bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel histone deacetylase inhibitor-based approach to eliminate microglia and retain astrocyte properties in glial cell culture
Authors: He Xi-Biao , Wu Yi , Huang Haozhi , Guo Fang 
Published: November 2021

ABSTRACTThe close association between astrocytes and microglia causes great difficulties to distinguish their individual roles in innate immune responses in central nervous system. Current chemical-based methods to eliminate microglia in glial cell culture introduce various molecular and functional alterations to astrocytes. Here, we describe a novel two-step approach to achieve a complete elimination of microglia without affecting the biological properties of co-cultured astrocytes by temporal treatment of histone deacetylase inhibitor trichostatin A (TSA). We verify TSA as a potent inducer for microglial-specific cell death, which also causes comprehensive gene expression changes in astrocytes. However, withdrawal of TSA not only ensures no microglia repopulation, but also restores all the gene expression changes in terms of astrocyte functions, including neurotrophic factors, glutamate and potassium transporters, and reactive astrocyte subtypes. By contrast, withdrawal of PLX5622, the commonly used colony-stimulating factor 1 receptor inhibitor neither prevents microglia repopulation nor restores the gene expression changes mentioned above. Using this method, we are able to discriminate differential roles of microglia and astrocytes in the induced expression of antiviral and pro-inflammatory cytokines upon various pathological stimuli including the spike protein of SARS-CoV-2. This simple and efficient method can be customized for the understanding of microglia-astrocyte interaction and the development of epigenetic therapies that target over-activated microglia in neuroinflammation-related diseases.
Assessing and enhancing foldability in designed proteins
Authors: Listov Dina , Lipsh-Sokolik Rosalie , Rosset Stéphane , Yang Che , Correia Bruno E , Fleishman Sarel J 
Published: November 2021

AbstractRecent advances in protein-design methodology have led to a dramatic increase in reliability and scale. With these advances, dozens and even thousands of designed proteins are automatically generated and screened. Nevertheless, the success rate, particularly in design of functional proteins, is low and fundamental goals such as reliable de novo design of efficient enzymes remain beyond reach. Experimental analyses have consistently indicated that a major reason for design failure is inaccuracy and misfolding relative to the design model. To address this challenge, we describe complementary methods to diagnose and ameliorate suboptimal regions in designed proteins: first, we develop a Rosetta atomistic computational mutation scanning approach to detect energetically suboptimal positions in designs (available on a web server https://pSUFER.weizmann.ac.il); second, we demonstrate that AlphaFold2 ab initio structure prediction flags regions that may misfold in designed enzymes and binders; and third, we focus FuncLib design calculations on suboptimal positions in a previously designed low-efficiency enzyme improving its catalytic efficiency by 330 fold. Furthermore, applied to a de novo designed protein that exhibited limited stability, the same approach markedly improved stability and expressibility. Thus, foldability analysis and enhancement may dramatically increase the success rate in design of functional proteins.
Improvement of muscle strength in a mouse model for congenital myopathy treated with HDAC and DNA methyltransferase inhibitors
Authors: Ruiz Alexis , Benucci Sofia , Duthaler Urs , Bachmann Christoph , Franchini Martina , Noreen Faiza , Pietrangelo Laura , Protasi Feliciano , Treves Susan , Zorzato Francesco 
Published: November 2021

AbstractTo date there are no therapies for patients with congenital myopathies, muscle disorders causing poor quality of life of affected individuals. In approximately 30% of the cases, patients with congenital myopathies carry either dominant or recessive mutations in the RYR1 gene; recessive RYR1 mutations are accompanied by reduction of RyR1 expression and content in skeletal muscles and are associated with fiber hypotrophy and muscle weakness. Importantly, muscles of patients with recessive RYR1 mutations exhibit increased content of class II histone de-acetylases and of DNA genomic methylation. We recently created a mouse model knocked-in for the p.Q1970fsX16+p.A4329D RyR1 mutations, which are isogenic to those carried by a severely affected child suffering from a recessive form of RyR1-related multi-mini core disease. The phenotype of the RyR1 mutant mice recapitulates many aspects of the clinical picture of patients carrying recessive RYR1 mutations. We treated the compound heterozygous mice with a combination of two drugs targeting DNA methylases and class II histone de-acetylases. Here we show that treatment of the mutant mice with drugs targeting epigenetic enzymes improves muscle strength, RyR1 protein content and muscle ultrastructure. This study provides proof of concept for the pharmacological treatment of patients with congenital myopathies linked to recessive RYR1 mutations.
Sequestration of LINE-1 in novel cytosolic bodies by MOV10 restricts retrotransposition
Authors: Arora Rajika , Bodak Maxime , Penouty Laura , Hackman Cindy , Ciaudo Constance 
Published: November 2021

AbstractLINE-1 (L1) are autonomous retroelements that have retained their ability to mobilize. Mechanisms regulating L1 mobility include DNA methylation in somatic cells and the Piwi-interacting RNA pathway in the germline. During pre-implantation stages of mouse embryonic development, however, both pathways are inactivated leading to a critical window necessitating alternate means of L1 regulation. We previously reported an increase in L1 levels in Dicer_KO mouse embryonic stem cells (mESCs). Intriguingly this was accompanied by only a marginal increase in retrotransposition, suggestive of additional mechanisms suppressing L1 mobility. Here, we demonstrate that L1 Ribonucleoprotein complexes (L1 RNP) accumulate as aggregates in Dicer_KO cytoplasm along with the RNA helicase MOV10. The combined overexpression of L1 RNAs and MOV10 is sufficient to create L1 RNP aggregates in stem cells. In Dicer_KO mESCs, MOV10 is upregulated due to the loss of its direct regulation by miRNAs. The newly discovered post-transcriptional regulation of Mov10 expression, and its role in preventing L1 retrotransposition by driving novel cytosolic aggregation affords alternate routes to explore for therapy and disease progression.
Deep and fast label-free Dynamic Organellar Mapping
Authors: Schessner Julia P. , Albrecht Vincent , Davies Alexandra K. , Sinitcyn Pavel , Borner Georg H.H. 
Published: November 2021

ABSTRACTThe Dynamic Organellar Maps (DOMs) approach combines cell fractionation and shotgun-proteomics for global profiling analysis of protein subcellular localization. Here, we have drastically enhanced the performance of DOMs through data-independent acquisition (DIA) mass spectrometry (MS). DIA-DOMs achieve twice the depth of our previous workflow in the same MS runtime, and substantially improve profiling precision and reproducibility. We leveraged this gain to establish flexible map formats scaling from rapid analyses to ultra-deep coverage. Our fastest format takes only ∼2.5h/map and enables high-throughput experimental designs. Furthermore, we introduce DOM-QC, an open-source software tool for in-depth standardized analysis of DOMs and other profiling data. We then applied DIA-DOMs to capture subcellular localization changes in response to starvation and disruption of lysosomal pH in HeLa cells, which revealed a subset of Golgi proteins that cycle through endosomes. DIA-DOMs offer a superior workflow for label-free spatial proteomics as a systematic phenotype discovery tool.
Salmonella Outer Membrane Vesicles contain tRNA Fragments (tRFs) that Inhibit Bacteriophage P22 infection
Authors: Houserova Dominika , Huang Yulong , Kasukurthi Mohan V. , Watters Brianna C. , Khan Fiza F. , Mehta Raj V. , Chaudhary Neil Y. , Roberts Justin T. , DeMeis Jeffrey D. , Hobbs Trevor K. , Ghee Kanesha R. , McInnis Cameron H. , Johns Nolan P. , Kegler Abrianna J. , Coley Alexander B. , Brown Cana L. , Hewes Jenny L. , McElyea Marie M. , Reeves Monica N. , Tran Tuan M. , Bauer Natalie R. , Huang Jingshan , Audia Jonathon P. , Foster John W. , Borchert Glen M. 
Published: November 2021

ABSTRACTSalmonella Outer Membrane Vesicles (OMVs) were recently shown to inhibit P22 bacteriophage infection. Furthermore, despite there being several published reports now independently describing (1) the marked prevalence of tRFs within secreted vesicle transcriptomes and (2) roles for specific tRFs in facilitating/inhibiting viral replication, there have been no examinations of the effects of vesicle-secreted tRFs on viral infection reported to date. Notably, while specific tRFs have been reported in a number of bacteria, the tRFs expressed by salmonellae have not been previously characterized. As such, we recently screened small RNA-seq datasets for the presence of recurrent, specifically excised tRFs and identified 31 recurrent, relatively abundant tRFs expressed by Salmonella enterica serovar Typhimurium (SL1344). What’s more, we find S. Typhimurium OMVs contain significant levels of tRFs highly complementary to known Salmonella enterica-infecting bacteriophage with 17 of 31 tRFs bearing marked complementarity to at least one known Salmonella enterica-infecting phage (averaging 97.4% complementarity over 22.9 nt). Most notably, tRNA-Thr-CGT-1-1, 44-73, bears 100% sequence complementary over its entire 30 nt length to 29 distinct, annotated Salmonella enterica-infecting bacteriophage including P22. Importantly, we find inhibiting this tRF in secreted OMVs improves P22 infectivity in a dose dependent manner whereas raising OMV tRF levels conversely inhibits P22 infectivity. Furthermore, we find P22 phage pre-incubation with OMVs isolated from naïve, control SL1344 S. Typhimurium, successfully rescues the ability of S. Typhimurium transformed with a specific tRNA-Thr-CGT-1-1, 44-73 tRF inhibitor to defend against P22. Collectively, these experiments confirm tRFs secreted in S. Typhimurium OMVs are directly involved with and required for the ability of OMVs to defend against bacteriophage predation. As we find the majority of OMV tRFs are highly complementary to an array of known Salmonella enterica-infecting bacteriophage, we suggest OMV tRFs may primarily function as a broadly acting, previously uncharacterized innate antiviral defense.
Platelets are dispensable for the ability of CD8+ T cells to accumulate, patrol, kill and reside in the liver
Authors: O’Connor James H. , McNamara Hayley A. , Cai Yeping , Coupland Lucy A. , Gardiner Elizabeth E. , Parish Christopher R. , McMorran Brendan J. , Ganusov Vitaly V. , Cockburn Ian A. 
Published: November 2021

AbstractEffector and memory CD8+ T cells accumulate in large numbers in the liver where they play key roles in the control of liver pathogens includingPlasmodium. It has also been proposed that liver may act as the main place for elimination of effector CD8+ T cells at the resolution of immune responses. Platelets and the integrin LFA-1 have been proposed to be critical for the accumulation of protective CD8+ T cells in the liver; conversely, asialo-glycoprotein (ASGP) expression on the surface of CD8+ T cells has been proposed to assist in elimination of effector T cells in the liver. Here we investigated the contributions of these interactions in the accumulation of CD8+ T cells activatedin vitroorin vivoby immunization withPlasmodiumparasites. UsingMpl-/-mice with constitutive thrombocytopaenia and antibody-mediated platelet depletion models we found that severe reduction in platelet concentration in circulation did not strongly influence the accumulation and protective function of CD8+ T cells in the liver in these models. Surprisingly, inhibition of ASGP receptors did not inhibit the accumulation of effector cells in the liver, but instead prevented these cells from accumulating in the spleen. We further found that enforced expression of ASGP on effector CD8+ T cells using ST3GalI knockout cells lead to their loss from the spleen. These data suggest that platelets play a marginal role in CD8+ T cell function in the liver. Furthermore, ASGP-expressing effector CD8+ T cells are retained in the liver but are lost from the spleen.
Novel genetic basis of resistance to Bt toxin Cry1Ac inHelicoverpa zea
Authors: Benowitz Kyle M. , Allan Carson W. , Degain Benjamin A. , Li Xianchun , Fabrick Jeffrey A. , Tabashnik Bruce E. , Carrière Yves , Matzkin Luciano M. 
Published: November 2021

AbstractCrops genetically engineered to produce insecticidal proteins from the bacteriumBacillus thuringiensis(Bt) have advanced pest management, but their benefits are diminished when pests evolve resistance. Elucidating the genetic basis of pest resistance to Bt toxins can improve resistance monitoring, resistance management, and design of new insecticides. Here, we investigated the genetic basis of resistance to Bt toxin Cry1Ac in the lepidopteranHelicoverpa zea, one of the most damaging crop pests in the United States. To facilitate this research, we built the first chromosome-level genome assembly for this species, which has 31 chromosomes containing 375 Mb and 15,482 predicted proteins. Using a genome-wide association study, fine-scale mapping, and RNA-seq, we identified a 250-kb quantitative trait locus (QTL) on chromosome 13 that was strongly associated with resistance in a strain ofH. zeathat had been selected for resistance in the field and lab. The mutation in this QTL contributed to but was not sufficient for resistance, which implies alleles in more than one gene contributed to resistance. This QTL contains no genes with a previously reported role in resistance or susceptibility to Bt toxins. However, in resistant insects, this QTL has a premature stop codon in a kinesin gene which is a primary candidate as a mutation contributing to resistance. We found no changes in gene sequence or expression consistently associated with resistance for 11 genes previously implicated in lepidopteran resistance to Cry1Ac. Thus, the results reveal a novel and polygenic basis of resistance.
Fibroblast-expressed LRRC15 suppresses SARS-CoV-2 infection and controls antiviral and antifibrotic transcriptional programs
Authors: Loo Lipin , Waller Matthew A. , Moreno Cesar L. , Cole Alexander J. , Stella Alberto Ospina , Pop Oltin-Tiberiu , Jochum Ann-Kristin , Ali Omar Hasan , Denes Christopher E. , Hamoudi Zina , Chung Felicity , Aggarwal Anupriya , Low Jason K. K. , Patel Karishma , Siddiquee Rezwan , Kang Taeyoung , Mathivanan Suresh , Mackay Joel P. , Flatz Lukas , Hesselson Daniel , Turville Stuart , Neely G. Gregory 
Published: November 2021

AbstractAlthough ACE2 is the primary receptor for SARS-CoV-2 infection, a systematic assessment of host factors that regulate binding to SARS-CoV-2 spike protein has not been described. Here we use whole genome CRISPR activation to identify host factors controlling cellular interactions with SARS-CoV-2. Our top hit was aTLR-related cell surface receptor calledleucine-rich repeat-containing protein 15(LRRC15).LRRC15expression was sufficient to promote SARS-CoV-2 Spike binding where they form a cell surface complex.LRRC15mRNA is expressed in human collagen-producing lung myofibroblasts and LRRC15 protein is induced in severe COVID-19 infection where it can be found lining the airways. Mechanistically, LRRC15 does not itself support SARS-CoV-2 infection, but fibroblasts expressing LRRC15 can suppress both pseudotyped and authentic SARS-CoV-2 infection intrans. Moreover, LRRC15 expression in fibroblasts suppresses collagen production and promotes expression of IFIT, OAS, and MX-family antiviral factors. Overall, LRRC15 is a novel SARS-CoV-2 spike-binding receptor that can help control viral load and regulate antiviral and antifibrotic transcriptional programs in the context of COVID-19 infection.
Genomic landscape of SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin
Authors: Perico Camila P. , De Pierri Camilla R. , Neto Giuseppe P. , Fernandes Danrley R. , Pedrosa Fabio O. , de Souza Emanuel M. , Raittz Roberto T. 
Published: November 2021

AbstractBrazil was the epicenter of worldwide pandemics at the peak of its second wave. The genomic/proteomic perspective of the COVID-19 pandemic in Brazil can bring new light to understand the global pandemics behavior. In this study, we track SARS-CoV-2 molecular information in Brazil using real-time bioinformatics and data science strategies to provide a comparative and evolutive panorama of the lineages in the country. SWeeP vectors represented the Brazilian and worldwide genomic/proteomic data from GISAID between 02/2020 – 08/2021. Clusters were analyzed and compared with PANGO lineages. Hierarchical clustering provided phylogenetic and evolutionary analysis of the lineages, and we tracked the P.1 (Gamma) variant origin. The genomic diversity based on Chao’s estimation allowed us to compare richness and coverage among Brazilian states and other representative countries. We found that epidemics in Brazil occurred in two distinct moments, with different genetic profiles. The P.1 lineages emerged in the second wave, which was more aggressive. We could not trace the origin of P.1 from the variants present in Brazil in 2020. Instead, we found evidence pointing to its external source and a possible recombinant event that may relate P.1 to the B.1.1.28 variant subset. We discussed the potential application of the pipeline for emerging variants detection and the stability of the PANGO terminology over time. The diversity analysis showed that the low coverage and unbalanced sequencing among states in Brazil could have allowed the silenty entry and dissemination of P.1 and other dangerous variants. This comparative and evolutionary analysis may help to understand the development and the consequences of the entry of variants of concern (VOC).
Mitochondrial calcium uptake regulates tumour progression in embryonal rhabdomyosarcoma
Authors: Chiu Hsin Yao , Loh Amos Hong Pheng , Taneja Reshma 
Published: November 2021

AbstractEmbryonal rhabdomyosarcoma (ERMS) is characterized by a failure of cells to complete skeletal muscle differentiation. Although ERMS cells are vulnerable to oxidative stress, the relevance of mitochondrial calcium homeostasis in oncogenesis is unclear. Here, we show that ERMS cell lines as well as primary tumours exhibit elevated expression of the Mitochondrial Calcium Uniporter (MCU). MCU knockdown resulted in impaired mitochondrial calcium uptake and a reduction in mitochondrial reactive oxygen species (mROS) levels. Phenotypically, MCU knockdown cells exhibited reduced cellular proliferation and motility, with an increased propensity to differentiatein vitroandin vivo. RNA-sequencing of MCU knockdown cells revealed a significant reduction in genes involved in TGFβ signalling that play prominent roles in oncogenesis and inhibition of myogenic differentiation. Interestingly, modulation of mROS production impacted TGFβ signalling. Our study elucidates mechanisms by which mitochondrial calcium dysregulation promotes tumour progression and suggests that targeting the MCU complex to restore mitochondrial calcium homeostasis could be a therapeutic avenue in ERMS.
Exploring the relationship between lifestyle, digital financial element and digital financial services experience
Authors: Bapat Dhananjay 
Published: November 2021

PurposeThe purpose of this study is to explore digital financial services experience, investigate the antecedents to digital financial services experience and examine familiarity as a moderator.Design/methodology/approachThe study uses dual methods: qualitative and quantitative. Multiple case studies are applied as a qualitative method to explore and capture recent development in rapidly changing digital finance. An empirical, survey-based approach is used to collect data from 258 respondents about their experiences with digital financial services experience using constructs, such as perceived ease of use, timeliness, lifestyle and digital financial element. The study used structural equation modeling using smart-PLS.FindingsUsing word count, hierarchy chart, items clustered by similarity and qualitative analysis by applying NVivo 12, the study validates the constructs and captures recent developments. Using smart PLS, the structural equation model reveals that the digital functional element positively affects the digital financial services experience. It is observed that lifestyle mediated between perceived ease of use and timeliness with digital financial services experience. Further, familiarity moderates the relationship between the digital financial element and digital financial services experience. Moreover, while this research analyzed the relationship regarding financial services customers, we suggest a comparative study between different entities.Originality/valueThe study can be considered one of its kind using qualitative and quantitative research methods. It integrates theory from both the information system and marketing domain. As the increased number of digital channels and interfaces has increased, companies need to understand how to improve the digital financial services experience.
A gardening and woodwork group in mental health: a step towards recovery
Authors: Sinnott Róisín , Rowlís Maria 
Published: November 2021

Purpose
This paper aims to evaluate the impact of an eight-week gardening and woodwork group programme on individuals’ recovery goals in an adult community mental health setting.

Design/methodology/approach
Seven individuals participated in the research. The programme was designed and facilitated by two occupational therapists (the authors) and one horticulture and trade skills facilitator. The goal attainment scale was used as a quantitative outcome measure as it allowed individuals to collaboratively set occupation-focused recovery-oriented goals. Due to the small sample size, descriptive statistics were used to analyse this data. Qualitative feedback was gathered through participant feedback forms when the programme ended.

Findings
Quantitative findings indicate positive results for individuals’ progression towards their recovery goals, with six out of seven participants either achieving or exceeding their goals. One person who attended only one out of eight groups had “worse than expected” goal achievement.

Originality/value
While there is evidence for the use of gardening and woodwork group therapy in mental health settings, most studies have relied on symptom-focused questionnaires or qualitative results rather than quantifiable recovery-oriented measures (Cipriani et al., 2017; Kamioka et al., 2014; Parkinson et al., 2011). It is hoped that this paper begins to bridge that gap and also outlines how recovery principles, gardening and woodwork can be incorporated into occupational therapy group programmes. This is of particular merit during the COVID-19 pandemic, which has led to a greater need for group intervention in outdoor settings, where social distancing can be comfortably facilitated.