bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extensive characterization of HIV-1 reservoirs reveals links to plasma viremia before and during analytical treatment interruption
Authors: Cole Basiel , Lambrechts Laurens , Boyer Zoe , Noppe Ytse , De Scheerder Marie-Angélique , Eden John-Sebastian , Vrancken Bram , Schlub Timothy E. , McLaughlin Sherry , Frenkel Lisa M. , Palmer Sarah , Vandekerckhove Linos 
Published: February 2021

SummaryThe HIV-1 reservoir is composed of cells harboring latent proviruses that are capable of contributing to viremia upon antiretroviral treatment (ART)interruption. Although this reservoir is known to be maintained by clonal expansion, the contribution of large, infected cell clones to residual viremia and viral rebound remains underexplored. Here, we conducted an extensive analysis on four ART-treated individuals who underwent an analytical treatment interruption (ATI). We performed subgenomic (V1-V3env), near full-length proviral and integration site sequencing, and used multiple displacement amplification to sequence both the integration site and provirus from single HIV-infected cells. We found eight proviruses that could phylogenetically be linked to plasma virus obtained before or during the ATI. This study highlights a role for HIV-infected cell clones in the maintenance of the replication-competent reservoir and suggests that infected cell clones can directly contribute to rebound viremia upon ATI.
Analytical Performance of a Standardized Kit for Mass Spectrometry-based Measurements of Human Glycosaminoglycans
Authors: Tamburro Davide , Bratulic Sinisa , Shameh Souad Abou , Soni Nikul K , Bacconi Andrea , Maccari Francesca , Galeotti Fabio , Mattsson Karin , Volpi Nicola , Nielsen Jens , Gatto Francesco 
Published: February 2021

AbstractGlycosaminoglycans (GAGs) are long linear sulfated polysaccharides implicated in processes linked to disease development such as mucopolysaccharidosis, respiratory failure, cancer, and viral infections, thereby serving as potential biomarkers. A successful clinical translation of GAGs as biomarkers depends on the availability of standardized GAG measurements. However, owing to the analytical complexity associated with the quantification of GAG concentration and structural composition, a standardized method to simultaneously measure multiple GAGs is missing. In this study, we sought to characterize the analytical performance of a ultra-high-performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (UHPLC-MS/MS)-based kit for the quantification of 17 GAG disaccharides. The kit showed acceptable linearity, selectivity and specificity, accuracy and precision, and analyte stability in the absolute quantification of 15 GAG disaccharides. In native human samples, here using urine as a reference matrix, the analytical performance of the kit was acceptable for the quantification of CS disaccharides. Intra- and inter-laboratory tests performed in an external laboratory demonstrated robust reproducibility of GAG measurements showing that the kit was acceptably standardized. In conclusion, these results indicated that the UHPLC-MS/MS kit was standardized for the simultaneous measurement of GAG disaccharides allowing for comparability of measurements and enabling translational research.SummaryAnalytical performance of a kit for standardized GAG measurements, based on an established UHPLC-MS/MS method
Selection on growth rate and local adaptation drive genomic adaptation during experimental range expansions in the protistTetrahymena thermophila
Authors: Moerman Felix , Fronhofer Emanuel A. , Altermatt Florian , Wagner Andreas 
Published: February 2021

AbstractPopulations that expand their range can undergo rapid evolutionary adaptation of life-history traits, dispersal behaviour, and adaptation to the local environment. Such adaptation may be aided or hindered by sexual reproduction, depending on the context.However, few studies have investigated the genomic causes and consequences or genetic architecture of such adaptation during range expansions.We here studied genomic adaptation during experimental range expansions of the protistTetrahymena thermophilain landscapes with a uniform environment or a pH-gradient. Specifically, we investigated two aspects of genomic adaptation during range expansion. Firstly, we investigated the genetic architecture of adaptation in terms of the underlying numbers of allele frequency changes from standing genetic variation andde novovariants. We focused on how sexual reproduction may alter this genetic architecture. Secondly, identified genes subject to selection caused by the expanding range itself, and directional selection due to the presence or absence of the pH-gradient. We focused this analysis on alleles with large frequency changes that occurred in parallel in more than one population to identify the most likely candidate targets of selection.We found that sexual reproduction altered genetic architecture both in terms ofde novovariants and standing genetic variation. However, sexual reproduction affected allele frequency changes in standing genetic variation only in the absence of long-distance gene flow. Adaptation to the range expansion affected genes involved in cell divisions and DNA repair, whereas adaptation to the pH-gradient additionally affected genes involved in ion balance, and oxidoreductase reactions. These genetic changes may result from selection on growth and adaptation to low pH.Our results suggest that the evolution of life-history and the adaptation to the local environment has a genetic basis during our range expansion experiment. In the absence of gene flow, sexual reproduction may have aided genetic adaptation. Gene flow may have swamped expanding populations with maladapted alleles, thus reducing the extent of evolutionary adaptation during range expansion. Sexual reproduction also altered the genetic architecture of our evolving populations viade novovariants, possibly by purging deleterious mutations or by revealing fitness benefits of rare genetic variants.
Chronic effects of short-term aerobic and anaerobic physical training on the ventral prostate of adult rats
Authors: Borges Rodrigo Miranda Ramos , Rocha Emerson Souza da , de Andrade Edila Monteiro , da Silva Nazaré Nagaywer Edno , Ortega Araújo Paulo Afonso , Cembraneli Pedro Nogarotto , Rocha Ruiz Thalles Fernando , Colleta Simone Jacovaci , Carlos Carla Patricia , Marques Vanessa Belentani , Taboga Sebastião Roberto , de Campos Gomes Fabiana , de Melo-Neto João Simão 
Published: February 2021

ABSTRACTAimsTo analyze the chronic effects of short-term aerobic and anaerobic physical training on prostate compartments, extracellular matrix, microvascularization, TGFβ, cyclooxygenase-2, inducible nitric oxide synthase (iNOS) and macrophage immunostaining, and ventral prostate histopathology in adult rats.Main methodsFifteen male rats (90 days old) were divided into three groups (n = 5/group): sedentary, aerobic (AE) (swimming), and anaerobic physical training (AN) (jumping), performed three days per week, for 8-weeks. The animals were sacrificed within 21 weeks of age. The ventral prostate was collected, weighed, and processed for histological and immunohistochemical analyses.Key findingsOur results show that AE increases blood capillaries and reduces the percentage and increases the thickness of smooth muscle. AN promotes increased iNOS levels in the prostatic tissue, and both modalities reduce TGFβ and elastic fibers, in addition to being protective against benign prostatic hyperplasia and atrophy.SignificanceDifferent physical training modalities can activate specific mechanisms that modify the prostate environment.
New loci and neuronal pathways for resilience to heat stress in animals
Authors: Cheruiyot Evans K. , Haile-Mariam Mekonnen , Cocks Benjamin G. , MacLeod Iona M. , Xiang Ruidong , Pryce Jennie E. 
Published: February 2021

AbstractClimate change and resilience to warming climates have implications for humans, livestock, and wildlife. The genetic mechanisms that confer thermotolerance to mammals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise; thus, the phenotypes used to measure an individual’s heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature-humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system (ITPR1, ITPR2,andGRIA4) and neuroactive ligand-receptor interaction functions for heat tolerance (NPFFR2, CALCR,andGHR), providing a novel insight that can help to develop genetic and management approaches to combat heat stress.Author summaryWhile understanding the genetic basis of heat tolerance is crucial in the context of global warming’s effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. The ability to tolerate heat varies across individuals, with substantial genetic control of this complex trait. Dairy cattle are excellent model in which to find genes associated with individual variations in heat tolerance since they significantly suffer from heat stress due to the metabolic heat of lactation. By genome-wide association studies of more than 29,000 cows with 15 million sequence variants and controlled phenotype measurements, we identify many new loci associated with heat tolerance. The biological functions of these loci are linked to the neuronal system and neuroactive ligand-receptor interaction functions. Also, several putative causal mutations for heat tolerance are at genomic sites that are otherwise evolutionarily conserved across 100 vertebrate species. Overall, our findings provide new insight into the molecular and biological basis of heat tolerance that can help to develop genetic and management approaches to combat heat stress.
Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells
Authors: Chen Xi , Saccon Elisa , Appelberg K. Sofia , Mikaeloff Flora , Rodriguez Jimmy Esneider , Vinhas Beatriz Sá , Frisan Teresa , Végvári Ákos , Mirazimi Ali , Neogi Ujjwal , Gupta Soham 
Published: February 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes Coronavirus disease 2019 (COVID-19) has caused a global health emergency. A key feature of COVID-19 is dysregulated interferon-response. Type-I interferon (IFN-I) is one of the earliest antiviral innate immune responses following viral infection and plays a significant role in the pathogenesis of SARS-CoV-2. In this study, using a proteomics-based approach, we identified that SARS-CoV-2 infection induces delayed and dysregulated IFN-I signaling in Huh7 cells. We demonstrate that SARS-CoV-2 is able to inhibit RIG-I mediated IFN-β production. Our results also confirm the recent findings that IFN-I pretreatment is able to reduce susceptibility of Huh7 cells to SARS-CoV-2, but not post-treatment. Moreover, senescent Huh7 cells, in spite of showing accentuated IFN-I response were more susceptible to SARS-CoV-2 infection, and the virus effectively inhibited IFIT1 in these cells. Finally, proteomic comparison between SARS-CoV-2, SARS-CoV and MERS-CoV revealed a distinct differential regulatory signature of interferon-related proteins emphasizing that therapeutic strategies based on observations in SARS-CoV and MERS-CoV should be used with caution. Our findings provide a better understanding of SARS-CoV-2 regulation of cellular interferon response and a perspective on its use as a treatment. Investigation of different interferon stimulated genes and their role in inhibition of SARS-CoV-2 pathogenesis may direct novel antiviral strategies.
Targetedin situcross-linking mass spectrometry and integrative modeling reveal the architectures of Nsp1, Nsp2, and Nucleocapsid proteins from SARS-CoV-2
Authors: Slavin Moriya , Zamel Joanna , Zohar Keren , Eliyahu Siona , Braitbard Merav , Brielle Esther , Baraz Leah , Stolovich-Rain Miri , Friedman Ahuva , Wolf Dana G , Rouvinski Alexander , Linial Michal , Schneidman-Duhovny Dina , Kalisman Nir 
Published: February 2021

AbstractAtomic structures of several proteins from the coronavirus family are still partial or unavailable. A possible reason for this gap is the instability of these proteins outside of the cellular context, thereby prompting the use of in-cell approaches.In situcross-linking and mass spectrometry (in situCLMS) can provide information on the structures of such proteins as they occur in the intact cell. Here, we applied targetedin situCLMS to structurally probe Nsp1, Nsp2, and Nucleocapsid (N) proteins from SARS-CoV-2, and obtained cross-link sets with an average density of one cross-link per twenty residues. We then employed integrative modeling that computationally combined the cross-linking data with domain structures to determine full-length atomic models. For the Nsp2, the cross-links report on a complex topology with long-range interactions. Integrative modeling with structural prediction of individual domains by the AlphaFold2 system allowed us to generate a single consistent all-atom model of the full-length Nsp2. The model reveals three putative metal binding sites, and suggests a role for Nsp2 in zinc regulation within the replication-transcription complex. For the N protein, we identified multiple intra- and inter-domain cross-links. Our integrative model of the N dimer demonstrates that it can accommodate three single RNA strands simultaneously, both stereochemically and electrostatically. For the Nsp1, cross-links with the 40S ribosome were highly consistent with recent cryo-EM structures. These results highlight the importance of cellular context for the structural probing of recalcitrant proteins and demonstrate the effectiveness of targetedin situCLMS and integrative modeling.
Speciation of theMycobacterium tuberculosiscomplex using mass spectrometry: a proof-of-concept
Authors: Robinne Simon , Saad Jamal , Morsli Madjid , Harouna Hamidou Zelika , Tazerart Fatah , Drancourt Michel , Baron Sophie Alexandra 
Published: February 2021

ABSTRACTMycobacteria that form theMycobacterium tuberculosiscomplex are responsible for deadly tuberculosis in animals and patients. Identification of these pathogens at the species level is of primary importance for treatment and source tracing, and currently relies on DNA analysis, including whole genome sequencing (WGS), which takes a whole day. In this study, we report on the unprecedented identification of theM. tuberculosiscomplex species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), with WGS as the comparative gold standard. In a first step, an optimised peptide extraction applied to 24 isolates otherwise identified in three of the 11M. tuberculosiscomplex species by WGS, yielded 94 MALDI-TOF spectra which clustered according to WGS identification. In a second step, 70/74 (95%) other isolates were correctly identified at the species level by this clustering method. This study is the first to report a MALDI-TOF-MS method of identification ofM. tuberculosiscomplex mycobacteria at the species level and is easily implantable in clinical microbiology laboratories.
Perturbation of BRMS1 interactome reveals pathways that impact cell migration
Authors: Zimmermann Rosalyn , Sardiu Mihaela E. , Manton Christa A. , Miah Md. Sayem , Banks Charles A.S. , Adams Mark K. , Koestler Devin C. , Hurst Douglas R. , Edmonds Mick D. , Washburn Michael P. , Welch Danny R. 
Published: February 2021

AbstractBreast Cancer Metastasis Suppressor 1 (BRMS1) expression is associated with longer patient survival in multiple cancer types. Understanding BRMS1 functionality will provide insights into both mechanism of action and will enhance potential therapeutic development. In this study, we confirmed that the C-terminus of BRMS1 is critical for metastasis suppression and hypothesized that critical protein interactions in this region would explain its function. Phosphorylation status at S237 regulates BRMS1 protein interactions related to a variety of biological processes, phenotypes [cell cycle (e.g., CDKN2A), DNA repair (e.g., BRCA1)], and metastasis [(e.g., TCF2 and POLE2)]. Presence of S237 also directly decreased MDA-MB-231 breast carcinoma migrationin vitroand metastasesin vivo. The results add significantly to our understanding of how BRMS1 interactions with Sin3/HDAC complexes regulate metastasis and expand insights into BRMS1’s molecular role, as they demonstrate that BRMS1 C-terminus involvement in distinct direct protein-protein interactions.
Escherichia coliS2P family intramembrane protease RseP is engaged in the regulated sequential cleavages of FecR in the ferric citrate signaling
Authors: Yokoyama Tatsuhiko , Niinae Tomoya , Tsumagari Kazuya , Imami Koshi , Ishihama Yasushi , Hizukuri Yohei , Akiyama Yoshinori 
Published: February 2021

AbstractEscherichia coliRseP, a member of the S2P family of intramembrane proteases, is involved in the activation of the σEextracytoplasmic stress response and elimination of remnant signal peptides. However, whether RseP has additional cellular functions is unclear. In this study, we attempted to identify new RseP substrates to explore still unknown physiological roles of this protease. Our mass spectrometry-based quantitative proteomic analysis revealed that the levels of several Fec system proteins encoded by thefecABCDEoperon (fecoperon) were significantly decreased in an RseP-deficient strain. The Fec system is responsible for the uptake of ferric citrate, and the transcription of thefecoperon is controlled by FecI, an alternative sigma factor, and its regulator FecR, a single-pass transmembrane protein. Assays with thefecoperon expression reporter demonstrated that the proteolytic activity of RseP is essential for the ferric citrate-dependent upregulation of thefecoperon. Analysis using the FecR protein and FecR-derived model proteins showed that FecR undergoes sequential processing at the membrane and that RseP participates in the last step of this sequential processing to generate the N-terminal cytoplasmic fragment of FecR that participates in the transcription of thefecoperon with FecI. Ferric citrate signal-dependent generation of this cleavage product is the essential and sufficient role of RseP in the transcriptional activation of thefecoperon. Our study unveiled thatE. coliRseP performs the intramembrane proteolysis of FecR, a novel physiological role that is essential for regulating iron uptake by the ferric citrate transport system.
In-planta Gene Targeting in Barley using Cas9, with and without Geminiviral Replicons
Authors: Lawrenson Tom , Hinchliffe Alison , Clarke Martha , Morgan Yvie , Harwood Wendy 
Published: February 2021

AbstractAdvances in the use of RNA-guided Cas9-based genome editing in plants have been rapid over the last few years. A desirable application of genome editing is gene targeting (GT), as it allows a wide range of precise modifications, however this remains inefficient especially in key crop species. Here we describe successful, heritable gene targeting in barley using anin-plantastrategy but fail to achieve the same using a wheat dwarf virus replicon to increase copy number of the repair template. Without the replicon, we were able to delete 150bp of the coding sequence of our target gene whilst simultaneously fusing in-frame mCherry in its place. Starting from 14 original transgenic plants, two plants appeared to have the required gene targeting event. From one of these T0 plants, three independent gene targeting events were identified, two of which were heritable. When the replicon was included, 39 T0 plants were produced and shown to have high copy numbers of the repair template. However, none of the 17 lines screened in T1 gave rise to significant or heritable gene targeting events despite screening twice the number of plants in T1 compared to the non-replicon strategy. Investigation indicated that high copy numbers of repair template created by the replicon approach cause false positive PCR results which are indistinguishable at the sequence level to true GT events in junction PCR screens widely used in GT studies. In the successful non-replicon approach, heritable gene targeting events were obtained in T1 and subsequently the T-DNA was found to be linked to the targeted locus. Thus, physical proximity of target and donor sites may be a factor in successful gene targeting.
Missing the sweet spot: one of the two N-glycans on human Gb3/CD77 synthase is expendable
Authors: Mikolajczyk Krzysztof , Bereznicka Anna , Szymczak-Kulus Katarzyna , Haczkiewicz-Lesniak Katarzyna , Szulc Bozena , Olczak Mariusz , Rossowska Joanna , Majorczyk Edyta , Kapczynska Katarzyna , Bovin Nicolai , Lisowska Marta , Kaczmarek Radoslaw , Miazek Arkadiusz , Czerwinski Marcin 
Published: February 2021

AbstractN-glycosylation is a ubiquitous posttranslational modification that may influence folding, subcellular localization, secretion, solubility and oligomerization of proteins. In this study, we examined the effects of N-glycans on the activity of human Gb3/CD77 synthase, which catalyzes the synthesis of glycosphingolipids with terminal Galα1→4Gal (Gb3 and the P1 antigen) and Galα1→4GalNAc disaccharides (the NOR antigen). The human Gb3/CD77 synthase contains two occupied N-glycosylation sites at positions N121and N203. Intriguingly, we found that while the N-glycan at N203is essential for activity and correct subcellular localization, the N-glycan at N121is dispensable and its absence did not reduce, but, surprisingly, even increased the activity of the enzyme. The fully N-glycosylated human Gb3/CD77 synthase and its glycoform missing the N121glycan correctly localized in the Golgi, whereas a glycoform without the N203site partially mislocalized in the endoplasmic reticulum. A double mutein missing both N-glycans was inactive and accumulated in the endoplasmic reticulum. Our results suggest that the decreased specific activity of human Gb3/CD77 synthase glycovariants results from their improper subcellular localization and, to a smaller degree, a decrease in enzyme solubility. Taken together, our findings show that the two N-glycans of human Gb3/CD77 synthase have opposing effects on its properties, revealing a dual nature of N-glycosylation and potentially a novel regulatory mechanism controlling the biological activity of proteins.