bluuebunny/crossref_metadata_2025_split huggingface dataset:
Malat1regulates female Th2 cell cytokine expression through controlling early differentiation and response to IL2
Authors: Gwynne Mags , West Katie A. , van Dongen Stijn , Kourtzelis Ioannis , Coverley Dawn , Teichmann Sarah A. , James Kylie R. , Hewitson James P. , Lagos Dimitris 
Published: October 2024

AbstractBeyond sex hormone and sex chromosome-driven mechanisms, little is known about cell intrinsic mediators of immune sexual dimorphism. We show thatMalat1is required for appropriate cytokine expression in female but not male Th2 cells.Malat1deficiency impairsin vitroTh2 differentiation of naïve CD4+T cells from female mice, characterised by transcriptome-wide effects and suppression of cytokine expression, particularly IL10. Mechanistically, naïve CD4+T cells fromMalat1−/−female mice demonstrate altered early activation kinetics, followed by impairment of the early differentiation gene expression programme, including up-regulation of an interferon responsive gene module. This is followed by suppression of IL2Rα and IL2Rγ expression and IL2-mediated differentiation. Male CD4+T cell activation and Th2 differentiation are not sensitive toMalat1loss due to stronger early activation, higher interferon responsive gene expression during early differentiation, maintenance of IL2Rα expression independently ofMalat1, and lower sensitivity to exogenous IL2 during late differentiation.In vivofemale, but not male,Malat1−/−mice demonstrate altered Th2 differentiation characterised by a reduction in IL10+Th2 cells in both lung and spleen following priming and challenge withSchistosoma mansonieggs, a model of lung type 2 inflammation. These findings revealMalat1as a determinant of immune sexual dimorphism.
Identifying simultaneous inhibition of riboflavin metabolism and MEK as a novel therapeutic strategy for pancreatic cancer
Authors: Ooshio Takako , Satoh Yusuke , Jiang Hui , Liu Tongwei , Fujii Kiyonaga , Ishikawa Takamasa , Igarashi Kaori , Saitoh Kaori , Kato Keiko , Mashima Tetsuo , Jin Shigeki , Matoba Kotaro , Mack Matthias , Osawa Tsuyoshi , Seimiya Hiroyuki , Soga Tomoyoshi , Sonoshita Masahiro 
Published: October 2024

AbstractPancreatic ductal adenocarcinoma (PDAC) remains a formidable challenge with a survival rate of approximately 10%, largely due to the lack of diagnostic and therapeutic options. To identify novel therapeutic targets for PDAC, we previously developed aDrosophila melanogastermodel, the ’4-hit’ fly, which mimics the alterations inKRAS,TP53,CDKN2A, andSMAD4genes observed in PDAC. Through whole-body genetic screening using the4-hitmodel, we identified riboflavin (RF) metabolism as a novel potential therapeutic target for PDAC. Additionally, transcript levels of four out of five genes that are involved in RF metabolism were elevated in human PDAC compared to non-tumor tissues. Roseoflavin (RoF), an antimetabolite of RF, resulted in a variety range of metabolic changes, decreased mitochondrial respiratory chain activity, and suppressed proliferation in cultured PDAC cells. Furthermore, the combination of RoF with the MEK inhibitor drug trametinib significantly suppressed the growth of human PDAC xenografts compared to either treatment alone. These findings underscore that dual targeting of RF metabolism and MEK represents a novel therapeutic strategy for PDAC.
Long-term warming inverts the relationship between ecosystem function and microbial resource acquisition
Authors: Shinfuku Melissa S. , DeAngelis Kristen M. 
Published: October 2024

AbstractSoil microbial traits drive ecosystem functions, which can explain the positive correlation between microbial functional diversity and ecosystem function. However, microbial adaptation to climate change related warming stress can shift microbial traits with direct implications for soil carbon cycling. Here, we investigated how long-term warming affects the relationship between microbial trait diversity and ecosystem function. Soils were sampled after 24 years of +5°C warming alongside unheated control soils from the Harvard Forest Long-Term Ecological Research site. Ecosystem function was estimated from six different enzyme activities and microbial biomass. Functional diversity was calculated from metatranscriptomics sequencing, where reads were assigned to yield, acquisition, or stress trait categories. We found that in organic horizon soils, warming decreased the richness of acquisition-related traits. In the mineral soils, we observed that heated soils exhibited a negative relationship with the richness of acquisition-related traits. These results suggest that microbial communities exposed to long-term warming are shifting away from a resource acquisition life history strategy.
3D Multiplexed Immunohistochemistry Using Opal-TSA Amplification for Enhanced Imaging of Pulmonary TB Lesions
Authors: Lata Suruchi , Yabaji Shivraj M. , O’Connell Aoife K , Gertje Hans P , Crossland Nicholas A , Kramnik Igor 
Published: October 2024

SummaryMycobacterium tuberculosishijacks the host immune system and persists for several years before the onset of active disease. Spatial characterization of epithelial compartments, immune cell populations and bacteria simultaneously within tissue specimens provide significant information about host pathogen interactions. Here, we present a protocol to detect multiple protein markers using Opal™-TSA conjugated fluorescent dyes in free floating 10% neutral buffered formalin fixed thick tissue sections (50-100 μm), with minimal additional tissue processing not requiring specialized equipment. Use of thick sections provides more information as compared to classic thin microtomy sections (3-10 μm), including the capacity for Z stacking and three-dimensional image rendering. Importantly, reduced tissue processing of samples with this method preserves endogenous fluorescent reporter signal. Use of Opal™-TSA conjugated fluorescent dyes enhances the sensitivity of low expressing proteins and supports the use of primary antibodies raised in the same species.Before you beginThis protocol describes the specific use of Mtb infected mouse lungs, but is applicable to any tissue type and species of origin.Institutional permissionsObtain institutional permission to perform animal studies and collect tissues under an approved Institutional Animal Care and Use Committee (IACUC) or Institutional Review Board protocol. Our protocol was approved by Boston University’s Institutional Animal Care and Use Committee (IACUC protocol number PROTO201800218).MiceB6J.C3-Sst1C3HeB/FejKrmn and B6. Sst1S, ifnb-YFP mice were developed in our laboratory (available from MMRRC stock # 043908-UNC).HighlightsCompatible with Opal™-TSA conjugated fluorescent dyes resulting in enhanced signal sensitivity with low background noiseReduced tissue processing preserves endogenous fluorescent reporter signalsCompatible with primary antibodies raised in the same speciesDoesn’t require specialized automated instrumentsGraphical Abstract
Vibrio mimicuscarrying the Type III Secretion System 2 (T3SS2) and TDH toxin ofVibrio parahaemolyticusin an integrative conjugative element context
Authors: Morgado Sergio Mascarenhas , da Fonseca Erica Lourenço , Paulo Vicente Ana Carolina 
Published: October 2024

AbstractObjectivesIdentify possible virulence factors in the genomes ofVibrio mimicusthat may be determinants of diarrheal cases/outbreaks.MethodsAllV. mimicusgenomes from Genbank were retrieved and the virulome was searched with Abricate using the VFDB database. Genomic islands (GIs) and integrative conjugative elements (ICEs) were identified using IslandViewer and ICEberg, respectively.ResultsFive ctx-negativeV. mimicusgenomes carrying the Type III Secretion System 2 (T3SS2) and the TDH/TRH toxin fromVibrio parahaemolyticuswere identified. The T3SS-positive genomes presented the phylotypes T3SS2α and T3SS2β and formed two clusters and one singleton throughout theV. mimicusphylogeny. Genomes carrying T3SS2α and T3SS2β were associated with thetdhandtrhgenes, respectively. Furthermore, genomic analyses characterized an integrative conjugative element (ICE) with a size of ∼150 kb carrying bothV. parahaemolyticusvirulence determinants.ConclusionsIn addition to looking for cholera toxin genes inV. mimicuscases/outbreaks, it is important to considerV. parahaemolyticustoxins such as TDH and TRH. Furthermore, an ICE was identified and characterized inV. mimicus, being associated with T3SS2 and the TDH toxin, which is worrying, as it can disseminate these virulence factors among Vibrio spp.
African origin haplotype protective for Alzheimer’s disease inAPOEε4 carriers: exploring potential mechanisms
Authors: Bertholim-Nasciben Luciana , Nuytemans Karen , Van Booven Derek , Rajabli Farid , Moura Sofia , Ramirez Aura M. , Dykxhoorn Derek M. , Wang Liyong , Scott William K. , Davis David A. , Vontell Regina T. , McInerney Katalina F. , Cuccaro Michael L. , Byrd Goldie S. , Haines Jonathan L. , Gearing Marla , Adams Larry D. , Pericak-Vance Margaret A. ,   ADSP, Young Juan I. , Griswold Anthony J. , Vance Jeffery M. 
Published: October 2024

AbstractAPOEε4 is the strongest genetic risk factor for Alzheimer’s disease (AD) with approximately 50% of AD patients carrying at least oneAPOEε4 allele. Our group identified a protective interaction betweenAPOEε4 with the African-specific A allele of rs10423769, which reduces the AD risk effect ofAPOEε4 homozygotes by approximately 75%. The protective variant lies 2Mb fromAPOEin a region of segmental duplications (SD) of chromosome 19 containing a cluster of pregnancy specific beta-1 glycoprotein genes (PSGs) and a long non-coding RNA. Using both short and long read sequencing, we demonstrate that rs10423769_A allele lies within a unique single haplotype inside this region of segmental duplication. We identified the protective haplotype in all African ancestry populations studied, including both West and East Africans, suggesting the variant has an old origin. Long-read sequencing identified both structural and DNA methylation differences between the protective rs10423769_A allele and non-protective haplotypes. An expanded variable number tandem repeat (VNTR) containing multiple MEF2 family transcription factor binding motifs was found associated with the protective haplotype (p-value = 2.9e-10). These findings provide novel insights into the mechanisms of this African-origin protective variant for AD inAPOEε4 carriers and supports the importance of including all ancestries in AD research.
A sequence-specific RNA acetylation catalyst
Authors: Thalalla Gamage Supuni , Howpay Manage Shereen , Sas-Chen Aldema , Nir Ronit , Burkhart Brett W. , Jhulki Isita , Link Courtney N. , Penikalapati Manini S. , Jones Jane E. , Iyer Lakshminarayan M. , Aravind L. , Santangelo Thomas J. , Schwartz Schraga , Meier Jordan L. 
Published: October 2024

AbstractN4-acetylcytidine (ac4C) is a ubiquitous RNA modification incorporated by cytidine acetyltransferase enzymes. Here, we report the biochemical characterization ofThermococcus kodakarensisNat10 (TkNat10), an RNA acetyltransferase involved in archaeal thermotolerance. We demonstrate that TkNat10’s catalytic activity is critical forT. kodakarensisfitness at elevated temperatures. Unlike eukaryotic homologs, TkNat10 exhibits robust stand-alone activity, modifying diverse RNA substrates in a temperature, ATP, and acetyl-CoA-dependent manner. Transcriptome-wide analysis reveals TkNat10 preferentially modifies unstructured RNAs containing a 5’-CCG-3’ consensus sequence. Using a high-throughput mutagenesis approach, we define sequence and structural determinants of TkNat10 substrate recognition. We find TkNat10 can be engineered to use non-native acyl-CoA donors, providing insight into its cofactor specificity. Finally, we demonstrate TkNat10’s utility for site-specific acetylation of RNA oligonucleotides, enabling analysis of ac4C-dependent RNA-protein interactions. Our findings establish a framework for understanding archaeal RNA acetylation and a new tool for studying the functional consequences of ac4C in diverse RNA contexts.
Crosstalk between three CRISPR-Cas types enables primed type VI-A adaptation inListeria seeligeri
Authors: Margolis Shally R. , Meeske Alexander J. 
Published: October 2024

SummaryCRISPR-Cas systems confer adaptive immunity to their prokaryotic hosts through the process of adaptation, where sequences are captured from foreign nucleic acids and integrated as spacers in the CRISPR array, and thereby enable crRNA-guided interference against new threats. While the Cas1-2 integrase is critical for adaptation, it is absent from many CRISPR-Cas loci, rendering the mechanism of spacer acquisition unclear for these systems. Here we show that the RNA-targeting type VI-A CRISPR system ofListeria seeligeriacquires spacers from DNA substrates through the action of a promiscuous Cas1-2 integrase encoded by a co-occurring type II-C system, in a transcription-independent manner. We further demonstrate that the type II-C integration complex is strongly stimulated by preexisting spacers in a third CRISPR system (type I-B) which imperfectly match phage targets and prime type VI-A adaptation. Altogether, our results reveal an unprecedented degree of communication among CRISPR-Cas loci encoded by a single organism.
Stoichiometry of HIV-1 Envelope Glycoprotein Protomers with Changes That Stabilize or Destabilize the Pretriggered Conformation
Authors: Zhang Zhiqing , Anang Saumya , Wang Qian , Nguyen Hanh T. , Chen Hung-Ching , Chiu Ta-Jung , Yang Derek , Smith Amos B. , Sodroski Joseph G. 
Published: October 2024

ABSTRACTDuring human immunodeficiency virus (HIV-1) entry into host cells, binding to the receptors, CD4 and CCR5/CXCR4, triggers conformational changes in the metastable envelope glycoprotein (Env) trimer ((gp120-gp41)3). CD4 binding induces Env to make transitions from its pretriggered conformation (PTC) to more “open” conformations that are sensitive to inhibition by antibodies, CD4-mimetic compounds (CD4mcs) and exposure to cold. Changes in functional membrane Envs have been identified that either stabilize or destabilize the PTC. Here, we investigate the stoichiometric requirements for the PTC-stabilizing and -destabilizing changes in the Env protomers. To this end, we generated viruses bearing Envs with mixed protomers exhibiting different degrees of PTC stability and determined the sensitivity of the viruses to cold (0°C) and, in some cases, to a CD4mc. The number of stabilized Env protomers required to achieve stabilization of the PTC was inversely related to the degree of PTC stabilization that resulted from the introduced Env change. For strongly stabilizing Env changes, modification of a single protomer was sufficient to achieve PTC stabilization; given adequate stability, the modified protomer can apparently constrain the conformation of the other two protomers to maintain the PTC. Weakly stabilizing Env changes needed to be present in all three protomers to achieve efficient stabilization of the PTC. In many cases, the PTC was disrupted when destabilizing changes were present in only a single protomer. These complementary results suggest that conformational symmetry among the protomers of the functional Env trimer is conducive to the integrity of the PTC.IMPORTANCEThe human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer consists of three protomers. In response to receptor binding, the flexible Env changes its conformation to mediate virus entry into host cells. The shape-shifting ability of Env also contributes to HIV-1’s capacity to evade the host immune system. The pretriggered (State-1) conformation (PTC) of Env is an important target for virus entry inhibitors and host antibodies, but is unstable and therefore incompletely characterized. Changes in Env amino acids that either stabilize or destabilize the PTC have been identified. Here, we define how many Env protomers need to be modified by these changes to achieve stabilization or destabilization of the PTC. These results can guide the placement of changes in the HIV-1 Env protomers to control the movement of the Env trimer from the PTC, allowing better characterization of this elusive conformation and testing of its utility in vaccines.
The life history traits of phages in a cocktail determine coinfection dynamics and efficacy
Authors: Khan Ruqaiyah , Chaudhari Harshali V. , Inamdar Mandar M. , Kondabagil Kiran 
Published: October 2024

AbstractPhage cocktails are preferred over single phages for efficacious and broader-spectrum therapy. An ideal phage cocktail should have a minimum number of phages with efficient infection kinetics and delay the emergence of resistance in bacterial populations. This study examined population dynamics of the common host and combinations of two phages (N4, KKE5P, and Ec_YwIITB1) through experimental and modeling approaches to gaining insights into how phage life history traits influence the outcome of infection in the short-term of approximately an infection cycle, and whether it is informative for developing efficacious cocktails. We tested the killing efficacy of a cocktail containing two divergent phages (N4 and Ec_YwIITB1) with similar adsorption rates but differed in their latency period. Because of the shorter latency period, phage N4 dominated under all conditions tested. The cocktail essentially behaves as a single phage. When two phages (N4 and KKE5P), with similar adsorption rates and latency periods but targeted different host receptors were used, it not only resulted in the efficient replication of both phages but also improved the suppression of the emergence of resistance when compared to the N4 and Ec_YwIITB1 combination, thus behaving like an ideal cocktail. The ODE-based mathematical model demonstrated predictive capabilities consistent with experimental observations and offered insights into infection dynamics. The model may aid in phage selection and optimizing cocktail formulation based on phage life history traits. This study highlights the need for thorough characterization of phage growth parameters and informed combinations of phages, as random combinations could lead to undesirable outcomes.
A randomized controlled trial of the effectiveness of a community-based rabies vaccination strategy
Authors: Lankester Felix , Lugelo Ahmed , Changalucha Joel , Anderson Danni , Duamor Christian Tetteh , Czupryna Anna , Lushasi Kennedy , Ferguson Elaine , Swai Emmanuel S. , Nonga Hezron , Sambo Maganga , Cleaveland Sarah , Wyke Sally , Johnson Paul C. D. , Hampson Katie 
Published: October 2024

SummaryBackgroundApproximately 60,000 people die from dog-mediated rabies annually. Low and heterogeneous coverage reduces the effectiveness of dog vaccination campaigns that can eliminate rabies. Campaigns typically involve teams travelling annually to villages to deliver cold chain stored vaccines from centralized headquarters. Thermotolerant vaccines enable novel decentralized delivery of locally-stored vaccines by communities throughout the year. We compared the effectiveness of annual team-based versus continuous community-based dog vaccination strategies.MethodsWe conducted a cluster randomized controlled trial across Mara region, Tanzania. Trial clusters were administrative wards (112, on average four villages each). For the team-based arm vaccinators hosted annual static-point clinics, whilst for the community-based arm, a ward-based animal health officer with a village community leader managed vaccinations using vaccines stored within the ward. We measured vaccination coverage, the primary outcome, twice annually per cluster (month 1 and 11) through household surveys over three years (November 2020 to October 2023) and examined spatial and temporal coverage variations as secondary outcomes.FindingsCommunity-based delivery achieved significantly higher coverage (49-62%) than team-based delivery (22-46%), and consistently exceeded the critical threshold for herd immunity (40%), Odds ratio (OR): 1.48-3.49. The lower less uniform coverage achieved through team-based delivery had a higher monthly probability of falling below the critical threshold (0.6, 95% CI: 0.38-0.81) vs 0.18 (95% CI: 0.04-0.40). Greater declines in coverage over the year were recorded in the team-based arm compared to the community-basedConclusionCommunity-based mass dog vaccination achieves higher more consistent coverage than team-based delivery across settings typical of many sub-Saharan African countries. This approach could play an important role in national rabies elimination programmes aiming to end human rabies deaths by 2030 as part of the global ‘zero by 30’ strategy.FundingDepartment of Health and Human Services of the National Institutes of Health (R01AI141712), Wellcome Trust (207569/Z/17/Z, 224520/Z/21/Z) and MSD Animal Health. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Small-Molecule Modulators of Lipid Raft Stability and Protein-Raft Partitioning
Authors: Stefanski Katherine M. , Huang Hui , Luu Dustin D. , Hutchison James M. , Saksena Nilabh , Fisch Alexander J. , Hasaka Thomas P. , Bauer Joshua A. , Kenworthy Anne K. , Van Horn Wade D. , Sanders Charles R. 
Published: October 2024

AbstractDevelopment of an understanding of membrane nanodomains colloquially known as “lipid rafts” has been hindered by a lack of pharmacological tools to manipulate rafts and protein affinity for rafts. We screened 24,000 small molecules for modulators of the affinity of peripheral myelin protein 22 (PMP22) for rafts in giant plasma membrane vesicles (GPMVs). Hits were counter-screened against another raft protein, MAL, and tested for impact on raft, leading to two classes of compounds. Class I molecules altered the raft affinity of PMP22 and MAL and also reduced raft formation in a protein-dependent manner. Class II molecules modulated raft formation in a protein-independent manner. This suggests independent forces work collectively to stabilize lipid rafts. Both classes of compounds altered membrane fluidity in cells and modulated TRPM8 channel function. These compounds provide new tools for probing lipid raft function in cells and for furthering our understanding of raft biophysics.TeaserCompounds have been discovered that modulate the affinity of membrane proteins for lipid rafts as well as raft formation.
The effects ofCDC45mutations on DNA replication and genome stability
Authors: Denkiewicz-Kruk Milena , Chaudhry Deepali , Krasilia Alina , Jedrychowska Malgorzata , Fijalkowska Iwona J. , Dmowski Michal 
Published: October 2024

AbstractCdc45 is a non-catalytic subunit of the CMG helicase complex and is recruited to the autonomously replicating sequence at the onset of DNA replication. Cdc45 protein is required for the initiation of the DNA replication process as well as for the nascent DNA strand synthesis. It interacts with Mcm2 and Psf1 elements of CMG helicase, as well as with Sld3, and initiation factor, and Pol2, the catalytic subunit of DNA polymerase epsilon (Pol ε). In this study, we analyzed the effects of amino acid substitutions in Cdc45 regions involved in the interaction of this protein with Mcm2-7 (Cdc45-1), Psf1 (Cdc45-26), and Sld3 (Cdc45-25, Cdc45-35). We found that mutations inCDC45result in defective DNA replication. At the restrictive temperature, mutant cells are unable to initiate DNA replication, while in permissive conditions, they demonstrate DNA synthesis delay. Moreover, we observed increased mutation rates, mainly dependent on DNA polymerase zeta (Pol ζ), as well as increased incidence of replication errors. These findings contribute to our understanding of Cdc45’s function in eukaryotic cells. Changes in the cell functioning observed in this study, related to the defect in Cdc45 function, may be helpful in understanding some diseases associated withCDC45.