bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strain-dependent inhibition ofClostridioides difficileby commensalClostridiaencoding the bile acid inducible(bai)operon
Authors: Reed A.D. , Nethery M.A. , Stewart A. , Barrangou R. , Theriot C.M. 
Published: January 2020

AbstractClostridioides difficileis one of the leading causes of antibiotic-associated diarrhea. Gut microbiota-derived secondary bile acids and commensalClostridiathat encode the bile acid inducible (bai) operon are associated with protection fromC. difficileinfection (CDI), although the mechanism is not known. In this study we hypothesized that commensalClostridiaare important for providing colonization resistance againstC. difficiledue to their ability to produce secondary bile acids, as well as potentially competing againstC. difficilefor similar nutrients. To test this hypothesis, we examined the ability of four commensalClostridiaencoding thebaioperon (C. scindensVPI 12708,C. scindensATCC 35704,C. hiranonis, andC. hylemonae) to convert CA to DCAin vitro, and if the amount of DCA produced was sufficient to inhibit growth of a clinically relevantC. difficilestrain. We also investigated the competitive relationship between these commensals andC. difficileusing anin vitroco-culture system. We found that inhibition ofC. difficilegrowth by commensalClostridiasupplemented with CA was strain-dependent, correlated with the production of ∼2 mM DCA, and increased expression ofbaioperon genes. We also found thatC. difficilewas able to outcompete all four commensalClostridiain anin vitroco-culture system. These studies are instrumental in understanding the relationship between commensalClostridiaandC. difficilein the gut, which is vital for designing targeted bacterial therapeutics. Future studies dissecting the regulation of thebaioperonin vitroandin vivoand how this affects CDI will be important.ImportanceCommensalClostridiaencoding thebaioperon such asC. scindenshave been associated with protection against CDI, however the mechanism for this protection is unknown. Herein, we show four commensalClostridiathat encode thebaioperon effectC. difficilegrowth in a strain-dependent manner, with and without the addition of cholate. Inhibition ofC. difficileby commensals correlated with the efficient conversion of cholate to deoxycholate, a secondary bile acid that inhibitsC. difficilegermination, growth, and toxin production. Competition studies also revealed thatC. difficilewas able to outcompete the commensals in anin vitroco-culture system. These studies are instrumental in understanding the relationship between commensalClostridiaandC. difficilein the gut, which is vital for designing targeted bacterial therapeutics.
A newSpirodela polyrhizagenome and proteome reveal a conserved chromosomal structure with high abundances of proteins favoring energy production
Authors: Harkess Alex , McLoughlin Fionn , Bilkey Natasha , Elliott Kiona , Emenecker Ryan , Mattoon Erin , Miller Kari , Czymmek Kirk , Vierstra Richard , Meyers Blake C. , Michael Todd P. 
Published: January 2020

AbstractDuckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family.Spirodela polyrhiza, the Greater Duckweed, has the largest body plan yet the smallest genome size in the family (1C = 150 Mb). Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination. We generated a highly contiguous, chromosome-scale assembly ofSpirodela polyrhizaline Sp7498 using Oxford Nanopore plus Hi-C scaffolding (Sp7498_HiC) which is highly syntenic with a related line (Sp9509). Both the Sp7498_HiC and Sp9509 genome assemblies reveal large chromosomal misorientations in a recent PacBio assembly of Sp7498, highlighting the necessity of orthogonal long-range scaffolding techniques like Hi-C and BioNano optical mapping. Shotgun proteomics of Sp7498 verified the expression of ∼2,250 proteins and revealed a high abundance of proteins involved in photosynthesis and carbohydrate metabolism among other functions. In addition, a strong increase in chloroplast proteins was observed that correlated to chloroplast density. This Sp7498_HiC genome was generated cheaply and quickly with a single Oxford Nanopore MinION flow cell and one Hi-C library in a classroom setting. Combining these data with a mass spectrometry-generated proteome illustrates the utility of duckweed as a model for genomics- and proteomics-based education.
Metabolic and Epigenomic Regulation of Th17/Treg Balance by the Polyamine Pathway
Authors: Wang Chao , Wagner Allon , Fessler Johannes , Avila-Pacheco Julian , Karminski Jim , Thakore Pratiksha , Zaghouani Sarah , Pierce Kerry , Bod Lloyd , Schnell Alexandra , DeTomaso David , Ron-Harel Noga , Haigis Marcia , Puleston Daniel , Pearce Erika , Soleimani Manoocher , Sobel Ray , Clish Clary , Regev Aviv , Yosef Nir , Kuchroo Vijay K. 
Published: January 2020

ABSTRACTCellular metabolism can orchestrate immune cell function. We previously demonstrated that lipid biosynthesis represents one such gatekeeper to Th17 cell functional state. Utilizing Compass, a transcriptome-based algorithm for prediction of metabolic flux, we constructed a comprehensive metabolic circuitry for Th17 cell function and identified the polyamine pathway as a candidate metabolic node, the flux of which regulates the inflammatory function of T cells. Testing this prediction, we found that expression and activities of enzymes of the polyamine pathway were enhanced in pathogenic Th17 cells and suppressed in regulatory T cells. Perturbation of the polyamine pathway in Th17 cells suppressed canonical Th17 cell cytokines and promoted the expression of Foxp3, accompanied by dramatic shift in transcriptome and epigenome, transitioning Th17 cells into a Treg-like state. Genetic and chemical perturbation of the polyamine pathway resulted in attenuation of tissue inflammation in an autoimmune disease model of central nervous system, with changes in T cell effector phenotype.
In Silico Modeling of Metabolic State in Single Th17 Cells Reveals Novel Regulators of Inflammation and Autoimmunity
Authors: Wagner Allon , Wang Chao , DeTomaso David , Avila-Pacheco Julian , Zaghouani Sarah , Fessler Johannes , Eyzaguirre Sequoia , Akama-Garren Elliot , Pierce Kerry , Ron-Harel Noga , Douglas Vivian Paraskevi , Haigis Marcia , Sobel Raymond A. , Clish Clary , Regev Aviv , Kuchroo Vijay K. , Yosef Nir 
Published: January 2020

ABSTRACTCellular metabolism, a key regulator of immune responses, is difficult to study with current technologies in individual cells Here, we present Compass, an algorithm to characterize the metabolic state of cells based on single-cell RNA-Seq and flux balance analysis. We applied Compass to associate metabolic states with functional variability (pathogenic potential) amongst Th17 cells and recovered a metabolic switch between glycolysis and fatty acid oxidation, akin to known differences between Th17 and Treg cells, as well as novel targets in amino-acid pathways, which we tested through targeted metabolic assays. Compass further predicted a particular glycolytic reaction (phosphoglycerate mutase — PGAM) that promotes an anti-inflammatory Th17 phenotype, contrary to the common understanding of glycolysis as pro-inflammatory. We demonstrate that PGAM inhibition leads non-pathogenic Th17 cells to adopt a pro-inflammatory transcriptome and induce autoimmunity in vivo. Compass is broadly applicable for characterizing metabolic states of cells and relating metabolic heterogeneity to other cellular phenotypes.
MK2-deficient mice are bradycardic and display delayed hypertrophic remodelling in response to a chronic increase in afterload
Authors: Ruiz Matthieu , Khairallah Maya , Dingar Dharmendra , Vaniotis George , Khairallah Ramzi J. , Lauzier Benjamin , Thibault Simon , Trépanier Joëlle , Shi Yanfen , Douillette Annie , Hussein Bahira , Nawaito Sherin Ali , Sahadevan Pramod , Nguyen Albert , Gillis Marc-Antoine , Sirois Martin G. , Gaestel Matthias , Stanley William C. , Fiset Céline , Tardif Jean-Claude , Allen Bruce G. 
Published: January 2020

AbstractMAP kinase-activated protein kinase-2 (MK2) is protein serine/threonine kinase activated by p38α/β. Herein we examined the cardiac phenotype of pan MK2-null (MK2−/−) mice. Survival curves for male MK2+/+and MK2−/−mice did not differ (Mantel-Cox test,P= 0.580). At 12-weeks of age, MK2−/−mice exhibited normal systolic function along with signs of possible early diastolic dysfunction; however, ageing was not associated with an abnormal reduction in diastolic function. Both R-R interval and P-R segment durations were prolonged in MK2-deficient mice. However, heart rates normalized when isolated hearts were perfusedex vivoin working mode. Ca2+transients evoked by field stimulation or caffeine were similar in ventricular myocytes from MK2+/+and MK2−/−mice. MK2−/−mice had lower body temperature and an age-dependent reduction in body weight. mRNA levels of key metabolic genes, includingPpargc1a,Acadm,Lipe, andUcp3were increased in hearts from MK2−/−mice. For equivalent respiration rates, mitochondria from MK2−/−hearts showed a significant decrease in Ca2+-sensitivity to mitochondrial permeability transition pore (mPTP) opening. Finally, the pressure overload-induced increase in heart weight/tibia length and decrease in systolic function were attenuated in MK2−/−mice two weeks, but not eight weeks, after constriction of the transverse aorta. Collectively, these results implicate MK2 in (i) autonomic regulation of heart rate, (ii) cardiac mitochondrial function, and (iii) the early stages of myocardial remodeling in response to chronic pressure overload.Key points summaryThe cardiac characterization of pan MK2-null mice showed:altered autonomic regulation of heart rateincreased expression of key metabolic genesdecreased Ca2+-sensitivity for MPTP openingdelayed hypertrophic remodeling in response to increased afterload
Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species
Authors: Ellegaard Kirsten M , Suenami Shota , Miyazaki Ryo , Engel Philipp 
Published: January 2020

AbstractMost bacterial species encompass strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet, little is known about the extent to which related microbial communities differ in diversity at this level and which underlying mechanisms may constrain and maintain strain-level diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two honey bee species,Apis melliferaandApis cerana,which have diverged about 6 mio years ago. While both host species are colonized by largely overlapping bacterial 16S rRNA phylotypes, we find that their communities are highly host-specific when analyzed with genomic resolution. Despite their similar ecology,A. melliferadisplayed a much higher extent of strain-level diversity and functional gene content in the microbiota thanA. cerana,per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota ofA. melliferarelative toA. cerana. Bee management practices, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota composition of these two key pollinator species. Our results illustrate that the gut microbiota of closely related animal hosts can differ vastly in genomic diversity despite sharing similar levels of diversity at the 16S rRNA gene. This is likely to have consequences for gut microbiota functioning and host-symbiont interactions, highlighting the need for metagenomic studies to understand the ecology and evolution of microbial communities.
Glial insulin regulates cooperative or antagonistic Golden goal/Flamingo interactions during photoreceptor axon navigation
Authors: Takechi Hiroki , Hakeda-Suzuki Satoko , Nitta Yohei , Ishiwata Yuichi , Sato Makoto , Sugie Atsushi , Suzuki Takashi 
Published: January 2020

SummaryTransmembrane protein Golden goal (Gogo) interacts with the atypical cadherin Flamingo to direct R8 photoreceptor axons in theDrosophilavisual system. However, the precise mechanisms underlying Gogo regulation during columnar- and layer-specific R8 axon targeting are unknown. Our studies demonstrated that the insulin secreted from surface and cortex glia switches the phosphorylation status of Gogo, thereby regulating its two distinct functions in this process. Nonphosphorylated Gogo mediates the initial recognition of the glial protrusion in the center of the medulla column, whereas phosphorylated Gogo suppresses horizontal filopodia extension by counteracting Flamingo to maintain one axon to one column ratio. Later, Gogo expression ceases during the midpupal developmental stage, thus allowing R8 filopodia to extend vertically into the M3 layer. These results demonstrate that the long- and short-range signaling between the glia and R8 axon growth cones regulates growth cone dynamics in a stepwise manner, and thus shape the entire organization of the visual system’s functional neuronal circuit.
DPSN: standardizing the short names of amplicon-sequencing primers to avoid ambiguity
Authors: Tan Yuxiang , Tian Yixia , Chen Junyu , Yin Zhinan , Yang Hengwen 
Published: January 2020

AbstractBackgroundAmplicon sequencing is the most widely used sequencing method to evaluate microbial diversity in virtually all environments. Thus, appropriate and specific primers are needed to amplify amplicon regions in amplicon sequencing. For this purpose, the community currently uses probeBase, which curates rRNA-targeted probes and primers.Main BodyWe found that 63.58% of the primers in probeBase have problematic issues in the short name, full name, and/or position. Furthermore, the current convention for short names causes ambiguity. We here introduce our new Database of Primer Scientific Names (DPSN), which is a manually curated database for the 173 primers in probeBase complete with a new short name convention. Building on the work of probeBase, we provide a more user-friendly and standardized system. The new short primer naming convention has three basic components: 5□ position on the sense strand, version, and direction. An additional character for the name of the taxonomic group is also added in front of the name for convenient use. Furthermore, DPSN contains primers for large subunit as well. In order to separate them from the primers for small subunit, a header character is also recommended.ConclusionAll 173 primers in probeBase were corrected according to this new rule, and are stored in DPSN, which is expected to facilitate accurate primer selection and better standardized communication in this field.Database URLThe DPSN database is available in a user-interactive website athttp://dpsn.leidailab.cn/
Virtual-freezing fluorescence imaging flow cytometry
Authors: Mikami Hideharu , Kawaguchi Makoto , Huang Chun-Jung , Matsumura Hiroki , Sugimura Takeaki , Huang Kangrui , Lei Cheng , Ueno Shunnosuke , Miura Taichi , Ito Takuro , Nagasawa Kazumichi , Maeno Takanori , Watarai Hiroshi , Yamagishi Mai , Uemura Sotaro , Ohnuki Shinsuke , Ohya Yoshikazu , Kurokawa Hiromi , Matsusaka Satoshi , Sun Chia-Wei , Ozeki Yasuyuki , Goda Keisuke 
Published: January 2020

ABSTRACTBy virtue of the combined merits of flow cytometry and fluorescence microscopy, imaging flow cytometry (IFC) has become an established tool for cell analysis in diverse biomedical fields such as cancer biology, microbiology, immunology, hematology, and stem cell biology. However, the performance and utility of IFC are severely limited by the fundamental trade-off between throughput, sensitivity, and spatial resolution. For example, at high flow speed (i.e., high throughput), the integration time of the image sensor becomes short, resulting in reduced sensitivity or pixel resolution. Here we present an optomechanical imaging method that overcomes the trade-off by virtually “freezing” the motion of flowing cells on the image sensor to effectively achieve 1,000 times longer exposure time for microscopy-grade fluorescence image acquisition. Consequently, it enables high-throughput IFC of single cells at >10,000 cells/s without sacrificing sensitivity and spatial resolution. The availability of numerous information-rich fluorescence cell images allows high-dimensional statistical analysis and accurate classification with deep learning, as evidenced by our demonstration of unique applications in hematology and microbiology.
Independent representations of reward-predicting cues and reward history in frontal cortical neurons
Authors: Kondo Masashi , Matsuzaki Masanori 
Published: January 2020

SummaryThe transformation of sensory inputs to appropriate goal-directed actions requires estimation of sensory-cue values based on outcome history. To clarify how cortical neurons represent an outcome-predicting cue and actual outcome, we conducted wide-field and two-photon calcium imaging of the mouse neocortex during performance of a classical conditioning task with two cues with different water-reward probabilities. Although licking behavior dominated the area-averaged activity over the whole dorsal neocortex, dorsomedial frontal cortex (dmFrC) affected other dorsal frontal cortical activities, and its inhibition extinguished differences in anticipatory licking between the cues. In individual frontal cortical neurons, the reward-predicting cue was not simultaneously represented with the current or past reward, but licking behavior was frequently multiplexed with the reward-predicting cue and current or past reward. Deep-layer neurons in dmFrC most strongly represented the reward-predicting cue and recent reward history. Our results suggest that these neurons ignite the cortical processes required to select appropriate actions.
A Highly Selective Chemical Probe for Activin Receptor-like Kinases ALK4 and ALK5
Authors: Hanke Thomas , Wong Jong Fu , Berger Benedict-Tilmann , Abdi Ismahan , Berger Lena Marie , Tesch Roberta , Tredup Claudia , Bullock Alex N. , Müller Susanne , Knapp Stefan 
Published: January 2020

AbstractThe transforming growth factor beta-receptor I/activin receptor-like kinase 5 (TGFBR1/ALK5) and its close homologue ALK4 are receptor protein kinases associated with the development of diverse diseases, including cancer, fibrosis, heart diseases and dysfunctional immune response. Therefore, ALK4/5 are among the most studied kinases and several inhibitors have been developed. However, current commercially available inhibitors either lack selectivity or have not been comprehensively characterized, limiting their value for studying ALK4/5 function in cellular systems. To this end, we report the characterization of the 2-oxo-imidazopyridine, TP-008, a potent chemical probe with dual activity for ALK4 and ALK5 as well as the development of a matching negative control compound. TP-008 has excellent cellular potency and strongly abrogates phosphorylation of the substrate SMAD2 (mothers against decapentaplegic homolog 2). Thus, this chemical probe offers an excellent tool for mechanistic studies on the ALK4/5 signaling pathway and the contribution of these targets to disease.
Consumption rate and dietary choice of cattle in species-rich mesic grasslands
Authors: Balogh Nóra , Tóthmérész Béla , Valkó Orsolya , Deák Balázs , Tóth Katalin , Molnár Zsolt , Vadász Csaba , Tóth Edina , Kiss Réka , Sonkoly Judit , Török Péter , Antal Károly , Budai Júlia Tüdősné , Miglécz Tamás , Kelemen András 
Published: January 2020

AbstractFor the improvement and maintenance of the desirable ecological value of grasslands it is necessary to manage them in a way which maintains their structure and their long-term functioning. Extensive grazing plays a crucial role in the seasonal biomass removal, thereby it prevents litter accumulation and shrub encroachment. Defoliation and biomass removal are among the most important effects of grazing on the vegetation, while the sufficient quantity and quality of plant biomass is an important ecosystem service for animal husbandry. In order to maintain the long term functioning of pastures it is important to gather information about the amount of consumed biomass and the dietary choice of the grazers. Therefore, we studied the direct effects of grazing on species-rich meadow steppes in Central-Hungary and the underlying mechanisms of dietary choice of cattle using trait-based approach. We asked the following questions: (i) What are the direct effects of grazing on the main biomass fractions (litter, moss, forbs and graminoids)? (ii) Which traits distinguish the preferred and non-preferred vascular plant species? The studied pastures were divided into two adjacent units, which were managed differently in the study year: the grazed units were managed by grazing for three months before the sampling date, while the control units remained ungrazed until the sampling. We collected above-ground biomass samples, measured leaf traits and shoot nitrogen content of plants. The consumption of the litter and moss biomass was negligible, while the reduction of the live biomass of vascular plants was 65%. Grazing significantly decreased the flowering success of plants. Cattle consumed species characterized by high specific leaf area and high nitrogen content. Based on our results we emphasize that, in order to ensure the reproduction of most plant species in the long term, it is unfavourable to graze an area every year in the same period. Instead, it is recommended to use grazing in a mosaic spatial and temporal pattern. The livestock carrying capacity of an area and the long-term management of grasslands can be carefully planned based on biomass measurements and the nutritional value of plants, which is well indicated by some easily measurable plant properties such as specific leaf area and the nitrogen content of species.
The Ketosynthase Domain Constrains the Design of Polyketide Synthases
Authors: Klaus Maja , Buyachuihan Lynn , Grininger Martin 
Published: January 2020

AbstractModular polyketide synthases (PKSs) produce complex, bioactive secondary metabolites in assembly line-like multistep reactions. Longstanding efforts to produce novel, biologically active compounds by recombining intact modules to new modular PKSs have mostly resulted in poorly active chimeras and decreased product yields. Recent findings demonstrate that the low efficiencies of modular chimeric PKSs also result from rate limitations in the transfer of the growing polyketide chain across the non-cognate module:module interface and further processing of the non-native polyketide substrate by the ketosynthase (KS) domain. In this study, we aim at disclosing and understanding the low efficiency of chimeric modular PKSs and at establishing guidelines for modular PKSs engineering. To do so, we work with a bimodular PKS testbed and systematically vary substrate specificity, substrate identity, and domain:domain interfaces of the KS involved reactions. We observe that KS domains employed in our chimeric bimodular PKSs are bottlenecks with regards to both substrate specificity as well as interaction with the ACP. Overall, our systematic study can explain in quantitative terms why early oversimplified engineering strategies based on the plain shuffling of modules mostly failed and why more recent approaches show improved success rates. We moreover identify two mutations of the KS domain that significantly increased turnover rates in chimeric systems and interpret this finding in mechanistic detail.