bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silicoapproach toward the identification of unique peptides from viral protein infection: Application to COVID-19
Authors: Orsburn Benjamin C. , Jenkins Conor , Miller Sierra M. , Neely Benjamin A , Bumpus Namandje N 
Published: March 2020

SummaryWe describe a method for rapid in silico selection of diagnostic peptides from newly described viral pathogens and applied this approach to SARS-CoV-2/COVID-19. This approach is multi-tiered, beginning with compiling the theoretical protein sequences from genomic derived data. In the case of SARS-CoV-2 we begin with 496 peptides that would be produced by proteolytic digestion of the viral proteins. To eliminate peptides that would cause cross-reactivity and false positives we remove peptides from consideration that have sequence homology or similar chemical characteristics using a progressively larger database of background peptides. Using this pipeline, we can remove 47 peptides from consideration as diagnostic due to the presence of peptides derived from the human proteome. To address the complexity of the human microbiome, we describe a method to create a database of all proteins of relevant abundance in the saliva microbiome. By utilizing a protein-based approach to the microbiome we can more accurately identify peptides that will be problematic in COVID-19 studies which removes 12 peptides from consideration. To identify diagnostic peptides, another 7 peptides are flagged for removal following comparison to the proteome backgrounds of viral and bacterial pathogens of similar clinical presentation. By aligning the protein sequences of SARS-CoV-2 field isolates deposited to date we can identify peptides for removal due to their presence in highly variable regions that may lead to false negatives as the pathogen evolves. We provide maps of these regions and highlight 3 peptides that should be avoided as potential diagnostic or vaccine targets. Finally, we leverage publicly deposited proteomics data from human cells infected with SARS-CoV-2, as well as a second study with the closely related MERS-CoV to identify the two proteins of highest abundance in human infections. The resulting final list contains the 24 peptides most unique and diagnostic of SARS-CoV-2 infections. These peptides represent the best targets for the development of antibodies are clinical diagnostics. To demonstrate one application of this we model peptide fragmentation using a deep learning tool to rapidly generate targeted LCMS assays and data processing method for detecting CoVID-19 infected patient samples.Graphical Abstract
Polysome fractionation analysis reveals features important for human nonsense-mediated mRNA decay
Authors: Lloyd James P. B. , French Courtney E. , Brenner Steven E. 
Published: March 2020

AbstractNonsense-mediated mRNA decay (NMD) is a translation-dependent mRNA surveillance pathway that eliminates transcripts with premature termination codons. Several studies have tried defined the features governing which transcripts are targeted to NMD. However, these approaches often rely on inhibiting core NMD factors, which often have roles in non-NMD processes within the cell. Based on reports that NMD-targeted transcripts are often bound by a single ribosome, we analyzed RNA-Seq data from a polysome fractionation experiment (TrlP-Seq) to characterize the features of NMD-targeted transcripts in human cells. This approach alleviates the need to inhibit the NMD pathway. We found that the exon junction complex (EJC) model, wherein an exon-exon junction located ≥50 nucleotides downstream of a stop codon is predicted to elicit NMD, was a powerful predictor of transcripts with high abundance in the monosome fraction (bound by a single ribosome). This was also true for the presence of an upstream open reading frame. In contrast, as 3’ UTR lengths increase, the proportion of transcripts that are most abundant in the monosome fraction does not increase. This suggests that either longer 3’ UTRs do not consistently act as potent triggers of NMD or that the degradation of these transcripts is mechanistically different to other NMD-targeted transcripts. Of the ribosome-associated transcripts annotated as “non-coding”, we find that a majority are bound by a single ribosome. Many of these transcripts increase in response to NMD inhibition, including the oncogenic SHNG15, suggesting many might be NMD targets. Finally, we found that retained intron transcripts without a premature termination codon are over-represented in the monosome fraction, suggesting an alternative mechanism is responsible for the low level of translation of these transcripts. In summary, our analysis finds that the EJC model is a powerful predictor of NMD-targeted transcripts, while the presence of a long 3’ UTR is not.
Positively selected modifications in the pore of TbAQP2 allow pentamidine to enterTrypanosoma brucei
Authors: Alghamdi Ali H. , Munday Jane C. , Campagnaro Gustavo D. , Gurvič Dominik , Svensson Fredrik , Okpara Chinyere E. , Kumar Arvind , Martin Abril Maria Esther , Milić Patrik , Watson Laura , Paape Daniel , Settimo Luca , Dimitriou Anna , Wielinska Joanna , Smart Graeme , Anderson Laura F. , Woodley Christopher M. , Ying Kelley Siu Pui , Ibrahim Hasan M.S. , Hulpia Fabian , Al-Salabi Mohammed I. , Eze Anthonius A. , Teka Ibrahim A. , Gudin Simon , Dardonville Christophe , Tidwell Richard R , Carrington Mark , O’Neill Paul M. , Boykin David W , Zachariae Ulrich , De Koning Harry P. 
Published: March 2020

AbstractMutations in theTrypanosoma bruceiaquaporin AQP2 are associated with resistance to pentamidine and melarsoprol. We show that TbAQP2 but not TbAQP3 was positively selected for increased pore size from a common ancestor aquaporin. We demonstrate that TbAQP2’s unique architecture permits pentamidine permeation through its central pore and show how specific mutations in highly conserved motifs affect drug permeation. Introduction of key TbAQP2 amino acids into TbAQP3 renders the latter permeable to pentamidine. Molecular dynamics demonstrates that permeation by dicationic pentamidine is energetically favourable in TbAQP2, driven by the membrane potential, although aquaporins are normally strictly impermeable for ionic species. We also identify the structural determinants that make pentamidine a permeant but exclude most other diamidine drugs. Our results have wide-ranging implications for optimising antitrypanosomal drugs and averting cross-resistance. Moreover, these new insights in aquaporin permeation may allow the pharmacological exploitation of other members of this ubiquitous gene family.
Chromatin-Bound PARP1 Correlates with Upregulation of Inflammatory Genes in Response to Long-Term Treatment with Veliparib
Authors: Alvarado-Cruz Isabel , Mahmoud Mariam , Khan Mohammed , Zhao Shilin , Oeck Sebastian , Meas Rithy , Clairmont Kaylyn , Quintana Victoria , Zhu Ying , Porciuncula Angelo , Wyatt Hailey , Ma Shuangge , Shyr Yu , Kong Yong , LoRusso Patricia M. , Laverty Daniel , Nagel Zachary D. , Schalper Kurt A. , Krauthammer Michael , Sweasy Joann B. 
Published: March 2020

AbstractPoly-ADP-ribose polymerase (PARP) inhibitors are active against cells and tumors with defects in homology-directed repair as a result of synthetic lethality. PARP inhibitors have been suggested to act by either catalytic inhibition or by PARP localization in chromatin. In this study, we treat human HCC1937BRCA1mutant and isogenicBRCA1-complemented cells for three weeks with veliparib, a PARP inhibitor. We show that long-term treatment with veliparib results in chromatin-bound PARP1 in theBRCA1mutant cells, and that this correlates with significant upregulation of inflammatory genes and activation of the cyclic GMP–AMP synthase (cGAS)/ signalling effector stimulator of interferon genes (STING) pathway. In contrast, long-term treatment of isogenicBRCA1-complemented cells with veliparib does not result in chromatin-associated PARP or significant upregulation of the inflammatory response. Our results suggest that long-term veliparib treatment may primeBRCA1mutant tumors for positive responses to immune checkpoint blockade.
Application of probioticBacillusspp. isolated from African nightcrawler (Eudrilus eugeniae) on Nile Tilapia (Oreochromis niloticusL.)
Authors: Samson J. , Quiazon K.M. , Choresca C. 
Published: March 2020

AbstractDue to the emergence of antibiotic-resistant pathogens, probiotics in aquaculture are used for the prevention of infectious microbial diseases and substitute for antibiotics and chemotherapeutics. In this study, we evaluated the effect of probioticBacillusspp. isolated from African nightcrawler (Eudrilus eugeniae) on the growth, feed utilization, and disease resistance of Nile tilapia (Oreochromis niloticus). Four probiotic strains ofBacillusspp. (ANSCI9, BFAR9, RM3, and RM10) were individually incorporated in the commercial diet (control) at 108CFU g-1of feed. The experimental fish were fed at 5% of their body weight for 30 days, and subjected to a 14-dayAeromonas hydrophilachallenge test afterward. The results showed the probiotic-treated groups have higher (P<0.05) average body weight (ABW) (4.51 ± 0.34 g) than the control (3.89 ± 0.17 g). The BFAR9 (2.73 ± 0.26 g) and RM10 (3.15 ± 0.30 g) showed higher (P<0.05) absolute growth (AG) than the control (2.20 ± 0.16 g). Furthermore, RM10 had higher (P<0.05) specific growth rate (SGR) (1.60 ± 0.10 % day-1) and relative growth rate (RGR) (181.39 ± 18.16 %) than the control (SGR=1.29 ± 0.07 % day-1; RGR=129.84 ± 9.77 %). Consequently, RM10 had significantly lower (P<0.05) feed conversion ratio (FCR) (1.99 ± 0.13) than the control (2.60 ± 0.16). The challenge test revealed that the probiotic-treated groups have higher (P<0.05) survival (81.25 ± 9.57 %) than the control (55.00 ± 19.15 %). These results revealed that the probioticBacillusspp. isolated fromE. eugeniaeimproved the growth, feed utilization, and the disease resistance of Nile tilapia.
Glycine receptors are not directly modulated by glutamate, AP5 or NMDA
Authors: Aubrey Karin , Sheipouri Diba , Vandenberg Robert , Otsu Yo 
Published: March 2020

3.AbstractReproducibility of research data is a significant problem with more than 60% of biological and medical researchers reporting they have failed to reproduce published data. General acceptance of incorrect results can mean that future data is incorrectly interpreted and progress significantly interrupted. Thus, replication studies play an essential role in corroborating research findings and validating future research objectives. Here, we attempted to replicate data demonstrating the neurotransmitter glutamate, as well as NMDA and AP5, acts as positive allosteric modulators of the inhibitory glycine receptor. Notably, it was shown that the amplitude of miniature glycinergic currents recorded in spinal cord slices were reversibly enhanced when extracellular glutamate concentrations were increased by the glutamate transporter antagonist TBOA. This finding indicates that endogenous fluctuations in extracellular [glutamate] permits cross-talk between excitatory and inhibitory synapses and likely plays a role in setting the spinal inhibitory glycinergic tone and modulating baseline neurotransmission. We re-evaluated the data in primary cultured spinal cord neurons, spinal cord slice andXenopus laevisoocytes expressing recombinant glycine receptors. Despite extensive efforts, we were unable to reproduce the finding that glutamate, AP5 or NMDA positively modulate glycine receptor currents. We paid careful attention to key aspects of the original study design, ensured rapid drug exposure by using fast-flow application and took into account receptor saturation and protocol deviations such as animal species. This study refutes the finding that glycine receptors are directly modulated by glutamate spill-over and suggests that glycinergic tone is independent of changes in excitatory activity.4.Significance StatementGlutamate spill-over onto inhibitory synapses has been reported to positively modulate glycine receptors and alter the inhibitory tone of the spinal cord. This finding has important implications for baseline spinal transmission and could play a role when chronic pain develops. However, we failed to replicate these results and did not observe any modulation of native or recombinant glycine receptor-mediated currents by AP5, NMDA or glutamate. This indicates that inhibitory glycine receptors operate independently of fluctuations in extracellular [glutamate].5.Visual AbstractN/A
Reshaping of theArabidopsis thalianaproteome landscape and co-regulation of proteins in development and immunity
Authors: Bassal Mona , Majovsky Petra , Thieme Domenika , Herr Tobias , Abukhalaf Mohammad , Ayash Mohamed , Al Shweiki MHD Rami , Proksch Carsten , Hmedat Ali , Ziegler Jörg , Neumann Steffan , Hoehenwarter Wolfgang 
Published: March 2020

AbstractProteome remodeling is a fundamental adaptive response and proteins in complex and functionally related proteins are often co-expressed. Using a deep sampling strategy we defineArabidopsis thalianatissue core proteomes at around 10,000 proteins per tissue and absolutely quantify (copy numbers per cell) nearly 16,000 proteins throughout the plant lifecycle. A proteome wide survey of global post translational modification revealed amino acid exchanges pointing to potential conservation of translational infidelity in eukaryotes. Correlation analysis of protein abundance uncovered potentially new tissue and age specific roles of entire signaling modules regulating transcription in photosynthesis, seed development and senescence and abscission. Among others, the data suggest a potential function of RD26 and other NAC transcription factors in seed development related to desiccation tolerance as well as a possible function of Cysteine-rich Receptor-like Kinases (CRKs) as ROS sensors in senescence. All of the components of ribosome biogenesis factor (RBF) complexes were co-expressed tissue and age specifically indicating functional promiscuity in the assembly of these little described protein complexes in Arabidopsis. Treatment of seedlings with flg22 for 16 hours allowed us to characterize proteome architecture in basal immunity in detail. The results were complemented with parallel reaction monitoring (PRM) targeted proteomics, phytohormone, amino acid and transcript measurements. We obtained strong evidence of suppression of jasmonate (JA) and JA-Ile levels by deconjugation and hydroxylation via IAA-ALA RESISTANT3 (IAR3) and JASMONATE-INDUCED OXYGENASE 2 (JOX2) under the control of JASMONATE INSENSITIVE 1 (MYC2). This previously unknown regulatory switch is another part of the puzzle of the as yet understudied role of JA in pattern triggered immunity. The extensive coverage of theArabidopsisproteome in various biological scenarios presents a rich resource to plant biologists that we make available to the community.
AnXist-dependent protein assembly mediatesXistlocalization and gene silencing
Authors: Pandya-Jones Amy , Markaki Yolanda , Serizay Jacques , Chitiashvilli Tsotne , Mancia Walter , Damianov Andrey , Chronis Costantinos , Papp Bernadett , Chen Chun-Kan , McKee Robin , Wang Xiao-Jun , Chau Anthony , Leonhardt Heinrich , Zheng Sika , Guttman Mitchell , Black Douglas L. , Plath Kathrin 
Published: March 2020

SummaryNuclear compartments play diverse roles in regulating gene expression, yet the molecular forces and components driving compartment formation are not well understood. Studying how the lncRNAXistestablishes the inactive-X-chromosome (Xi)-compartment, we found that theXistRNA-binding-proteins PTBP1, MATR3, TDP43, and CELF1 form a condensate to create an Xi-domain that can be sustained in the absence ofXist. The E-repeat-sequence ofXistserves a multivalent binding-platform for these proteins. Without the E-repeat,Xistinitially coats the X-chromosome during XCI onset but subsequently disperses across the nucleus with loss of gene silencing. Recruitment of PTBP1, MATR3, TDP-43 or CELF1 to ΔE-Xistrescues these phenotypes, and requires both self-association of MATR3 and TDP-43 and a heterotypic PTBP1-MATR3-interaction. Together, our data reveal thatXistsequesters itself within the Xi-territory and perpetuates gene silencing by seeding a protein-condensate. Our findings uncover an unanticipated mechanism for epigenetic memory and elucidate the interplay between RNA and RNA-binding-proteins in creating compartments for gene regulation.
Estimating plasmid conjugation rates: a new computational tool and a critical comparison of methods
Authors: Huisman Jana S. , Benz Fabienne , Duxbury Sarah J.N. , de Visser J. Arjan G.M. , Hall Alex R. , Fischer Egil A.J. , Bonhoeffer Sebastian 
Published: March 2020

AbstractPlasmids are important vectors for the spread of genes among diverse populations of bacteria. However, there is no standard method to determine the rate at which they spread horizontally via conjugation. Here, we compare commonly used methods on simulated and experimental data, and show that the resulting conjugation rate estimates often depend strongly on the time of measurement, the initial population densities, or the initial ratio of donor to recipient populations. Differences in growth rate, e.g. induced by sub-lethal antibiotic concentrations or temperature, can also significantly bias conjugation rate estimates. We derive a new ‘end-point’ measure to estimate conjugation rates, which extends the well-known Simonsen method to include the effects of differences in population growth and conjugation rates from donors and transconjugants. We further derive analytical expressions for the parameter range in which these approximations remain valid. We present an easy to use R package and web interface which implement both new and previously existing methods to estimate conjugation rates. The result is a set of tools and guidelines for accurate and comparable measurement of plasmid conjugation rates.HighlightsWe present an R package and Shiny app to estimate conjugation rates from experimental dataWe highlight the diversity of existing measures used to estimate conjugation ratesWe show these measures are biased for populations with differing growth and conjugation rates from donors or transconjugantsWe develop a new ‘end-point’ measure which accounts for such differences in growth and conjugation rates
SPIN reveals genome-wide landscape of nuclear compartmentalization
Authors: Wang Yuchuan , Zhang Yang , Zhang Ruochi , van Schaik Tom , Zhang Liguo , Sasaki Takayo , Hupkes Daniel Peric , Chen Yu , Gilbert David M. , van Steensel Bas , Belmont Andrew S. , Ma Jian 
Published: March 2020

AbstractChromosomes segregate differentially relative to distinct subnuclear structures, but this genome-wide compartmentalization, pivotal for modulating genome function, remains poorly understood. New genomic mapping methods can reveal chromosome positioning relative to specific nuclear structures. However, computational methods that integrate their results to identify overall intranuclear chromo-some positioning have not yet been developed. We report SPIN, a new method to identify genome-wide nuclear spatial localization patterns. As a proof-of-principle, we use SPIN to integrate nuclear compartment mapping (TSA-seq and DamID) and chromatin interaction data (Hi-C) from K562 cells to identify 10 spatial compartmentalization states genome-wide relative to nuclear speckles, lamina, and nucleoli. These SPIN states show novel patterns of genome spatial organization and their relation to genome function (transcription and replication timing). Comparisons of SPIN states with Hi-C sub-compartments and lamina-associated domains (LADs) from multiple cell types suggest constitutive compartmentalization patterns. By integrating different readouts of higher-order genome organization, SPIN provides critical insights into nuclear spatial and functional compartmentalization.
CRISPR-Csy4-mediated editing of rotavirus double-stranded RNA genome
Authors: Papa Guido , Venditti Luca , Braga Luca , Schneider Edoardo , Giacca Mauro , Petris Gianluca , Burrone Oscar R. 
Published: March 2020

ABSTRACTCRISPR-nucleases have been widely applied for editing cellular and viral genomes, but nuclease-mediated genome editing of double-stranded RNA (dsRNA) viruses has not yet been reported. Here, by engineering CRISPR-Csy4 nuclease to localise to rotavirus viral factories, we achieved the first nuclease-mediated genome editing of rotavirus, an important human and livestock pathogen with a multi-segmented dsRNA genome. Rotavirus replication intermediates cleaved by Csy4 were repaired through the formation of defined deletions in the targeted genome segments in a single replication cycle. Using CRISPR-Csy4-mediated editing of rotavirus genome, we labelled for the first time the products of rotavirus secondary transcription made by newly assembled viral particles during rotavirus replication, demonstrating that this step largely contributes to the overall production of viral proteins. We anticipate that the nuclease-mediated cleavage of dsRNA virus genomes will promote a new level of understanding of viral replication and host-pathogen interactions, offering the opportunity to develop new therapeutics.
O-GlcNAcylation of SAMHD1 Indicating a Link between Metabolic Reprogramming and Anti-HBV Immunity
Authors: Hu Jie , Gao Qingzhu , Yang Yang , Xia Jie , Zhang Wanjun , Chen Yao , Zhou Zhi , Chang Lei , Hu Yuan , Zhou Hui , Liang Li , Li Xiaosong , Long Quanxin , Wang Kai , Huang Ailong , Tang Ni 
Published: March 2020

AbstractViruses hijack the host cell machinery to promote viral replication; however, the mechanism by which metabolic reprogramming regulates innate antiviral immunity in the host remains elusive. Herein, we found that Hepatitis B virus (HBV) infection upregulates glucose transporter 1expression, promotes hexosamine biosynthesis pathway (HBP) activity, and enhances O-linked β-N-acetylglucosamine (O-GlcNAc) modification of downstream proteins. HBP-mediated O-GlcNAcylation positively regulates host antiviral response against HBVin vitroandin vivo. Mechanistically, O-GlcNAc transferase (OGT)-mediated O-GlcNAcylation of sterile alpha motif and histidine/aspartic acid domain-containing protein 1 (SAMHD1) on Ser93 stabilizes SAMHD1 and enhances its antiviral activity. In addition, O-GlcNAcylation of SAMHD1 promoted its antiviral activity against human immunodeficiency virus-1in vitro. In conclusion, the results of our study reveal a link between HBP, O-GlcNAc modification, and innate antiviral immunity by targeting SAMHD1. Therefore, the results of this study demonstrate a strategy for the potential treatment of HBV infection by modulating HBP activity.