bluuebunny/crossref_metadata_2025_split huggingface dataset:
Room-temperature serial synchrotron crystallography of apo PTP1B
Authors: Sharma Shivani , Ebrahim Ali , Keedy Daniel A. 
Published: July 2022

AbstractRoom-temperature X-ray crystallography provides unique insights into protein conformational heterogeneity, but a common hurdle is obtaining sufficiently large protein crystals. Serial synchrotron crystallography (SSX) helps address this hurdle by allowing the use of many medium- to small-sized crystals. We have used a recently introduced serial sample support chip system to obtain the first SSX structure of a human phosphatase, specifically Protein Tyrosine Phosphatase 1B (PTP1B) in the unliganded (apo) state. In previous apo room-temperature structures, the active site and allosteric sites adopted alternate conformations, including open and closed conformations for the active-site WPD loop and for a distal allosteric site. By contrast, in our SSX structure, the active site is best fit with a single conformation, but the distal allosteric site is best fit with alternate conformations. This observation argues for additional nuance in interpreting the nature of allosteric coupling in this protein. Overall, our results illustrate the promise of serial methods for room-temperature crystallography, as well as future avant-garde crystallography experiments, for PTP1B and other proteins.
Defining the optimal intranasal administration strategy for inactivated poliovirus vaccine
Authors: Kraan Heleen , Willems Geert-Jan , Soema Peter C. 
Published: July 2022

AbstractMucosal immunity plays a pivotal role in protection against infection and the transmission of pathogens from person to person. Ideally, novel vaccines should be easy and safe to administer, provide mucosal immunity, be safe to manufacture, and be affordable for low-income countries. Alternative delivery strategies, such as the intranasal route, may fulfill at least some of these preferred vaccine characteristics. Moreover, vaccination via mucosal routes has the potential to evoke strong mucosal immunity at the entry site.In the current study, the potential of the intranasal route was investigated for an inactivated polio vaccine based on Sabin strains (sIPV). Different vaccination regimes for intranasal administration of sIPV were evaluated by measuring both systemic and mucosal immune responses in mice. Heterologous prime-boost schedules using a combination of parenteral and mucosal administration showed to elicit virus neutralizing antibody titers in serum and polio-specific IgA titers at different mucosal sites in mice that were vaccinated with sIPV. Moreover, the inclusion of an adjuvant was able to further enhance immune responses. Intranasal administration of adjuvanted sIPV combined with a regular intramuscular sIPV vaccination can significantly improve mucosal immune responses while maintaining systemic immune responses, which can lead to better protection against polio infection and possibly prevent virus transmission. An intranasally delivered inactivated polio vaccine might be of value for use in routine vaccination or outbreak control, and therefore, a helpful tool towards polio-eradication.
Bioengineered niches that recreate physiological extracellular matrix organisation to support long-term haematopoietic stem cells
Authors: Donnelly Hannah , Ross Ewan , Xiao Yinbo , Hermantara Rio , Taqi Aqeel , Sebastian Doherty-Boyd W. , Cassels Jennifer , Tsimbouri Penelope. M. , Dunn Karen M , Hay Jodie , Cheng Annie , Jain Nikhil , West Christopher , Wheadon Helen , Michie Alison M , Peault Bruno , West Adam G. , Salmeron-Sanchez Manuel , Dalby Matthew J. 
Published: July 2022

AbstractLong-term reconstituting haematopoietic stem cells (LT-HSCs) are used to treat blood disorders via allogeneic stem cell transplantation (alloSCT), to engraft and repopulate the blood system. The very low abundance of LT-HSCs and their rapid differentiation duringin vitroculture hinders their clinical utility. Previous developments using stromal feeder layers, defined media cocktails, and bioengineering have enabled HSC expansion in culture, but of mostly short-term HSCs (ST-HSC) and progenitor populations at the expense of naïve LT-HSCs. Here, we report the creation of a bioengineered LT-HSC maintenance niche that recreates physiological extracellular matrix organisation, using soft collagen type-I hydrogels to drive nestin expression in perivascular stromal cells (PerSCs or pericytes). We demonstrate that nestin, which is expressed by HSC-supportive bone marrow stromal cells, is cytoprotective and, via regulation of metabolism, is important for HIF-1α expression in PerSCs. When CD34+veHSCs were added to the bioengineered niches comprising nestin/HIF-1α expressing PerSCs, LT-HSC numbers were maintained with normal clonal andin vivoreconstitution potential, without media supplementation. We provide proof-of-concept that our bioengineered niches can support the survival of CRISPR edited HSCs. Successful editing of LT-HSCs ex vivo can have potential impact on the treatment of blood disorders.
Hitchhiking of bactericidal/permeability-increasing protein-like gene with the fibromelanosis locus in Kadaknath black-bone-chicken
Authors: Shinde Sagar Sharad , Sharma Ashutosh , Vijay Nagarjun 
Published: August 2022

AbstractBlack-bone-chicken (BBC) meat is popular for its distinctive taste and texture. A complex chromosomal rearrangement at the fibromelanosis (Fm) locus on the 20th chromosome results in increased expression of the endothelin-3 (EDN3) gene and is responsible for melanin hyperpigmentation in BBC. We use public long-read sequencing data of the silkie breed to resolve high-confidence haplotypes at theFmlocus spanning both Dup1 and Dup2 regions and establish that theFm_2scenario is correct of the three possible scenarios of the complex chromosomal rearrangement. The relationship between Chinese and Korean BBC breeds with Kadaknath native to India is underexplored. Our data from whole-genome re-sequencing establishes that all BBC breeds, including Kadaknath, share the complex chromosomal rearrangement junctions at the fibromelanosis (Fm) locus. We also identify twoFmlocus proximal regions (∼70Kb and ∼300 Kb) with signatures of selection unique to Kadaknath. These regions harbor several genes with protein-coding changes, with the Bactericidal/permeability-increasing-protein-like (BPIL) gene having two Kadaknath-specific changes within protein domains. Our results indicate that protein-coding changes in theBPILgene hitchhiked with theFmlocus in Kadaknath due to close physical linkage. Identifying thisFmlocus proximal selective sweep sheds light on the genetic distinctiveness of Kadaknath compared to other BBC.
The Effects of Depression on The Neural Correlates of Reward Sensitivity in Poverty
Authors: Perera-W.A. Hiran , Khairuddin Rozainee , Salehuddin Khazriyati 
Published: August 2022

AbstractExisting studies have identified that depression and depressive symptoms are associated with reduced sensitivity to feedback processing, which is a core ability that determines the success of human actions. However, a key individual difference which is the socioeconomic status (SES) has been largely ignored in this field because the recent trend of research has suggested how it relates to various cognitive domain-specific neural systems. Because depression is a widespread mental health condition that is more prevalent among the poor, it can potentially play a role in the association between poverty and feedback processing. With a sample of 80 adults recruited from low to high-income communities, the current study examined the role of depression on the relationship between poverty and feedback processing by using feedback negativity (FN) event-related potential (ERP), which is a well-known ERP component that is indexed by response feedback indicating losses versus gains. Consistent with previous studies, high depressive symptoms were associated with reduced FN amplitude across our sample. SES was negatively associated with FN and depressive symptoms, which indicates reduced reward sensitivity to feedback among the low-SES individuals who are also mostly depressed. However, no association between SES and reward sensitivity was observed when it was controlled for depression. Findings in this study suggest the importance of partial out the variance accounted for by depression when studying responses to reward sensitivity in poverty.
The 3D Structural Architecture of the Human Hand Area is Non-Topographic
Authors: Doehler Juliane , Northall Alicia , Liu Peng , Fracasso Alessio , Chrysidou Anastasia , Speck Oliver , Lohmann Gabriele , Wolbers Thomas , Kuehn Esther 
Published: August 2022

AbstractThe functional topography of the human primary somatosensory cortex (S1) hand area is a widely studied model system to understand sensory organization and plasticity. It is so far unclear whether or not the underlying 3D structural architecture also shows a topographic organization. We used 7T MRI data to quantify layer-specific myelin, iron and mineralization in relation to population receptive field maps of individual finger representations in Brodman area 3b (BA 3b) of human S1 in female and male younger adults. This 3D description allowed us to identify a characteristic profile of layer-specific myelin and iron deposition in the BA 3b hand area, but revealed an absence of structural differences, an absence of low-myelin borders, and high similarity of 3D microstructure profiles between individual fingers. However, structural differences and borders were detected between the hand and face areas. We conclude that the 3D structural architecture of the human hand area is non-topographic, unlike in some monkey species, which suggests a high degree of flexibility for functional finger organization and a new perspective on human topographic plasticity.Significance StatementUsing ultra-high field MRI, we provide the first comprehensivein vivodescription of the 3D structural architecture of the human BA 3b hand area in relation to functional population receptive field (pRF) maps. High similarity of precise finger-specific 3D profiles, together with an absence of structural differences and an absence of low-myelin borders between individual fingers, reveal the 3D structural architecture of the human hand area to be non-topographic. This suggests reduced structural limitations to cortical plasticity and reorganization, and allows for shared representational features across fingers.
Genome-wide epistasis analysis in Parkinson’s disease between populations with different genetic ancestry reveals significant variant-variant interactions
Authors: Cisterna-Garcia Alejandro , Bustos Bernabe I. , Bandres-Ciga Sara , Leal Thiago P. , Sarihan Elif I. , Jok Christie , Blauwendraat Cornelis , Nalls Mike A. , Krainc Dimitri , Singleton Andrew B. ,   International Parkinson’s Disease Genomics Consortium (IPDGC), Mata Ignacio F. , Lubbe Steven J. , Botia Juan A. 
Published: August 2022

AbstractGenome-wide association studies (GWAS) have increased our understanding of Parkinson’s disease (PD) genetics through the identification of common disease-associated variants. However, much of the heritability remains unaccounted for and we hypothesized that this could be partly explained by epistasis. Here, we developed a genome-wide non-exhaustive epistasis screening pipeline calledVariant-variant interaction through variable thresholds(VARI3) and applied it to diverse PD GWAS cohorts. First, as a discovery cohort, we used 14 cohorts of European ancestry (14,671 cases and 17,667 controls) to identify candidate variant-variant interactions. Next, we replicated significant results in a cohort with a predominately Latino genetic ancestry (807 cases and 690 controls). We identified 14 significant epistatic signals in the discovery stage, with genes showing enrichment in PD-relevant ontologies and pathways. Next, we successfully replicated two of the 14 interactions, where the signals were located nearbySNCAand withinMAPTandWNT3. Finally, we determined that the epistatic effect on PD of those variants was similar between populations. In brief, we identified several epistatic signals associated with PD and replicated associations despite differences in the genetic ancestry between cohorts. We also observed their biological relevance and effect on the phenotype usingin silicoanalysis.
Enhanced viral infectivity and reduced interferon production are associated with high pathogenicity for influenza viruses
Authors: Li Ke , McCaw James M. , Cao Pengxing 
Published: July 2022

AbstractEpidemiological and clinical evidence indicates that humans infected with the 1918 pandemic influenza virus and highly pathogenic avian H5N1 influenza viruses often displayed severe lung pathology. High viral load and extensive infiltration of macrophages are the hallmarks of highly pathogenic (HP) influenza viral infections. However, it remains unclear what biological mechanisms primarily determine the observed difference in the kinetics of viral load and macrophages between HP and low pathogenic (LP) viral infections, and how the mechanistic differences are associated with viral pathogenicity. In this study, we develop a mathematical model of viral dynamics that includes the dynamics of different macrophage populations and interferon. We fit the model to in vivo kinetic data of viral load and macrophage level from BALB/c mice infected with an HP or LP strain of H1N1/H5N1 virus using Bayesian inference. Our primary finding is that HP viruses has a higher viral infection rate, a lower interferon production rate and a lower macrophage recruitment rate compared to LP viruses, which are strongly associated with more severe tissue damage (quantified by a higher percentage of epithelial cell loss). We also quantify the relative contribution of macrophages to viral clearance and find that macrophages do not play a dominant role in direct clearance of free virus although their role in mediating immune responses such as interferon production is crucial. Our work provides new insight into the mechanisms that convey the observed difference in viral and macrophage kinetics between HP and LP infections and establishes an improved model fitting framework to enhance the analysis of new data on viral pathogenicity.Author SummaryInfections with highly pathogenic (HP) influenza virus (e.g., the 1918 pandemic virus) often lead to serious morbidity and mortality. HP influenza virus infection is characterised by rapid viral growth rate, high viral load and excessive infiltration of macrophages to the lungs. Despite extensive study, we do not yet fully understand what biological processes leading to the observed viral and macrophage dynamics and therefore viral pathogenicity. Experimental studies have previously suggested that bot viral factors (e.g., viral proteins) and host factors (e.g., the host immune response) play a role to enhance viral pathogenicity. Here, we utilise in vivo kinetic data of viral load and macrophages and fit a viral dynamic model the data. Our model allow us to explore the biological mechanisms that contribute to the difference viral and macrophage dynamics between HP and LP infections. This study improves our understanding of the role of interferon on distinguishing immunodynamics between HP and LP infections. Our findings may contribute to the development of next-generation treatment which rely upon an understanding of the host different immunological response to HP influenza viruses.
Early events marking lung fibroblast transition to profibrotic state in idiopathic pulmonary fibrosis
Authors: Jia Minxue , Rosas Lorena , Kapetanaki Maria G. , Tabib Tracy , Sebrat John , Cruz Tamara , Bondonese Anna , Mora Ana L. , Lafyatis Robert , Rojas Mauricio , Benos Panayiotis .V. 
Published: August 2022

ABSTRACTBackgroundIdiopathic Pulmonary Fibrosis (IPF) is an age-associated progressive lung disease with accumulation of scar tissue impairing gas exchange. Previous high-throughput studies elucidated the role of cellular heterogeneity and molecular pathways in advanced disease. However, critical pathogenic pathways occurring in the transition of fibroblasts from normal to profibrotic have been largely overlooked.MethodsWe used single cell transcriptomics (scRNA-seq) from lungs of healthy controls and IPF patients (lower and upper lobes). We identified fibroblast subclusters, genes and pathways associated to early disease. Immunofluorescence assays validated the role of MOXD1 early in fibrosis.FindingsWe identified four distinct fibroblast subgroups, including one marking the normal-to-profibrotic state transition. Our results show for the first time that global downregulation of ribosomal proteins and significant upregulation of the majority of copper-binding proteins, including MOXD1, mark the IPF transition. We find no significant differences in gene expression in IPF upper and lower lobe samples, which were selected to have low and high degree of fibrosis, respectively.InterpretationEarly events during IPF onset in fibroblasts include dysregulation of ribosomal and copper-binding proteins. Fibroblasts in early stage IPF have already acquired a profibrotic phenotype while hallmarks of advanced disease, including fibroblast foci and honeycomb formation, are still not evident. The new transitional fibroblasts we discover could prove very important for studying the role of fibroblast plasticity in disease progression and help develop early diagnosis tools and therapeutic interventions targeting earlier disease states.
New genetic tools enable dissection of a global stress response in the early-branching speciesFusobacterium nucleatum
Authors: Ponath Falk , Zhu Yan , Cosi Valentina , Vogel Jörg 
Published: July 2022

ABSTRACTFusobacterium nucleatum, long known as a common oral microbe, has recently garnered attention for its ability to colonize tissues and tumors elsewhere in the human body. Clinical and epidemiological research has now firmly establishedF. nucleatumas an oncomicrobe associated with several major cancer types. However, with the current research focus on host associations, little is known about gene regulation inF. nucleatumitself, including global stress response pathways that typically ensure the survival of bacteria outside their primary niche. This is due to the phylogenetic distance of Fusobacteriota to most model bacteria, their limited genetic tractability, and paucity of known gene functions. Here, we characterize a global transcriptional stress response network governed by the extracytoplasmic function sigma factor, σE. To this aim, we developed several new genetic tools for this anaerobic bacterium, including four different fluorescent marker proteins, inducible gene expression, scarless gene deletion, and transcriptional and translational reporter systems. Using these tools, we identified a σEresponse partly reminiscent of phylogenetically distant Proteobacteria but induced by exposure to oxygen. AlthoughF. nucleatumlacks canonical RNA chaperones such as Hfq, we uncovered conservation of the non-coding arm of the σEresponse in form of the non-coding RNA FoxI. This regulatory small RNA (sRNA) acts as an mRNA repressor of several membrane proteins, thereby supporting the function of σE. In addition to the characterization of a global stress response inF. nucleatum, the genetic tools developed here will enable further discoveries and dissection of regulatory networks in this early-branching bacterium.SIGNIFICANCE STATEMENTFusobacterium nucleatumis an abundant member of the oral microbiome that can spread throughout the body and colonize secondary sites, including cancer tissues where it promotes tumor progression. Understanding howF. nucleatumis able to adapt to this new environment might open new therapeutic opportunities, but we currently lack basic molecular knowledge of gene regulation in this phylogenetically distinct bacterium. We developed much-needed genetic tools for use inF. nucleatumand with their aid uncovered a stress response mediated by the transcriptional activator σEand an associated small RNA. Our findings in an early-branching bacterium reveal surprising parallels to and differences from the σEresponse in well-characterized model bacteria and provide a framework that will accelerate research into the understudied phylum Fusobacteriota.
TraC of the conjugative plasmid pKM101 is secreted as a monomer in outer membrane vesicles and stimulates conjugation
Authors: Amro Jaafar , Baron Christian 
Published: July 2022

AbstractGram-negative bacteria use membrane-bound type IV secretion systems to assemble pili on the cell surface, followed by cell-cell contact with recipient cells and transfer of plasmid DNA. The process at the cell-cell contact stage of conjugative DNA transfer is not well understood. We here present a biochemical and genetic characterization of the TraC protein that is a minor component of the pili determined by the IncN plasmid pKM101 from Escherichia coli. The cellular and secreted forms of TraC are monomers, TraC preferentially localizes at the cell poles and it is also detected in extracellular membrane vesicles. Purified TraC does not impact the infection with bacteriophages, but we detect binding of TraC to recipient cells and partial complementation of a traC deletion strain by the addition of purified TraC. These results suggest that the protein contributes to conjugation at the cell-cell contact stage.
Crowding-induced phase separation and solidification by co-condensation of PEG in NPM1-rRNA condensates
Authors: André Alain A.M. , Yewdall N. Amy , Spruijt Evan 
Published: July 2022

ABSTRACTThe crowdedness of the cell calls for adequate intracellular organization. Biomolecular condensates, formed by liquid-liquid phase separation of intrinsically disordered proteins and nucleic acids, are important organizers of cellular fluids. To underpin the molecular mechanisms of protein condensation, cell-free studies are often used where the role of crowding is not investigated in detail. Here, we investigate the effects of macromolecular crowding on the formation and material properties of a model heterotypic biomolecular condensate, consisting of nucleophosmin (NPM1) and ribosomal RNA (rRNA). We studied the effect of the macromolecular crowding agent PEG, which is often considered an inert crowding agent. We observed that PEG could induce both homotypic and heterotypic phase separation of NPM1 and NPM1-rRNA, respectively. Crowding increases the condensed concentration of NPM1 and decreases its equilibrium dilute phase concentration, while no significant change in the concentration of rRNA in the dilute phase was observed. Interestingly, the crowder itself is concentrated in the condensates, suggesting that co-condensation rather than excluded volume interactions underlie the enhanced phase separation by PEG. Fluorescence recovery after photobleaching (FRAP) measurements indicated that both NPM1 and rRNA become immobile at high PEG concentrations, indicative of a liquid-to-gel transition. Together, these results shed new light onto the role of synthetic crowding agents in phase separation, and demonstrate that condensate properties determined in vitro depend strongly on the addition of crowding agents.STATEMENT OF SIGNIFICANCELiquid-liquid phase separation of proteins and nucleic acids leads to the formation of biomolecular condensates. To mimic biomolecular condensates in vitro, polymeric crowding agents, such as PEG, are often added. Such crowding agents are considered to make in vitro solutions more physiologically relevant, by mimicking the high cellular macromolecule concentrations. However, these crowding agents are commonly selected for their commercial availability and solubility in water, and their influence on phase separation and the physicochemical properties of condensates are seldom studied. Here we use biophysical methods to show that PEG induces phase separation of a model condensate through co-condensation rather than volume exclusion. As a consequence, crowding changes the partitioning, concentrations and viscoelastic properties of the condensates significantly, which sheds new light onto studies aimed at quantifying the material properties of biomolecular condensates.