bluuebunny/crossref_metadata_2025_split huggingface dataset:
IL-17A-mediated alterations in gut microbiota composition, particularly changes in Prevotella abundance, impact Treg function in CNS Autoimmunity
Authors: Shahi Shailesh K. , Ghimire Sudeep , Jensen Samantha N. , Lehman Peter , Rux Allison G , Turner Ti-Ara , Borcherding Nicholas , Gibson-Corley Katherine N. , Ganesan Sukirth M. , Karandikar Nitin J. , Mangalam Ashutosh K. 
Published: May 2022

AbstractA disrupted equilibrium among gut microbiota, IL-17A-producing CD4 T-cells (Th17), and regulatory CD4 T-cells (Treg) have been linked with the pathobiology of multiple sclerosis (MS). While gut microbiota can regulate both Treg and Th17 cells, the impact of IL-17A on this gut-immune connection remains unclear. Utilizing HLA-DR3 transgenic mouse model of MS, we show that IL-17A deficiency (HLA-DR3.IL17A-/-) resulted in milder disease characterized by increased Tregs and expansion of Treg-promoting gut microbes, includingPrevotella. Cohousing HLA-DR3 mice with HLA-DR3.IL17A-/-transferred the milder disease phenotype and associated microbiota changes to DR3 mice, highlighting the dominant role of gut microbiota in Treg induction and disease amelioration. DR3.IL17A-/-mice also showed a higher abundance of functional pathways linked with short-chain fatty acid synthesis and elevated IL-10 in dendritic cells. Enrichment of the Treg-promoting PPAR signaling pathway expression in the colon of HLA-DR3.IL17A-/-mice and followingPrevotellaadministration in HLA-DR3 mice underscores the importance of gut microbiota in IL-17A-mediated immune regulation. Thus, our study uncovers a previously unappreciated role for IL-17A in shaping gut microbiota and immune regulation, with far-reaching implications for MS treatment.One-Sentence SummaryIL-17A modulates Treg and gut microbiota to control EAE
The effect of sleep continuity disruption on multimodal emotion processing and regulation: a laboratory-based, randomized, controlled experiment in good sleepers
Authors: Reid MJ. , Omlin X. , Espie CA. , Sharman R. , Tamm S. , Kyle SD. 
Published: May 2022

AbstractPrevious research shows that experimental sleep deprivation alters emotion processing, suggesting a potential mechanism linking sleep disruption to mental ill-health. Extending previous work, we experimentally disrupted sleep continuity in good sleepers and assessed next-day emotion processing and regulation using tasks with established sensitivity to depression. In a laboratory-based study, 51 good sleepers (37 female; mean age = 24 years, SD= 3.63) were randomized to one night (23:00-07:00) of uninterrupted sleep (n=24) or sleep continuity disruption (n=27). We assessed emotion perception, attention, and memory the following day. Participants also completed an emotion regulation task and measures of self-reported affect, anxiety, sleepiness, overnight declarative memory consolidation, and psychomotor vigilance. Confirming the effects of the manipulation, sleep continuity disruption led to a marked decrease in polysomnography-defined total sleep time (229.98 mins vs 434.57 mins), increased wake-time after sleep onset (260.66 mins vs 23.84 mins) and increased sleepiness (d=0.81). Sleep continuity disruption led to increased anxiety (d=0.68), decreased positive affect (d=-0.62), reduced overnight declarative memory consolidation (d=-1.08) and reduced psychomotor vigilance [longer reaction times (d=0.64) and more lapses (d=0.74)], relative to control. However, contrary to our hypotheses, experimental sleep disruption had no effect on perception of, or bias for, emotional facial expressions, emotional memory for words, or emotion regulation following worry induction. In conclusion, one night of sleep continuity disruption had no appreciable effect on objective measures of emotion processing or emotion regulation in response to worry induction, despite clear effects on memory consolidation, vigilance, and self-reported affect and anxiety.
A Chalcone Synthase-Like Bacterial Protein Catalyzes Heterocyclic C-Ring Cleavage of Naringenin to Alter Bioactivity Against Nuclear Receptors in Colonic Epithelial Cells
Authors: Gülşan Ebru Ece , Nowshad Farrhin , Leigh Meredith Davis , Crott Jimmy W , Safe Stephen , Jayaraman Arul , Lee Kyongbum 
Published: May 2022

SummaryThe human gut microbiota contributes enzymatic functions that are unavailable to host cells and play crucial roles in host metabolism, nutrient processing and regulating immune functions. As dietary compounds that are only partially absorbed, flavonoids are available for metabolism by gut microbiota, leading to diverse bioactive products. Combining prediction of enzyme promiscuity, metabolomics, and in vitro model systems, we identified a bacterial enzyme that can catalyze heterocyclic C-ring cleavage of naringenin. Culture experiments using a wild-type and mutant strain of Bacillus subtilis confirmed that the enzyme is a chalcone synthase-like polyketide synthase. The prediction-validation methodology developed in this work could be used to systematically characterize the products of gut bacterial flavonoid metabolism and identify the responsible enzymes and species. Further, we demonstrated that naringenin and its ring cleavage metabolites differentially engage the AhR and NR4A in intestinal epithelial cells. Our results suggest that the abundance of selected gut bacterial species impacts the profile of bioactive flavonoids and flavonoid-derived metabolites and thereby influences inflammatory responses in the intestine. These results are significant for understanding the mechanisms of gut microbiota-dependent effects of dietary flavonoids.
Polarly Localized WPR Proteins Interact With PAN Receptors And The Actin Cytoskeleton During Maize Stomatal Development
Authors: Nan Qiong , Char Si Nian , Yang Bing , Bennett Eric J. , Yang Bing , Facette Michelle R. 
Published: May 2022

ABSTRACTPolarization of cells prior to asymmetric cell division is crucial for correct cell divisions, cell fate and tissue patterning. In maize stomatal development, polarization of subsidiary mother cells prior to asymmetric division is controlled by the BRK-PAN-ROP pathway. Two catalytically inactive receptor-like kinases, PAN2 and PAN1, are required for correct division plane positioning. Proteins in the BRK-PAN-ROP pathway are polarized in subsidiary mother cells, with the polarization of each protein dependent on the previous one. As most of the known proteins in this pathway do not physically interact, possible interactors that might participate in the pathway are yet to be described. We identified WPR proteins as new players during subsidiary mother cell polarization. WPRs physically interact with PAN receptors, and polarly accumulate in subsidiary mother cells. The polarized localization of WPR proteins depends on PAN2 but not PAN1. CRISPR-Cas9- induced mutations result in division plane defects in subsidiary mother cells, and ectopic expression of WPR-RFP results in stomatal defects and alterations to the actin cytoskeleton. We show certain WPR proteins directly interact with F-actin through their N-terminus. Our data implicate WPR proteins as potentially regulating actin filaments, which providing insight into their molecular function. Together, these results demonstrate that WPR proteins are important for cell polarization.One-sentence summaryFour related proteins, identified via their physical interaction with the receptor PAN2, are polarly localized prior to asymmetric division in stomatal lineage cells, and interact with F-actin.
Run-on sequencing reveals nascent transcriptomics of the human microbiome
Authors: Vill Albert C. , Rice Edward J. , De Vlaminck Iwijn , Danko Charles G. , Brito Ilana L. 
Published: May 2022

ABSTRACTPrecise regulation of transcription initiation and elongation enables bacteria to control cellular responses to environmental stimuli. RNAseq is the most common tool for measuring the transcriptional output of bacteria, comprising predominantly mature transcripts. To gain further insight into transcriptional dynamics, it is necessary to discriminate actively transcribed loci from those represented in the total RNA pool. One solution is to capture RNA polymerase (RNAP) in the act of transcription, but current methods are restricted to culturable and genetically tractable organisms. Here, we apply precision run-on sequencing (PRO-seq) to profile nascent transcription, a method amenable to diverse species. We find that PRO-seq is well-suited to profile small, structured, or post-transcriptionally modified RNAs, which are often excluded from RNAseq libraries. When PRO-seq is applied to the human microbiome, we identify taxon-specific RNAP pause motifs. We also uncover concurrent transcription and cleavage of guide RNAs and tRNA fragments at active CRISPR and tRNA loci. We demonstrate the specific utility of PRO-seq as a tool for exploring transcriptional dynamics in diverse microbial communities.
Implications for food safety of the size and location of fragments of lead shotgun pellets embedded in hunted carcasses of small game animals intended for human consumption
Authors: Green Rhys E. , Taggart Mark A. , Pain Deborah J. , Smithson Keturah 
Published: May 2022

AbstractCarcasses of common pheasants (Phasianus colchicus) killed by hunters using shotguns are widely used or sold in the United Kingdom and elsewhere for human consumption. Almost all of the birds are shot using shotgun pellets composed principally of lead (Pb). Lead shotgun pellets often fragment on impact within the bodies of gamebirds, leaving small lead particles in the meat that are difficult for consumers to detect and remove and from which a greater proportion of lead is likely to be absorbed. Chronic exposure to even low levels of lead is associated with negative health effects in humans and especially in groups particularly vulnerable to the effects of lead, which include young children and pregnant women. Our study used a high-resolution computerised tomography X-ray scanner to locate, in three dimensions, metal fragments embedded within carcasses of eight pheasants sold for human consumption in the UK. Small radio-dense fragments (<2 mm diameter), assumed to be metallic lead, were present in all of the pheasant carcasses examined (mean number: 39 per carcass) and many were too small (<0.1 mm diameter) and too distant from the nearest large shotgun pellet for it to be practical for consumers to detect and remove them without discarding a large proportion of otherwise usable meat. Consumers of carcasses of pheasants killed using lead shotgun ammunition are likely to be exposed to elevated levels of dietary lead, even if careful food preparation is practiced to remove shotgun pellets and the most damaged tissue.
Quantifying the fraction of new mutations that are recessive lethal
Authors: Wade Emma E. , Kyriazis Christopher C. , Cavassim Maria Izabel A. , Lohmueller Kirk E. 
Published: May 2022

AbstractThe presence and impact of recessive lethal mutations has been widely documented in diploid outcrossing species. However, precise estimates in different species of the proportion of mutations that are recessive lethal remain limited. Here, we attempt to quantify the fraction of new mutations that are recessive lethal using Fit∂a∂i, a commonly-used method for inferring the distribution of fitness effects (DFE) using the site frequency spectrum. Using simulations, we demonstrate that Fit∂a∂i cannot accurately estimate the fraction of recessive lethal mutations, as expected given that Fit∂a∂i assumes that all mutations are additive by default. Consistent with the idea that mis-specification of the dominance model can explain this performance, we find that Fit∂a∂i can accurately infer the fraction of additive lethal mutations. Moreover, we demonstrate that in both additive and recessive cases, inference of the deleterious non-lethal portion of the DFE is minimally impacted by a small proportion (<10%) of lethal mutations. Finally, as an alternative approach to estimate the proportion of mutations that are recessive lethal, we employ models of mutation-selection-drift balance using existing genomic parameters and segregating recessive lethals estimates for humans and Drosophila melanogaster. In both species, we find that the segregating recessive lethal load can be explained by a very small fraction (<1%) of new nonsynonymous mutations being recessive lethal. Our results refute recent assertions of a much higher recessive lethal mutation fraction (4-5%), while highlighting the need for additional information on the joint distribution of selection and dominance coefficients.
Circular mRNA encoded PROTAC (RiboPROTAC) as a new platform for the degradation of intracellular therapeutic targets
Authors: Yang Jiali , Sun Jiaojiao , Zhu Jiafeng , Du Yaran , Tan Yiling , Wei Lixiang , Zhao Yang , Hou Qiangbo , Zhang Yan , Sun Zhenhua , Zuo Chijian 
Published: May 2022

AbstractAlthough proteolysis targeting chimera (PROTAC) technology that hijacking the ubiquitin-proteasome system (UPS) to artificially degrade protein is an emerging promising technology for many undruggable targets, it still faces several challenges, such as the difficulty to select high specificity molecule to protein of interest (POI), and only few of the E3-ligase are suitable for PROTAC mediated protein degradation. Protein-based PROTAC, termed BioPROTAC, owns the advantage of specificity but lacks membrane permeability. Here, we develop a new targeted protein degrading platform, which we termed RiboPROTAC, by encoding BioPROTAC protein degraders with circular mRNA (cmRNA) and delivering intracellularly. In this way, intracellular protein GFP and nuclear protein PCNA were successfully degraded. For PCNA targeting, not only the level of target protein is strongly decreased, but also the cell function related is strongly interfered, such as cell proliferation, apoptosis, as well as the cell cycle. What is more, for the first time, we observed that degrading PCNA with RiboPROTAC causes immunogenic cell death (ICD), although not strong, but was verified in vivo. Importantly, our in vivo results demonstrated that cmRNA encoded PCNA degrader exhibited significant tumor suppression effect, thus we provide the first proof of concept for the application of RiboPROTAC as potential mRNA therapeutic. We consider that RiboPROTAC is a new and superior PROTAC technology for targeting the undruggable targets.
A method to enrich polypeptidyl-tRNAs to capture snapshots of translation in the cell
Authors: Yamakawa Ayako , Niwa Tatsuya , Chadani Yuhei , Kobo Akinao , Taguchi Hideki 
Published: May 2022

AbstractLife depends on proteins, which all exist in nascent states when the growing polypeptide chain is covalently attached to a tRNA within the ribosome. Although the nascent chains; i.e., polypeptidyl-tRNAs (pep-tRNAs), are considered as merely transient intermediates during protein synthesis, recent advances have revealed that they are directly involved in a variety of cell functions, such as gene expression control. An increasing appreciation for fine-tuning at translational levels demands a general method to handle the pep-tRNAs on a large scale. Here, we developed a method termed peptidyl-tRNA enrichment using organic extraction and silica adsorption (PETEOS), and then identify their polypeptide moieties by mass spectrometry. As a proof-of-concept experiment using Escherichia coli, we identified ∼800 proteins derived from the pep-tRNAs, which were markedly biased towards the N-termini in the proteins, reflecting that PETEOS captured the intermediate pep-tRNA population during translation. Furthermore, we observed the changes in the pep-tRNA set in response to heat shock or antibiotic treatments. In summary, PETEOS will complement conventional methods for profiling nascent chains such as ribosome profiling.Significance StatementIn the central dogma of biology, RNA and protein are usually regarded as two completely independent molecular species. However, they are combined into a single species called peptidyl-tRNA (pep-tRNA) during the translation process in the ribosome. Despite the importance of pep-tRNAs as precursors of all proteins in the cell, a general method to analyze pep-tRNAs on a large scale was lacking. Taking advantage of the properties of pep-tRNAs as RNA and protein, we developed a method to enrich the pep-tRNAs by organic solvent extraction and silica column separation. The method, termed PETEOS, not only provides a unique approach to examine the nascent state of proteins but also may be effective in capturing snapshots of translation status in the cell.
Saturation mutagenesis of a predicted ancestral Syk-family kinase
Authors: Hobbs Helen T. , Shah Neel H. , Shoemaker Sophie R. , Amacher Jeanine F. , Marqusee Susan , Kuriyan John 
Published: May 2022

ABSTRACTMany tyrosine kinases cannot be expressed readily in E. coli, limiting facile production of these proteins for biochemical experiments. We used ancestral sequence reconstruction to generate a spleen tyrosine kinase (Syk) variant that can be expressed in bacteria and purified in soluble form, unlike the human members of this family (Syk and ZAP-70). The catalytic activity, substrate specificity, and regulation by phosphorylation of this Syk variant are similar to the corresponding properties of human Syk and ZAP-70. Taking advantage of the ability to express this novel Syk-family kinase in bacteria, we developed a two-hybrid assay that couples the growth of E.coli in the presence of an antibiotic to successful phosphorylation of a bait peptide by the kinase. Using this assay, we screened a site-saturation mutagenesis library of the kinase domain of this reconstructed Syk-family kinase. Sites of loss-of-function mutations identified in the screen correlate well with residues established previously as critical to function and/or structure in protein kinases. We also identified activating mutations in the regulatory hydrophobic spine and activation loop, which are within key motifs involved in kinase regulation. Strikingly, one mutation in an ancestral Syk-family variant increases the soluble expression of the protein by 75-fold. Thus, through ancestral sequence reconstruction followed by deep mutational scanning, we have generated Syk-family kinase variants that can be expressed in bacteria with very high yield.
Ancestral Body Plan and Adaptive Radiation of Sauropterygian Marine Reptiles
Authors: Wang Wei , Shang Qinghua , Cheng Long , Wu Xiao-Chun , Li Chun 
Published: May 2022

SUMMARYMesozoic was the age of reptiles that not only occupied the land and sky but also adapted to the sea. Sauropterygia, from turtle-like placodonts, lizard-like pachypleurosaurs, and predatory nothosaurs to long-necked pistosaurs including plesiosaurs, is one of the most predominant lineages among secondarily aquatic reptiles. However, we know little about the early evolution of sauropterygians involving the morphological gaps among aforementioned sub-groups and their ancestral body-plan, because the Early Triassic fossil remains are scarce shortly after their origin. Here we report a skeleton from the Early Triassic in South China, representing the oldest known complete specimen related to Sauropterygia. It can be referred to Hanosaurus hupehensis and shows a mosaic morphology combining the characters of multiple sauropterygian sub-lineages. We constructed an updated character matrix obtaining the hitherto most comprehensive phylogeny of Triassic sauropterygians, and Hanosaurus hupehensis is stably resolved as the basal-most member of the Sauropterygiformes (clade nov.). Sauropterygians were previously considered using limb propulsion for the movement that is distinguishable from ichthyosaurs and other marine reptiles, but this skeleton reflects an ancestral body plan of sauropterygians unexpectedly developing an elongate trunk and four short limbs, being different from most sauropterygians but more convergently similar to the basal members of other marine reptilian lineages in body shape. After this convergence, we confirm the rapid adaptive radiation of sauropterygiform reptiles following the end-Permian mass extinction. Our results provide an evolutionary framework of sauropterygian marine reptiles and highlight the integrations of both convergences and divergences when an emerging animal lineage arises.
A highly contiguous, scaffold-level nuclear genome assembly for the Fever tree (Cinchona pubescens Vahl) as a novel resource for research in the Rubiaceae
Authors: Canales Nataly Allasi , Pérez-Escobar Oscar A. , Powell Robyn F. , Töpel Mats , Kidner Catherine , Nesbitt Mark , Maldonado Carla , Barnes Christopher J. , Rønsted Nina , Przelomska Natalia A. S. , Leitch Ilia J. , Antonelli Alexandre 
Published: May 2022

AbstractBackgroundThe Andean Fever tree (Cinchona L.; Rubiaceae) is the iconic source of bioactive quinine alkaloids, which have been vital to treating malaria for centuries. C. pubescens Vahl, in particular, has been an essential source of income for several countries within its native range in north-western South America. However, an absence of available genomic resources is essential for placing the Cinchona species within the tree of life and setting the foundation for exploring the evolution and biosynthesis of quinine alkaloids.FindingsWe address this gap by providing the first highly contiguous and annotated nuclear and organelle genome assemblies for C. pubescens. Using a combination of ∼120 Gb of long sequencing reads derived from the Oxford Nanopore PromethION platform and 142 Gb of short-read Illumina data. Our nuclear genome assembly comprises 603 scaffolds comprising a total length of 904 Mb, and the completeness represents ∼85% of the genome size (1.1 Gb/1C). This draft genome sequence was complemented by annotating 72,305 CDSs using a combination of de novo and reference-based transcriptome assemblies. Completeness analysis revealed that our assembly is moderately complete, displaying 83% of the BUSCO gene set and a small fraction of genes (4.6%) classified as fragmented. Additionally, we report C. pubescens plastome with a length of ∼157 Kb and a GC content of 37.74%. We demonstrate the utility of these novel genomic resources by placing C. pubescens in the Gentianales order using additional plastid and nuclear datasets.ConclusionsOur study provides the first genomic resource for C. pubescens, thus opening new research avenues, including the provision of crucial genetic resources for analysis of alkaloid biosynthesis in the Fever tree.
Top-down modulation of the retinal code via histaminergic neurons of the hypothalamus
Authors: Warwick Rebekah A. , Riccitelli Serena , Heukamp Alina S. , Yaakov Hadar , Ankri Lea , Mayzel Jonathan , Gilead Noa , Parness-Yossifon Reut , Rivlin-Etzion Michal 
Published: May 2022

SummaryThe mammalian retina is considered an autonomous circuit, yet work dating back to Ramon y Cajal indicates that it receives inputs from the brain. How such inputs affect retinal processing has remained unknown. We identified brain-to-retina projections of histaminergic neurons from the mouse hypothalamus, which densely innervated the dorsal retina. Histamine application, or chemogenetic activation of histaminergic axons, altered spontaneous and light-evoked activity of various retinal ganglion cells (RGCs), including direction-selective RGCs. These cells exhibited broader directional tuning and gained responses to high motion velocities. Such changes could improve vision when objects move fast across the visual field (e.g. while running), which fits with the known increased activity of histaminergic neurons during arousal. In humans, an antihistamine drug non-uniformly modulated visual sensitivity across the visual field, indicating an evolutionary conserved function of the histaminergic system. Our findings expose a previously unappreciated role for brain-to-retina projections in modulating retinal function.