNPA1 from the RPA-telomeric DNA complex. We speculate that this telomere specific RPA-DNA-hnRNPA1 complex is an important structure in telomere protection.One Sentence SummaryAt the single-stranded ends of human telomeres, the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) binds to and modulates conformational dynamics of the ssDNA binding protein RPA forming a ternary complex which is controlled by telomeric repeat-containing RNA (TERRA).
Metabolic alterations unravel the materno–fetal immune responses with disease severity in pregnant women infected with SARS-CoV-2
Authors: Hora Sandhya , Pahwa Prabhjyoti , Siddiqui Hamda , Saxena Anoushka , Kashyap Minal , Sevak Jayesh Kumar , Singh Ravinder , Javed Maryam , Yadav Pushpa , Kale Pratibha , Ramakrishna Gayatri , Rathore Asmita , Maras Jaswinder Singh , Tyagi Shakun , Sarin Shiv kumar , Trehanpati Nirupama 
Published: May 2023

AbstractBackgroundPregnancy being immune compromised state, COVID-19 disease poses high risk of premature delivery and threat to fetus. Plasma metabolome regulates immune cellular responses and we aimed to analyze the plasma secretome, metabolome and immune cells in COVID-19 positive pregnant mother and cord blood.MethodsCOVID-19 RT-PCR positive pregnant females (n=112) asymptomatic (n=82), or with mild (n=21) or moderate (n=9) disease and control healthy pregnant (n=10) females were included. Mother’s blood and cord blood (n=80) was analysed for untargeted metabolome profiling and plasma cytokines by high-resolution mass spectrometry (MS) and multiplex cytokine bead array. Immune scan in mothers was done using flow cytometry.ResultsIn asymptomatic SARS-CoV-2 infection, --the amino acid metabolic pathways such as glycine, serine, L-lactate and threonine metabolism was upregulated, riboflavin and tyrosine metabolism, downregulated. In mild to moderate disease, the pyruvate and NAD+metabolism (energy metabolic pathways) were mostly altered. In addition to raised TNF-α, IFN-α, IFN-γ, IL-6 cytokine storm, IL-9 was increased in both mothers and neonates. Pyruvate and NAD+metabolic pathways along with IL-9 and IFN-γ had impact on non-classical monocytes, increased CD4 T cells and B cells but depleted CD8+T cells. Cord blood mimicked the mother’s metabolomic profiles by showing altered valine, leucine, isoleucine, glycine, serine, threonine in asymptomatic and NAD+and riboflavin metabolism in mild and moderate disease subjects.ConclusionsOur results demonstrate a graduated immune-metabolomic interplay in mother and fetus in pregnant females with different degrees of severity of COVID-19 disease. IL-9 and IFN- γ regulated pyruvate, lactate TCA metabolism and riboflavin metabolism with context to disease severity are hall marks of this materno-fetal metabolome.HighlightsSARS-CoV-2 infection alters energy consumption metabolic pathways during pregnancy.Pregnant women with mild to moderate COVID-19 show increased energy demands, and consume stored glucose by upregulating pyruvate and NAD+metabolism.Increased TNF-α and IL-9 in mild COVID-19 disease involve TCA cycle to produce lactate and consume stored glucose by up regulating pyruvate and nicotinamide and nicotinate metabolism.With mild to moderate disease, raised IL-9 and TNF-α, decreased riboflavin pathway, exhaustion of T and B cells cause pathogenesis.Cord blood mimics the metabolic profile of mother’s peripheral blood, SARS- CoV-2 infection reshapes immune-metabolic profiles of mother-infant dyad.Graphical Abstract
Identification and mapping ofRpi-blb4in diploid wild potato speciesSolanum bulbocastanum
Authors: Li Jie , Kaur Amanpreet , Harrower Brian , Armstrong Miles , Dou Daolong , Wang Xiaodan , Hein Ingo 
Published: May 2023

AbstractMore than 170 years after causing the potato famine in Ireland, late blight is still considered one of the most devastating crop diseases. Commercial potato breeding efforts depend on natural sources of resistance to protect crops from the rapidly evolving late blight pathogen,Phytophthora infestans. We have identified and mapped a novel broad-spectrum disease resistance gene effective againstP. infestansfrom the wild, diploid potato speciesSolanum bulbocastanum. Diagnostic resistance gene enrichment sequencing (dRenSeq) was used to confirm the uniqueness of the identified resistance. RenSeq and GenSeq-based mapping of the resistance, referred to asRpi-blb4, alongside recombinant screening, positioned the locus responsible for the resistance to potato Chromosome 5. The interval spans approximately 2.3 MB and corresponds to the DM reference genome positions of 11.25 and 13.56 Mb.
In-section Click-iT detection and super-resolution CLEM: Shedding light on nucleolar ultrastructure and S-phase progression in plants
Authors: Franek M , Koptasikova L , Miksatko J , Pospisil J , Liebl D , Esner M , Macickova E , Dvorackova M , Fajkus J 
Published: May 2023

AbstractCorrelative light and electron microscopy (CLEM) is an essential tool that allows for localisation of a particular target molecule(s) and their spatial correlation with the ultrastructural map of subcellular features at the nanometer scale. Adoption of these advanced imaging methods has been limited in plant biology, due to challenges with plant tissue permeability, fluorescence labelling efficiency, indexing of features of interest throughout the complex 3D volume and their re-localization on micrographs of ultrathin cross-sections. Here, we demonstrate an imaging approach based on tissue processing and embedding into methacrylate resin followed by imaging of serial sections by both, single-molecule localization microscopy and transmission electron microscopy for correlative analysis. Importantly, we demonstrate that the use of a particular type of embedding resin is not only compatible with single-molecule localization microscopy but shows a dramatic improvement in fluorophore blinking behavior relative to the whole-mount approaches. Here we used commercially available Click-iT ethynyl-deoxyuridine cell proliferation kit to visualize the DNA replication sites of wild-typeArabidopsis thalianaseedlings, as well as FASCIATA1 and NUCLEOLIN1 mutants and applied our on-section CLEM imaging workflow for the analysis of S-phase progression and nucleolar organization in mutant plants with aberrant nucleolar phenotypes.
KLIPP - a precision CRISPR approach to target structural variant junctions in cancer
Authors: Yang Huibin , Hulbatte Radhika Suhas , Kelleher Alan , Gratsch Natalie , Wang Yin , Palmbos Philip L. , Ljungman Mats 
Published: May 2023

AbstractCurrent cancer therapies typically give rise to dose-limiting normal tissue toxicity. We have developed KLIPP, a precision cancer approach that specifically kills cancer cells using CRISPR/Cas9 technology. The approach consists of guide RNAs that target cancer-specific structural variant junctions to nucleate two parts of a dCas9-conjugated endonuclease, Fok1, leading to its activation. We show that KLIPP causes induction of DNA double strand breaks (DSBs) at the targeted junctions and cell death. When cancer cells were grown orthotopically in mice, activation of Fok1 at only two junctions led to the disappearance of tumor cells in 7/11 mice. This therapeutic approach has high specificity for tumor cells and is independent of tumor-specific drivers. Individualized translation of KLIPP to patients would be transformative and lead to consistent and simplified cancer treatment decisions.
Thrombocytopenia Independently Leads to Monocyte Immune Dysfunction
Authors: Li Chen , Ture Sara K. , Nieves-Lopez Benjamin , Blick-Nitko Sara K. , Maurya Preeti , Livada Alison C. , Stahl Tyler J. , Kim Minsoo , Pietropaoli Anthony P. , Morrell Craig N. 
Published: May 2023

AbstractIn addition to their well-studied hemostatic functions, platelets are immune cells. Platelets circulate at the interface between the vascular wall and leukocytes, and transient platelet-leukocyte complexes are found in both healthy and disease states, positioning platelets to provide physiologic cues of vascular health and injury. Roles for activated platelets in inducing and amplifying immune responses have received an increasing amount of research attention, but our past studies also showed that normal platelet counts are needed in healthy conditions to maintain immune homeostasis. We have now found that thrombocytopenia (a low platelet count) leads to monocyte dysfunction, independent of the cause of thrombocytopenia, in a manner that is dependent on direct platelet-monocyte CD47 interactions that regulate monocyte immunometabolism and gene expression. Compared to monocytes from mice with normal platelet counts, monocytes from thrombocytopenic mice had increased toll-like receptor (TLR) responses, including increased IL-6 production. Furthermore,ex vivoco-incubation of resting platelets with platelet naïve bone marrow monocytes, induced monocyte metabolic programming and durable changes in TLR agonist responses. Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) on monocytes from thrombocytopenic mice showed persistently open chromatin at LPS response genes and resting platelet interactions with monocytes induced histone methylation in a CD47 dependent manner. Using mouse models of thrombocytopenia and sepsis, normal platelet numbers were needed to limit monocyte immune dysregulation andIL6expression in monocytes from human patients with sepsis also inversely correlated with patient platelet counts. Our studies demonstrate that in healthy conditions, resting platelets maintain monocyte immune tolerance by regulating monocyte immunometabolic processes that lead to epigenetic changes in TLR-related genes. This is also the first demonstration of sterile cell interactions that regulate of innate immune-metabolism and monocyte pathogen responses.
GRK2 Kinases in the Primary Cilium Initiate SMOOTHENED-PKA Signaling in the Hedgehog Cascade
Authors: Walker Madison F. , Zhang Jingyi , Steiner William , Ku Pei-I , Zhu Ju-Fen , Michaelson Zachary , Yen Yu-Chen , Lee Annabel , Long Alyssa B. , Casey Mattie J. , Poddar Abhishek , Nelson Isaac B. , Arveseth Corvin D. , Nagel Falko , Clough Ryan , LaPotin Sarah , Kwan Kristen M. , Schulz Stefan , Stewart Rodney A. , Tesmer John J. G. , Caspary Tamara , Subramanian Radhika , Ge Xuecai , Myers Benjamin R. 
Published: May 2023

ABSTRACTDuring Hedgehog (Hh) signal transduction in development and disease, the atypical G protein-coupled receptor (GPCR) SMOOTHENED (SMO) communicates with GLI transcription factors by binding the protein kinase A catalytic subunit (PKA-C) and physically blocking its enzymatic activity. Here we show that GPCR kinase 2 (GRK2) orchestrates this process during endogenous Hh pathway activation in the vertebrate primary cilium. Upon SMO activation, GRK2 rapidly relocalizes from the ciliary base to the shaft, triggering SMO phosphorylation and PKA-C interaction. Reconstitution studies reveal that GRK2 phosphorylation enables active SMO to bind PKA-C directly. Lastly, the SMO-GRK2-PKA pathway underlies Hh signal transduction in a range of cellular andin vivomodels. Thus, GRK2 phosphorylation of ciliary SMO, and the ensuing PKA-C binding and inactivation, are critical initiating events for the intracellular steps in Hh signaling. More broadly, our study suggests an expanded role for GRKs in enabling direct GPCR interactions with diverse intracellular effectors.
Improving xylose consumption inRhodotorula toruloidesthrough heterologous expression of xylose reductase and xylulokinase
Authors: de Oliveira Paola Monteiro , Pinheiro Marina Julio , De Biaggi Juliano Sabedotti , Tšitšerin Artjom , Tammekivi Eliise , Herodes Koit , Bonturi Nemailla , Lahtvee Petri-Jaan 
Published: May 2023

AbstractThe oleaginous yeastRhodotorula toruloidesis a promising host for sustainable bioproduction due to its capacity to naturally utilize xylose present in lignocellulosic biomass, an abundant and renewable resource. However, its xylose consumption pathway is still not completely understood. To better understand the potential limitations in xylose utilization inR. toruloides, heterologous xylose reductase fromScheffersomyces stipitis, together with the native and heterologous xylulokinases from three different microorganisms (Scheffersomyces stipitis, Candida intermedia, andEscherichia coli) were overexpressed solely and in combination. The overexpression of xylulokinases showed more significant improvements in terms of xylose consumption rate compared to the single overexpression of xylose reductase. When the heterologous xylulokinase fromEscherichia coliwas overexpressed, the specific xylose consumption rate was improved by 66% and the maximum specific growth rate by 30% compared to the parental strain. The xylose specific consumption rate increased by 146% and the maximum specific growth rate increased by 118% when heterologous genes for xylose reductase and xylulokinase fromE. coliwere overexpressed together. These results suggest that the low expression of xylulokinase inR. toruloides, which has been reported previously, could limit its sugar consumption, while supporting higher lipid accumulation in this yeast.
The marine natural microbiome mediates physiological outcomes in host nematodes
Authors: Xue Yiming , Xie Yusu , Cao Xuwen , Zhang Liusuo 
Published: May 2023

AbstractNematodes are the most abundant metazoans in marine sediments, many of which are bacterivores, however how habitat bacteria effects physiological outcomes in marine nematodes remains largely unknown. Here, we used aLitoditis marinainbred line to assess how native bacteria modulates host nematode physiology. We characterized seasonal dynamic bacterial compositions inL. marinahabitats, and examined the impacts of 448 habitat bacteria isolates onL. marinadevelopment, then focused on HQbiome with 73 native bacteria, of which we generated 72 whole genomes sequences. Unexpectedly, we found that the effects of marine native bacteria on the development ofL. marinaand its terrestrial relativeCaenorhabditis eleganswere significantly positively correlated. Next, we reconstructed bacterial metabolic networks and identified several bacterial metabolic pathways positively correlated withL. marinadevelopment (e.g., ubiquinol and hemebbiosynthesis), while pyridoxal 5’-phosphate biosynthesis pathway was negatively associated. Through single metabolite supplementation, we verified CoQ10, hemeb, Acetyl-CoA, and acetaldehyde promotedL. marinadevelopment, while vitamin B6 attenuated growth. Notably, we found that only four development correlated metabolic pathways were shared betweenL. marinaandC. elegans. Furthermore, we identified two bacterial metabolic pathways correlated withL. marinalifespan, while a distinct one inC. elegans. Strikingly, we found that glycerol supplementation significantly extendedL. marinabut notC. eleganslongevity. Moreover, we comparatively demonstrated the distinct gut microbiota characteristics and their effects onL. marinaandC. elegansphysiology. Our integrative approach will provide a microbe–nematodes framework for microbiome mediated effects on host animal fitness.
Perceived Clinical Readiness of Senior Medical Students as Outcomes of Online Clerkship in the Philippines: New Normal in Medical Education
Authors: Abear Adam James A. , Benitez Marie Bernice P. , Cabrillos Krissha Marie S. , Casaña Adrian V. , Doctora Ma. Theresa Mae P. , Ellema Joan Marie D. , Fuentes Bianca Louise U. , Lam Justin Riley Y. , Mendoza John Emmanuel C. , Tan Shairah P. , Tan Shannon D. 
Published: May 2023

ABSTRACTTITLEPerceived Clinical Readiness of Senior Medical Students as Outcomes 0f Online Clerkship in the Philippines: New Normal in Medical EducationINTRODUCTIONCOVID-19 formed new challenges to the medical institutions; it resulted in the transition from the usual face-to-face classes and direct clerkship training within the hospital to a new remote learning with online lectures and virtual clinical experience. Given the new online interactive setting, problems were raised given the limited patient care and interaction as well as restricted bedside teaching opportunities and its impact on how medical students can acquire and hone their clinical skills.OBJECTIVETo determine the perceived clinical readiness of the medical clerks in the new normal setting in the Philippines.METHODOLOGYConvenience sampling was used to gather respondents who were asked to answer an online survey questionnaire. The questions pertained to: academic training profile, clinical skills, patient management, communication, understanding clinical guidelines, and personal development. After analyzing the data, the scales of readiness from these subjects were gathered.RESULTSThe medical clerks in the Philippines perceived that they were ready with regards to understanding clinical guidelines, communication, personal development, and patient management. They were moderately ready in the different clinical skills in the departments of Family and Community Medicine, Internal Medicine, Pediatrics, Surgery and Obstetrics and Gynecology with some specific skills in Surgery and Obstetrics and Gynecology being perceived as less ready than the rest.CONCLUSIONThe impact of the pandemic has disrupted the student’s confidence and readiness. This shows that online clerkship in this time of pandemic may have provided learning to a certain degree but it is not enough to replace what face-to-face training could offer.
Transcriptional changes consistent with impaired neuronal differentiation, angiogenesis, and tumor plasticity induced in human subpallial telencephalic organoid-glioblastoma chimeras
Authors: Chiola Simone , Yang Jingye , Ullah H M Arif , Napan Kandy , Huang Qiju , Gamboa Nicholas , Youssef Osama , Colman Howard , Cheshier Samuel H. , Shcheglovitov Alex 
Published: May 2023

AbstractGlioblastoma multiforme (GBM) is one of the most aggressive and therapy-resistant brain tumors prevalent in both adults and children. Despite extensive research to understand GBM pathology, it remains unclear how neural cells in the human brain interact with GBM cells to support their brain propagation and therapy resistance and whether GBM cells exert any influence on the properties of human neural cells. In this study, we co-culture human stem cell-derived subpallial telencephalic organoids with patient-derived proneural or mesenchymal GBM spheroids to investigate their reciprocal interactions. We show that both proneural and mesenchymal GBM spheroids readily fuse and propagate with human organoids, forming organoid-GBM chimeras, without the need for exogenous growth factors. GBM cells within the chimeras adapt by modulating gene expression profiles consistent with diminished proliferation, heightened hypoxia, increased angiogenesis, and proneural-to-mesenchymal transition in proneural GBM. Both proneural or mesenchymal GBMs also exert an impact on the properties of neural cells in the chimeras, leading to the suppression of neuronal genes and an upregulation expression of genes associated with hypoxia and angiogenesis. Collectively, this study identifies specific genes and molecular pathways that can be altered in GBM and neural cells by reciprocal interactions in a human developing brain-like environment for an increased understanding of GBM pathology and future therapy development.
Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs
Authors: Olsen Johan G. , Prestel Andreas , Kassem Noah , Broendum Sebastian S. , Shamim Hossain Mohammad , Simonsen Signe , Grysbæk Martin , Mortensen Josefine , Rytkjær Louise Lund , Haxholm Gitte W. , Marabini Riccardo , Carr Antony M. , Crehuet Ramon , Nielsen Olaf , Kragelund Birthe B. 
Published: May 2023

AbstractDNA regulation, replication and repair are processes fundamental to all known organisms and the sliding clamp proliferating cell nuclear antigen (PCNA) is central to all these processes. S-phase delaying protein 1 (Spd1) fromS. pombe, an intrinsically disordered protein that causes checkpoint activation by inhibiting the enzyme ribonucleotide reductase, has one of the most divergent PCNA binding motifs known. Using NMR spectroscopy,in vivoassays, X-ray crystallography, calorimetry, and Monte Carlo simulations, an additional PCNA binding motif in Spd1, a PIP-box, is revealed. The two tandemly positioned, low affinity sites exchange rapidly on PCNA exploiting the same binding sites. Increasing or decreasing the binding affinity between Spd1 and PCNA through mutations of either motif compromised the ability of Spd1 to cause checkpoint activation in yeast. These results pinpoint a role for PCNA in Spd1-mediated checkpoint activation and suggest that its tandemly positioned short linear motifs create a neatly balanced competition-based system, involving PCNA, Spd1 and the small ribonucleotide reductase subunit, Suc22R2. Similar mechanisms may be relevant in other PCNA binding ligands where divergent binding motifs so far have gone under the PIP-box radar.
Phage activity againstStaphylococcus aureusis impaired in plasma and synovial fluid
Authors: Mutti Michele , Moreno David Sáez , Restrepo-Córdoba Marcela , Visram Zehra , Resch Grégory , Corsini Lorenzo 
Published: May 2023

AbstractS. aureus is a pathogen that frequently causes severe morbidity and phage therapy is being discussed as an alternative to antibiotics for the treatment of S. aureus infections. In this in vitro and animal study, we demonstrated that the activity of anti-staphylococcal phages is severely impaired in plasma and synovial fluid. Despite phage replication in these matrices, lysis of the bacteria was slower than phage propagation, and no reduction of the bacterial population was observed. This phage inhibition is due to a 99% reduction of phage adsorption, already at 10% plasma concentration. Coagulation factors bind S. aureus resulting in the formation of aggregates and blood clots that protect the bacterium from the phages. This was confirmed by the finding that purified fibrinogen is sufficient to impair phage activity. In contrast, dissolution of the clots by tissue plasminogen activator (tPA) partially restored phage activity. Consistent with these in vitro findings, phage treatment did not reduce bacterial burdens in a neutropenic mouse S. aureus thigh infection model. In summary, phage treatment of S. aureus infections may be fundamentally challenging, and more investigation is needed prior to proceeding to in-human trials.