bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deletion of proU suppresses proQ phenotypes in Escherichia coli
Authors: Smith-Frieday Michelle N. , Kerr Craig H. , Wood Janet M. 
Published: March 2022

ABSTRACTThe ProQ protein interacts as an RNA chaperone with diverse RNA molecules in Escherichia coli. ProQ is implicated in the bacterial osmotic stress response. When the osmotic pressure is high, cells maintain their hydration by accumulating organic solutes denoted osmolytes. Transporters ProP and ProU (which is ProVWX) mediate osmolyte accumulation by Escherichia coli. Mutations at proQ impair ProP activity by reducing ProP levels (the ProQ transport phenotype) but do not impair ProU activity or reduce the level of ProX. The proQ- bacteria are longer than proQ+ bacteria during growth in either low or high salinity medium and they grow slowly at high salinity (the ProQ growth phenotype). In addition, spherical cells with crescent-shaped, nucleic acid-rich foci appear and cells lyse (the ProQ morphological phenotypes). In this work, the proQ transport phenotype was suppressed by deletions of proU, or by an insertion of IS5 in proU, when proP was expressed from the chromosome or from the heterologous, plasmid-based PBAD promoter. A point mutation disrupting the Walker B motif of ProV inactivated ProU but did not suppress the transport phenotype. ProP activities and ProP levels varied in parallel, so proQ and proU act at the same level to regulate ProP expression. Deletion of the proU operon also suppressed the growth and morphological phenotypes. The proU locus may overlap the gene encoding a regulatory sRNA that acts with ProQ, contributing to cellular morphogenesis and osmotic stress tolerance, or the relationship between ProQ and proU may be indirect.
Spatiotemporal changes in genetic diversity and structure of a recent fish invasion in eastern North America
Authors: Bernos Thaïs A. , Avlijaš Sunčica , Hill Jaclyn , Morissette Olivier , Ricciardi Anthony , Mandrak Nicholas E. , Jeffries Kenneth M. 
Published: March 2022

AbstractIntroduced and geographically expanding populations experience similar eco-evolutionary challenges, including founder events, genetic bottlenecks, and novel environments. Theory predicts that reduced genetic diversity resulting from such genetic phenomena limits the colonization success of introduced populations. We examined an invasive population of a Eurasian freshwater fish, Tench (Tinca tinca), that has been expanding geographically in eastern North America for three decades. Using genomic data, we evaluated evidence for single versus multiple introductions and the connectivity of the population across the entire range in which it has been spreading. Tench exhibited low levels of genetic diversity, a lack of marked population subdivision across time and space, and evidence of a recent genetic bottleneck. These results suggest that the invasion stemmed from a single introduction, consistent with the reported invasion history. Furthermore, the large genetic neighbourhood size and weak within-population genetic substructure suggest high connectivity across the invaded range, despite the large area occupied, and no evidence of substantial diminution of genetic diversity from the invasion core to the margins. As eradicating the species within a ~112 km radius would be necessary to prevent recolonization, eradicating Tench is likely not feasible at watershed—and possibly local—scales. Management should instead focus on reducing abundance in priority conservation areas to mitigate adverse impacts. Our study supports the argument that introduced populations can thrive despite recent bottlenecks and low levels of genetic diversity, and it suggests that landscape heterogeneity and population demographics can generate variability in spatial patterns of genetic diversity within a single range expansion.
Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening
Authors: Roy Anu , Alhammad Yousef M. , McDonald Peter , Johnson David K. , Zhuo Junlin , Wazir Sarah , Ferraris Dana , Lehtiö Lari , Leung Anthony K.L. , Fehr Anthony R. 
Published: March 2022

ABSTRACTThe emergence of several zoonotic viruses in the last twenty years, especially the pandemic outbreak of SARS-CoV-2, has exposed a dearth of antiviral drug therapies for viruses with pandemic potential. Developing a diverse drug portfolio will be critical for our ability to rapidly respond to novel coronaviruses (CoVs) and other viruses with pandemic potential. Here we focus on the SARS-CoV-2 conserved macrodomain (Mac1), a small domain of non-structural protein 3 (nsp3). Mac1 is an ADP-ribosylhydrolase that cleaves mono-ADP-ribose (MAR) from target proteins, protects the virus from the anti-viral effects of host ADP-ribosyltransferases, and is critical for the replication and pathogenesis of CoVs. In this study, a luminescent-based high-throughput assay was used to screen ∼38,000 small molecules for those that could inhibit Mac1-ADP-ribose binding. We identified 5 compounds amongst 3 chemotypes that inhibit SARS-CoV-2 Mac1-ADP-ribose binding in multiple assays with IC50 values less than 100µM, inhibit ADP-ribosylhydrolase activity, and have evidence of direct Mac1 binding. These chemotypes are strong candidates for further derivatization into highly effective Mac1 inhibitors.
Therapeutic targeting of differentiation state-dependent metabolic vulnerabilities in DIPG
Authors: Mbah Nneka E. , Myers Amy L. , Chung Chan , Thompson Joyce K. , Hong Hanna S. , Sajjakulnukit Peter , Nwosu Zeribe C. , Shan Mengrou , Sweha Stefan R. , Maydan Daniella D. , Chen Brandon , Zhang Li , Magnuson Brian , Zui Zirui , Wahl Daniel R. , Franchi Luigi , Agnihotri Sameer , Koschmann Carl J. , Venneti Sriram , Lyssiotis Costas A. 
Published: March 2022

ABSTRACTH3K27M diffuse intrinsic pontine gliomas (DIPG) exhibit cellular heterogeneity comprising less-differentiated, stem-like glioma cells that resemble oligodendrocyte precursors (OPC) and more differentiated astrocyte (AC)-like cells. H3K27M DIPG stem-like cells exhibit tumor-seeding capabilities in vivo, a feature lost or greatly diminished in the more differentiated AC-like cells. In this study, we established isogenic in vitro models of DIPG that closely recapitulated the OPC-like and AC-like phenotypes of DIPG cells. Using these tools, we performed transcriptomics, metabolomics, and bioenergetic profiling to identify metabolic programs operative in the different cellular states. From this, we defined new strategies to selectively target metabolic vulnerabilities within the specific tumor populations. Namely, we showed that the AC-like cells exhibited a more mesenchymal phenotype and were thus sensitized to ferroptotic cell death. In contrast, OPC-like cells upregulated cholesterol metabolism and mitochondrial oxidative phosphorylation (OXPHOS) and were accordingly more sensitive to statins and OXPHOS inhibitors. Additionally, statins and OXPHOS inhibitors showed efficacy and extended survival in preclinical orthotopic models established with stem-like H3K27M DIPG cells. Together, this study demonstrates that cellular subtypes within DIPGs harbor distinct metabolic vulnerabilities that can be uniquely and selectively targeted for therapeutic gain.
Double knockout CRISPR screen in cancer resistance to T cell cytotoxicity
Authors: Park Jonathan J. , Codina Adan , Ye Lupeng , Lam Stanley , Guo Jianjian , Clark Paul , Zhou Xiaoyu , Peng Lei , Chen Sidi 
Published: March 2022

AbstractImmunotherapy has transformed cancer treatments; however, a large fraction of patients encounter resistance. Such resistance is mediated by complex factors, often involving interactions between multiple genes. Thus, it is crucially important to identify genetic interactions between genes that are significantly mutated in cancer patients and those involved in immune responses, ideally the ones that currently have chemical compounds for direct targeting. To systematically interrogate such genetic interactions that mediate cancer cells’ response to T cell killing, we designed an asymmetric CRISPR/Cas9 dual perturbation library targeting the matched combinations between significantly mutated tumor suppressors and immune resistance genes. We performed a combinatorial double knockout screen on 1,159 gene pairs and identified those where joint loss-of-function renders altered cellular response to T cell cytotoxicity. With individual double knockout constructs we validated these genetic interactions including Jak1-Trp53, Jak1-Kmt2d, and Ifngr1-Kmt2d. Interactions between significantly mutated tumor suppressors and potentially druggable immune resistance genes may offer insights on potential new concepts of how to target clinically relevant cancer mutations with currently available agents. This study also provides a technology platform and an asymmetric CRISPR double knockout library for interrogating genetic interactions between cancer mutations and immune resistance pathways under various settings.
Impact of Delta and Vaccination on SARS-CoV-2 transmission risk: Lessons for Emerging Breakthrough infections
Authors: Sriraman Kalpana , Shaikh Ambreen , Vaswani Smriti , Mestry Tejal , Patel Grishma , Sakthivel Shalini , Oswal Vikas , Kadam Pratibha , Nilgiriwala Kayzad , Shah Daksha , Gomare Mangala , Mistry Nerges 
Published: March 2022

AbstractWith the continuous emergence of SARS-CoV-2 variants of concern and implementation of mass-scale interventions like vaccination, understanding factors affecting disease transmission has critical implications for control efforts. Here we used a simple adapted N95 mask sampling method to demonstrate the impact of circulating SARS-CoV-2 variants and vaccination on 92 COVID-19 patients to expel virus into the air translating to a transmission risk. Between July and September 2021, when the Delta was the dominant circulating strain in Mumbai, we noted a two-fold increase in the proportion of people expelling virus (95%), about an eighty-fold increase in median viral load and a three-fold increase in high emitter type (41%; people expelling >1000 viral copy numbers in 30 minutes) compared to initial strains of 2020. Eight percent of these patients continued to be high emitters even after eight days of symptom onset, suggesting a probable increased transmission risk for Delta strain even at this stage. There was no significant difference in expelling pattern between partial, full and un-vaccinated individuals suggesting similar transmission risk. We noted significantly more infections among vaccinated study patients and their household members than unvaccinated, probably due to increased duration from vaccination and/or increased risk behaviour upon vaccination due to lower perceived threat. This study provides biological evidence for possible continued transmission of the Delta strain even with vaccination, emphasizing the need to continue COVID-19 appropriate behaviour. The study also indicates that the mask method may be useful for screening future vaccine candidates, therapeutics or interventions for their ability to block transmission.
Recurrent SARS-CoV-2 Mutations in Immunodeficient Patients
Authors: Wilkinson Sam AJ , Richter Alex , Casey Anna , Osman Husam , Mirza Jeremy D , Stockton Joanne , Quick Josh , Ratcliffe Liz , Sparks Natalie , Cumley Nicola , Poplawski Radoslaw , Nicholls Sam , Kele Beatrix , Harris Kathryn ,   The COVID-19 Genomics UK (COG-UK) consortium, Peacock Thomas P , Loman Nicholas J 
Published: March 2022

AbstractLong-term SARS-CoV-2 infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COG-UK dataset. The spike gene receptor binding domain (RBD) and N-terminal domains (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, - T30I was determined to be the most recurrent frequently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation.There is an apparent selective pressure for mutations which aid intra-host transmission or persistence which are often different to mutations which aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted.
Cell-specific regulation of gene expression using splicing-dependent frameshifting
Authors: Ling Jonathan P. , Bygrave Alexei M. , Santiago Clayton P. , Carmen-Orozco Rogger P. , Trinh Vickie , Yu Minzhong , Li Yini , Han Jeong , Taneja Kamil , Liu Ying , Dongmo Rochinelle , Babola Travis A. , Parker Patrick , Jiang Lizhi , Leavey Patrick J. , Smith Jennifer J. , Vistein Rachel , Gimmen Megan Y. , Dubner Benjamin , Helmenstine Eric , Teodorescu Patric , Karantanos Theodore , Ghiaur Gabriel , Kanold Patrick O. , Bergles Dwight , Langmead Ben , Sun Shuying , Nielsen Kristina J. , Peachey Neal , Singh Mandeep S. , Dalton W. Brian , Rajaii Fatemeh , Huganir Richard L. , Blackshaw Seth 
Published: March 2022

AbstractPrecise and reliable cell-specific gene delivery remains technically challenging. Here we report a splicing-based approach for controlling gene expression whereby separate translational reading frames are coupled to the inclusion or exclusion of cell-specific alternative exons. Candidate exons are identified by analyzing thousands of publicly available RNA sequencing datasets and filtering by cell specificity, sequence conservation, and local intron length. This method, which we denote splicing-linked expression design (SLED), can be combined in a Boolean manner with existing techniques such as minipromoters and viral capsids. SLED vectors can leverage the strong expression of constitutive promoters, without sacrificing precision, by decoupling the tradeoff between promoter strength and selectivity. We generated SLED vectors to selectively target all neurons, photoreceptors, or excitatory neurons, and demonstrated that specificity was retainedin vivowhen delivered using AAVs. We further demonstrated the utility of SLED by creating what would otherwise be unobtainable research tools, specifically a GluA2 flip/flop reporter and a dual excitatory/inhibitory neuronal calcium indicator. Finally, we show the translational potential of SLED by rescuing photoreceptor degeneration inPrph2rds/rdsmice and by developing an oncolytic vector that can selectively induce apoptosis in SF3B1 mutant cancer cells. The flexibility of SLED technology enables new avenues for basic and translational research.
The 3D structure of lipidic fibrils of α-synuclein
Authors: Frieg Benedikt , Antonschmidt Leif , Dienemann Christian , Geraets James A. , Najbauer Eszter E. , Matthes Dirk , de Groot Bert L. , Andreas Loren B. , Becker Stefan , Griesinger Christian , Schröder Gunnar F. 
Published: March 2022

Abstractα-synuclein (αSyn) is abundant in neurons, but its misfolding and abnormal fibrillization are associated with severe neurodegenerative diseases. Although interactions between αSyn and phospholipid membranes are relevant during αSyn fibril assembly, insights into the interactions of αSyn fibrils with phospholipids have remained elusive. Here, we present six novel polymorphic atomic structures of αSyn fibrils aggregated in the presence of phospholipids. The structures reveal that phospholipids favor a novel protofilament fold, mediate an unusual arrangement of protofilaments, and fill the central cavities between the protofilaments. These findings provide a structural rationale for fibril-induced lipid extraction, a mechanism likely to be involved in the development of α-synucleinopathies.
Characterizing circadian connectome ofO. tenuiflorumusing an integrated network theoretic framework
Authors: Singh Vikram , Singh Vikram 
Published: March 2022

AbstractOcimum tenuiflorum(Tulsi) is among the most valuable medicinal plants as almost every part of this herb and the essential oil it produces possess pharmaceutical properties that have been utilized since ancient times to cure a large number of diseases. Like in other plants, circadian clock in Tulsi regulate important physiological processes like growth, development, defenceetc. by anticipating environmental cues. In the present work, identification and characterization of core circadian clock and clock associated proteins in Tulsi genome is reported. We mined 24 core clock (CC) proteins in 56 template plant genomes to build their hidden Markov models (HMMs). These HMMs were used to identify 24 core clock proteins inO. tenuiflorumwhich were further subjected to functional annotation. A hybrid network theoretic methodology comprising of random walk with restart (RWR) and graphlet degree vectors (GDV) was implemented to explore the local topology of the interologous, Tulsi protein interaction network (TulsiPIN) and mine CC associated raw candidate proteins. Statistical and biological significance of the raw candidates was determined using permutation and enrichment tests. A total of 70 putative CC associated proteins were identified which were further subjected to functional annotation.
Peptidoglycan recognition protein S2 is crucial for activation the Toll pathway against Israeli acute paralysis virus infection in honey bee Apis mellifera
Authors: Deng Yanchun , Yang Sa , Zhao Hongxia , Luo Ji , Lu Zhiqiang , Hou Chunsheng 
Published: March 2022

AbstractAlthough honey bee responses to pathogens have been systematically described in the past decades, antiviral signalling pathways mechanisms are not thoroughly characterized. To decipher direct antiviral roles of an immune pathway, we firstly used the infectious clone of Israeli acute paralysis virus (IAPV) to screen 42 immune genes involved in mTOR, MAPK, Toll, Endocytosis, Jak-STAT pathway and homeobox protein, heat shock protein, as well as antimicrobial peptides (AMPs), and found that Toll pathway was a potential predominant immune pathway in Apis mellifera. Consistent with this, only dsRNA-PGRP-S2 treated A. mellifera significantly exhibited impaired activation of Toll pathway, promoting susceptibility to the IAPV infection. Finally, immunofluorescence results confirmed that the Toll pathway was initiated by peptidoglycan recognition protein S2 (PGRP-S2) interacting with Toll protein. Co-immunoprecipitation findings also further preliminarily confirmed PGRP-S2 directly interacting with viral capsid protein IAPV-VP3 to induce the activation of the Toll pathway in A. mellifera. These findings highlight that the Toll pathway is demanded efficient inhibitions of IAPV replication as a specific antiviral pathway in A. mellifera, and PGRP-S2, acting as a pattern recognition receptor, could be a new approach for control of the viral disease.Author summaryHoney bee viruses, particularly IAPV, had been implicated in the colony decline with a global distribution resulting in insufficient pollination services. However, little is known about the antiviral mechanism of honey bee. In this study, we found that the Toll pathway was required for A. mellifera against IAPV infection and initiated by PGRP-S2. We also confirmed that dsRNA-PGRP-S2 treated A. mellifera exhibited impaired Toll pathway activation and promoted susceptibility to the IAPV infection. As a result, we employed co-immunoprecipitation technique to identify the interaction between the PGRP-S2 with Toll. Moreover, it was found the PGRP-S2 directly recognized IAPV-VP3 to activate the immune pathway against IAPV infection. Our work provides novel evidence that honey bees own a specific antiviral immune pathway and suggests that targeting PGRP-S2 could be a new approach for controlling the viral disease.
Effects of Sanhuang plaster on expression of MyD88, TRAF6, MIP-1β and IL-23 in rats infected by MRSA
Authors: Pan Haibang , Chen Qian , Fu Qi , Wang Tianming , Li Xiaoli , Li Richeng , Liu Mei , Guo Tiankang 
Published: March 2022

AbstractObjective: To investigate the effects of Sanhuang plaster on expression of myeloid differentiation factor 88 (MyD88), tumor necrosis factor receptor-related factor 6 (TRAF6), macrophage inflammatory protein-lβ (MIP-1β) and its mediated cytokine interleukin-23 (IL-23) in soft tissues of rats infected by methicillin-resistant Staphylococcus aureus (MRSA). Methods: Ninety-six healthy rats were randomly divided into normal control group, model control group, Mupirocin group, high, medium and low dose groups of Sanhuang plaster, with 16 rats in each group. MRSA bacterial liquid was used to make skin and soft tissue infection models. The rats in the normal control group and the model control group were not given any treatment measures. The high, medium, and low dose groups of Sanhuang plaster were given to the affected area with Sanhuang plaster, and the Mupirocin group was given to the affected area for treatment for 10 days. The wound pathological changes were observed. The levels of MIP-1β and IL-23 in serum and infected tissues of rats in each group were measured by ELISA. The mRNA expressions of MyD88, TRAF6, MIP-lβ and IL-23 were measured by Quantitative Real-time PCR, and Western blot was used to measure MyD88 and TRAF6 protein expression. Results: Compared with the model control group, the general condition of the Sanhuang plaster groups was significantly improved, and the pathological damage was reduced. The MIP-1β and IL-23 levels in the serum and infected tissues of the high dose group of Sanhuang plaster, the mRNA expressions of MyD88, TRAF6, MIP-1β and IL-23and in large and medium dose groups of Sanhuang plaster, and the protein expressions of Myd88 and TRAF6 in high dose of Sanhuang plaster were significantly decreased (p<0.05 or p<0.01). Conclusion: Sanhuang plaster may play a role in promoting healing of infected wounds by down-regulating the expression levels of MyD88, TRAF6, and MIP-1β, and inhibiting the abnormal secretion of cytokine IL-23.