bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-cell transcriptome landscape of circulating CD4+T cell populations in human autoimmune diseases
Authors: Yasumizu Yoshiaki , Takeuchi Daiki , Morimoto Reo , Takeshima Yusuke , Okuno Tatsusada , Kinoshita Makoto , Morita Takayoshi , Kato Yasuhiro , Wang Min , Motooka Daisuke , Okuzaki Daisuke , Nakamura Yamami , Mikami Norihisa , Arai Masaya , Zhang Xuan , Kumanogoh Atsushi , Mochizuki Hideki , Ohkura Naganari , Sakaguchi Shimon
Published: May 2023

CD4+T cells are a key mediator of various autoimmune diseases; however, how they contribute to disease development remains obscure primarily because of their cellular heterogeneity. Here, we evaluated CD4+T cell subpopulations by decomposition-based transcriptome characterization together with canonical clustering strategies. This approach identified 12 independent transcriptional gene programs governing whole CD4+T cell heterogeneity, which can explain the ambiguity of canonical clustering. In addition, we performed a meta-analysis using public single-cell data sets of over 1.8M peripheral CD4+T cells from 953 individuals by projecting cells onto the reference and cataloged cell frequency and qualitative alterations of the populations in 20 diseases. The analyses revealed that the 12 transcriptional programs were useful in characterizing each autoimmune disease and predicting its clinical status. Moreover, genetic variants associated with autoimmune diseases showed disease-specific enrichment within the 12 gene programs. The results collectively provide a landscape of single-cell transcriptomes of CD4+T cell subpopulations involved in autoimmune disease.
Discordance between gut-derived appetite hormones and energy intake in humans
Authors: Hengist Aaron , Sciarrillo Christina M. , Guo Juen , Walter Mary , Hall Kevin D.
Published: May 2023

Gut-derived hormones affect appetite and are thought to play an important role in body weight regulation. Dietary macronutrient composition can influence gut-derived appetite hormone concentrations, thereby providing theoretical basis for why some diets might facilitate weight loss better than others. We investigated postprandial gut-derived appetite hormones in 20 inpatient adults after 2 weeks of eating either a low carbohydrate (LC) or a low fat (LF) diet followed by the alternate diet in random order. A LC meal resulted in significantly greater postprandial GLP-1, GIP, and PYY but lower ghrelin compared to an isocaloric LF meal (allp≤0.02). However, differences in gut-derived appetite hormones were incommensurate with subsequent ad libitum energy intake over the rest of the day, which was 551±103 kcal (p<0.0001) greater with the LC as compared to the LF diet. The effects of gut-derived appetite hormones on ad libitum energy intake can be dominated by other diet-related factors, at least in the short-term.

Graphical Abstract
Estimating county-level flu vaccination in the United States
Authors: Tiu Andrew , Bansal Shweta
Published: May 2023

In the United States, influenza vaccines are an important part of public health efforts to blunt the effects of seasonal influenza epidemics. This in turn emphasizes the importance of understanding the spatial distribution of influenza vaccination coverage. Despite this, high quality data at a fine spatial scale and spanning a multitude of recent flu seasons are not readily available. To address this gap, we develop county-level counts of vaccination across five recent, consecutive flu seasons and fit a series of regression models to these data that account for bias. We find that the spatial distribution of our bias-corrected vaccination coverage estimates is generally consistent from season to season, with the highest coverage in the Northeast and Midwest but is spatially heterogeneous within states. We also observe a negative relationship between a county’s vaccination coverage and social vulnerability. Our findings stress the importance of quantifying flu vaccination coverage at a fine spatial scale, as relying on state or region-level estimates misses key heterogeneities.
Glucocorticoid-driven gene expression in circulating monocytes and neutrophils in health and severe inflammation
Authors: Molendijk Arthur , Koenderman Leo
Published: May 2023

Glucocorticoids (GCs) are used as anti-inflammatory and immunosuppressive drugs in many immune mediated diseases, but their use in sepsis and shock is controversial. This is caused in part by a lack of information regarding the responding cell types and GC-regulated genesin vivo. We used public blood transcriptomic datasets and GC-induced query genes to obtain 2 robust gene expression correlation signatures of GC induction, either in the absence or in the presence of severe inflammation. GC signature 1 originated from circadian cortisol with biases for gene expression in NK cells and neutrophils. GC signature 2 originated from GC in severe inflammation, mainly with biases for gene expression in monocytes and neutrophils. Many genes upregulated by GC treatment in septic shock and burn shock were also present as high-ranking genes in GC signatures, which pointed to their direct regulation by GC. Robust GC signatures were also obtained from dataset collections of monocytes and neutrophils, separately, and predicted cellular effects. Additionally, gene induction by GC was put into a wider framework of gene expression in circulating monocytes and neutrophils in health and systemic inflammation. We present and interpret a large number of GC-regulated genes in different blood cells and tissues, and select 2 whole blood transcriptomic biomarker gene sets, GC-1 and GC-2, for monitoring cortisol action in health, and in severe inflammation, respectively. GC signature 2 was found in sepsis and many other inflammatory diseases, both from treatment with GC, and from endogenous GC.
Rapid Online Assessment of Reading (ROAR): Evaluation of an Online Tool for Screening Reading Skills in a Developmental-Behavioral Pediatrics Clinic
Authors: Barrington Elizabeth P. , Sarkisian Sadie Mae , Feldman Heidi M. , Yeatman Jason D.
Published: May 2023

Objective

Reading difficulties frequently co-occur with other neurodevelopmental/behavioral conditions. It is difficult to assess reading routinely in Developmental-Behavioral Pediatrics (DBP) clinical practice due to time/resource constraints. Rapid Online Assessment of Reading (ROAR) is a gamified assessment that children take in a web-browser without adult supervision. This study’s purpose was to evaluate ROAR as a screening tool for reading difficulties in a DBP clinic.

Method

Patients, ages 6-14 years, attending a DBP clinic, were invited to participate. Children took ROAR and completed the Woodcock-Johnson Letter-Word Identification (LWID) and Word Attack (WA). Basic Reading Skills (BRS), a standardized aggregate score of LWID and WA, was used as the gold standard assessment. The strength of association between age-adjusted standard score on ROAR and BRS was calculated. BRS scores < 90 (bottom quartile of sample) were deemed poor reader. Receiver Operating Characteristic (ROC) curve analysis was used to assess the quality of ROAR as a screening test.

Results

A total of 41 children, 78% boys, mean age 9.5 years (SD 2.0 years), completed the study. The correlation of ROAR standard score with BRS was r = 0.66, p<0.001. ROC curve classification analysis with ROAR scores accurately classified poor readers with an area under the curve (AUC) of 0.90.

Conclusion

ROAR is a useful screening tool for children to take before attending a DBP clinic to identify children at high risk for reading difficulties. Assessment of the tool during a busy clinic was challenging and a larger replication is warranted.
Reconciling the efficacy and effectiveness of masking on epidemic outcomes
Authors: Yang Wan , Shaman Jeffrey
Published: May 2023

Mask wearing in public settings has been broadly implemented as a means to mitigate the COVID-19 pandemic. However, the reported effectiveness of masking has been much lower than laboratory measures of efficacy, and this large discrepancy has cast doubt on the utility of masking. Here, we develop an agent-based model that comprehensively accounts for individual masking behaviors and infectious disease dynamics, and test the impact of masking on epidemic outcomes. Using realistic inputs of mask efficacy and contact data at the individual level, the model reproduces the lower effectiveness as reported in randomized controlled trials. Model results demonstrate that transmission within households, where masks are rarely used, can substantially lower effectiveness, and reveal the interaction of nonlinear epidemic dynamics, control measures (e.g., masking and social distancing), and potential measurement biases. Overall, model results show that, at the individual level, consistent masking can reduce the risk of first infection, and, over time, reduce the frequency of repeated infection. At the population level, masking can provide direct protection to mask wearers, as well as indirect protection to non-wearers, collectively reducing epidemic intensity. These findings suggest it is prudent for individuals to use masks during an epidemic, and for policy makers to recognize the less-than-ideal effectiveness of masking when devising public health interventions.

Significance statement

During the COVID-19 pandemic, mask wearing in public settings has been a key control measure. However, the low effectiveness reported for masking has cast doubt on its validity. Here, we develop an agent-based model to interrogate influencing factors. Using realistic inputs of mask efficacy and contact data, the model reproduces the lower effectiveness reported in real-world settings. Testing shows that transmission within-household where masks are rarely used can substantially lower effectiveness. Nonetheless, the model results support the effectiveness of masking at both the individual and population levels, albeit at less-than-ideal levels. Overall, these findings indicate it is prudent for individuals to use masks during an epidemic, and for policy makers to recognize the less-than-ideal effectiveness of masking when devising interventions.
Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development
Authors: Darbellay Fabrice , Ramisch Anna , Lopez-Delisle Lucille , Kosicki Michael , Visel Axel , Andrey Guillaume
Published: May 2023

The precisely orchestrated differentiation of chondrocytes during skeleton development is a critical determinant of human height and body shape and disruptions of this process can cause severe skeletal abnormalities. The ultimate size and shape of each of over 200 bones depends on the intricate spatiotemporal regulation of chondrogenic and chondrocyte differentiation genes, but the genomic architecture coordinating these events remains poorly defined. Here we provide a comprehensive map of transcriptional enhancers specifically active in chondrocytes and show that they provide a mechanistic framework through which noncoding genetic variants can influence human stature. We isolated limb and trunk fetal chondrocytes from mice with aCol2a1fluorescent regulatory sensor and used RNA-seq to identify 780 genes that are specifically expressed during chondrogenesis. To create cell type-specific enhancer maps, we performed ATAC-seq to map open chromatin regions and ChIP-seq for H3K27ac, an enhancer-associated histone modification, and identified 2’704 putative chondrogenic enhancer regions. Most (74%) of these enhancers showedpan-chondrogenic activity, with smaller populations being restricted to limb (18%) or trunk (8%) chondrocytes only. We found that chondrogenic enhancers are enriched for the binding of several chondrogenic transcription factors including SOX9. Finally, we find that genetic variation overlapping chondrogenic enhancers explains a higher fraction of the heritability of human adult height than the one overlapping non-chondrogenic enhancers. This data provides a comprehensive mapping of the chondrogenic enhancer repertoire, paving the way to interpreting the role of non-coding sequence polymorphisms in phenotypic variation and bone diseases.
A global LC-MS2-based methodology to identify and quantify anionic phospholipids in plant samples
Authors: Genva Manon , Fougère Louise , Bahammou Delphine , Mongrand Sébastien , Boutté Yohann , Fouillen Laetitia
Published: May 2023

Anionic phospholipids (PS, PA, PI, PIPs) are low abundant phospholipids with impactful functions in cell signaling, membrane trafficking and cell differentiation processes. They can be quickly metabolized and can transiently accumulate at define spots within the cell or an organ to respond to physiological or environmental stimuli. As even a small change in their composition profile will produce a significant effect on biological processes, it is crucial to develop a sensitive and optimized analytical method to accurately detect and quantify them. While thin layer chromatography (TLC) separation coupled with gas chromatography (GC) detection methods already exist, they do not allow for precise, sensitive and accurate quantification of all anionic phospholipid species. Here we developed a method based on high performance liquid chromatography (HPLC) combined with two-dimensional mass spectrometry (MS2) by MRM mode to detect and quantify all molecular species and classes of anionic phospholipids in one-shot. This method is based on a derivatization step by methylation that greatly enhances the ionization, the separation of each peaks, the peak resolution as well as the limit of detection and quantification for each individual molecular species, and more particularly for PA and PS. Our method universally works in various plant samples. Remarkably, we identified that PS is enriched with very long chain fatty acids in the roots but not in aerial organs ofArabidopsis thaliana. Our work thus paves the way to new studies on how the composition of anionic lipids is finely tuned during plant development and environmental responses.

Significance Statement

While anionic phospholipids have key functions in plant cellular processes, their low concentration in biological samples and their low stability during the analysis complicate their quantification. Here, we present the first one-shot analytical method for the profiling and quantification of all anionic phospholipid classes and species from plant tissues with unprecedented sensitivity. This method open the way to future studies requiring a fine quantification of anionic phospholipids to understand their role in plant cell processes.
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

Silencing 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

Neural 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

Although 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.

Teaser

The 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

Improving 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

Brain 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

Changes 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

In 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

Kufs 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.
Passive diffusion accounts for the majority of intracellular vesicle transport
Authors: Sittewelle Méghane , Royle Stephen J.
Published: May 2023

During membrane trafficking, a vesicle formed at the donor compartment must travel to the acceptor membrane before fusing. For large carriers, it is established that this transport is motor-driven; however, the mode by which small vesicles, which outnumber larger carriers, are transported is poorly characterized. Here we show that intracellular nanovesicles (INVs), a substantial class of small vesicles, are highly mobile within cells and that this mobility depends almost entirely on passive diffusion (0.1–0.3 µm2s−1). Using single particle tracking, we describe how other small trafficking vesicles have a similar diffusive mode of transport, that contrasts with the motor-dependent movement of larger endolysosomal carriers. We also demonstrate that a subset of INVs are involved in constitutive secretion and that delivery of cargo to the plasma membrane during exocytosis is decreased when diffusion of INVs is specifically restricted. Our results suggest that passive diffusion is sufficient to explain the majority of small vesicle transport.
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

The 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

Molecular 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.
Elongator is a microtubule polymerase selective for poly-glutamylated tubulin
Authors: Planelles-Herrero Vicente José , Genova Mariya , Bittleston Alice , McNally Kerrie E. , Degliesposti Gianluca , Magiera Maria M. , Janke Carsten , Derivery Emmanuel
Published: May 2023

Elongator is a tRNA-modifying complex that regulates the fidelity of protein translation. Recently, a moonlighting function of Elongator has been identified in regulating polarization of the microtubule cytoskeleton during asymmetric cell division. Elongator induces symmetry breaking of the anaphase midzone by selectively stabilizing microtubules on one side of the spindle. This polarizes the segregation of signalling endosomes containing cell-fate determinants to only one daughter cell, thus contributing to cell fate determination. Here, we unravelled the molecular mechanism by which Elongator controls microtubule dynamics. Elongator binds simultaneously to the tip of microtubules and also to free GTP-tubulin heterodimers via their C-terminal tails. Elongator thereby locally increases tubulin concentration at microtubule ends, which stabilizes microtubules by increasing their growth speed and decreasing their catastrophe rate. We show that the Elp123 and Elp456 subcomplexes bind to microtubules and free tubulin heterodimers, respectively, and that these activities must be coupled for Elongator to stabilize microtubules. Surprisingly, we found that Elp456 has strong selectivity towards polyglutamylated tubulin dimers. Hence, microtubules assembled by Elongator become selectively enriched with polyglutamylated tubulin. Therefore, Elongator can rewrite the tubulin code of growing microtubules, placing it at the core of cytoskeletal dynamics and polarization during asymmetric cell division.
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

Metagenomic 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

Since 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.

IMPORTANCE

Due 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

Strategies 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.
Preferences reveal separable valuation systems in prefrontal-limbic circuits
Authors: Stoll Frederic M. , Rudebeck Peter H.
Published: May 2023

Individual preferences for the flavor of different foods and fluids exert a strong influence on behavior. Most current theories posit that preferences are integrated with other state variables in orbitofrontal cortex (OFC), which is thought to derive the relative subjective value of available options to drive choice behavior. Here we report that instead of a single integrated valuation system in OFC, another separate one is centered in ventrolateral prefrontal cortex (vlPFC) in macaque monkeys. Specifically, we found that OFC and vlPFC preferentially represent outcome flavor and outcome probability, respectively, and that preferences are separately integrated into these two aspects of subjective valuation. In addition, vlPFC, but not OFC, represented the outcome probability for the two options separately, with the difference between these representations reflecting the degree of preference. Thus, there are at least two separable valuation systems that work in concert to guide choices and that both are biased by preferences.
Ketosis regulates K+ion channels, strengthening brain-wide signaling disrupted by age
Authors: van Nieuwenhuizen Helena , Chesebro Anthony G. , Polizu Claire , Clarke Kieran , Strey Helmut H. , Weistuch Corey , Mujica-Parodi Lilianne R.
Published: May 2023

Aging is associated with impaired signaling between brain regions when measured using resting-state fMRI. This age-related destabilization and desynchronization of brain networks reverses itself when the brain switches from metabolizing glucose to ketones. Here, we probe the mechanistic basis for these effects. First, we established their neuronal basis using two datasets acquired from resting-state EEG (Lifespan:standard diet, 20-80 years, N = 201;Metabolic:individually weight-dosed and calorically-matched glucose and ketone ester challenge,μage= 26.9 ± 11.2 years, N = 36). Then, using the multi-scale Larter-Breakspear neural mass model, we identified the unique set of mechanistic parameters consistent with our clinical data. Together, our results implicate potassium (K+) gradient dysregulation as a mechanism for age-related neural desynchronization and its reversal with ketosis, the latter finding of which is consistent with direct measurement of ion channels.
Bayesian updating for self-assessment explains social dominance and winner-loser effects
Authors: Perkes Ammon , Laskowski Kate
Published: May 2023

In animal contests, winners of previous contests often keep winning and losers keep losing. This coupling of previous experiences to future success, referred to as the winner-loser effect, plays a key role in stabilizing the resulting dominance hierarchies. Despite their importance, the cognitive mechanisms through which these effects occur are unknown. Identifying the mechanisms behind winner-loser effects requires identifying plausible models and generating predictions that can be used to test these alternative hypotheses. Winner-loser effects are often accompanied by a change in the aggressiveness of experienced individuals, which suggests individuals may be adjusting their self-assessment of their abilities after each contest. This updating of a prior estimate can be effectively described by Bayesian updating, and here we implement an agent-based model with continuous Bayesian updating to explore whether this is a plausible explanation of winner-loser effects. We first show that Bayesian updating reproduces known empirical results of typical dominance interactions. We then provide a series of testable predictions that can be used in future empirical work to distinguish Bayesian updating from simpler mechanisms. Our work demonstrates the utility of Bayesian updating as a mechanism to explain and ultimately predict changes in behaviour after salient social experiences.
The Non-Phototrophic Hypocotyl3 (NPH3)-domain protein NRL5 is a trafficking-associated GTPase essential for drought resistance
Authors: Upadhyay-Tiwari Neha , Huang Xin-Jie , Lee Yi-Chen , Singh Shashi Kant , Hsu Chuan-Chi , Huang Shih-Shan , Verslues Paul E.
Published: May 2023

The mechanisms of plant resistance to low water potential (ψw) during drought are unclear but may involve signaling and trafficking at the plasma membrane as well as metabolic reprogramming, including proline accumulation. Forward genetic screening using aProline Dehydrogenase 1(ProDH1) promoter:reporterline identified a mutant with extreme low ψwhypersensitivity due to a single amino acid substitution (P335L) in the Non-Phototrophic Hypocotyl3 (NPH3) domain of NPH3/RPT2-Like5 (NRL5)/Naked Pins in Yucca8 (NPY8). Further experiments found that NRL5, and other NPH3-domain proteins, are GTPases. NRL5 interacted with RAB small GTPases and the SNARE proteins VAMP721/722 and had polar localization. NRL5P335Lhad greatly reduced GTPase activity, impaired RAB and VAMP721/722 interaction and disrupted polar localization. These data demonstrate that NRL5-mediated restraint of proline catabolism is required for drought resistance and also more broadly define unexpected functions of the NPH3 domain such that the role of NPH3-domain proteins in signaling, trafficking, and cellular polarity can be critically re-evaluated.

One-Sentence Summary

A protein containing the plant-specific NPH3-domain has GTPase activity, trafficking interaction and drought resistance function.
Copine-6 is a Ca2+sensor for activity-induced AMPA receptor exocytosis
Authors: Anson Tan Jing Zhi , Jang Se Eun , Batallas-Borja Ana , Bhembre Nishita , Chandra Mintu , Zhang Lingrui , Guo Huimin , Ringuet Mitchell T. , Widagdo Jocelyn , Collins Brett M. , Anggono Victor
Published: May 2023

The recruitment of synaptic AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors underlies the strengthening of neuronal connectivity during learning and memory. This process is triggered by NMDA (N-methyl-D-aspartate) receptor-dependent postsynaptic Ca2+influx. Synaptotagmin (Syt)-1 and −7 have been proposed as Ca2+-sensors for AMPA receptor exocytosis, but are functionally redundant. Here we identify a cytosolic C2 domain-containing Ca2+-binding protein Copine-6 that forms a complex with AMPA receptors. Loss of Copine-6 expression impairs activity-induced exocytosis of AMPA receptors in primary hippocampal neurons, which is rescued by wild-type Copine-6, but not Ca2+-binding mutants. In contrast, Copine-6 loss-of-function has no effects on steady-state expression or tetrodotoxin-induced synaptic upscaling of surface AMPA receptors. Loss of Syt-1/-7 significantly reduces Copine-6 protein expression. Interestingly, overexpression of wild-type Copine-6, but not the Ca2+-binding mutant, restores activity-dependent exocytosis of AMPA receptors in Syt-1/-7 double-knockdown neurons. We conclude that Copine-6 is a postsynaptic Ca2+-sensor that mediates AMPA receptor exocytosis during synaptic potentiation.