bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypothalamic melanin-concentrating hormone neurons integrate food-motivated appetitive and consummatory processes
Authors: Subramanian Keshav S. , Lauer Logan Tierno , Hayes Anna M. R. , Décarie-Spain Léa , McBurnett Kara , Donohue Kristen N. , Kao Alicia E. , Bashaw Alexander G. , Burdakov Denis , Noble Emily E. , Schier Lindsey A. , Kanoski Scott E. 
Published: October 2022

AbstractThe lateral hypothalamic area (LHA) integrates homeostatic processes and reward-motivated behaviors. Here we show that LHA neurons that produce melanin-concentrating hormone (MCH) are dynamically responsive to both food-directed appetitive and consummatory processes. Specifically, our results reveal that MCH neuron Ca+2activity increases in response to both discrete and contextual food-predictive cues and is correlated with food-motivated responses. MCH neuron activity also increases during eating and this response is highly predictive of caloric consumption and declines throughout a meal, thus supporting a role for MCH neurons in the positive feedback consummatory process known as appetition. These physiological MCH neural responses are functionally-relevant as chemogenetic MCH neuron activation promotes appetitive behavioral responses to food-predictive cues and increases meal size. Finally, MCH neuron activation enhances preference for a noncaloric flavor paired with intragastric glucose. Collectively, these data identify a hypothalamic neural population that orchestrates both food-motivated appetitive and intake-promoting consummatory processes.
The C-terminal domain of RNase H and the C-terminus amino acid residue regulate virus release and autoprocessing of a defective HIV-1 possessing M50I and V151I changes in integrase
Authors: Imamichi Tomozumi , Chen Qian , Hao Ming , Chang Weizhong , Yang Jun 
Published: October 2022

AbstractPreviously, we reported that an HIV-1 variant containing Met-to-Ile change at codon 50 and Val-to-Ile mutation at codon 151 of integrase (IN), HIV(IN:M50I/V151I), was an impaired virus. Despite the mutations being in IN, the virus release was significantly suppressed (p < 0.0001) and the initiation of autoprocessing was inhibited; the mechanism of the defect remains unknown. In the current study, we attempted to identify the critical domains or amino acid (aa) residue(s) that promote defects in HIV(IN:M50I/V151I), using a series of variants, including truncated or aa-substituted RNase H (RH) or IN. The results demonstrated that virus release and the initiation of autoprocessing were regulated by the C-terminal domains (CTDs) of RH and IN. Further studies illustrated that Asp at codon 109 of RH CTD and Asp at the C terminus of IN induces the defect. This result indicated that the CTD of RH and IN in GagPol and particular aa positions in RH and IN regulated the virus release and the initiation of autoprocessing, and these sites could be potential targets for the developing new therapies.
The regulatory landscape of the yeast phosphoproteome
Authors: Leutert Mario , Barente Anthony S. , Fukuda Noelle K. , Rodriguez-Mias Ricard A. , Villén Judit 
Published: October 2022

SummaryThe cellular ability to react to environmental fluctuations depends on signaling networks that are controlled by the dynamic activities of kinases and phosphatases. To gain insight into these stress-responsive phosphorylation networks, we generated a quantitative mass spectrometry-based atlas of early phosphoproteomic responses inSaccharomyces cerevisiaeexposed to 101 environmental and chemical perturbations. We report phosphosites on 59% of the yeast proteome, with 18% of the proteome harboring a phosphosite that is regulated within 5 minutes of stress exposure. We identify shared and perturbation-specific stress response programs, uncover dephosphorylation as an integral early event, and dissect the interconnected regulatory landscape of kinase-substrate networks, as we exemplify with TOR signaling. We further reveal functional organization principles of the stress-responsive phosphoproteome based on phosphorylation site motifs, kinase activities, subcellular localizations, shared functions, and pathway intersections. This information-rich map of 25,000 regulated phosphosites advances our understanding of signaling networks.HighlightsUltra-deep reference yeast phosphoproteome covers 36,000 phosphorylation sites and reveals general principles of eukaryotic protein phosphorylation.High-dimensional quantitative atlas of early phosphoproteomic responses of yeast across 101 environmental and chemical perturbations identifies 25,000 regulated perturbation-phosphosite pairs.Identification of shared and perturbation-specific stress response phosphorylation programs reveals the importance of dephosphorylation as an early stress response.Dissection of the TOR signaling network uncovers subnetworks with differential stress responsiveness and points of pathway cross-talkIdentification of functional organization of the phosphoproteome by dimensionality reduction and co-regulation analysis.
Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis)
Authors: Wang Yongsheng , Wang Huihui , Wang Huiyuan , Zhou Ruifan , Wu Ji , Zhang Zekun , Jin Yandong , Li Tao , Kohnen Markus V. , Liu Xuqing , Wei Wentao , Chen Kai , Gao Yubang , Ding Jiazhi , Zhang Hangxiao , Liu Bo , Lin Chentao , Gu Lianfeng 
Published: October 2022

AbstractCircular RNAs are endogenous non-coding RNAs with covalently closed structures, which have important functions in plants. However, their biogenesis, degradation, and function upon treatment with gibberellins (GA) and auxins (NAA) remain unknown. Here, we systematically identified and characterized expression patterns, evolutionary conservation, genomic features, and internal structures of circRNAs using RNase R-treated libraries from moso bamboo (Phyllostachys edulis) seedlings. Moreover, we investigated the biogenesis of circRNAs dependent on both cis- and trans-regulation. We determined details regarding the function of circRNAs, including their roles in regulating microRNA-related genes and modulating the alternative splicing of their linear counterparts. Importantly, we developed a customized degradome sequencing approach to detect microRNA-mediated cleavage of circRNAs. Finally, we present a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with gibberellins (GA) and auxins (NAA). Collectively, our study uncovers important features of circRNAs including overall characteristics, biogenesis, function, and microRNA-mediated degradation of circRNAs in moso bamboo.
Century-long timelines of herbarium genomes predict plant stomatal response to climate change
Authors: Lang Patricia L.M. , Erberich Joel M. , Lopez Lua , Weiß Clemens L. , Amador Gabriel , Fung Hannah F. , Latorre Sergio M. , Lasky Jesse R. , Burbano Hernán A. , Expósito-Alonso Moisés , Bergmann Dominique 
Published: October 2022

AbstractDissecting plant responses to the environment is key to understanding if and how plants adapt to anthropogenic climate change. Stomata, plants’ pores for gas exchange, are expected to decrease in density following increased CO2concentrations, a trend already observed in multiple plant species. However, it is unclear if such responses are based on genetic changes and evolutionary adaptation. Here we make use of extensive knowledge of 43 genes in the stomatal development pathway and newly generated genome information of 191A. thalianahistorical herbarium specimens collected over the last 193 years to directly link genetic variation with climate change. While we find that the essential transcription factors SPCH, MUTE and FAMA, central to stomatal development, are under strong evolutionary constraints, several regulators of stomatal development show signs of local adaptation in contemporary samples from different geographic regions. We then develop a polygenic score based on known effects of gene knock-out on stomatal development that recovers a classic pattern of stomatal density decrease over the last centuries without requiring direct phenotype observation of historical samples. This approach combining historical genomics with functional experimental knowledge could allow further investigations of how different, even in historical samples unmeasurable, cellular plant phenotypes have already responded to climate change through adaptive evolution.One sentence summaryUsing a molecular-knowledge based genetic phenotype proxy, historical whole-genomeA. thalianatimelines compared with contemporary data indicate a shift of stomatal density following climate-associated predictions.
PhenoScore: AI-based phenomics to quantify rare disease and genetic variation
Authors: Dingemans Alexander J M , Hinne Max , Truijen Kim M G , Goltstein Lia , van Reeuwijk Jeroen , de Leeuw Nicole , Schuurs-Hoeijmakers Janneke , Pfundt Rolph , Diets Illja J , den Hoed Joery , de Boer Elke , Coenen-van der Spek Jet , Jansen Sandra , van Bon Bregje W , Jonis Noraly , Ockeloen Charlotte , Vulto-van Silfhout Anneke T , Kleefstra Tjitske , Koolen David A , Van Esch Hilde , Lyon Gholson J , Alkuraya Fowzan S , Rauch Anita , Marom Ronit , Baralle Diana , van der Sluijs Pleuntje J , Santen Gijs W E , Kooy R Frank , van Gerven Marcel A J , Vissers Lisenka E L M , de Vries Bert B A 
Published: October 2022

AbstractWhile both molecular and phenotypic data are essential when interpreting genetic variants, prediction scores (CADD, PolyPhen, and SIFT) have focused on molecular details to evaluate pathogenicity — omitting phenotypic features. To unlock the full potential of phenotypic data, we developed PhenoScore: an open source, artificial intelligence-based phenomics framework. PhenoScore combines facial recognition technology with Human Phenotype Ontology (HPO) data analysis to quantify phenotypic similarity at both the level of individual patients as well as of cohorts. We prove PhenoScore’s ability to recognize distinct phenotypic entities by establishing recognizable phenotypes for 25 out of 26 investigated genetic syndromes against clinical features observed in individuals with other neurodevelopmental disorders. Moreover, PhenoScore was able to provide objective clinical evidence for two distinctADNP-related phenotypes, that had already been established functionally, but not yet phenotypically. Hence, PhenoScore will not only be of use to unbiasedly quantify phenotypes to assist genomic variant interpretation at the individual level, such as for reclassifying variants of unknown clinical significance, but is also of importance for detailed genotype-phenotype studies.
Vague retellings of personal narratives in temporal lobe epilepsy
Authors: D’Aprano Fiore , Malpas Charles B. , Roberts Stefanie E. , Saling Michael M. 
Published: October 2022

AbstractAside from deficits identified in lexical retrieval, individuals with temporal lobe epilepsy (TLE) exhibit clinical oddities, such as circumstantiality in their language production. This becomes particularly evident when elicitation tasks impose minimal structure, or when impersonal narratives are retold over consecutive occasions. Personal reminiscence is highly specific and localised in time, placing specific demands on cognitive-linguistic systems. It is presumed that the nature of this elicitation paradigm will produce a unique psycholinguistic phenotype in those with TLE. Among controls there is a compression of output for impersonal narratives, but the opposite effect when personal narratives are retold. To investigate the micro- and macrolinguistic processes underpinning personal discourse production in TLE, we examined the elicited language output of in 15 surgically naïve individuals with TLE and 14 healthy controls. Participants were asked to recall and re-tell an autobiographical memory on four immediately consecutive occasions, representing an alternative unstructured elicitation. Following transcription and coding of output, a detailed multi-level discourse analysis of output volume, fluency, cohesion, and coherence was conducted. There were significant group by trial interactions for the number of novel units, the number of non-progression units, and for the proportion of non-progression to novel content. As anticipated, a distinctly different pattern emerged in TLE when compared with controls who did not compress their output volume across repetitions but instead produced greater novelty, and a more coherent and refined account over time. Individuals with TLE consistently told a less distinct story across repetitions, with disturbances in fluency, cohesion, and coherence. This reflects a reduced capacity to produce a coherent mental representation, in all likelihood related to the neurolinguistic demands of recalling and retelling specific personal events.
Microbial diversity and community dynamics in an active, high CO2subsurface rift ecosystem
Authors: Lipus Daniel , Jia Zeyu , Sondermann Megan , Bussert Robert , Bartholomäus Alexander , Yang Sizhong , Wagner Dirk , Kallmeyer Jens 
Published: October 2022

AbstractThe Eger Rift subsurface is characterized by frequent seismic activity and consistently high CO2concentrations, making it a unique deep biosphere ecosystem and a suitable site to study the interactions between volcanism, tectonics, and microbiological activity. Pulses of geogenic H2during earthquakes may provide substrates for methanogenic and chemolithotrophic processes, but very little is currently known about the role of subsurface microorganisms and their cellular processes in this type of environment. To assess the impact of geologic activity on microbial life, we analyzed the geological, geochemical, and microbiological composition of rock and sediment samples from a 240 m deep drill core, running across six lithostratigraphic zones. In addition, we evaluated diversity as well as metabolic attributes of bacterial and archaeal communities. Our investigation revealed a distinct low biomass community, with a surprisingly diverse Archaea population, providing strong support that methanogenic archaea reside in the Eger subsurface. Geochemical analysis revealed sulfate and sodium concentrations as high as 1000 mg L−1in sediment samples from a depth between 50 and 100 m and in weathered rock samples collected below 200 m.Most microbial signatures could be assigned to common soil and water bacteria, which together with the occurrence of freshwater Cyanobacteria at specific depths, emphasize the heterogenous, groundwater movement driven nature of this terrestrial subsurface environment. Although not as frequently and abundantly as initially expected, our investigations also found evidence for anaerobic, autotrophic, and acidophilic communities in Eger Rift sediments, as sulfur cycling taxa likeThiohalophilusandDesulfosporosinuswere specifically enriched at depths below 100 m. The detection of methanogenic, halophilic, and ammonia oxidizing archaeal populations demonstrate that the unique features of the Eger Rift subsurface environment provide the foundation for diverse types of microbial life, including the microbial utilization of geologically derived CO2and when available H2, as a primary energy source.
Physico-chemical characterization of single bacteria and spores using optical tweezers
Authors: Nilsson Daniel P.G. , Jonsmoen Unni Lise , Malyshev Dmitry , Öberg Rasmus , Wiklund Krister , Andersson Magnus 
Published: October 2022

ABSTRACTSpore-forming pathogenic bacteria are adapted for adhering to surfaces, and their endospores can tolerate strong chemicals making decontamination difficult. Understanding the physico-chemical properties of bacteria and spores is therefore essential in developing antiadhesive surfaces and disinfection techniques. However, measuring physico-chemical properties in bulk does not show the heterogeneity between cells. Characterizing bacteria on a single-cell level can provide mechanistic clues usually hidden in bulk measurements. This paper shows how optical tweezers can be applied to characterize single bacteria and spores, and how physico-chemical properties related to adhesion, fluid dynamics, biochemistry, and metabolic activity can be assessed.
A quorum of mechano-sensing fungal consortia
Authors: García-Navarrete M. , Sanchis D. Ruiz , Sánchez-Muñoz I. , González-Ruiz S. , Avdovic M. , Atienza-Sanz S. , Wabnik K. 
Published: October 2022

SummaryBacteria use Quorum sensing (QS) to coordinate gene expression in dense cell populations. Here, we show that eukaryoteS. Cerevisiaeuses an alternative strategy, the quorum mechano-sensing (QMS), to resolve growth conflicts in the fungal consortia. QMS connects the biomechanical signal perception through adhesin FLO11 and transmembrane histidine kinase SLN1, triggering an intracellular signaling cascade for the cell density-dependent regulation of gene expression. Both cis and trans interactions of FLO11 are required for the inhibition of SLN1 and involve the extracellular fibronectin type III-like domain of FLO11. Genetic deletion of FLO11 removes inhibition of SLN1, associated with the spontaneous activation of gene expression whereas overproduction of FLO11 strengthens the inhibitory effect of FLO11 on SLN1. Therefore, adjusting the amount of FLO11 directly scales with the level of SLN1 inhibition, forecasting the outcome of growth competition at the macroscopic scale. Furthermore, the integration of an orthogonal synthetic circuit downstream of SLN1 allows for QMS-controlled regulation of gene expression in cell populations. Our study reveals a molecular pathway connecting FLO11 adhesion to SLN1-dependent intracellular regulation of gene expression in fungi. FLO11 and SLN1 coordinate kin recognition and growth conflict resolution through gene expression in dense fungal populations. This study challenges the classical view of chemically-driven QS and provides new strategies for controlling population growth through quorum mechano-sensing.
Transposons repressed by H3K27me3 were co-opted as cis-regulatory elements of H3K27me3 controlled protein coding genes during evolution of plants
Authors: Hisanaga Tetsuya , Romani Facundo , Wu Shuangyang , Kowar Teresa , Lintermann Ruth , Jamge Bhagyshree , Montgomery Sean A. , Axelsson Elin , Dierschke Tom , Bowman John L. , Fujiwara Takayuki , Hirooka Shunsuke , Miyagishima Shin-ya , Dolan Liam , Schubert Daniel , Berger Frédéric 
Published: October 2022

SummaryThe mobility of transposable elements (TEs) contributes to evolution of genomes1,2. Meanwhile, their uncontrolled activity causes genomic instability and therefore expression of TEs is silenced by host genomes3,4. TEs are marked with DNA and H3K9 methylation that are associated with silencing in flowering plants5, animals, and fungi6. Yet, in distantly related eukaryotes TEs are instead marked by H3K27me3 deposited by the Polycomb Repressive Complex 2 (PRC2)7–11, an epigenetic mark associated with gene silencing in multicellular eukaryotes12–15. It was therefore proposed that the ancestral activity of PRC2 was the deposition of H3K27me3 to silence TEs16.To test this hypothesis we obtained mutants deprived of PRC2 activity and used genomics to analyze the role of PRC2 in extant species along the lineage of Archaeplastida. While in the red algaCyanidioschyzon merolaemore TEs than genes were repressed by PRC2, an opposite trend was observed in bryophytesMarchantia polymorphaandAnthoceros agrestis. In the red alga, TEs silenced by H3K27me3 are in subtelomeres but in bryophytes, TEs and genes marked by H3K27me3 form coregulated transcriptional units. The latter trend was also observed in the flowering plantArabidopsis thaliana, and we identified cis-elements recognised by transcription factors in TEs flanking genes repressed by PRC2.Together with the silencing of TEs by PRC2 in ciliates that diverged early from an ancestor common with Archaeplastida, our findings support the hypothesis that PRC2 deposited H3K27me3 to silence TEs in early lineages of eukaryotes. During evolution, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation that control networks of genes regulated by PRC2.HighlightsH3K27me3 marks a decreasing proportion of TEs during evolution of plantsThe polycomb repressive complex 2 represses TEs in red algae and bryophytesH3K27me3-marked TEs in flowering plants contain transcription factor binding sitesTranscription factors bind TEs and regulate networks of genes controlled by PRC2
Exposing New Taxonomic Variation with Inflammation – A Murine Model-Specific Genome Database for Gut Microbiome Researchers
Authors: Leleiwi Ikaia , Rodriguez-Ramos Josue , Shaffer Michael , Sabag-Daigle Anice , Kokkinias Katherine , Flynn Rory M , Daly Rebecca A , Kop Linnea FM , Solden Lindsey M , Ahmer Brian M. M. , Borton Mikayla A , Wrighton Kelly C 
Published: October 2022

AbstractBackgroundThe murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminatedSalmonellainteractions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs.ResultsHere we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated andSalmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~42.4 Gbps/sample), we reconstructed 2,281 bacterial and 4,129 viral draft genomes.Salmonellachallenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of theAlistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation resistant strains.ConclusionsThis CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on howSalmonellaremodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches.Salmonella-induced inflammation suppressedAlistipesand other dominant members, while rarer commensals likeLactobacillusandEnterococcusendure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally.