bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ralstonia solanacearumalters root developmental programs in auxin-dependent and independent manners
Authors: Zhang Lu , Yu Gang , Xue Hao , Li Meng , Lozano-Durán Rosa , Macho Alberto P. 
Published: June 2022

ABSTRACTMicrobial pathogens and other parasites can modify the development of their hosts, either as a target or a side effect of their virulence activities. The plant pathogenic bacteriumRalstonia solanacearum, causal agent of the devastating bacterial wilt disease, is a soil-borne microbe that invades host plants through their roots, and later proliferates in xylem vessels. In this work, we studied the early stages ofR. solanacearuminfection in the model plantArabidopsis thaliana, using anin vitroinfection system. In addition to the previously reported inhibition of primary root length and increase in root hair formation at the root tip, we observed an earlier xylem differentiation duringR. solanacearuminfection that occurs in a HrpG-dependent manner, suggesting that the pathogen actively promotes the development of the vascular system upon invasion of the root. Moreover, we found that the phytohormone auxin, of which the accumulation is promoted by the bacterial infection, is required for theR. solanacearum-triggered induction of root hair formation, but not earlier xylem differentiation. Altogether, our results shed light on the capacity ofR. solanacearumto induce alterations of root developmental pathways and on the role of auxin in this process.
Using a Whole Genome Co-expression Network to Inform the Functional Characterisation of Predicted Genomic Elements fromMycobacterium tuberculosisTranscriptomic Data
Authors: Stiens Jennifer , Tan Yen Yi , Joyce Rosanna , Arnvig Kristine B. , Kendall Sharon L. , Nobeli Irene 
Published: June 2022

ABSTRACTA whole genome co-expression network was created usingMycobacterium tuberculosistranscriptomic data from publicly available RNA-sequencing experiments covering a wide variety of experimental conditions. The network includes expressed regions with no formal annotation, including putative short RNAs and untranslated regions of expressed transcripts, along with the protein-coding genes. These unannotated expressed transcripts were among the best-connected members of the module sub-networks, making up more than half of the ‘hub’ elements in modules that include protein-coding genes known to be part of regulatory systems involved in stress response and host adaptation. This dataset provides a valuable resource for investigating the role of non-coding RNA, and conserved hypothetical proteins, in transcriptomic remodelling. Based on their connections to genes with known functional groupings and correlations with replicated host conditions, predicted expressed transcripts can be screened as suitable candidates for further experimental validation.
Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform
Authors: Siepe Dirk H. , Henneberg Lukas T. , Wilson Steven C. , Hess Gaelen T. , Bassik Michael C. , Zinn Kai , Garcia K. Christopher 
Published: June 2022

ABSTRACTSecreted proteins, which include cytokines, hormones and growth factors, are extracellular ligands that control key signaling pathways mediating cell-cell communication within and between tissues and organs. Many drugs target secreted ligands and their cell-surface receptors. Still, there are hundreds of secreted human proteins that either have no identified receptors (“orphans”) and are likely to act through cell surface receptors that have not yet been characterized. Discovery of secreted ligand-receptor interactions by high-throughput screening has been problematic, because the most commonly used high-throughput methods for protein-protein interaction (PPI) screening do not work well for extracellular interactions. Cell-based screening is a promising technology for definition of new ligand-receptor interactions, because multimerized ligands can enrich for cells expressing low affinity cell-surface receptors, and such methods do not require purification of receptor extracellular domains. Here, we present a proteo-genomic cell-based CRISPR activation (CRISPRa) enrichment screening platform employing customized pooled cell surface receptor sgRNA libraries in combination with a magnetic bead selection-based enrichment workflow for rapid, parallel ligand-receptor deorphanization. We curated 80 potentially high value orphan secreted proteins and ultimately screened 20 secreted ligands against two cell sgRNA libraries with targeted expression of all single-pass (TM1) or multi-pass (TM2+) receptors by CRISPRa. We identified previously unknown interactions in 12 of these screens, and validated several of them using surface plasmon resonance and/or cell binding. The newly deorphanized ligands include three receptor tyrosine phosphatase (RPTP) ligands and a chemokine like protein that binds to killer cell inhibitory receptors (KIR’s). These new interactions provide a resource for future investigations of interactions between the human secreted and membrane proteomes.
The DEAD-box RNA helicase Dhx15 controls glycolysis and arbovirus replication in Aedes aegypti mosquito cells
Authors: Machado Samara Rosendo , Qu Jieqiong , Koopman Werner J.H. , Miesen Pascal 
Published: June 2022

AbstractAedes aegypti mosquitoes are responsible for the transmission of arthropod-borne (arbo)viruses including dengue and chikungunya virus (CHIKV), but in contrast to human hosts, arbovirus infected mosquitoes are able to efficiently control virus replication to sub-pathological levels. Yet, our knowledge about the molecular interactions of arboviruses with their mosquito hosts is largely incomplete. Here, we aimed to identify and characterize novel host genes that control arbovirus replication in Aedes mosquitoes. RNA binding proteins (RBPs) are well known to regulate immune signaling pathways in all kingdoms of life. We therefore performed a knockdown screen targeting 461 genes encoding predicted RBPs in Aedes aegypti Aag2 cells and identified 15 genes with antiviral activity against a Sindbis reporter virus. Amongst these, three DEAD-box RNA helicases, AAEL004419/Dhx15, AAEL008728 and AAEL004859 also acted as antiviral factors in dengue and CHIKV infections. Here, we explore the mechanism of Dhx15 in regulating an antiviral transcriptional response in mosquitoes by silencing Dhx15 in Aag2 cells followed by deep-sequencing of poly-A enriched RNAs. Dhx15 knockdown in uninfected or CHIKV-infected cells resulted in differential expression of 856 and 372 genes, respectively. Interestingly, amongst the consistently downregulated genes, glycolytic process was the most strongly enriched GO term as the expression of all core enzymes of the glycolytic pathway was reduced, suggesting that Dhx15 regulates glycolytic function. A decrease in lactate production supported the observation that Dhx15 silencing functionally impaired glycolysis. Modified rates of glycolytic metabolism have been implicated in controlling the replication of several classes of viruses and strikingly, infection of Aag2 cells with CHIKV by itself also resulted in the decrease of several glycolysis genes. Our data suggests that Dhx15 regulates replication of CHIKV, and possibly other arboviruses, by controlling glycolysis in mosquito cells.
In vivo virological efficacy of monoclonal antibodies and direct antiviral agents against the SARS-CoV-2 BA.1 and BA.2 Omicron sublineages
Authors: Mazzotta V , Cozzi Lepri A , Colavita F , Rosati S , Lalle E , Cimaglia C , Paulicelli J , Mastrorosa I , Vergori A , Girardi E , Garbuglia AR , Vaia F , Nicastri E , Antinori A 
Published: June 2022

ABSTRACTBackgroundOmicron variant questioned the efficacy of the approved therapies for the early COVID-19. I In vitro data show retained neutralizing activity against BA.1 and BA.2 for remdesivir (RDV), molnupiravir (MLN), and nirmatrelvir/ritonavir (NRM/r), while poor efficacy for Sotrovimab (STR) against BA.2. No data about the risk of clinical failure and in vivo antiviral activity are available.Material and methodsSingle-center observational comparison study enrolling all consecutive patients with a confirmed SARS-CoV-2 Omicron (BA.1 or BA.2) diagnosis and who met eligibility criteria for treatment with RDV, MLN, NRM/r, or STR. Treatment allocation was subject to drug availability, time from symptoms onset, and comorbidities. Patients were followed through day 30. Nasopharyngeal swab (NPS) VL was measured on day 1 (D1) and D7 and was expressed by log2 cycle threshold (CT) scale. Comparisons between groups were made by Chi-square and Wilcoxon paired-test. Primary endpoint was D1-D7 VL variation. Potential decrease in VL and average treatment effect (ATE) were calculated from fitting marginal linear regression models weighted for calendar month of infusion, duration of symptoms, and immunodeficiency. Secondary endpoints were the proportion of D7 undetectable VL in NPS and clinical outcomes compared by treatment groups using a Chi-square test.ResultsA total of 521 pts received treatments (STR 202, MLN 117, NRM/r 84, and RDV 118): female 250 (48%), median age 66 yrs (IQR 55-76), 90% vaccinated; 15% with negative baseline serology. At D1, median time from symptoms onset was 3 days (2,4). 378 (73%) pts were infected with BA.1 and 143 (27%) with BA.2. D1 mean viral load was 4.12 log2 (4.16 for BA.1 and 4.01 for BA.2). The adjusted analysis showed that NRM/r significantly reduced VL compared to all the other drugs in pts infected with BA.1 while no evidence for a difference vs. MLP was seen in those infected with BA.2. MLN had comparable activity to STR against BA.1 and to NRM/r against BA.2. There was no significant difference between STR and RDV for BA.2.At D7, 35/521 (6.7%) pts had undetectable VL. Of these, 31 were infected with BA.1 [9 (9%) MLN, 7 (14%) NRM/r, 7 (8%) RDV, and 8 (5%) STR)], and only 4 with BA.2, all treated with NRM/r. After 30 days of follow-up, 9/568 pts experienced COVID-19-related clinical failure [7/226 STR (5 BA.1) and 2/87 NRM /r (2 BA.1)].ConclusionsIn this analysis of in vivo early VL reductions, NRM/r appears to be the drug showing the greatest antiviral activity regardless of the VoC, together with MLN, although the latter limited to people with BA.2. In the Omicron era, due to the high prevalence of vaccinated people and the lower probability of hospital admission, VL decrease can be a valuable surrogate of drug activity.
Genetic susceptibility to earlier ovarian ageing increases de novo mutation rate in offspring
Authors: Stankovic Stasa , Shekari Saleh , Huang Qin Qin , Gardner Eugene J. , Owens Nick D. L. , Azad Ajuna , Hawkes Gareth , Kentistou Katherine A. , Beaumont Robin N. , Day Felix R. , Zhao Yajie ,   The Genomics England Research Consortium, Kennedy Kitale , Wood Andrew R. , Weedon Michael N. , Ong Ken K. , Wright Caroline F. , Hoffmann Eva R. , Hurles Matthew E. , Ruth Katherine S. , Martin Hilary C. , Perry John R. B. , Murray Anna 
Published: June 2022

AbstractHuman genetic studies have provided substantial insight into the biological mechanisms governing ovarian ageing, yet previous approaches have been largely restricted to assessing common genetic variation. Here we report analyses of rare (MAF<0.1%) protein-coding variants in the exomes of 106,973 women from the UK Biobank study, implicating novel genes with effect sizes up to ∼5 times larger than previously discovered in analyses of common variants. These include protein truncating variants in ZNF518A, which shorten reproductive lifespan by promoting both earlier age at natural menopause (ANM, 5.61 years [4.04-7.18], P=2*10-12) and later puberty timing in girls (age at menarche, 0.56 years [0.15-0.97], P=9.2*10-3). By integrating ChIP-Seq data, we demonstrate that common variants associated with ANM and menarche are enriched in the binding sites of ZNF518A. We also identify further links between ovarian ageing and cancer susceptibility, highlighting damaging germline variants in SAMHD1 that delay ANM and increase all-cause cancer risk in both males (OR=2.1 [1.7-2.6], P=4.7*10-13) and females (OR=1.61 [1.31-1.96], P=4*10-6). Finally, we demonstrate that genetic susceptibility to earlier ovarian ageing in women increases de novo mutation rate in their offspring. This provides direct evidence that female mutation rate is heritable and highlights an example of a mechanism for the maternal genome influencing child health.
Health-Related Quality of Life Among Critical Ill Patients After Move Out of ICU - A Systematic Review Protocol
Authors: Li Yao , Fang Dan , Wu Qiao 
Published: June 2022

AbstractIntroductionthe impact of critical illness is profound on patients resulting in physical, mental and social consequences and a poor health-related quality of life (HRQOL). Several studies investigated HRQOL among patients after moving out of the Intensive care unit (ICU). We will propose a systematic review of these studies.MethodWe will search PubMed, Web of Science, EMBASE, CINAHL (Cumulative Index to Nursing and Allied Health Literature), Cochrane Library and open grey paper that reported HRQOL of ICU survivors from January 2012 to January 2022 in the English language. We will exact HRQOL data. Risk of bias will use the QUADAS-2 tool. The strength of results depends on the quality of studies.Strengths and limitations of this studyThis study will focus on general ICU survivors and make sure our results are generalizableThe information about HRQOL is updated, and the follow-up period was extended. We will focus on recently ten-year studies. We will be glad to see whether the HRQOL improved.This study will analyze the factors associated with HRQOL after patients moved out of ICU.This study will not perform a meta-analysis due to the heterogeneous population.Ethics and disseminationWe do not require ethical approval because our review will be based on published material.Trial registration numberPROSPERO CRD 42022304279
The Chlamydia trachomatis type III secreted effector protein CteG induces centrosome amplification through interactions with centrin-2
Authors: Steiert Brianna , Icardi Carolina M. , Faris Robert , Klingelhutz Aloysius J. , Yau Peter M. , Weber Mary M. 
Published: June 2022

AbstractThe centrosome is the main microtubule organizing center of the cell and is crucial for mitotic spindle assembly, chromosome segregation, and cell division. Centrosome duplication is tightly controlled, yet several pathogens, most notably oncogenic viruses, perturb this process leading to increased centrosome numbers. Infection by the obligate intracellular pathogen Chlamydia trachomatis (C.t.) correlates with blocked cytokinesis, supernumerary centrosomes, and multipolar spindles; however, the mechanisms behind how C.t. induces these cellular abnormalities from the confines of its inclusion, remain largely unknown. Here we show that the type III secreted effector protein, CteG, binds to centrin-2 (CETN2), a key structural component of centrosomes and regulator of centriole duplication. This interaction requires a functional calcium binding EF hand 4 of CETN2, which is recognized via the C-terminus of CteG. Significantly, we show that deletion of CteG, or knockdown of CETN2, significantly impairs chlamydia’s ability to induce centrosome amplification. Uniquely, we have identified the first bacterial effector to target centrins, crucial regulators of the eukaryotic cell cycle. These findings have not only allowed us to begin addressing how C.t. induces gross cellular abnormalities during infection, but also indicate that obligate intracellular bacteria may contribute to cellular transformation events that negatively impact host physiology even when the pathogen is long removed. Understanding the consequences of CteG-CETN2 interactions, its impact on centrosome amplification, and the long-term effect this has on host cells could explain why chlamydial infection leads to an increased risk of cervical or ovarian cancer.Significance StatementThe presence of more than two centrosomes is a hallmark of many types of cancer, including cervical and ovarian cancers of which Chlamydia trachomatis (C.t.) infection is a significant risk factor. Despite the importance of this problem, how C.t. orchestrates these drastic changes in the host cell remains poorly understood. Here, we describe how C.t. uses a single effector protein, CteG, to drive centrosome amplification via manipulation of a key regulator of centriole duplication, centrin-2. This work begins to define how C.t. induces centrosome amplification to promote its replication while potentially contributing to devastating long-term negative consequences for normal host physiology. Further it may help elucidate why chlamydial infection leads to an increased cancer risk.
Mapping Responsive Genomic Elements to Heat Stress in a Maize Diversity Panel
Authors: Liang Zhikai , Myers Zachary A. , Petrella Dominic , Engelhorn Julia , Hartwig Thomas , Springer Nathan M. 
Published: June 2022

AbstractMany plant species exhibit genetic variation for tolerating environmental stress. A transcriptome investigation of over 100 maize inbreds revealed manycis- andtrans-acting eQTLs that influence the expression response to heat stress. Thecis-acting eQTL in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. Thecis-acting variants for heat stress responsive expression likely result from distinct promoter activities and the differential heat responses of the alleles were confirmed for selected genes using transient expression assays. Global foot-printing of transcription factor binding was performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.
Common patterns of hydrolysis initiation in P-loop fold nucleoside triphosphatases
Authors: Kozlova Maria I. , Shalaeva Daria N. , Dibrova Daria V. , Mulkidjanian Armen Y 
Published: June 2022

AbstractIn ubiquitous P-loop fold nucleoside triphosphatases (also known as Walker NTPases), hydrolysis of ATP or GTP is initiated by interaction with an activating partner (usually another protein domain), which is accompanied by insertion of stimulatory moiety(ies) (usually arginine or lysine residues) into the catalytic site. After inspecting over 3600 Mg-NTP-containing structures of P-loop NTPases, we identified those with stimulator(s) inserted into catalytic sites and analysed the patterns of stimulatory interactions. In most cases, at least one stimulator twists gamma-phosphate counter-clockwise by linking the oxygen atoms of alpha- and gamma-phosphates; the twisted gamma-phosphate is stabilized by a hydrogen bond with the backbone amino group of the fourth residue of the Walker A motif. In the remaining cases, the stimulators only interact with gamma-phosphate. The ubiquitous mechanistic interaction of diverse stimulators with the gamma phosphate group suggests its twist/rotation as the trigger for NTP hydrolysis.
Metabotyping of Andean pseudocereals and characterization of emerging mycotoxins
Authors: Vásquez-Ocmín Pedro G. , Marti Guillaume , Gadea Alice , Cabanac Guillaume , Vásquez-Briones Juan A. , Casavilca-Zambrano Sandro , Ponts Nadia , Jargeat Patricia , Haddad Mohamed , Bertani Stéphane 
Published: June 2022

AbstractPseudocereals are best known for three crops derived from the Andes: quinoa (Chenopodium quinoa, Chenopods I), canihua (C. pallidicaule, Chenopods I), and kiwicha (Amaranthus caudatus). Their grains are recognized for their nutritional benefits; however, there is a higher level of polyphenism and the chemical foundation that would rely with such polyphenism has not been thoroughly investigated. Meanwhile, the chemical food safety of pseudocereals remains poorly documented. Here we applied untargeted and targeted metabolomics approach by LC-MS to achieve both:i) a comprehensive chemical mapping of pseudocereal samples collected in the Andes to classify them according to their chemotype;ii) a quantification of their contents in emerging mycotoxins. An inventory of the fungal community was also realized with the aims to better know the filamentous fungi present in these grains and try to parallel this information with the presence of the molecules produced, especially mycotoxins. Metabotyping permitted to add new insights into the chemotaxonomy of pseudocereals, confirming the previously established phylotranscriptomic clades: Chenopods I (clusters quinoa and canihua), and Amaranthaceae s.s. (cluster kiwicha). Moreover, we report for the first time the presence of mycotoxins in pseudocereals. Sixteen samples of Peru (out of 27) and one sample from France (out of one) were contaminated with Beauvericin, an emerging mycotoxin. There were several mycotoxigenic fungi detected, includingAspergillus sp.,Penicillium sp., andAlternaria sp., but notFusaria.Highlights▪Twenty-seven grain samples of Andean pseudocereals were profiled by LC-HRMS.▪Untargeted metabolomics was used to differentiate varieties from the whole metabolome dataset.▪Five mycotoxins were quantify using targeted metabolomics.▪Sixteen samples of Peru and one sample from France were contaminated with Beauvericin.▪An inventory of the fungal community infesting the Andean pseudocereal samples was documented.
Natural Antimicrobial Peptides Self-assemble as α/β Chameleon Amyloids
Authors: Ragonis-Bachar Peleg , Rayan Bader , Barnea Eilon , Engelberg Yizhaq , Upcher Alexander , Landau Meytal 
Published: June 2022

ABSTRACTAmyloid protein fibrils and some antimicrobial peptides (AMPs) share biophysical and structural properties. This observation suggests that ordered self-assembly can act as an AMP-regulating mechanism, and, vice versa, that human amyloids play a role in host defense against pathogens, as opposed to their common association with neurodegenerative and systemic diseases. Based on previous structural information on toxic amyloid peptides, we developed a sequence-based bioinformatics platform and, led by its predictions, experimentally identified 14 fibril-forming AMPs (ffAMPs) from living organisms, which demonstrated cross-β and cross-α amyloid properties. The results support the amyloid-antimicrobial link. The high prevalence of ffAMPs produced by amphibians and marine creatures among other species suggests that they confer unique advantageous properties in distinctive environments, potentially providing stability and adherence properties. Most of the newly identified 14 ffAMPs showed lipid-induced and/or time-dependent secondary structure transitions in the fibril form, indicating structural and functional cross-α/β chameleons. Specifically, ffAMP cytotoxicity against human cells correlated with inherent or lipid-induced α-helical fibril structure. The findings raise hypotheses about the role of fibril secondary structure switching in regulation of processes, such as the transition between a stable storage conformation and an active state with toxicity against specific cell types.