bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vivo analysis of the contribution of proprotein convertases to the processing of FGF23
Authors: Rifai Omar Al , Susan-Resiga Delia , Essalmani Rachid , Creemers John W.M. , Seidah Nabil G. , Ferron Mathieu 
Published: January 2021

ABSTRACTFibroblast growth factor 23 (FGF23) is a hormone secreted from fully differentiated osteoblasts and osteocytes that inhibits phosphate reabsorption by kidney proximal tubules. The full-length (i.e., intact) protein mediates FGF23 endocrine functions, while endoproteolytic cleavage at a consensus cleavage sequence for the proprotein convertases (PCs) inactivates FGF23. Two PCs, furin and PC5, were shown to cleave FGF23in vitroat RHTR179↓, but whether they are fulfilling this function in vivo is currently unknown. To address this question we used here mice lacking either or both furin and PC5 in cell-specific manners and mice lacking the paired basic amino acid-cleaving enzyme 4 (PACE4) in all cells. Our analysis shows that furin inactivation in osteoblasts and osteocytes results in a 25% increase in circulating intact FGF23, without any significant impact on serum phosphate levels, whether mice are maintained on a normal or a low phosphate diet. Under conditions of iron deficiency, FGF23 is normally processed in control mice, but its processing is impaired in mice lacking furin in osteoblasts and osteocytes. In contrast, FGF23 is normally cleaved following erythropoietin or IL-1β injections in mice lacking furin or both furin and PC5, and in PACE4-deficient mice. Altogether, these studies suggest that furin is only partially responsible for FGF23 cleavage under certain conditionsin vivo. The processing of FGF23 may therefore involve the redundant action of multiple PCs or of other peptidases in osteoblasts, osteocytes and hematopoietic cells.
Circadian Alterations Increase with Progression in a Patient-Derived Cell Culture Model of Breast Cancer
Authors: Lin Hui-Hsien , Taylor Stephanie R. , Farkas Michelle E. 
Published: January 2021

AbstractCircadian rhythms are critical regulators of many physiological and behavioral functions; disruption of this time-tracking system can elicit the development of various diseases, including breast cancer. While multiple studies have used cell lines to study the correlation between altered circadian rhythms and cancer, these cells generally have different genetic backgrounds and do not mirror the changes that occur with disease development. Isogenic cell models can represent and recapitulate changes across cancer progression. Hence in the present study, a patient-derived breast cancer model, the 21T series, was used to evaluate changes to circadian oscillations of core clock protein transcription and translation as cells progress from normal to malignant states. Three cell lines from the series were used: H16N2, from normal breast epithelium; 21PT, from Atypical Ductal Hyperplasia; and 21MT, from Invasive Metastatic Carcinoma. Both of the cancerous cell lines are HER2 positive. We assessed the transcriptional profiles of two core circadian clock proteins, BMAL1 and PER2, which represent a positive and negative component of the molecular oscillator. In the normal H16N2 cells,BMAL1andPER2both possessed rhythmic mRNA oscillations with close to standard periods and the expected anti-phase relationship. However, in the cancerous cells, consistent changes were observed: both clock genes had periods that deviated farther from normal and did not have an anti-phase relationship. To provide a more complete understanding of circadian alterations in breast cancer, luciferase reporters and real-time luminometry should be used in future studies.
Functional Genetic Biomarkers of Alzheimer’s Disease and Gene Expression from Peripheral Blood
Authors: Ni Andrew , Sethi Amish ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: January 2021

AbstractDetecting Alzheimer’s Disease (AD) at the earliest possible stage is key in advancing AD prevention and treatment but is challenged by normal aging processes in addition to other confounding neurodegenerative diseases. Recent genome-wide association studies (GWAS) have identified associated alleles, but it has been difficult to transition from non-coding genetic variants to underlying mechanisms of AD. Here, we sought to reveal functional genetic variants and diagnostic biomarkers underlying AD using machine learning techniques. We first developed a Random Forest (RF) classifier using microarray gene expression data sampled from the peripheral blood of 744 participants in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. After initial feature selection, 5-fold cross-validation of the 100-gene RF classifier achieved an accuracy of 99.04%. The high accuracy of the RF classifier supports the possibility of a powerful and minimally invasive tool for screening of AD. Next, unsupervised clustering was used to validate and identify relationships among differentially expressed genes (DEGs) the RF selected revealing 3 distinct AD clusters. Results suggest downregulation of global sulfatase and oxidoreductase activities in AD through mutations in SUMF1 and SMOX respectively. Then, we used Greedy Fast Causal Inference (GFCI) to find potential causes of AD within DEGs. In the causal graph, HLA-DPB1 and CYP4A11 emerge as hub genes, furthering the discussion of the immune system’s role in AD. Finally, we used Gene Set Enrichment Analysis (GSEA) to determine the biological pathways and processes underlying the DEGs that were highly correlated with AD. Cell activation in the immune system, glycosaminoglycan (GAG) binding, vascular dysfunction, oxidative stress, and the neuronal apoptotic process were revealed to be significantly enriched in AD. This study further advances the possibility of low-cost and noninvasive genetic screening for AD while also providing potential gene targets for further experimentation.
AsmMix: A pipeline for high quality diploidde novoassembly
Authors: Wu Pei , Liu Chao , Wang Ou , Zhao Xia , Chen Fang , Cheng Xiaofang , Zhu Hongmei 
Published: January 2021

AbstractIn this paper, we report a pipeline, AsmMix, which is capable of producing both contiguous and high-quality diploid genomes. The pipeline consists of two steps. In the first step, two sets of assemblies are generated: one is based on co-barcoded reads, which are highly accurate and haplotype-resolved but contain many gaps, the other assembly is based on single-molecule sequencing reads, which is contiguous but error-prone. In the second step, those two sets of assemblies are compared and integrated into a haplotype-resolved assembly with fewer errors. We test our pipeline using a dataset of human genome NA24385, perform variant calling from those assemblies and then compare against GIAB Benchmark. We show that AsmMix pipeline could produce highly contiguous, accurate, and haplotype-resolved assemblies. Especially the assembly mixing process could effectively reduce small-scale errors in the long read assembly.
Acute Endotheliitis (Type 3 Hypersensitivity Vasculitis) in Ten COVID-19 Autopsy Brains
Authors: Rhodes Roy H. , Love Gordon L. , Da Silva Lameira Fernanda , Sadough Maryam Shahmirzadi , Fox Sharon E. , Heide Richard S. Vander 
Published: January 2021

AbstractCentral nervous system (CNS) involvement in COVID-19 may occur through direct SARS-CoV-2 invasion through peripheral or cranial nerves or through vascular endothelial cell infection. The renin-angiotensin system may play a major part in CNS morbidity. Effects of hypoxia have also been implicated in CNS lesions in COVID-19. This communication reports on ten consecutive autopsies of individuals with death due to COVID-19 with decedent survival ranging from 30 minutes to 84 days after admission. All ten brains examined had neutrophilic microvascular endotheliitis present in variable amounts and variably distributed. Importantly, this acute stage of type 3 hypersensitivity vasculitis can be followed by fibrinoid necrosis and inner vascular wall sclerosis, but these later stages were not found. These results suggest that a vasculitis with autoimmune features occurred in all ten patients. It is possible that viral antigen in or on microvascular walls or other antigen-antibody complexes occurred in all ten patients proximate to death as a form of autoimmune vasculitis.
SARS-CoV-2 RECoVERY: a multi-platform open-source bioinformatic pipeline for the automatic construction and analysis of SARS-CoV-2 genomes from NGS sequencing data
Authors: De Sabato Luca , Vaccari Gabriele , Knijn Arnold , Ianiro Giovanni , Di Bartolo Ilaria , Morabito Stefano 
Published: January 2021

AbstractBackgroundSince its first appearance in December 2019, the novelSevere Acute Respiratory Syndrome Coronavirus type 2(SARS-CoV-2), spread worldwide causing an increasing number of cases and deaths (35,537,491 and 1,042,798, respectively at the time of writing,https://covid19.who.int). Similarly, the number of complete viral genome sequences produced by Next Generation Sequencing (NGS), increased exponentially. NGS enables a rapid accumulation of a large number of sequences. However, bioinformatics analyses are critical and require combined approaches for data analysis, which can be challenging for non-bioinformaticians.ResultsA user-friendly and sequencing platform-independent bioinformatics pipeline, named SARS-CoV-2 RECoVERY (REconstruction of CoronaVirus gEnomes & Rapid analYsis) has been developed to build SARS-CoV-2 complete genomes from raw sequencing reads and to investigate variants. The genomes built by SARS-CoV-2 RECoVERY were compared with those obtained using other software available and revealed comparable or better performances of SARS–CoV2 RECoVERY. Depending on the number of reads, the complete genome reconstruction and variants analysis can be achieved in less than one hour. The pipeline was implemented in the multi-usage open-source Galaxy platform allowing an easy access to the software and providing computational and storage resources to the community.ConclusionsSARS-CoV-2 RECoVERY is a piece of software destined to the scientific community working on SARS-CoV-2 phylogeny and molecular characterisation, providing a performant tool for the complete reconstruction and variants’ analysis of the viral genome. Additionally, the simple software interface and the ability to use it through a Galaxy instance without the need to implement computing and storage infrastructures, make SARS-CoV-2 RECoVERY a resource also for virologists with little or no bioinformatics skills.Availability and implementationThe pipeline SARS-CoV-2 RECoVERY (REconstruction of COronaVirus gEnomes & Rapid analYsis) is implemented in the Galaxy instance ARIES (https://aries.iss.it).
Optimized CRISPR-mediated gene knock-in reveals FOXP3-independent control of human Treg identity
Authors: Lam Avery J. , Lin David T.S. , Gillies Jana K. , Uday Prakruti , Pesenacker Anne M. , Kobor Michael S. , Levings Megan K. 
Published: January 2021

SummaryTreg cell therapy is a promising curative approach for a variety of immune-mediated conditions. CRISPR-based genome editing allows precise insertion of transgenes through homology-directed repair, but use in human Tregs has been limited. We report an optimized protocol for CRISPR-mediated gene knock-in in human Tregs with high-yield expansion. To establish a benchmark of human Treg dysfunction, we targeted the master transcription factor FOXP3 in naive and memory Tregs. Although FOXP3-knockout Tregs upregulated cytokine expression, effects on suppressive capacity manifested slowly and primarily in memory Tregs. Moreover, FOXP3-knockout Tregs retained their characteristic phenotype and had few changes in their DNA methylation landscape, with FOXP3 maintaining methylation at regions enriched for AP-1 binding sites. Thus, while FOXP3 is important for human Treg development, it has a limited role in maintaining mature Treg identity. Optimized gene knock-in with human Tregs will enable mechanistic studies and the development of tailored, next-generation Treg cell therapies.
Idiosyncratic purifying selection on metabolic enzymes in the long-term evolution experiment withEscherichia coli
Authors: Maddamsetti Rohan 
Published: January 2021

AbstractBacteria, Archaea, and Eukarya all share a common set of metabolic reactions. This implies that the function and topology of central metabolism has been evolving under purifying selection over deep time. Central metabolism may similarly evolve under purifying selection during longterm evolution experiments, although it is unclear how long such experiments would have to run (decades, centuries, millennia) before signs of purifying selection on metabolism appear. I hypothesized that central and superessential metabolic enzymes would show evidence of purifying selection in the long-term evolution experiment withEscherichia coli(LTEE). I also hypothesized that enzymes that specialize on single substrates would show stronger evidence of purifying selection in the LTEE than generalist enzymes that catalyze multiple reactions. I tested these hypotheses by analyzing metagenomic time series covering 62,750 generations of the LTEE. I find mixed support for these hypotheses, because the observed patterns of purifying selection are idiosyncratic and population-specific. To explain this finding, I propose the Jenga hypothesis, named after a children’s game in which blocks are removed from a tower until it falls. The Jenga hypothesis postulates that loss-of-function mutations degrade costly, redundant, and nonessential metabolic functions. Replicate populations can therefore follow idiosyncratic trajectories of lost redundancies, despite purifying selection on overall function. I tested the Jenga hypothesis by simulating the evolution of 1,000 minimal genomes under strong purifying selection. As predicted, the minimal genomes converge to different metabolic networks. Strikingly, the core genes common to all 1,000 minimal genomes show consistent signatures of purifying selection in the LTEE.Significance StatementPurifying selection conserves organismal function over evolutionary time. However, few studies have examined the role of purifying selection during adaptation to novel environments. I tested metabolic enzymes for purifying selection in an ongoing long-term evolution experiment withEscherichia coli.While some populations show signs of purifying selection, the overall pattern is inconsistent. To explain these findings, I propose the Jenga hypothesis, in which loss-of-function mutations first degrade costly, redundant, and nonessential metabolic functions, after which purifying selection begins to dominate. I then tested several predictions of the Jenga hypothesis using computational simulations. On balance, the simulations confirm that we should find evidence of purifying selection on the metabolic pathways that sustain growth in a novel environment.
Human Cytomegalovirus uses a Host Stress Response to Balance the Elongation of Saturated/Monounsaturated and Polyunsaturated Very Long Chain Fatty Acids
Authors: Xi Yuecheng , Lindenmayer Lena , Kline Ian , von Einem Jens , Purdy John G. 
Published: January 2021

ABSTRACTStress and virus infection are known to regulate lipid metabolism in cells. Human cytomegalovirus infection induces fatty acid (FA) elongation and increases the cellular abundance of lipids with very long-chain FA tails (VLCFAs). While reprogramming of metabolism can be stress-related, the role of stress in HCMV reprogramming of lipid metabolism is poorly understood. In this study, we engineered cells to knockout PKR-like ER kinase (PERK) in the ER stress pathway and measured lipid changes using lipidomics to determine if PERK is needed for lipid changes associated with HCMV infection. We found that in HCMV-infected cells, PERK promotes the increase in the levels of phospholipids with saturated FA (SFA) and monounsaturated FA (MUFA) VLCFAs tails. Consistent with the SFA/MUFA lipidome changes, PERK enhances the protein levels of FA elongase 7 (ELOVL7), which elongates SFA and MUFA VLCFAs. Additionally, we found that increases in the elongation of polyunsaturated fatty acids (PUFAs) associated with HCMV infection was independent of PERK and that lipids with PUFA tails accumulated in HCMV-infected PERK knockout cells. Consistent with the PUFA lipidome changes, the protein levels of ELOVL5, which elongates PUFAs, are increased by HCMV infection through a PERK-independent mechanism. These observations show that PERK differentially regulates ELOVL7 and ELOVL5, creating a balance between the synthesis of lipids with SFA/MUFA tails and PUFA tails. Additionally, we found that PERK was necessary for virus replication and the infectivity of released viral progeny. Overall, our findings indicate that PERK—and more broadly, ER stress—may be necessary for membrane biogenesis needed to generate infectious HCMV virions.IMPORTANCEHCMV is a common herpesvirus that establishes lifelong persistent infections. While infection is asymptomatic in most people, HCMV causes life-threatening illnesses in immunocompromised people, including transplant recipients and cancer patients. Additionally, HCMV infection is a leading cause of congenital disabilities. HCMV replication relies on lipid synthesis. Here, we demonstrated that the ER stress mediator, PERK, controls fatty acid (FA) elongation and cellular abundance of several types of lipids following HCMV infection. Specifically, we found that PERK promotes FA elongase 7 synthesis of lipids with saturated/monounsaturated very long-chain FA tails which are important for building the viral membrane of infectious HCMV virions. Overall, our study shows that PERK is an essential host factor that supports HCMV replication and promotes lipidome changes caused by HCMV infection.
Type IV competence pili inStreptococcus pneumoniaeare highly dynamic structures that retract to promote DNA uptake
Authors: Lam Trinh , Ellison Courtney K. , Dalia Ankur B. , Eddington David T. , Morrison Donald A. 
Published: January 2021

SUMMARYThe competence pili of transformable Gram-positive species form a subset of the diverse and widespread class of extracellular filamentous organelles known as type IV pili (T4P). In Gram-negative bacteria, T4P act through dynamic cycles of extension and retraction to carry out diverse activities including attachment, motility, protein secretion, and DNA uptake. It remains unclear whether T4P in Gram-positive species exhibit this same dynamic activity, and their mechanism of action for DNA uptake remains unclear. They are hypothesized to either (1) passively form transient cavities in the cell wall to facilitate DNA passage, (2) act as static adhesins to enrich DNA near the cell surface for subsequent uptake by membrane-embedded transporters, or (3) play an active role in translocating bound DNA via their dynamic activity. Here, using a recently described pilus labeling approach, we demonstrate that pneumococcal competence pili are highly dynamic structures that rapidly extend and retract from the cell surface. By labeling ComGC with bulky adducts, we further demonstrate that pilus retraction is essential for natural transformation. Together, our results indicate that Gram-positive type IV competence pili are dynamic and retractile structures that play an active role in DNA uptake.Short summaryCompetent pneumococci kill non-competent cells on contact. Retractable DNA-binding fibers in the class of type IV pili may provide a key tool for retrieving DNA segments from cell wreckage for internalization and recombination.
Laboratory diagnostics of tomato spotted wilt virus by PCR
Authors: Morozova O.N. , Zvyagintseva D. D. , Beloshapkina O.O. 
Published: January 2021

AbstractTomato spotted wilt virus is a widespread and harmful virus. It affects a wide range of host plants. The outward signs of TSWV lesions are different on different cultures. For the early diagnosis of TSWV, molecular diagnostic methods such as PCR must be used. In the course of this work, primers were developed for the diagnosis of tomato bronzing virus by real-time PCR and classical PCR. We also compared the specificity and sensitivity of various test systems for the diagnosis of tomato bronzing virus. In the course of this comparison, it was found that the self-assembly test system and the Syntol test system can be recommended for laboratory diagnostics of tomato spotted wilt virus.
Hierarchy-guided Neural Networks for Species Classification
Authors: Elhamod Mohannad , Diamond Kelly M. , Maga A. Murat , Bakis Yasin , Bart Henry L. , Mabee Paula , Dahdul Wasila , Leipzig Jeremy , Greenberg Jane , Avants Brian , Karpatne Anuj 
Published: January 2021

AbstractSpecies classification is an important task that is the foundation of industrial, commercial, ecological, and scientific applications involving the study of species distributions, dynamics, and evolution.While conventional approaches for this task use off-the-shelf machine learning (ML) methods such as existing Convolutional Neural Network (ConvNet) architectures, there is an opportunity to inform the ConvNet architecture using our knowledge of biological hierarchies among taxonomic classes.In this work, we propose a new approach for species classification termed Hierarchy-Guided Neural Network (HGNN), which infuses hierarchical taxonomic information into the neural network’s training to guide the structure and relationships among the extracted features. We perform extensive experiments on an illustrative use-case of classifying fish species to demonstrate thatHGNNoutperforms conventional ConvNet models in terms of classification accuracy, especially under scarce training data conditions.We also observe thatHGNNshows better resilience to adversarial occlusions, when some of the most informative patch regions of the image are intentionally blocked and their effect on classification accuracy is studied.