bluuebunny/crossref_metadata_2025_split huggingface dataset:
H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment
Authors: Harris C. Jake , Zhong Zhenhui , Ichino Lucia , Feng Suhua , Jacobsen Steven E. 
Published: May 2023

ABSTRACTSilencing pathways prevent transposable element (TE) proliferation and help to maintain genome integrity through cell division. Silenced genomic regions can be classified as either euchromatic or heterochromatic, and are targeted by genetically separable epigenetic pathways. In plants, the RNA-directed DNA methylation (RdDM) pathway targets mostly euchromatic regions, while CMT DNA methyltransferases are mainly associated with heterochromatin. However, many epigenetic features - including DNA methylation patterning - are largely indistinguishable between these regions, so how the functional separation is maintained is unclear. The linker histone H1 is preferentially localized to heterochromatin and has been proposed to restrict RdDM from encroachment. To test this hypothesis, we followed RdDM genomic localization in anh1mutant by performing ChIP-seq on the largest subunit, NRPE1, of the central RdDM polymerase, Pol V. Loss of H1 resulted in NRPE1 enrichment predominantly in heterochromatic TEs. Increased NRPE1 binding was associated with increased chromatin accessibility inh1, suggesting that H1 restricts NRPE1 occupancy by compacting chromatin. However, RdDM occupancy did not impact H1 localization, demonstrating that H1 hierarchically restricts RdDM positioning. H1 mutants experience major symmetric (CG and CHG) DNA methylation gains, and by generating anh1/nrpe1double mutant, we demonstrate these gains are largely independent of RdDM. However, loss of NRPE1 occupancy from a subset of euchromatic regions inh1corresponded to loss of methylation in all sequence contexts, while at ectopically bound heterochromatic loci, NRPE1 deposition correlated with increased methylation specifically in the CHH context. Additionally, we found that H1 similarly restricts the occupancy of the methylation reader, SUVH1, and polycomb-mediated H3K27me3. Together, the results support a model whereby H1 helps maintain the exclusivity of heterochromatin by preventing encroachment from other competing pathways.
Adaptation invariant concentration discrimination in an insect olfactory system
Authors: Ling D. , Zhang L. , Saha D. , Chen A. B. , Raman B. 
Published: May 2023

AbstractNeural responses evoked by a stimulus reduce upon repetition. While this adaptation allows the sensory system to attend to novel cues, does information about the recurring stimulus particularly its intensity get compromised? We explored this issue in the locust olfactory system. We found that locusts’ innate behavioral response to odorants varied with repetition and stimulus intensity. Counter-intuitively, the stimulus-intensity dependent differences became significant only after adaptation had set in. Adaptation also altered responses of individual neurons in the antennal lobe (neural network downstream to insect antenna). These response variations to repetitions of the same stimulus were unpredictable and inconsistent across intensities. Although both adaptation and intensity decrements resulted in an overall reduction in spiking activities across neurons, these changes could be disentangled and information about stimulus intensity robustly maintained by ensemble neural responses. In sum, these results show how information about odor intensity can be preserved in an adaptation-invariant manner.
Neuronal mechanism of the encoding of socially familiar faces in the striatum tail
Authors: Kunimatsu Jun , Amita Hidetoshi , Hikosaka Okihide 
Published: May 2023

AbstractAlthough we can quickly locate a familiar person even in a crowd, the underlying neuronal mechanism remains unclear. Recently, we found that the striatum tail (STRt), which is part of the basal ganglia, is sensitive to long-term reward history. Here, we show that long-term value-coding neurons are involved in the detection of socially familiar faces. Many STRt neurons respond to facial images, especially to those of socially familiar persons. Additionally, we found that these face-responsive neurons also encode the stable values of many objects based on long-term reward experiences. Interestingly, the strength of neuronal modulation of social familiarity bias (familiar or unfamiliar) and object value bias (high-valued or low-valued) were positively correlated. These results suggest that both social familiarity and stable object-value information are mediated by a common neuronal mechanism. This mechanism may contribute to the rapid detection of familiar faces in real-world contexts.TeaserThe common mechanism mediating social familiarity and stable object-value information may contribute to rapid detection of familiar faces.
Phosphoribulokinase abundance is not limiting the Calvin-Benson-Bassham cycle inChlamydomonas reinhardtii
Authors: Boisset Nicolas D. , Favoino Giusi , Meloni Maria , Jomat Lucile , Cassier-Chauvat Corinne , Zaffagnini Mirko , Lemaire Stéphane D. , Crozet Pierre 
Published: May 2023

AbstractImproving photosynthetic efficiency in plants and microalgae is of utmost importance to support the growing world population and to enable the bioproduction of energy and chemicals. Limitations in photosynthetic light conversion efficiency can be directly attributed to kinetic bottlenecks within the Calvin-Benson-Bassham cycle (CBBC) responsible for carbon fixation. A better understanding of these bottlenecksin vivois crucial to overcome these limiting factors through bio-engineering. The present study is focused on the analysis of phosphoribulokinase (PRK) in the unicellular green algaChlamydomonas reinhardtii. We have characterized a PRK knock-out mutant strain and showed that in the absence of PRK, Chlamydomonas cannot grow photoautotrophically while functional complementation with a synthetic construct allowed restoration of photoautotrophy. Nevertheless, using standard genetic elements, the expression of PRK was limited to 40% of the reference level in complemented strains and could not restore normal growth in photoautotrophic conditions suggesting that the CBBC is limited. We were subsequently able to overcome this initial limitation by improving the design of the transcriptional unit expressing PRK using diverse combinations of DNA parts including PRK endogenous promoter and introns. This enabled us to obtain strains with PRK levels comparable to the reference strain and even overexpressing strains. A collection of strains with PRK levels between 16% and 250% of WT PRK levels was generated and characterized. Immunoblot and growth assays revealed that a PRK content of ≈86% is sufficient to fully restore photoautotrophic growth. This result suggests that PRK is present in moderate excess in Chlamydomonas. Consistently, the overexpression of PRK did not increase photosynthetic growth indicating that that the endogenous level of PRK in Chlamydomonas is not limiting the Calvin-Benson-Bassham cycle under optimal conditions.
Success versus failure in cognitive control: meta-analytic evidence from neuroimaging studies on error processing
Authors: Cieslik Edna C. , Ullsperger Markus , Gell Martin , Eickhoff Simon B. , Langner Robert 
Published: May 2023

AbstractBrain mechanisms of error processing have often been investigated using response interference tasks and focusing on the posterior medial frontal cortex, which is also implicated in resolving response conflict in general. Thereby, the role other brain regions may play has remained undervalued. Here, activation likelihood estimation meta-analyses were used to synthesize the neuroimaging literature on brain activity related to committing errors versus responding successfully in interference tasks and to test for commonalities and differences. The salience network and the temporoparietal junction were commonly recruited irrespective of whether responses were correct or incorrect, pointing towards a general involvement in coping with situations that call for increased cognitive control. The dorsal posterior cingulate cortex, posterior thalamus, and left superior frontal gyrus showed error-specific convergence, which underscores their consistent involvement when performance goals are not met. In contrast, successful responding revealed stronger convergence in the dorsal attention network and lateral prefrontal regions. Underrecruiting these regions in error trials may reflect failures in activating the task-appropriate stimulus-response contingencies necessary for successful response execution.
DNA methylation responses to stress across different plant species
Authors: Van Antro Morgane , Ivanovic Slavica , Postuma Maarten , McIntyre Lauren M. , van der Putten Wim H. , Vergeer Philippine , Verhoeven Koen J.F. 
Published: May 2023

SummaryChanges in environments trigger plant DNA methylation responses, potentially modulating stress responses. Studies on stress-induced DNA methylation typically focus on single species, limiting our understanding of what are general and specific responses between species.Using reduced-representation bisulfite sequencing epiGBS, we compared DNA methylation stress-responses across seven plant species. Because methylation can be targeted at transposable elements (TEs) and because environmental plasticity may be particularly relevant in asexual species, we hypothesize that genome size and reproduction mode explain differences in methylation responses between species.We show that enrichment of environmentally-induced methylation responses in genes and TEs is a general feature across plant species. While previous studies have emphasized methylation responses in CHH-cytosines, we observed that cytosines in all sequence contexts (CG, CHG, CHH) are equally likely to respond to stress. Larger-genome species showed a higher proportion of stress-responding cytosines, and asexual species showed more cytosines with a strong methylation response to stress than sexually responding species.Our study highlights the role of TEs in methylome plasticity and identifies causes of variation in methylome plasticity. This provides guidance to extrapolating results from models to other plant species, and may contribute to better understanding of functionality of the response.
Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons
Authors: Rayamajhi Dheeraj , Ege Mert , Ukhanov Kirill , Ringers Christa , Zhang Yiliu , Jeong Inyoung , D’Gama Percival P. , Li Summer Shijia , Cosacak Mehmet Ilyas , Kizil Caghan , Park Hae-Chul , Yaksi Emre , Martens Jeffrey R. , Brody Steven L. , Jurisch-Yaksi Nathalie , Roy Sudipto 
Published: May 2023

ABSTRACTIn vertebrates, olfactory receptors localize on multiple cilia elaborated on dendritic knobs of olfactory sensory neurons (OSNs). Although olfactory cilia dysfunction can cause anosmia, how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1, a forkhead domain-containing transcription factor linked with motile cilia biogenesis, is expressed in OSNs and required for olfactory epithelium (OE) formation. In keeping with the immotile nature of olfactory cilia, we observed that ciliary motility genes are repressed in zebrafish, mouse, and human OSNs. Strikingly, we also found that besides ciliogenesis, Foxj1 controls the differentiation of the OSNs themselves by regulating their cell type-specific gene expression, such as that ofolfactory marker protein(omp) involved in odor-evoked signal transduction. In line with this, response to bile acid, an odor detected by OMP-positive OSNs, was significantly diminished infoxj1mutant zebrafish. Taken together, our findings establish how the canonical Foxj1-mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of immotile olfactory cilia and for development of the OSNs.
Neuronal lipofuscinosis caused by Kufs disease/CLN4DNAJC5mutations but not by a CSPα/DNAJC5 deficiency
Authors: López-Begines Santiago , Lavado-Roldán Ángela , Mesa-Cruz Cristina , Mavillard Fabiola , Borjini Nozha , Wiersma Vera I. , Aguado Carolina , Luján Rafael , Scheper Wiep , Nieto-González José L. , Fernández-Chacón Rafael 
Published: May 2023

ABSTRACTKufs disease/CLN4 is an autosomal dominant neurodegenerative disorder that affects young adults, caused by mutations in the DNAJC5 gene that encodes the synaptic vesicle co-chaperone Cysteine String Protein α (CSPα/DNAJC5). The Leu115Arg and Leu116Δ mutations in humans are known to independently cause the disease, although the underlying mechanisms are unknown. To investigate the disease mechanisms in vivo, we generated three independent mouse lines overexpressing different versions of CSPα/DNAJC5 under the neuron-specific Thy1 promoter: wild-type (WT), Leu115Arg, and Leu116Δ. Mice expressing mutant CSPα/DNAJC5 are viable and do not show any significant increase in morbidity or mortality. However, we observed the presence of pathological lipofuscinosis in the mutants, indicated by autofluorescent punctate structures labeled with antibodies against ATP synthase subunit C, which were absent in the WT transgenic line. Additionally, transmission electron microscopy revealed intracellular structures resembling granular osmiophilic deposits (GRODs), observed in Kufs disease patients, in the mutants but not in non-transgenic controls or the WT transgenic mice. Notably, conventional, or conditional knockout mice lacking CSPα/DNAJC5 did not exhibit any signs of increased lipofuscinosis or GRODs. Our novel mouse models thus provide a valuable tool to investigate the molecular mechanisms underlying Kufs disease/CLN4. We conclude that DNAJC5 mutations cause neuronal lipofuscinosis through a cell-autonomous gain of a novel but pathological function of CSPα/DNAJC5.
The influence of the larval microbiome on susceptibility to Zika virus is mosquito genotype dependent
Authors: Accoti Anastasia , Multini Laura C. , Diouf Babakar , Becker Margaret , Vulcan Julia , Sylla Massamba , Yap Dianne aster Y , Khanipov Kamil , Weaver Scott C. , Diallo Mawlouth , Gaye Alioune , Dickson Laura B. 
Published: May 2023

AbstractThe microbiome of the mosquitoAedes aegyptiis largely determined by the environment and influences mosquito susceptibility for arthropod-borne viruses (arboviruses). Larval interactions with different bacteria can influence adultAe. aegyptireplication of arboviruses, but little is known about the role that mosquito host genetics play in determining how larval-bacterial interactions shapeAe aegyptisusceptibility to arboviruses. To address this question, we isolated single bacterial isolates and complex microbiomes fromAe. aegyptilarvae from various field sites in Senegal. Either single bacterial isolates or complex microbiomes were added to two different genetic backgrounds ofAe. aegyptiin a gnotobiotic larval system. Using 16S amplicon sequencing we show that similarities in bacterial community structures when given identical microbiomes between different genetic backgrounds ofAe. aegyptiwas dependent on the source microbiome, and the abundance of single bacterial taxa differed betweenAe. aegyptigenotypes. Using single bacterial isolates or the entire preserved complex microbiome, we tested the ability of specific microbiomes to drive differences in infection rates for Zika virus in different genetic backgrounds ofAe. aegypti. We observed that the proportion of Zika virus-infected adults was dependent on the interaction between the larval microbiome andAe. aegyptihost genetics. By using the larval microbiome as a component of the environment, these results demonstrate that interactions between theAe. aegyptigenotype and its environment can influence Zika virus infection. AsAe. aegyptiexpands and adapts to new environments under climate change, an understanding of how different genotypes interact with the same environment will be crucial for implementing arbovirus transmission control strategies.
Sensitivity-enhanced magnetic resonance reveals hydrogen intermediates during active [Fe]-hydrogenase catalysis
Authors: Kaltschnee Lukas , Pravdivtsev Andrey N. , Gehl Manuel , Huang Gangfeng , Stoychev Georgi L. , Riplinger Christoph , Keitel Maximilian , Neese Frank , Hövener Jan-Bernd , Auer Alexander A. , Griesinger Christian , Shima Seigo , Glöggler Stefan 
Published: May 2023

AbstractMolecular hydrogen (H2) is considered an eco-friendly future energy-carrier and an alternative to fossil fuel1and thus, major efforts are directed towards identifying efficient and economical hydrogen catalysts.2,3Efficient hydrogen catalysis is used by many microorganisms, some of them producing H2from organic materials and others consuming it.4-6To metabolize H2, these microorganisms use enzymes called hydrogenases.7,8For the future development of efficient catalysts a detailed analysis of the catalytic mechanisms of such hydrogenases is required and existing analytical techniques could not provide a full understanding.9Consequently, new analytical technologies are of utmost importance to unravel natures’ blueprints for highly efficient hydrogen catalysts. Here, we introduce signal-enhanced or hyperpolarized, nuclear magnetic resonance (NMR) to study hydrogenases under turnover conditions. So far undiscovered hydrogen species of the catalytic cycle of [Fe]-hydrogenases, are revealed and thus, extend the knowledge regarding this class of enzymes. These findings pave new pathways for the exploration of novel hydrogen metabolismsin vivo. We furthermore envision that the results contribute to the rational design of future catalysts to solve energy challenges of our society.
De novosynthesis of a conjugative system from human gut metagenomic data for targeted delivery of Cas9 antimicrobials
Authors: Hamilton Thomas A. , Joris Benjamin R. , Shrestha Arina , Browne Tyler S. , Rodrigue Sébastien , Karas Bogumil J. , Gloor Gregory B. , Edgell David R. 
Published: May 2023

ABSTRACTMetagenomic sequence represents an untapped source of genetic novelty, particularly for conjugative systems that could be used for plasmid-based delivery of Cas9-derived antimicrobial agents. However, unlocking the functional potential of conjugative systems purely from metagenomic sequence requires the identification of suitable candidate systems as starting scaffolds forde novoDNA synthesis. Here, we developed a bioinformatics approach that searches through the metagenomic ‘trash bin’ for conjugative systems present on contigs that are typically excluded from common metagenomic analysis pipelines. Using a human metagenomic gut dataset representing 2805 taxonomically distinct units, we identified 1598 contigs containing conjugative systems with a differential distribution in human cohorts. We synthesizedde novoan entireCitrobacterspp. conjugative system of 54 kb and containing at least 47 genes, pCitro, and found that pCitro conjugates fromEscherichia colitoCitrobacter rodentiumwith a 30-fold higher frequency than toE. coli, and is compatible withCitrobacterresident plasmids. Mutations in thetraVandtraYconjugation components of pCitro inhibited conjugation. We showed that pCitro can be re-purposed as an antimicrobial delivery agent by programming it with the TevCas9 nuclease andCitrobacter-specific sgRNAs to killC. rodentium. Our study reveals a trove of uncharacterized conjugative systems in metagenomic data and describes an experimental framework to animate these large genetic systems as novel target-adapted delivery vectors for Cas9-based editing of bacterial genomes.
Proteasome activity is required for reovirus entry into cells
Authors: Abad Andrew T. , McNamara Andrew J. , Danthi Pranav 
Published: May 2023

ABSTRACTSince viruses have limited coding capacity in their genomes, they use host cell machinery to complete virtually every stage of their replication cycle. Mammalian orthoreovirus (reovirus) is comprised of two concentric protein shells, the inner core and the outer capsid. Following attachment to its receptor, reovirus enters the cell by receptor-mediated endocytosis. Within endosomes reovirus utilizes host acid-dependent proteases to process the viral outer capsid. Specifically, the outer capsid protein σ3 is degraded and μ1 is cleaved to form the disassembly intermediate infectious subvirion particles (ISVPs). ISVPs undergo additional conformational changes into ISVP*s that release small peptides which mediate the penetration of endosomal membranes.Membrane penetration allows for delivery of the remaining viral core into the cytoplasm for subsequent gene expression. Here, we describe that the ubiquitin proteasome system controls an entry step of reovirus particles. We show that chemically inhibiting the proteasome blocks infection at a stage following ISVP formation but prior to transcriptional activation of cores. Specifically, inhibition of the proteasome prevents conformational changes in μ1 characteristic of ISVP-to-ISVP* conversion. In the absence of these conformational changes, cores are unable to be delivered and become transcriptionally active, thereby blocking viral replication. This work highlights a previously unknown way in which reovirus relies on host factors for successful replication.IMPORTANCEDue to their limited genetic capacity, viruses are reliant on multiple host systems to replicate successfully. Mammalian orthoreovirus (reovirus) is commonly used as a model system for understanding host-virus interactions. In this study, we identify the host ubiquitin proteasome system as a regulator of reovirus entry. Inhibition of the proteasome using a chemical inhibitor blocks reovirus uncoating. Blocking these events reduces subsequent replication of the virus. This work identifies that additional host factors controls reovirus entry.
Novel taxonomic and functional diversity of bacteria from the upper digestive tract of chicken
Authors: Rios-Galicia Bibiana , Sáenz Johan Sebastian , Yergaliyev Timur , Roth Christoph , Camarinha-Silva Amélia , Seifert Jana 
Published: May 2023

AbstractStrategies to increase the production rate of chicken for human consumption alter the natural process of microbial colonisation and the nutritional performance of the animal. The lack of sufficient reference genomes limits the interpretation of sequencing data and restrain the study of complex functions. In this study, 43 strains obtained from crop, jejunum and ileum of chicken were isolated, characterised and genome analysed to observe their metabolic profiles, adaptive strategies and to serve as future references. Eight isolates represent new species that colonise the upper gut intestinal tract and present consistent adaptations that enable us to predict their ecological role, expanding our knowledge on the adaptive functions. Molecular characterisation confirmed the classification ofClostridium anaeroviscerissp. nov. (DSM 113860= LMG 32675),Clostridium butanolproducens(DSM 115076= LMG 32878),Ligilactobacillus hohenheimiussp. nov. (DSM 113870= LMG 32876),Limosilactobacillus gallussp. nov. (DSM 113833 =LMG 32623),Limosilactobacillus aviumsp. nov. (DSM 113849= LMG 32671), Limosilactobacillus pullumsp. nov. (DSM 115077 =LMG 32877),Limosilactobacillus digestussp. nov. (DSM113835= LMG 32625) andLimosilactobacillus difficilesp. nov. (DSM 114195= LMG 32875). Strains ofLimosilactobacilluswere found to be more abundant in the crop, whileLigilactobacillusdominated the ileal digesta. Isolates from crop encode a high number of glycosidases specialized in complex polysaccharides compared to strains isolated from jejunum and ileum. These results represent the first approach for the isolation and detection of bacteria from the chicken’s upper digestive tract and describe the functional diversity of bacteria inhabiting these regions, improving the potential handling of chicken microbiota with biotechnological applications.