bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic analysis across patient iPSC-based models and human post-mortem hippocampal tissue reveals early cellular dysfunction, progression, and prion-like spread of Alzheimer’s disease pathogenesis
Authors: Pomeshchik Yuriy , Velasquez Erika , Gil Jeovanis , Klementieva Oxana , Gidlöf Ritha , Sydoff Marie , Bagnoli Silvia , Nacmias Benedetta , Sorbi Sandro , Westergren-Thorsson Gunilla , Gouras Gunnar K. , Rezeli Melinda , Roybon Laurent 
Published: February 2023

AbstractThe hippocampus is a primary region affected in Alzheimer’s disease (AD). Because AD postmortem brain tissue is not available prior to symptomatic stage, we lack understanding of early cellular pathogenic mechanisms. To address this issue, we examined the cellular origin and progression of AD pathogenesis in patient-based model systems including iPSC-derived brain cells transplanted into the mouse brain hippocampus. Notably, proteomic analysis of the graft enabled the identification of proteomic alterations in AD patient brain cells, associated with increased levels of β-sheet structures and Aβ42 peptides. Interestingly, the host cells surrounding the AD graft also presented alterations in cellular biological pathways. Furthermore, proteomic analysis across human iPSC-based models and human post-mortem hippocampal tissue projected coherent longitudinal cellular changes indicative of disease progression from early to end stage AD. Our data showcase patient-based models to study the cellular origin, progression, and prion-like spread of AD pathogenesis.Highlights-AD patient iPSC-derived brain cells survive in the hippocampus of immunodeficient mice 6 months post-transplantation.-Proteomic analysis of the grafts reveals profound alterations in cellular biological pathways in iPSC-derived hippocampal cells despite absence of senile plaques.-Proteomic alterations within transplanted AD iPSC-derived hippocampal cells are reminiscent of early/prodromal AD.-AD-grafted cells induce proteomic changes in host mouse cells.
Surface Energy and Viscoelastic Characteristics ofStaphylococcus epidermidisandCutibacterium acnesBiofilm on Commercial Skin Constructs versus agar
Authors: Razgaleh S. A. , Wrench Andrew , Jones A-Andrew D. 
Published: February 2023

ABSTRACTBiofilms are recalcitrant to both study and infectious disease treatment as it requires not only the study or management of single organism behavior, but also many dynamical interactions including but not limited to bacteria-bacteria, bacteria-host, bacteria-nutrients, and bacteria-material across multiple time scales. This study performs comparative and quantitative research of two materials used in biofilm research, TSA agar and skin epidermal, to reveal how adhesion effects viscoelastic properties of biofilms at long time scales. We show that the host surface stressors, such as wettability and surface energy, impact the biofilm’s mechanical integrity and viscoelastic properties. While it is known that the bacteria-material interface influences initial biofilm formation and external stress influences mature biofilm function, this study examines the influence of the bacteria-material interface on mature biofilms. These mechanical viscoelastic properties have the potential to determine metabolite and pathogenesis pathways which means that the platform researchers use to study impacts the outcome.
Aberrant activation of Wnt/β-Catenin signaling pathway drives the expression of poor prognosis-associated microRNAs in adrenocortical cancer with a major impact on miR-139-5p and its host gene PDE2A
Authors: Cristante Justine , El Sayed Soha Reda , Denis Josiane , Ragazzon Bruno , Hantel Constanze , Chabre Olivier , Guyon Laurent , Cherradi Nadia 
Published: February 2023

AbstractAdrenocortical carcinoma (ACC) is a rare malignancy with dismal prognosis. Deregulated microRNA (miRNA) expression has been implicated in ACC aggressiveness. Nevertheless, the mechanisms underlying such deregulations remain unknown. Aberrant Wnt/β-Catenin signaling has been reported in about 40% of ACC and is associated with poor outcome. Here, we investigated the link between constitutive activation of Wnt/β-Catenin pathway and miRNA expression alterations in ACC. Inducible shRNA-mediated gene silencing of β-Catenin (β-Cat) was performed in ACC cells expressing constitutively active β-Catenin. The miRnome of ACC cells was analyzed using RNA-Sequencing. Selected miRNAs and mRNAs were validated using quantitative PCR and functional experiments with an emphasis on miR-139-5p, its host gene phosphodiesterase 2A (PDE2A) and its target gene N-Myc Downstream-Regulated Gene 4 (NDRG4). Prognostic values of Wnt/β-Catenin pathway components or mutational status and their correlations with miRNA/mRNA expressions were determined in COMETE-ENSAT and TCGA cohorts. We carried out the first miRnome analysis in β-Catenin-deficient (β-Cat-) ACC cells. Twelve upregulated miRNAs and 42 downregulated miRNAs among which miR-139-5p and miRNAs of the 14q32 locus were identified in β-Cat-cells. Downregulation of selected poor prognosis-associated miRNAs was confirmed using RT-qPCR. Remarkably, the expression of the intronic miR-139-5p was decreased by 90% in β-Cat-cells with a concomitant repression of its host gene PDE2A and upregulation of its target gene NDRG4. In ACC patients, miR-139-5p levels were highly correlated with the levels of PDE2A and anti-correlated with those of NDRG4. MiR-139-5p and PDE2A expressions were higher in patients with mutations in components of Wnt/β-Catenin signaling pathway or high expression of LEF1, with LEF1 proving a better predictor of prognosis than Wnt/β-Catenin signaling pathway mutational status. Our findings indicate that in addition to inducing protein-coding genes in ACC, constitutively active Wnt/β-Catenin signaling upregulates the expression of a subset of miRNAs involved in tumour aggressiveness and poor clinical outcome.
Acute stress modulates social approach and social maintenance in adult zebrafish
Authors: Cook Alex , Beckmann Holger , Azap Rutkay , Ryu Soojin 
Published: February 2023

ABSTRACTStress alters social functioning in a complex manner. An important variable determining the final effects of stress is stressor intensity. However, the precise relationship between stressor intensity and social behavior is not well understood. Here we investigate the effects of varying acute stressor intensity exposure on social behavior using adult zebrafish. We first establish a novel test using adult zebrafish that allows distinguishing fish’s drive to approach a social cue and its ability to engage and maintain social interaction within the same behavioral paradigm. Next, we combined this test with a new method to deliver an acute stress stimulus of varying intensities. Our results show that both social approach and social maintenance are reduced in adult zebrafish upon acute stress exposure in an intensity-dependent manner. Interestingly, lower stress intensity reduces social maintenance without affecting the social approach, while a higher stress level is required to alter social approach. These results provide evidence for a direct correlation between acute stressor intensity and social functioning and suggest that distinct steps in social behavior are modulated differentially by the acute stress level.SIGNIFICANCE STATEMENTAcute stress exposure has a potent effect on social behavior in many animals including humans. However, so far the effect of different stressor intensity on distinct steps of social behavior has not been directly tested. Here, using zebrafish, we develop a new social behavior paradigm and a new graded acute stressor delivery method in order to test the relationship between acute stressor intensity and social behavior. Our results show that acute stress modulates both social approach and social maintenance in an intensity-dependent manner but social maintenance is affected at lower stress intensity than social approach. Thus, this work reveals that distinct steps in social behavior are differentially modulated by the acute stress level.
SARS-COV-2 NSP5 Antagonizes MHC II Expresion by Subverting Histone Deacetylase 2
Authors: Taefehshokr Nima , Lac Alex , Vrieze Angela M , Dickson Brandon H , Guo Peter N , Jung Catherine , Blythe Eoin N , Fink Corby , Aktar Amena , Dikeakos Jimmy D , Dekaban Gregory A , Heit Bryan 
Published: February 2023

SARS-CoV-2 interferes with antigen presentation by downregulating MHC II on antigen presenting cells, but the mechanism mediating this process is unelucidated. Herein, analysis of protein and gene expression in human antigen presenting cells reveals that MHC II is downregulated by the SARS-CoV-2 main protease, NSP5. This suppression of MHC II expression occurs via decreased expression of the MHC II regulatory protein CIITA. This downregulation of CIITA is independent of NSP5’s proteolytic activity, but rather, NSP5 delivers HDAC2 to IRF3 at an IRF binding site within the CIITA promoter. Here, HDAC2 deacetylates and inactivates the CIITA promoter. This loss of CIITA expression prevents further expression of MHC II, with this suppression alleviated by ectopic expression of CIITA or knockdown of HDAC2. These results identify a mechanism by which SARS-CoV-2 limits MHC II expression, thereby delaying or weakening the subsequent adaptive immune response.ImportanceSARS-CoV-2 alters the expression of many immunoregulatory proteins to limit and delay the host antiviral response, thereby producing a more severe and longer-lasting infection. Preventing and limiting the activation of helper T cells by reducing MHC II expression on antigen presenting cells is one of these strategies, but while this mechanism was identified early in the pandemic, the mechanism allowing SARS-CoV-2 to limit MHC II expression has remained unclear. Herein, we demonstrate that this occurs via a tripartite interaction between viral NSP5 and host HDAC2 and IRF3, where a complex of NSP5 and HDAC2 is recruited to IRF3 bound to the promoter of CIITA—the master regulator of MHC II expression—with the delivery of HDAC2 then mediating the deacetylation of the CIITA promoter and the suppression of MHC II expression.
Neonatal Subarachnoid Hemorrhage Disrupts Multiple Aspects of Cerebellar Development
Authors: Butler David F. , Skibo Jonathan , Traudt Christopher M. , Millen Kathleen J. 
Published: February 2023

AbstractOver the past decade, survival rates for extremely low gestational age neonates (ELGANs; <28 weeks gestation) has markedly improved. Unfortunately, a significant proportion of ELGANs will suffer from neurodevelopmental dysfunction. Cerebellar hemorrhagic injury (CHI) has been increasingly recognized in the ELGANs population and may contribute to neurologic dysfunction; however, the underlying mechanisms are poorly understood. To address this gap in knowledge, we developed a novel model of early isolated posterior fossa subarachnoid hemorrhage (SAH) in neonatal mice and investigated both acute and long-term effects. Following SAH on postnatal day 6 (P6), we found significant decreased levels of proliferation with the external granular layer (EGL), thinning of the EGL, decreased Purkinje cell (PC) density, and increased Bergmann glial (BG) fiber crossings at P8. At P42, CHI resulted in decreased PC density, decreased molecular layer interneuron (MLI) density, and increased BG fiber crossings. Results from both Rotarod and inverted screen assays did not demonstrate significant effects on motor strength or learning at P35-38. Treatment with the anti-inflammatory drug Ketoprofen did not significantly alter our findings after CHI, suggesting that treatment of neuro-inflammation does not provide significant neuroprotection post CHI. Further studies are required to fully elucidate the mechanisms through which CHI disrupts cerebellar developmental programming in order to develop therapeutic strategies for neuroprotection in ELGANs.
Helminth infection impacts hematopoiesis
Authors: Wijshake Tobias , Wang Jipeng , Rose Joseph , Marlar-Pavey Madeleine , Collins James J. , Agathocleous Michalis 
Published: February 2023

AbstractHelminth infections are common in animals. However, the impact of a helminth infection on the function of hematopoietic stem cells (HSCs) and other hematopoietic cells has not been comprehensively defined. Here we describe the hematopoietic response to infection of mice withSchistosoma mansoni,a parasitic flatworm which causes schistosomiasis. We analyzed the frequency or number of hematopoietic cell types in the bone marrow, spleen, liver, thymus, and blood, and observed multiple hematopoietic changes caused by infection. Schistosome infection impaired bone marrow HSC function after serial transplantation. Functional HSCs were present in the infected liver. Infection blocked bone marrow erythropoiesis and augmented spleen erythropoiesis, observations consistent with the anemia and splenomegaly prevalent in schistosomiasis patients. This work defines the hematopoietic response to schistosomiasis, a debilitating disease afflicting more than 200 million people, and identifies impairments in HSC function and erythropoiesis.
cGAS-activating lupus autoantibody for cancer immunotherapy
Authors: Chen Xiaoyong , Tang Xiangjun , Cuffari Benedette J. , Tang Caroline , Gao Xingchun , Noble Philip W. , Young Melissa R. , Turk Olivia M. , Shirali Anupama , Gera Joseph , Nishimura Robert N. , Zhou Jiangbing , Hansen James E. 
Published: February 2023

AbstractCytoplasmic DNA triggers a cGAS-mediated signaling cascade that promotes an innate immune response and is potentially actionable in cancer immunotherapy. Here we show that a cytoplasmic-localizing lupus anti-DNA autoantibody activates cGAS and facilitates an immune-mediated prolongation of survival in orthotopic models of glioblastoma (GBM). Mechanistically, cellular penetration and blood-brain barrier crossing by the anti-DNA autoantibody is linked to nucleoside transport. Pulldown, knockdown, signaling, and cytotoxicity assays demonstrate autoantibody association with and activation of cGAS. In orthotopic GBM models, the autoantibody localizes to brain tumor, increases tumor CD8+ T cell content, and prolongs survival in immunocompetent but not immunodeficient mice. This work introduces the new concept of a cGAS-activating anti-DNA autoantibody, which impacts theories on mechanisms of autoimmunity and has translational applications in cancer immunotherapy.
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale
Authors: Mendelevich Asia , Gupta Saumya , Pakharev Aleksei , Teodosiadis Athanasios , Mironov Andrey A. , Gimelbrant Alexander A. 
Published: February 2023

AbstractMotivationAnalysis of allele-specific expression is strongly affected by the technical noise present in RNA-seq experiments. Previously, we showed that technical replicates can be used for precise estimates of this noise, and we provided a tool for correction of technical noise in allele-specific expression analysis. This approach is very accurate but costly due to the need for two or more replicates of each library. Here, we develop a spike-in approach that is highly accurate at only a small fraction of the cost.ResultsWe show that a distinct RNA added as a spike-in before library preparation reflects technical noise of the whole library and can be used in large batches of samples. We experimentally demonstrate the effectiveness of this approach using combinations of RNA from species distinguishable by alignment, namely, mouse, human, andC.elegans. Our new approach,controlFreq, enables highly accurate and computationally efficient analysis of allele-specific expression in (and between) arbitrarily large studies at an overall cost increase of ~ 5%.AvailabilityAnalysis pipeline for this approach is available at GitHub asRpackagecontrolFreq(github.com/gimelbrantlab/controlFreq).Contactagimelbrant@altius.org
Drug repurposing for Leishmaniasis with Hyperbolic Graph Neural Networks
Authors: Lau Yenson , Gutierrez Jahir M. , Volkovs Maksims , Zuberi Saba 
Published: February 2023

AbstractLeishmanisis, a neglected tropical disease caused by protozoan parasites of the genusLeishmania, affects millions of individuals living in poverty across the world and is second to malaria in parasitic causes of death. Although current drugs for treating leishmaniasis exist, these are either highly toxic, ineffective, or expensive. For this reason, there is an urgent need to identify affordable, safer, and more effective treatments. Drug repurposing is a promising method for identifying existing molecules with the potential to treat leishmaniasis. Here, we present a deep learning model for drug repurposing based on hyperbolic graph neural networks. We leverage experimentally validated protein-drug interactions and molecular descriptors across three different parasites to train and validate our model. The final network model shows significant gains over the best baseline model, with an 11.6% increase in precision of the top scoring 0.5% protein-drug pairs. Finally, our model identified two experimental drugs that could target threeL. majorproteins involved in drug resistance and cell cycle regulation, which play an essential role in ensuring the parasite’s survival inside the host.Author summaryLeishmanisis is a deadly and neglected tropical disease. Current treatments are ineffective, highly toxic, and unaffordable for the majority of affected individuals who live in extreme poverty. To accelerate the discovery and development of novel treatments against this disease, we develop a model that proposes existing drugs with the potential to treat leishmaniasis. Our methodology is based on hyperbolic graph neural networks, a class of deep learning models that can incorporate protein-drug interaction information from similar but well-studied parasites, in addition to utilizing chemical and molecular features. Empirically, this additional information leads to improved predictions of drug interactions withL. majorproteins. Overall, the protein-drug pairs predicted by our model suggests two existing drugs that could target essential pathways for growth and survival ofLeishmaniaparasites, which could be exploited either as a booster to increase the therapeutic effect of an existing anti-leishmaniasis drug, or as a novel chemotherapeutic treatment against the disease.
The long and short of it: Benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies
Authors: Cook Ryan , Brown Nathan , Rihtman Branko , Michniewski Slawomir , Redgwell Tamsin , Clokie Martha , Stekel Dov J , Chen Yin , Scanlan David J , Hobman Jon L , Nelson Andrew , Jones Michael A , Smith Darren , Millard Andrew 
Published: February 2023

AbstractViral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid approaches that combine long and short read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio technologies have been applied to viral metagenomics, it is not known to what extent different technologies will impact the reconstruction of the viral community.Thus, we constructed a mock phage community of previously sequenced phage genomes and sequenced using Illumina, Nanopore, and PacBio sequencing technologies and tested a number of different assembly approaches. When using a single sequencing technology, Illumina assemblies were the best at recovering phage genomes. Nanopore- and PacBio-only assemblies performed poorly in comparison to Illumina in both genome recovery and error rates, which both varied with the assembler used. The best Nanopore assembly had errors that manifested as SNPs and INDELs at frequencies ~4x and 120x higher than found in Illumina only assemblies respectively. While the best PacBio assemblies had SNPs at frequencies ~3.5 x and 12x higher than found in Illumina only assemblies respectively. Despite high read coverage, long-read only assemblies failed to recover a complete genome for any of the 15 phage, down sampling of reads did increase the proportion of a genome that could be assembled into a single contig.Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short read only assemblies. When using a single technology, Illumina only was the best approach. The differences in genome recovery and error rates between technology and assembler had downstream impacts on gene prediction, viral prediction, and subsequent estimates of diversity within a sample. These findings will provide a starting point for others in the choice of reads and assembly algorithms for the analysis of viromes.Data SummaryAll reads from virome sequencing were submitted to the ENA under study PRJEB56639. The assemblies are provided via FigShare (https://figshare.com/s/2d9b5121eb421d370455).Author NotesEight Supplementary Tables and nine Supplementary Figures are available with the online version of this article.
Overcoming resolution loss due to thermal magnetic field fluctuations from phase plates in transmission electron microscopy
Authors: Axelrod Jeremy J. , Petrov Petar N. , Zhang Jessie T. , Remis Jonathan , Buijsse Bart , Glaeser Robert M. , Mȕller Holger 
Published: February 2023

AbstractWe identify thermal magnetic field fluctuations, caused by thermal electron motion (“Johnson noise”) in electrically conductive materials, as a potential resolution limit in transmission electron microscopy with a phase plate. Specifically, resolution loss can occur if the electron diffraction pattern is magnified to extend phase contrast to lower spatial frequencies, and if conductive materials are placed too close to the electron beam. While our initial implementation of a laser phase plate (LPP) was significantly affected by these factors, a redesign eliminated the problem and brought the performance close to the expected level. The resolution now appears to be limited by residual Johnson noise arising from the electron beam liner tube in the region of the LPP, together with the chromatic aberration of the relay optics. These two factors can be addressed during future development of the LPP.
Tunable biomimetic bacterial membranes from binary and ternary lipid mixtures and their application in antimicrobial testing
Authors: Krok Emilia , Stephan Mareike , Dimova Rumiana , Piatkowski Lukasz 
Published: February 2023

AbstractReconstruction of accurate yet simplified mimetic models of cell membranes is a very challenging goal of synthetic biology. To date, most of the research focuses on the development of eukaryotic cell membranes, while reconstitution of their prokaryotic counterparts has not been fully addressed, and the proposed models do not reflect well the complexity of bacterial cell envelopes. Here, we describe the reconstitution of biomimetic bacterial membranes with an increasing level of complexity, developed from binary and ternary lipid mixtures. Giant unilamellar vesicles composed of phosphatidylcholine (PC) and phosphatidylethanolamine (PE); PC and phosphatidylglycerol (PG); PE and PG; PE, PG and cardiolipin (CA) at varying molar ratios were successfully prepared by the electroformation method. Each of the proposed mimetic models focuses on reproducing specific membrane features such as membrane charge, curvature, leaflets asymmetry, or the presence of phase separation. GUVs were characterized in terms of size distribution, surface charge, and lateral organization. Finally, the developed models were tested against the lipopeptide antibiotic daptomycin. The obtained results showed a clear dependency of daptomycin binding efficiency on the amount of negatively charged lipid species present in the membrane. We anticipate that the models proposed here can be applied not only in antimicrobial testing but also serve as platforms for studying fundamental biological processes in bacteria as well as their interaction with physiologically relevant biomolecules.