bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polygonum Cillinervepolysaccharide inhibits Transmissible gastroenteritis virus by regulating microRNA-181
Authors: Duan Xueqin , Li Huicong , Tan Xuewen , Liu Nishang , Wang Xingchen , Zhang Weimin , Liu Yingqiu , Ma Wuren , Wu Yi , Ma Lin , Fan Yunpeng 
Published: November 2023

AbstractTransmissible gastroenteritis virus (TGEV) is an important pathogen that can cause changes in the expression profile of cell miRNA. In this study, PCP could treat piglets infected with TGEV by in vivo experiment. High-throughput sequencing technology was used to detect that 9 miRNAs were up-regulated and 17 miRNAs were down-regulated during PCP inhibition of TGEV infection in PK15 cells. Meanwhile, miR-181 was related to the target genes of key proteins of apoptosis pathway. PK15 was treated with different PCP after transfection of miR-181 mimic or inhibitor. Real-time PCR was used to detect the effect of TGEV replication, electron microscopy, TEM and Hoechst fluorescence staining were used to detect the biological function of the treated cells, and western blot (WB) was used to detect the expression of key signaling factors cyt C, caspase 9 and P53 in the apoptotic signaling pathway. The results showed that compared with the control group, 250 μg/mL PCP significantly inhibited the replication of TGEV gRNA and gene N (P< 0.01). PK15 cells in PCP groups (250 and 125 μg/mL) had uniform cell morphology and a small number of floating cells by microscopic, no typical virus structure was observed in 250 μg/mL PCP group under TEM, and apoptosis staining showed that 250 μg/mL PCP significantly reduced the number of apoptotic cells. PCP may inhibit TGEV-induced apoptosis through Caspase-dependent mitochondrial pathway after transfection of miR-181. The above results provided a theoretical basis for further research on the mechanism of PCP anti-TGEV.
Novel hypervariable erythrocyte surface expressed recombinant proteins show promise as serological markers of exposure toPlasmodium falciparuminfection
Authors: Vasileva Hristina , Chopo-Pizarro Ana , Ooko Michael , Dumont Elin , Wu Lindsey , Ssewanyana Isaac , Last Anna , Tetteh Kevin K.A. 
Published: November 2023

AbstractMalaria caused byPlasmodium spp. leads to significant morbidity and mortality, particularly in Sub-Saharan African countries withPlasmodium falciparumbeing the predominant infectious species. The pathogenesis ofP. falciparumdepends on multiple host and parasitic factors, one of which is the evasion of host immune response due to antigenic variability during the blood stage of infection. The understudied infected erythrocyte expressed protein families STEVOR and RIFIN characterize with antigenic hypervariability and are associated with clinical outcome of the infection and protective acquired immunity based on their topology and localization. We have used two molecular tag methods for successful expression of members of STEVOR and RIFIN protein families as recombinant proteins inE. coliexpression system. We have further established the antigenicity of those recombinants and have used Ugandan cohort samples with variousP. falciparuminfectious status and have compared the seropositivity rate to those recombinants in different age groups against already established short- and long-term markers of infection. We have demonstrated age-dependent immunity acquisition against the tested recombinants, and we have suggested the potential use of STEVOR and RIFIN recombinants as novel markers ofP. falciparuminfection in serosurveillance. Due to the hypervariability of those protein members we propose that further, more extensive research using a library of expressed variants is needed to strengthen the conclusions made in this study.
Replication poison treated BRCA1-deficient breast cancers are prone to MRE11 over-resection resulting in single strand DNA accumulation and mitotic catastrophe
Authors: Tabet Imene , Orhan Esin , Candiello Ermes , Fenou Lise , Velazquez Carolina , Orsetti Beatrice , Rodier Geneviève , Jacot William , Ribeyre Cyril , Sardet Claude , Theillet Charles 
Published: November 2023

AbstractBRCA1, BRCA2 and RAD51, key players of homologous recombination (HR) repair, are also involved in stalled DNA replication fork protection and repair. BRCA1-deficiency is encountered in 25% of Triple Negative Breast Cancer (TNBC). Here we investigated the sensitivity ofBRCA1-deficient TNBC cell models to gemcitabine a frequently used replication poison that does not alter DNA structure. We show that BRCA1-deficient models, in contrast to their isogenicBRCA1-proficient counterparts, are superiorly sensitive to gemcitabine, accumulate massive levels of single strand DNA (ssDNA), in absence of RPA and RAD51 signals and elevated double strand break (DSB) numbers leading to cell death.Remarkably, ssDNA accumulation in gemcitabine-treated BRCA1-deficient cells was strongly diminished by the MRE11 inhibitor mirin, while it did not affect ssDNA levels resulting from PARP inhibitor olaparib treatment. The central role of MRE11 DNA resection strongly suggested that replication fork reversal may be important in response to replication poisoning by gemcitabine in BRCA1-deficient models. Furthermore, we demonstrate that gemcitabine-treatedBRCA1-deficient cells showing massive ssDNA accumulation slipped into mitosis and produced mitotic bridges and micronuclei (MN) showing strong BrdU and γH2AX staining. Noticeably these BrdU-positive MN and DNA bridges triggered cGAS sensing.Our data, thus, strongly suggest that gemcitabine treatment could be beneficial inBRCA1-deficient TNBC both in terms of cancer cell death, but possibly as well in terms of antitumor immune response.
Deployment of aVibrio choleraeordered transposon mutant library in a quorum-competent genetic background
Authors: Grant Nkrumah A. , Donkor Gracious Yoofi , Sontz Jordan T. , Soto William , Waters Christopher M. 
Published: November 2023

AbstractVibrio cholerae, the causative agent of cholera, has sparked seven pandemics in recent centuries, with the current one being the most prolonged.V. cholerae’spathogenesis hinges on its ability to switch between low and high cell density gene regulatory states, enabling transmission between host and the environment. Previously, a transposon mutant library forV. choleraewas created to support investigations aimed toward uncovering the genetic determinants of its pathogenesis. However, subsequent sequencing uncovered a mutation in the geneluxOof the parent strain, rendering mutants unable to exhibit high cell density behaviors. In this study, we used chitin-independent natural transformation to move transposon insertions from these low cell density mutants into a wildtype genomic background. Library transfer was aided by a novel gDNA extraction we developed using thymol, which also showed high lysis-specificity forVibrio. The resulting Grant Library comprises 3,102 unique transposon mutants, covering 79.8% ofV. cholerae’sopen reading frames. Whole genome sequencing of randomly selected mutants demonstrates 100% precision in transposon transfer to cognate genomic positions of the recipient strain. Notably, in no instance did theluxOmutation transfer into the wildtype background. Our research uncovered density-dependent epistasis in growth on inosine, an immunomodulatory metabolite secreted by gut bacteria that is implicated in enhancing gut barrier functions. Additionally, Grant Library mutants retain the plasmid that enables rapid, scarless genomic editing. In summary, the Grant Library reintroduces organismal relevant genetic contexts absent in the low cell density locked library equivalent.Significance StatementOrdered transposon mutant libraries are essential tools for catalyzing research by providing access to null mutants of all non-essential genes. Such a library was previously generated forVibrio cholerae, but whole genome sequencing revealed that this library was made using a parent strain that is unable to exhibit cell-cell communication known as quorum sensing. Here, we utilize natural competence combined with a novel, high-throughput genomic DNA extraction method to regenerate the signaling incompetentV. choleraeordered transposon mutant library in quorum sensing competent strain. Our library provides researchers with a powerful tool to understandV. choleraebiology within a genetic context that influences how it transitions from an environmentally benign organism to a disease-causing pathogen.
The N6-methyladenosine demethylase ALKBH5 regulates the hypoxic HBV transcriptome
Authors: Tsukuda Senko , Harris James M , Magri Andrea , Balfe Peter , Wing Peter AC , Siddiqui Aleem , McKeating Jane A 
Published: November 2023

AbstractChronic hepatitis B is a global health problem and current treatments only suppress hepatitis B virus (HBV) infection, highlighting the need for new curative treatments. Oxygen levels influence HBV replication and we previously reported that hypoxia inducible factors (HIFs) activate the basal core promoter to transcribe pre-genomic RNA. Application of a probe-enriched long-read sequencing method to map the HBV transcriptome showed an increased abundance of all viral RNAs under low oxygen or hypoxic conditions. Importantly, the hypoxic-associated increase in HBV transcripts was dependent on N6-methyladenosine (m6A) modifications and an m6A DRACH motif in the 5’ stem loop of pre-genomic RNA defined transcript half-life under hypoxic conditions. Given the essential role of m6A modifications in the viral transcriptome we assessed the oxygen-dependent expression of RNA demethylases and bio-informatic analysis of published single cell RNA-seq of murine liver showed an increased expression of the RNA demethylase ALKBH5 in the peri-central low oxygen region.In vitrostudies with a human hepatocyte derived HepG2 cell line showed increased ALKBH5 gene expression under hypoxic conditions. Silencing the demethylase reduced the levels of HBV pre-genomic RNA and host gene (CA9, NDRG1, VEGFA, BNIP3, FUT11, GAP and P4HA1) transcripts and this was mediated via reduced HIFα expression. In summary, our study highlights a previously unrecognized role for ALKBH5 in orchestrating viral and cellular transcriptional responses to low oxygen.Author SummaryOxygen levels influence HBV replication and hypoxia inducible factors (HIFs) activate HBV transcription. Long-read sequencing and mapping the HBV transcriptome showed an increased abundance of all viral RNAs under hypoxic conditions that was dependent on N6-methyladenosine modifications. Investigating the oxygen-dependent expression of RNA demethylases identified ALKBH5 as a hypoxic activated gene and silencing its expression showed a key role in regulating HBV and host gene expression under hypoxic conditions.
Bioremediation of Atrazine and its Metabolite Using Multiple Enzymes Delivered by aBacillus thuringiensisSpore Display System
Authors: Hsu Shu-Yu , Hsieh Hsin-Yeh , Stewart George C. , Lin Chung-Ho 
Published: November 2023

ABSTRACTAtrazine (ATR), a widely used herbicide in the United States, has contaminated ground and surface water. The persistence in the environment, the carcinogenic characteristic, and the endocrine disruption activity of ATR raises public health concerns. To provide a clean source of drinking water, it is imperative to remediate ATR and its metabolites without toxic by-products. A green technology,Bacillus thuringiensisspore-based display system, has been developed to express a high density of enzymes on the spore surface. TheB. thuringiensisspore can serve as a bioparticle to deliver enzymes to different environments and enhance the stability and shelf-life of enzymes expressed on their surface. A cluster of enzymes, AtzA, AtzB, AtzC, AtzD, AtzE, and AtzF, found inPseudomonas sp.strain ADP, remediates ATR to CO2and NH3in the degradation pathway. AtzA-bearing spores were generated, and they successfully demonstrated the capability of converting ATR to its metabolite, hydroxyatrazine (HA) [Hsiehet al.2020]. In this study, AtzB, a hydroxyatrazineN-ethylaminohydrolase that hydrolyzes HA toN-isopropylammelide (NiPA), was expressed on theBacillusspores by fusingatzBto the gene encoding the attachment domain of the BclA spore surface nap layer protein. The results showed that 1 mg AtzB-bearing spores degraded 50% of HA to NiPA in water within 12 hours. The Kmand Vmaxof AtzB-bearing spores with HA as a substrate were 25.28 µM and 1.26 nmole NiPA h-1mg-1spores, respectively. The optimal ratio of 1:2 for AtzA-bearing to AtzB-bearing spores was applied and successfully converted 90% ATR to NiPA in the water after 96 hours of incubation. The surface water with the addition of 34.5 nM (7.5 µg L-1) of ATR was treated with a combination of AtzA-bearing and AtzB-bearing spores in a 96-hour time course study. Over 80% of applied ATR in surface water was degraded and ATR concentration was below the United States Environmental Protection Agency maximum contaminant level, 13.8 nM (3 µg L-1) within 24 hours. At the end of 96 hours. ATR in surface water was completely converted to NiPA. We have successfully demonstrated the application of multienzyme bioremediation of ATR using theBacillusspore-based display system in the surface water in the laboratory.
Covalent Degrader of the Oncogenic Transcription Factor β-Catenin
Authors: Gowans Flor A. , Forte Nafsika , Hatcher Justin , Huang Oscar W. , Wang Yangzhi , Poblano Belen E. Altamirano , Wertz Ingrid E. , Nomura Daniel K. 
Published: November 2023

Abstractβ-catenin (CTNNB1) is an oncogenic transcription factor that is important in cell-cell adhesion and transcription of cell proliferation and survival genes that drives the pathogenesis of many different types of cancers. However, direct pharmacological targeting of CTNNB1 has remained challenging deeming this transcription factor as “undruggable.” Here, we have performed a screen with a library of cysteine-reactive covalent ligands to identify a monovalent degrader EN83 that depletes CTNNB1 in a ubiquitin-proteasome-dependent manner. We show that EN83 directly and covalently targets CTNNB1 through targeting four distinct cysteines within the armadillo repeat domain—C439, C466, C520, and C619—leading to a destabilization of CTNNB1. Using covalent chemoproteomic approaches, we show that EN83 directly engages CTNNB1 in cells with a moderate degree of selectivity. We further demonstrate that direct covalent targeting of three of these four cysteines--C466, C520, and C619--in cells contributes to CTNNB1 degradation in cells. We also demonstrate that EN83 can be further optimized to yield more potent CTNNB1 binders and degraders. Our results show that chemoproteomic approaches can be used to covalently target and degrade challenging transcription factors like CTNNB1 through a destabilization-mediated degradation.
Development ofCorynebacterium glutamicumas a monoterpene production platform
Authors: Luckie Bridget A. , Kashyap Meera , Pearson Allison N. , Chen Yan , Liu Yuzhong , Valencia Luis E. , Romero Alexander Carrillo , Hudson Graham A. , Tao Xavier B. , Wu Bryan , Petzold Christopher J. , Keasling Jay D. 
Published: November 2023

AbstractMonoterpenes are commonly known for their role in the flavors and fragrances industry and are also gaining attention for other uses like insect repellant and as potential renewable fuels for aviation.Corynebacterium glutamicum,a Generally Recognized as Safe microbe, has been a choice organism in industry for the annual million ton-scale bioproduction of amino acids for more than 50 years; however, efforts to produce monoterpenes inC. glutamicumhave remained relatively limited. In this study, we report a further expansion of theC. glutamicumbiosynthetic repertoire through the development and optimization of a mevalonate-based monoterpene platform. In the course of our plasmid design iterations, we increased flux through the mevalonate-based bypass pathway, measuring isoprenol production as a proxy for monoterpene precursor abundance and demonstrating the highest reported titers inC. glutamicumto date at nearly 1500 mg/L. Our designs also evaluated the effects of backbone, promoter, and GPP synthase homolog origin on monoterpene product titers. Monoterpene production was further improved by disrupting competing pathways for isoprenoid precursor supply and by implementing a biphasic production system to prevent volatilization. With this platform, we achieved 321.1 mg/L of geranoids, 723.6 mg/L of 1,8-cineole, and 227.8 mg/L of linalool. Furthermore, we determined thatC. glutamicumfirst oxidizes geraniol through an aldehyde intermediate before it is asymmetrically reduced to citronellol. Additionally, we demonstrate that the aldehyde reductase, AdhC, possesses additional substrate promiscuity for acyclic monoterpene aldehydes.HighlightsDesign of a mevalonate-based monoterpene production platform inC. glutamicumHighest production titers of geranoids, eucalyptol, and linalool reported inC. glutamicumto dateIdentification of citronellal as an intermediate in the reduction of geraniol to citronellol byC. glutamicum
Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator
Authors: Adeleye Samuel A. , Yadavalli Srujana S. 
Published: November 2023

AbstractIn many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners.Escherichia colicells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint particular residues in QueE that contribute distinctly to each of its functions – Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria likeSalmonella typhimuriumandKlebsiella pneumoniaealso cause filamentation in these organisms, but the more distant counterparts fromPseudomonas aeruginosaandBacillus subtilislack this ability. By comparative analysis ofE. coliQueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueE’s secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of “one gene, one enzyme, one function”, which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.Author SummaryIn stressful environments, proteins in many organisms can take on extra roles. WhenEscherichia colibacteria are exposed to antimicrobial compounds, the cell activates the PhoQ/PhoP signaling system, increasing the production of an enzyme called QueE. QueE is usually involved in the formation of queuosine (Q) tRNA modification. When cells make abundant QueE, it interacts with a vital division protein, FtsZ, disrupting division and causing elongation − a “moonlighting” function. Detailed study of QueE reveals specific regions involved in Q biosynthesis or cell division. QueE in organisms closely related toE. colialso has dual roles, while distant relatives are unifunctional. Comparative analysis identifies a uniqueE. coliQueE region regulating cell division. This study shows QueE’s versatility in linking and impacting distinct cellular processes such as RNA metabolism, protein translation, cell division, and stress response.
NK and NKT cells in the pathogenesis of Hidradenitis suppurativa: Novel therapeutic strategy through targeting of CD2
Authors: Kashyap Mahendra P. , Mishra Bharat , Sinha Rajesh , Jin Lin , Kumar Nilesh , Goliwas Kayla F. , Deshane Jessy , Elewski Boni E. , Elmets Craig A. , Athar Mohammad , Shahid Mukhtar M. , Raman Chander 
Published: November 2023

AbstractHidradenitis suppurativa (HS) is a chronic debilitating inflammatory skin disease with poorly understood pathogenesis. Single-cell RNAseq analysis of HS lesional and healthy individual skins revealed that NKT and NK cell populations were greatly expanded in HS, and they expressed elevated CD2, an activation receptor. Immunohistochemistry analyses confirmed significantly expanded numbers of CD2+ cells distributed throughout HS lesional tissue, and many co-expressed the NK marker, CD56. While CD4+ T cells were expanded in HS, CD8 T cells were rare. CD20+ B cells in HS were localized within tertiary follicle like structures. Immunofluorescence microscopy showed that NK cells (CD2+CD56dim) expressing perforin, granzymes A and B were enriched within the hyperplastic follicular epidermis and tunnels of HS and juxtaposed with apoptotic cells. In contrast, NKT cells (CD2+CD3+CD56bright) primarily expressed granzyme A and were associated with α-SMA expressing fibroblasts within the fibrotic regions of the hypodermis. Keratinocytes and fibroblasts expressed high levels of CD58 (CD2 ligand) and they interacted with CD2 expressing NKT and NK cells. The NKT/NK maturation and activating cytokines, IL-12, IL-15 and IL-18, were significantly elevated in HS. Inhibition of cognate CD2-CD58 interaction with blocking anti-CD2 mAb in HS skin organotypic cultures resulted in a profound reduction of the inflammatory gene signature and secretion of inflammatory cytokines and chemokines in the culture supernate. In summary, we show that a cellular network of heterogenous NKT and NK cell populations drives inflammation, tunnel formation and fibrosis in the pathogenesis of HS. Furthermore, CD2 blockade is a viable immunotherapeutic approach for the management of HS.
Mass media campaigns and the ‘file drawer problem’: a Delphi study of how to avoid campaign failure
Authors: Kite James , Thomas Margaret , Bellew Bill , Bauman Adrian , Grunseit Anne 
Published: November 2023

AbstractMass media campaigns are frequently used to address public health issues. Considering the considerable cost, there has been surprisingly little analysis of why campaigns sometimes fail. This study used a modified Delphi approach to explore the mechanisms that can lead to failure and to identify what can be done to avoid or overcome common mistakes in campaign planning, implementation, and evaluation. Through interviews and a survey with 28 public health social marketing and mass media campaign experts, we identified four systemic factors that drive success: long-term strategic thinking and commitment, understanding the campaign context, doing and learning from evaluation, and fostering strong relationships. The factors did not operate in isolation, rather good (or poor) execution in one area was likely to influence performance in another. The experts also emphasised that a change of political context could drastically affect one or more of the identified factors. Our analysis showed that campaign failures are not simply individuals making mistakes. Systemic issues throughout the planning, execution, and evaluation phases need to be addressed if campaign outcomes are to improve.