bluuebunny/crossref_metadata_2025_split huggingface dataset:
Set2 and H3K36 regulate theDrosophilamale X chromosome in a context-specific manner, independent from MSL complex spreading
Authors: Salzler Harmony R. , Vandadi Vasudha , Matera A. Gregory 
Published: May 2024

AbstractDosage compensation inDrosophilainvolves upregulating male X-genes two-fold. This process is carried out by the MSL (male-specific lethal) complex, which binds high-affinity sites and spreads to surrounding genes. Current models of MSL spreading focus on interactions of MSL3 (male-specific lethal 3) with histone marks; in particular, Set2- dependent H3 lysine-36 trimethylation (H3K36me3). However, Set2 might affect DC via another target, or there could be redundancy between canonical H3.2 and variant H3.3 histones. Further, it is difficult to parse male-specific effects from those that are simply X- specific. To discriminate among these possibilities, we employed genomic approaches inH3K36(residue) andSet2(writer) mutants. The results confirm a role for Set2 in X-gene regulation, but show that expression trends in males are often mirrored in females. Instead of global male-specific reduction of X-genes inSet2/H3K36mutants, the effects were heterogeneous. We identified cohorts of genes whose expression was significantly altered following loss of H3K36 or Set2, but the changes were in opposite directions, suggesting that H3K36me states have reciprocal functions. In contrast toH4K16Rcontrols, analysis of combinedH3.2K36R/H3.3K36Rmutants neither showed consistent reduction in X-gene expression, nor any correlation with MSL3 binding. Examination of other developmental stages/tissues revealed additional layers of context-dependence. Our studies implicate BEAF-32 and other insulator proteins in Set2/H3K36-dependent regulation. Overall, the data are inconsistent with the prevailing model wherein H3K36me3 directly recruits the MSL complex. We propose that Set2 and H3K36 support DC indirectly, via processes that are utilized by MSL but common to both sexes.
Topoisomerase I is an Evolutionarily Conserved Key Regulator for Satellite DNA Transcription
Authors: Teng Zhen , Yang Lu , Zhang Qian , Chen Yujue , Wang Xianfeng , Zheng Yiran , Tian Aiguo , Tian Di , Lin Zhen , Deng Wu-Min , Liu Hong 
Published: May 2024

AbstractRepetitive satellite DNAs, divergent in nucleic-acid sequence and size across eukaryotes, provide a physical site for centromere assembly to orchestrate chromosome segregation during the cell cycle. These non-coding DNAs are transcribed by RNA polymerase (RNAP) II and the transcription has been shown to play a role in chromosome segregation, but a little is known about the regulation of centromeric transcription, especially in higher organisms with tandemly-repeated-DNA-sequence centromeres. Using RNA interference knockdown, chemical inhibition and AID/IAA degradation, we show that Topoisomerase I (TopI), not TopII, promotes the transcription of α-satellite DNAs, the main type of satellite on centromeres in human cells. Mechanistically, TopI localizes to centromeres, binds RNAP II and facilitates RNAP II elongation on centromeres. Interestingly, in response to DNA double-stranded breaks (DSBs) induced by chemotherapy drugs or CRSPR/Cas9, α-satellite transcription is dramatically stimulated in a DNA damage checkpoint-independent but TopI-dependent manner. These DSB-induced α-satellite RNAs were predominantly derived from the α-satellite high-order repeats of human centromeres and forms into strong speckles in the nucleus. Remarkably, TopI-dependent satellite transcription also exists in mouse 3T3 andDrosophilaS2 cells and inDrosophilalarval imaginal wing discs and tumor tissues. Altogether, our findings herein reveal an evolutionally conserved mechanism with TopI as a key player for the regulation of satellite transcription at both cellular and animal levels.
Differences in size and number of embryonic type-II neuroblast lineages correlate with divergent timing of central complex development between beetle and fly
Authors: Rethemeier Simon , Fritzsche Sonja , Mühlen Dominik , Bucher Gregor , Hunnekuhl Vera S. 
Published: May 2024

AbstractDespite its conserved basic structure, the morphology of the insect brain and the timing of its development underwent evolutionary adaptations. However, little is known about the developmental processes that create this diversity. The central complex is a brain centre required for multimodal information processing and an excellent model to understand neural development and divergence. It is produced in large parts by type-II neuroblasts, which produce intermediate progenitors, another type of cycling precursor, to increase their neural progeny. These neural stem cells are believed to be conserved among insects, but little is known on their molecular characteristics in insects other than flies.Tribolium castaneumhas emerged as a valuable new insect model for brain development and evolution. However, type-II neuroblast lineages and their role in central complex development have so far not been studied in this beetle.Using CRISPR-Cas9 we created a fluorescent enhancer trap marking expression ofTribolium fez/earmuff, a key marker for type-II neuroblast derived intermediate progenitors. Using combinatorial labelling of further markers includingTc-pointed,Tc-deadpan,Tc-asenseandTc-prosperowe characterized the type-II neuroblast lineages present in theTriboliumembryo and their sub-cell-types. Intriguingly, we found 9 type-II neuroblast lineages per hemisphere in theTriboliumembryo whileDrosophilaproduces only 8 per brain hemisphere. In addition, these lineages are significantly larger at the embryonic stage ofTriboliumthan they are inDrosophilaand contain more intermediate progenitors. Finally, we mapped these lineages to the domains of early expressed head patterning genes. Notably,Tc-otdis absent from all type-II neuroblasts and intermediate progenitors, whereasTc-six3marks an anterior subset of the type-II-lineages. The placodal markerTc-six4specifically marks the territory where anterior medial type-II neuroblasts differentiate.In conclusion, we identified a conserved pattern of gene expression in holometabolan central complex forming type-II neuroblast lineages, and conserved head patterning genes emerged as new candidates for conferring spatial identity to individual lineages. The higher number and greater lineage size of the embryonic type-II neuroblasts in the beetle correlate with a previously described embryonic phase of central complex formation which is not found in the fly. These findings stipulate further research on the causal link between timing of stem cell activity and temporal and structural differences in central complex development.
A heterocyclic compound inhibits viral release by inducing cell surface BST2/Tetherin/CD317/HM1.24
Authors: Nyame Perpetual , Togami Akihiro , Yoshida Tomofumi , Masunaga Takuya , Monira Begum MST , Terasawa Hiromi , Monde Nami , Tahara Yurika , Tanaka Reiko , Tanaka Yuestu , Appiah-Kubi Joyce , Amesimeku Wright Ofotsu , Hossain Md Jakir , Otsuka Masami , Yoshimura Kazuhisa , Ikeda Terumasa , Sawa Tomohiro , Satou Yorifumi , Fujita Mikako , Maeda Yosuke , Tateishi Hiroshi , Monde Kazuaki 
Published: May 2024

AbstractThe introduction of combined antiretroviral therapy (cART) has greatly improved the quality of life of human immunodeficiency virus type 1 (HIV-1)-infected individuals. Nonetheless, the ever-present desire to seek out a full remedy for HIV-1 infections makes the discovery of novel antiviral medication compelling. Owing to this, a new late-stage inhibitor, Lenacapavir/Sunlenca, an HIV multi-phase suppressor, was clinically authorized in 2022. Besides unveiling cutting-edge antivirals inhibiting late-stage proteins or processes, newer therapeutics targeting host restriction factors hold promise for the curative care of HIV-1 infections. Notwithstanding, bone marrow stromal antigen 2 (BST2)/Tetherin/CD317/HM1.24, which entraps progeny virions is an appealing HIV-1 therapeutic candidate. In this study, a novel drug screening system was established, using the Jurkat/Vpr-HiBiT T cells, to identify drugs that could obstruct HIV-1 release; the candidate compounds were selected from the Ono Pharmaceutical compound library. Jurkat T cells expressing Vpr-HiBiT were infected with NL4-3, and the amount of virus release was quantified indirectly by the amount of Vpr-HiBiT incorporated into the progeny virions. Subsequently, the candidate compounds that suppressed viral release were used to synthesize the heterocyclic compound, HT-7, which reduces HIV-1 release with less cellular toxicity. Notably, HT-7 increased cell surface BST2 coupled with HIV-1 release reduction in Jurkat cells but not Jurkat/KO-BST2 cells. Seemingly, HT-7 impeded simian immunodeficiency virus (SIV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) release. Concisely, these results suggest that the reduction in viral release, following HT-7 treatment, resulted from the modulation of cell surface expression of BST2 by HT-7.ImportanceA collection of scientific strategies has been revealed to find long-term cure for HIV-1 infection. One of these techniques, the therapeutic approach, involves harnessing late events that are not targeted by current medication. The regulator of HIV-1 assembly and release, the HIV-1 Gag protein, has emerged as a prospective inhibitor. We set up a high-efficiency, economically viable, and facile screening system for the identification of late-stage inhibitors. Herein, we discovered a heterocyclic compound that inhibits HIV-1 release. This newly high- performance testing technique can be employed in virological research for investigating HIV- 1 late-stage processes.
Growth ofStaphylococcus aureusin the presence of oleic acid shifts the glycolipid fatty acid profile and increases resistance to antimicrobial peptides
Authors: Raskovic Djuro , Alvarado Gloria , Hines Kelly M. , Xu Libin , Gatto Craig , Wilkinson Brian J. , Pokorny Antje 
Published: May 2024

AbstractStaphylococcus aureusreadily adapts to various environments and quickly develops antibiotic resistance, which has led to an increase in multidrug-resistant infections. Hence,S. aureuspresents a significant global health issue and its adaptations to the host environment are crucial for understanding pathogenesis and antibiotic susceptibility. WhenS. aureusis grown conventionally, its membrane lipids contain a mix of branched-chain and straight-chain saturated fatty acids. However, when unsaturated fatty acids are present in the growth medium, they become a major part of the total fatty acid composition. This study explores the biophysical effects of incorporating straight-chain unsaturated fatty acids intoS. aureusmembrane lipids. Membrane preparations from cultures supplemented with oleic acid showed more complex differential scanning calorimetry scans than those grown in tryptic soy broth alone. When grown in the presence of oleic acid, the cultures exhibited a transition significantly above the growth temperature, attributed to the presence of glycolipids with long-chain fatty acids causing acyl chain packing frustration within the bilayer. Functional aspects of the membrane were assessed by studying the kinetics of dye release from unilamellar vesicles induced by the antimicrobial peptide mastoparan X. Dye release was slower from liposomes prepared from cells grown in oleic acid-supplemented cultures, suggesting that changes in membrane lipid composition and biophysics protect the cell membrane against peptide-induced lysis. These findings underscore the intricate relationship between the growth environment, membrane lipid composition, and the physical properties of the bacterial membrane, which should be considered when developing new strategies against S. aureus infections.
The tricellular junction protein ILDR2 in glomerulopathies: insights and implications
Authors: Siegerist Florian , Kliewe Felix , Hammer Elke , Schakau Paul , Chi Soh Joanne Ern , Weber Claudia , Puelles Victor , Lindemeyer Maja , Reichelt-Wurm Simone , Drenic Vedran , Chatziantoniou Christos , Chadjichristos Christos E. , Zhang Yiying , Banas Miriam C. , Nauck Matthias , Völker Uwe , Endlich Nicole 
Published: May 2024

SummaryThe tricellular tight junctions are crucial for the regulation of paracellular flux at tricellular junctions, where tricellulin (MARVELD2) and angulins (ILDR1, ILDR2 or LSR) are localized. The role of ILDR2 in podocytes, specialized epithelial cells in the kidney, is still unknown. We investigated the role of ILDR2 in glomeruli and its influence on blood filtration. Western blots, scRNA-seq and superresolution microscopy showed a strong expression of MARVELD2 and ILDR2 in podocytes that colocalizes with the podocyte-specific claudin CLDN5. Co-immunoprecipitation revealed that ILDR2 directly binds CLDN5. In glomerulopathies, induced by nephrotoxic serum and by DOCA-salt heminephrectomy, ILDR2 was strongly upregulated. Furthermore,Ildr2knockout mice exhibited glomerular hypertrophy and decreased podocyte density, however, did not develop effacement of podocyte foot processes or proteinuria. LC-MS/MS proteomic analysis of isolated glomeruli showed an increase in matrix proteins such as fibronectin and agrin. This suggests a protective role of ILDR2 in glomerulopathies.
Transient interdomain interactions modulate the monomeric structural ensemble and self-assembly of Huntingtin Exon 1
Authors: Mohanty Priyesh , Phan Tien Minh , Mittal Jeetain 
Published: May 2024

AbstractPolyglutamine expansion (≥ 36 residues) within the N-terminal exon-1 of Huntingtin (Httex1) leads to Huntington’s disease, a neurodegenerative condition marked by the presence of intranuclear Htt inclusions. Notably, the polyglutamine tract in Httex1 is flanked by an N-terminal coiled-coil domain - N17 (17 amino acids), which undergoes self-association to promote the formation of soluble Httex1 oligomers and brings the aggregation-prone polyQ tracts in close spatial proximity. However, the mechanisms underlying the subsequent conversion of soluble oligomers into insoluble β-rich aggregates with increasing polyQ length, remain unclear. Current knowledge suggests that expansion of the polyQ tract increases its helicity, and this favors its oligomerization and aggregation. In addition, studies utilizing photocrosslinking, conformation-specific antibodies and a stable coiled-coil heterotetrametric system fused to polyQ indicate that domain “cross-talk” (i.e., interdomain interactions) may play a role in the emergence of toxic conformations and the conversion of Httex1 oligomers into fibrillar aggregates. Here, we performed extensive atomistic molecular dynamics (MD) simulations (aggregate time ∼ 0.7 ms) to uncover the interplay between structural transformation and domain “cross-talk” on the conformational ensemble and oligomerization landscape of Httex1. Notably, our MD-derived ensembles of N17-polyQ monomers validated against13C NMR chemical shifts indicated that in addition to elevated α- helicity, polyQ expansion also favors transient, interdomain (N17-polyQ) interactions which result in the emergence of β-sheet conformations. Further, interdomain interactions competed with increased polyQ tract α-helicity to modulate the stability of N17-mediated dimers and thereby promoted a heterogenous dimerization landscape. Finally, we observed that the C-terminal proline-rich domain (PRD) promoted condensation of Httex1 through self-interactions involving its P10/P11tracts while also interacting with N17 to suppress its α-helicity. In summary, our study demonstrates a significant role for domain “cross-talk” in modulating the monomeric structural ensemble and self-assembly of Httex1.
Global biogeography of N2-fixing microbes:nifHamplicon database and analytics workflow
Authors: Morando Michael , Magasin Jonathan , Cheung Shunyan , Mills Matthew M. , Zehr Jonathan P. , Turk-Kubo Kendra A. 
Published: May 2024

AbstractMarine nitrogen (N) fixation is a globally significant biogeochemical process carried out by a specialized group of prokaryotes (diazotrophs), yet our understanding of their ecology is constantly evolving. Although marine dinitrogen (N2)-fixation is often ascribed to cyanobacterial diazotrophs, indirect evidence suggests that non-cyanobacterial diazotrophs (NCDs) might also be important. One widely used approach for understanding diazotroph diversity and biogeography is polymerase chain reaction (PCR)-amplification of a portion of thenifHgene, which encodes a structural component of the N2-fixing enzyme complex, nitrogenase. An array of bioinformatic tools exists to processnifHamplicon data, however, the lack of standardized practices has hindered cross-study comparisons. This has led to a missed opportunity to more thoroughly assess diazotroph biogeography, diversity, and their potential contributions to the marine N cycle. To address these knowledge gaps a bioinformatic workflow was designed that standardizes the processing ofnifHamplicon datasets originating from high-throughput sequencing (HTS). Multiple datasets are efficiently and consistently processed with a specialized DADA2 pipeline to identify amplicon sequence variants (ASVs). A series of customizable post-pipeline stages then detect and discard spuriousnifHsequences and annotate the subsequent quality-filterednifHASVs using multiple reference databases and classification approaches. This newly developed workflow was used to reprocess nearly all publicly availablenifHamplicon HTS datasets from marine studies, and to generate a comprehensivenifHASV database containing 7909 ASVs aggregated from 21 studies that represent the diazotrophic populations in the global ocean. For each sample, the database includes physical and chemical metadata obtained from the Simons Collaborative Marine Atlas Project (CMAP). Here we demonstrate the utility of this database for revealing global biogeographical patterns of prominent diazotroph groups and highlight the influence of sea surface temperature. The workflow andnifHASV database provide a robust framework for studying marine N2fixation and diazotrophic diversity captured bynifHamplicon HTS. Future datasets that target understudied ocean regions can be added easily, and users can tune parameters and studies included for their specific focus. The workflow and database are available, respectively, in GitHub (https://github.com/jdmagasin/nifH-ASV-workflow) and Figshare (https://doi.org/10.6084/m9.figshare.23795943.v1).
Psilocybin facilitates fear extinction: importance of dose, context, and serotonin receptors
Authors: Woodburn Samuel C. , Levitt Caleb M. , Koester Allison M. , Kwan Alex C. 
Published: May 2024

ABSTRACTA variety of classic psychedelics and MDMA have been shown to enhance fear extinction in rodent models. This has translational significance because a standard treatment for posttraumatic stress disorder (PTSD) is prolonged exposure therapy. However, few studies have investigated psilocybin’s potential effect in fear learning paradigms. More specifically, the extents to which dose, timing of administration, and serotonin receptors may influence psilocybin’s effect on fear extinction are not understood. In this study, we used an auditory delay fear conditioning paradigm to determine the effects of psilocybin on fear extinction, extinction retention, and fear renewal in male and female mice. Psilocybin robustly enhances fear extinction when given acutely prior to testing for all doses tested. Psilocybin exerts long-term effects to elevate extinction retention and suppress fear renewal in a novel context, though these changes were sensitive to dose. Administration of psilocybin prior to fear learning or immediately after extinction yielded no change in behavior, indicating that concurrent extinction experience is necessary for the drug’s effects. Co-treatment with a 5-HT2Areceptor antagonist blocked psilocybin’s effects for extinction, extinction retention and fear renewal, whereas 5-HT1Areceptor antagonism attenuated only the effect on fear renewal. Collectively, these results highlight dose, context, and serotonin receptors as crucial factors in psilocybin’s ability to facilitate fear extinction. The study provides preclinical evidence to support investigating psilocybin as a pharmacological adjunct for extinction-based therapy for PTSD.
HEPN-AbiV is an RNase in the antiphage system AbiV
Authors: Zhu Xiaojun , Morency Carlee , Picard Marie-Ève , Mosterd Cas , McAlister Jason A. , Perrault-Jolicoeur Alice , Geddes-McAlister Jennifer , Shi Rong , Moineau Sylvain 
Published: May 2024

AbstractProkaryotes and eukaryotes possess defense systems, which can be either innate or acquired, to protect against viral infections. At the bacterial population level, abortive infection (Abi) serves as an innate immune defense mechanism against phage invasion. The AbiV antiviral system is prevalent in several bacterial genomes and exhibits diverse characteristics in terms of gene composition and evolution. Our investigation into theLactococcusAbiV system revealed a novel two-component system,abiV1andabiV2, both of which are essential for its function as a type III toxin-antitoxin system. The toxin component AbiV (product ofabiV1) is an RNase belonging to the HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding) superfamily as it carries the consensus Rx4-6H motif.In vivoassays coupled with mass spectrometry showed that the lactococcal AbiV was expressed in the presence or absence of phages whilein vitroexperiments demonstrated that AbiV1 degraded ribosomal RNA but not mRNA. On the other hand, the antitoxin component (abiV2) was found to function as an RNA molecule that inhibited the nuclease activity of the AbiV1 toxin. The structural characterization of AbiV revealed that this RNase utilizes a large patch of positively charged area across the dimer to anchor RNA molecules. In addition, we showed that the AbiV N-terminal region (amino acids 1 to 23) is crucial for its RNase activity as a truncated AbiV lacking this segment adopted distinct conformational states incompatible with RNA binding. This study provided novel insights into the mode of action of the antiviral system AbiV.
PI3 kinase-unrelated effects of LY294002 and LY303511 on serotonin-induced Ca2+and cAMP signaling
Authors: Kotova Polina D. , Dymova Ekaterina A. , Rogachevskaja Olga A. , Kolesnikov Stanislav S. 
Published: May 2024

ABSTRACTThe phosphoinositide 3-kinase (PI3K) is involved in regulation of multiple intracellular processes. Although the inhibitory analysis is generally employed for validating a physiological role of PI3K, increasing body of evidence suggests that PI3K inhibitors can exhibit PI3K-unrelated activity as well. Here we studied effects of PI3K inhibitor LY294002 and its inactive analogue LY303511 on Ca2+and cAMP signals initiated by serotonin. In the present study several monoclonal HEK293 cell lines were used, in particular, monitoring of Ca2+signals were carried out on Fura-2 loaded cells expressed recombinant serotonin 5-HT2Creceptors, cAMP signals were studied on cells expressed the genetically encoded cAMP sensor Pink Flamindo and recombinant 5-HT4receptors, for monitoring PI3K activity cells stably expressed the genetically encoded PIP3sensor PH(Akt)-Venus were used. It turned out that LY294002 suppressed Ca2+signals initiated by activation 5-HT2Creceptors irrespectively of PI3K inhibition, but did not affect cAMP responses initiated by 5-HT4receptors. In turn LY303511 suppressed cAMP signals initiated by 5-HT4receptors, and elicited Ca2+transients exclusively in cells expressed 5-HT2Creceptors. Based on these facts and the results of the inhibitory analysis, we hypothesize that the described effects may be due to the activity of LY294002 and LY303511 on the serotonin 5-HT2Cand 5-HT4receptors.