bluuebunny/crossref_metadata_2025 huggingface dataset:
RBMS1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon
Authors: Yu Johnny , Culbertson Bruce , Asgharian Hosseinali , Navickas Albertas , Fish Lisa , Olegario John Paolo , Hänisch Benjamin , Weinberg Ethan M , Dienstmann Rodrigo , Warren Robert S , Goodarzi Hani
Published: January 2020

Broad dysregulation of gene expression control is a hallmark of cancer progression. Identifying the underlying master regulators that drive pathological gene expression is a key challenge in precision oncology. Here, we have developed a network analytical framework, named PRADA, that identifies oncogenic RNA-binding proteins through the systematic detection of coordinated changes in their target regulons. Application of this approach to data collected from clinical samples, patient-derived xenografts, and cell line models of colon cancer metastasis revealed the RNA-binding protein RBMS1 as a suppressor of colon cancer progression. We observed that silencing RBMS1 results in increased metastatic capacity in xenograft mouse models, and that restoring its expression blunts metastatic liver colonization. We have found that RBMS1 functions as a post-transcriptional regulator of RNA stability by directly binding and stabilizing ~80 target mRNAs. Measurements in more than 180 clinical samples as well as survival analyses in publicly available datasets, have shown that RBMS1 silencing and the subsequent downregulation of its targets are strongly associated with disease progression and poor survival in colon cancer patients. Together, our findings establish a role for RBMS1 as a previously unknown regulator of RNA stability and as a suppressor of colon cancer metastasis with clinical utility for risk stratification of patients.

Significance

By applying a new analytical approach to transcriptomic data from clinical samples and models of colon cancer progression, we have uncovered RBMS1 as a suppressor of metastasis and as a post-transcriptional regulator of RNA stability. Notably, RBMS1 silencing and downregulation of its targets are negatively associated with patient survival.
p.E152K-STIM1 mutation deregulates Ca2+signaling contributing to chronic pancreatitis
Authors: Burgos Miguel , Philippe Reginald , Antigny Fabrice , Buscaglia Paul , Masson Emmanuelle , Mukherjee Sreya , Dubar Pauline , Le Maréchal Cédric , Campeotto Florence , Lebonvallet Nicolas , Frieden Maud , Llopis Juan , Domingo Beatriz , Stathopulos Peter B. , Ikura Mitsuhiko , Brooks Wesley , Guida Wayne , Chen Jian-Min , Ferec Claude , Capiod Thierry , Mignen Olivier
Published: January 2020

Since deregulation of intracellular Ca2+can lead to intracellular trypsin activation and STIM1 (stromal interaction molecule-1) protein is the main regulator of Ca2+homeostasis in pancreatic acinar cells, we explored the Ca2+signaling in 37 STIM1 variants found in three pancreatitis patient cohorts. Extensive functional analysis of one particular variant, p.E152K, identified in three patients, provided a plausible link between dysregulated Ca2+signaling within pancreatic acinar cells and chronic pancreatitis susceptibility. Specifically, p.E152K, located within the STIM1 EF-hand and sterile α-motif domain, increased the release of Ca2+from the endoplasmic reticulum in patient-derived fibroblasts and transfected HEK293T cells. This event was mediated by altered STIM1-sarco/endoplasmic reticulum calcium transport ATPase (SERCA) interactions and enhanced SERCA pump activity leading to increased Store Operated Calcium Entry (SOCE). In the pancreatic AR42J cells expressing the p.E152K variant, Ca2+-signaling perturbations correlated with defects in trypsin activation and secretion, and increased cytotoxicity after cholecystokinin stimulation.

Summary statement

p.E152K-STIM1 variant found in pancreatitis patients leads to intracellular changes in calcium homeostasis through SERCA interaction, enabling intracellular trypsin activation and pancreatic acinar cell death.
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

Clostridioides 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.

Importance

CommensalClostridiaencoding 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

Duckweeds 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

Cellular 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

Cellular 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

MAP 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 summary

The cardiac characterization of pan MK2-null mice showed:

altered autonomic regulation of heart rate

increased expression of key metabolic genes

decreased Ca2+-sensitivity for MPTP opening

delayed 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

Most 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

Transmembrane 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

Background

Amplicon 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 Body

We 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.

Conclusion

All 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 URL

The 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

By 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

The 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

The 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

For 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

Modular 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.
Dietary supplementation with PUFAs rescues the eggshell defects caused byseipinmutations inC. elegans
Authors: Bai Xiaofei , Huang Leng-Jie , Chen Sheng-Wen , Nebenfuehr Ben , Wysolmerski Brian , Wu Jui-Ching , Olson Sara K. , Golden Andy , Wang Chao-Wen
Published: January 2020

SEIPIN, an ER membrane protein, plays critical roles in lipid droplet (LD) formation and lipid storage. Dysfunction of SEIPIN causes a variety of human diseases, including lipodystrophy, neuropathies, and male and female infertility. However, the cellular and molecular mechanisms of SEIPIN in causing these diseases are poorly understood. To address such mechanisms, we investigated the functional roles ofR01B10.6 (seip-1), the soleSEIPIN1ortholog inC. elegans,using CRISPR/Cas9 gene editing, and transcriptional assays. SEIP-1::mScarlet is widely expressed throughout development inC. elegans. Three full gene deletion mutants, generated by CRISPR/Cas9, displayed penetrant embryonic lethality. EM imaging and the visualization of reporter genes revealed that the lipid-rich permeability barrier, the innermost layer of theC. elegansembryonic eggshell, was defective or missing. Intriguingly, depletion of SEIP-1 revealed a perturbed gene expression pattern for fatty acid biosynthesis enzymes, in agreement with the disrupted permeability barrier formation phenotype of the embryos. Lastly, dietary supplementation of PUFAs rescued the embryonic lethality and defective permeability barrier in the deletion mutants. In sum, our study suggests that SEIP-1 may maternally regulate LD biogenesis and maintain lipid homeostasis to orchestrate the formation of the lipid-rich permeability barrier, which is crucial for eggshell formation and embryogenesis.
Proteogenomic single cell analysis of skeletal muscle myocytes
Authors: Fomchenko Katherine M. , Verma Rohan X. , Kannan Suraj , Lin Brian L. , Yang Xiaoping , Nieuwenhuis Tim O. , Patil Arun H. , Fox-Talbot Karen , McCall Matthew N. , Kwon Chulan , Kass David A. , Rosenberg Avi Z. , Halushka Marc K.
Published: January 2020

Skeletal muscle myocytes have evolved into slow and fast-twitch types. These types are functionally distinct as a result of differential gene and protein expression. However, an understanding of the complexity of gene and protein variation between myofibers is unknown. We performed deep, whole cell, single cell RNA-seq on intact and fragments of skeletal myocytes from the mouse flexor digitorum brevis muscle. We compared the genomic expression data of 171 of these cells with two human proteomic datasets. The first was a spatial proteomics survey of mosaic patterns of protein expression utilizing the Human Protein Atlas (HPA) and the HPASubC tool. The second was a mass-spectrometry (MS) derived proteomic dataset of single human muscle fibers. Immunohistochemistry and RNA-ISH were used to understand variable expression. scRNA-seq identified three distinct clusters of myocytes (a slow/fast 2A cluster and two fast 2X clusters). Utilizing 1,605 mosaic patterned proteins from visual proteomics, and 596 differentially expressed proteins by MS methods, we explore this fast 2X division. Only 36 genes/proteins had variable expression across all three studies, of which nine are newly described as variable between fast/slow twitch myofibers. An additional 414 genes/proteins were identified as variable by two methods. Immunohistochemistry and RNA-ISH generally validated variable expression across methods presumably due to species-related differences. In this first integrated proteogenomic analysis of mature skeletal muscle myocytes we confirm the main fiber types and greatly expand the known repertoire of twitch-type specific genes/proteins. We also demonstrate the importance of integrating genomic and proteomic datasets.
Regulation of human development by ubiquitin chain editing of chromatin remodelers
Authors: Beck David B. , Basar Mohammed A. , Asmar Anthony J. , Thompson Joyce , Oda Hirotsugu , Uehara Daniela T. , Saida Ken , D’Souza Precilla , Bodurtha Joann , Mu Weiyi , Barañano Kristin W. , Miyake Noriko , Wang Raymond , Kempers Marlies , Nishimura Yutaka , Okada Satoshi , Kosho Tomoki , Dale Ryan , Mitra Apratim , Macnamara Ellen ,   Undiagnosed Diseases Network, Matsumoto Naomichi , Inazawa Johi , Walkiewicz Magdalena , Tifft Cynthia J. , Aksentijevich Ivona , Kastner Daniel L. , Rocha Pedro P. , Werner Achim
Published: January 2020

Embryonic development occurs through commitment of pluripotent stem cells to differentiation programs that require highly coordinated changes in gene expression. Chromatin remodeling of gene regulatory elements is a critical component of how such changes are achieved. While many factors controlling chromatin dynamics are known, mechanisms of how different chromatin regulators are orchestrated during development are not well understood. Here, we describe LINKED (LINKage-specific-deubiquitylation-deficiency-inducedEmbryonicDefects) syndrome, a novel multiple congenital anomaly disorder caused by hypomorphic hemizygous missense variants in the deubiquitylase OTUD5/DUBA. Studying LINKED mutations in vitro, in mouse, and in models of neuroectodermal differentiation of human pluripotent stem cells, we uncover a novel regulatory circuit that coordinates chromatin remodeling pathways during early differentiation. We show that the K48-linkage-specific deubiquitylation activity of OTUD5 is essential for murine and human development and, if reduced, leads to aberrant cell-fate specification. OTUD5 controls differentiation through preventing the degradation of multiple chromatin regulators including ARID1A/B and HDAC2, mutation of which underlie developmental syndromes that exhibit phenotypic overlap with LINKED patients. Accordingly, loss of OTUD5 during early differentiation leads to less accessible chromatin at neural and neural crest enhancers and thus aberrant rewiring of gene expression networks. Our work identifies a novel mechanistic link between phenotypically related developmental disorders and an essential function for linkagespecific ubiquitin editing of substrate groups (i.e. chromatin remodeling complexes) during early cellfate decisions – a regulatory concept, we predict to be a general feature of embryonic development.
Low-N protein engineering with data-efficient deep learning
Authors: Biswas Surojit , Khimulya Grigory , Alley Ethan C. , Esvelt Kevin M. , Church George M.
Published: January 2020

Protein engineering has enormous academic and industrial potential. However, it is limited by the lack of experimental assays that are consistent with the design goal and sufficiently high-throughput to find rare, enhanced variants. Here we introduce a machine learning-guided paradigm that can use as few as 24 functionally assayed mutant sequences to build an accurate virtual fitness landscape and screen ten million sequences viain silicodirected evolution. As demonstrated in two highly dissimilar proteins, avGFP and TEM-1 β-lactamase, top candidates from a single round are diverse and as active as engineered mutants obtained from previous multi-year, high-throughput efforts. Because it distills information from both global and local sequence landscapes, our model approximates protein function even before receiving experimental data, and generalizes from only single mutations to propose high-functioning epistatically non-trivial designs. With reproducible >500% improvements in activity from a single assay in a 96-well plate, we demonstrate the strongest generalization observed in machine-learning guided protein function optimization to date. Taken together, our approach enables efficient use of resource intensive high-fidelity assays without sacrificing throughput, and helps to accelerate engineered proteins into the fermenter, field, and clinic.
The 2019-new coronavirus epidemic: evidence for virus evolution
Authors: Benvenuto Domenico , Giovannetti Marta , Ciccozzi Alessandra , Spoto Silvia , Angeletti Silvia , Ciccozzi Massimo
Published: January 2020

There is concern about a new coronavirus, the 2019-nCoV, as a global public health threat. In this article, we provide a preliminary evolutionary and molecular epidemiological analysis of this new virus. A phylogenetic tree has been built using the 15 available whole genome sequence of 2019-nCoV and 12 whole genome sequences highly similar sequences available in gene bank (5 from SARS, 2 from MERS and 5 from Bat SARS-like Coronavirus). FUBAR analysis shows that the Nucleocapsid and the Spike Glycoprotein has some sites under positive pressure while homology modelling helped to explain some molecular and structural differences between the viruses. The phylogenetic tree showed that 2019.nCoV significantly clustered with Bat SARS-like Coronavirus sequence isolated in 2015, whereas structural analysis revealed mutation in S and nucleocapsid proteins. From these results, 2019nCoV could be considered a coronavirus distinct from SARS virus, probably transmitted from bats or another host where mutations conferred upon it the ability to infect humans.
Pioneer transcription factors in chromatin remodeling: the kinetic proofreading view
Authors: Schiessel Helmut , Blossey Ralf
Published: January 2020

Pioneer transcription factors are a recently defined class of transcription factors which can bind directly to nucleosomal DNA; they play a key role in gene activation in certain pathways. Here we quantify their role in the initiation of nucleosome displacement within the kinetic proofreading scenario of chromatin remodeling. The model allows to perform remodeling efficiency comparisons for scenarios involving different types of transcription factors and remodelers as a function of their binding and unbinding rates and concentrations. Our results demonstrate a novel way to fine-tune the specificity of processes that modify the chromatin structure in transcriptional initiation.
Variation in maize chlorophyll biosynthesis alters plant architecture
Authors: Khangura Rajdeep S. , Johal Gurmukh S. , Dilkes Brian P.
Published: January 2020

Chlorophyll is a tetrapyrrole metabolite essential for photosynthesis in plants. Theoil yellow1(oy1) gene of maize encodes subunit I of Magnesium chelatase, the enzyme catalyzing the first committed step of chlorophyll biosynthesis. A range of chlorophyll contents and net CO2assimilation rates can be achieved in maize by combining a semi-dominant mutant allele,Oy1-N1989,and cis-regulatory alleles encoded by the Mo17 inbred calledvery oil yellow1(vey1). We previously demonstrated that these allelic interactions can delay reproductive maturity. In this study, we demonstrate that multiple gross morphological traits respond to a reduction in chlorophyll. We found that stalk width, number of lateral branches (tillers), and branching of the inflorescence decline with a decrease in chlorophyll level. Chlorophyll variation suppressed tillering in multiple maize mutants includingteosinte branched1,grassy tiller1, andTillering1as well as thetiller number1QTL responsible for tillering in many sweet corn varieties. In contrast to these traits, plant height showed a non-linear response to chlorophyll levels. Weak suppression ofOy1-N1989byvey1B73resulted in a significant increase in mutant plant height. This was true in multiple mapping populations, isogenic inbreds, and hybrid backgrounds. Enhancement of theOy1-N1989mutants by thevey1Mo17allele reduced chlorophyll contents and plant height in mapping populations and isogenic inbred background. We demonstrate that the effects of reduced chlorophyll content on plant growth and development are complex and that the genetic relationship depends on the trait. We propose that growth control for branching and architecture are downstream of energy balance sensing.
Ancestry-agnostic estimation of DNA sample contamination from sequence reads
Authors: Zhang Fan , Flickinger Matthew , Taliun Sarah A. Gagliano ,   InPSYght Psychiatric Genetics Consortium, Abecasis Gonçalo R. , Scott Laura J. , McCaroll Steven A. , Pato Carlos N. , Boehnke Michael , Kang Hyun Min
Published: January 2020

Detecting and estimating DNA sample contamination are important steps to ensure high-quality genotype calls and reliable downstream analysis. Existing methods rely on population allele frequency information for accurate estimation of contamination rates. Correctly specifying population allele frequencies for each individual in early stage of sequence analysis is impractical or even impossible for large-scale sequencing centers that simultaneously process samples from multiple studies across diverse populations. On the other hand, incorrectly specified allele frequencies may result in substantial bias in estimated contamination rates. For example, we observed that existing methods often fail to identify 10% contaminated samples at a typical 3% contamination exclusion threshold when genetic ancestry is misspecified. Such an incomplete screening of contaminated samples substantially inflates the estimated rate of genotyping errors even in deeply sequenced genomes and exomes. We propose a robust statistical method that accurately estimates DNA contamination and is agnostic to genetic ancestry of the intended or contaminating sample. Our method integrates the estimation of genetic ancestry and DNA contamination in a unified likelihood framework by leveraging individual-specific allele frequencies projected from reference genotypes onto principal component coordinates. Our method can also be used for estimating genetic ancestries, similar to LASER or TRACE, but simultaneously accounting for potential contamination. We demonstrate that our method robustly estimates contamination rates and genetic ancestries across populations and contamination scenarios. We further demonstrate that, in the presence of contamination, genetic ancestry inference can be substantially biased with existing methods that ignore contamination, while our method corrects for such biases.
FiXR: a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments
Authors: Roig-Solvas Biel , Brooks Dana H. , Makowski Lee
Published: January 2020

Ab initio reconstruction methods have revolutionized the capabilities of small-angle X-ray scattering (SAXS), allowing the data-driven discovery of previously unknown molecular conformations, exploiting optimization heuristics and assumptions behind the composition of globular molecules. While these methods have been successful for the analysis of small particles, their impact on fibrillar assemblies has been more limited. The micrometre-range size of these assemblies and the complex interaction of their periodicities in their scattering profiles indicate that the discovery of fibril structures from SAXS measurements requires novel approaches beyond extending existing tools for molecular discovery. In this work, it is proposed to use SAXS measurements, together with diffraction theory, to infer the electron distribution of the average cross-section of a fiber. This cross-section is modeled as a discrete electron density with continuous support, allowing representations beyond binary distributions. Additional constraints, such as non-negativity or smoothness/connectedness, can also be added to the framework. The proposed approach is tested using simulated SAXS data from amyloid β fibril models and using measured data of Tobacco mosaic virus from SAXS experiments, recovering the geometry and density of the cross-sections in all cases. The approach is further tested by analyzing SAXS data from different amyloid β fibril assemblies, with results that are in agreement with previously proposed models from cryo-EM measurements. The limitations of the proposed method, together with an analysis of the robustness of the method and the combination with different experimental sources, are also discussed.
Digitalizing supply chains potential benefits and impact on lean operations
Authors: Haddud Abubaker , Khare Anshuman
Published: January 2020

Purpose

New technological trends continue to emerge, and businesses adopt them in different capacity in a pursuit of improving current ways of doing things and to gain competitive advantages over rivals. One of the key business functions that is impacted by the implementation of different disruptive technologies is the supply chain management. As a result, there is a continuous need to identify where digitalizing supply chains may provide businesses with benefits to capitalize such gains. This study aims to examine potential impacts of digitalizing supply chains on five selected lean operations practices through the identification of key areas and benefits under each of these practices.

Design/methodology/approach

Data were collected from 74 participants mainly from the academic community and who were university scholars through the use of an online survey. The used online survey consists of six main parts in total, but three were included in this paper and these were designed to gather data about participants’ general information, level of influence of seven technological trends on supply chain performance and management and potential impact of digitalizing supply chains on five lean operations practices.

Findings

The authors were able to confirm the significant impact of digitalizing supply chains on the five examined lean operations practices. Most of the examined potential impacts were found to improve certain areas that directly improve the practices of the explored five lean operations practices as well as the overall supply chain and business performance. They were also able to determine the level of influence of the seven examined enabling technologies on supply chain performance and management.

Originality/value

To the best of the authors’ knowledge, this study is the first of its kind. Although some literature explored different aspects related to the concept of Industry 4.0 and digitalizing supply chains, no study has specifically explored potential impacts of digitalizing supply chains on lean operations. The results from this study can be beneficial to academic scholars interested in the researched themes, business professionals specializing in supply chain management and lean operations, organizations within different industrial sectors particularly manufacturing where lean thinking is adopted and any other party interested in understanding more about the impact of digitalizing supply chain on lean operations and on an overall business performance.
Investigation and optimization of textured thrust bearings with spirally distributed dimples using multi-objective optimization method
Authors: Li Qiang , Wang Yujun , Zhang Shuo , Xu Wei-Wei , Bai Lu , Wang Zhenbo
Published: January 2020

Purpose

Surface textures have been widely used in thrust bearings as a means of enhancing the tribological performance. The effect of textures with a spiral distribution on the lubrication characteristics of thrust bearings has not been fully covered. This paper aims to investigate and find the optimal structure and distribution parameters of textures with the maximum loading capacity and minimum friction force as goals.

Design/methodology/approach

Combining the multi-objective optimization method based on the non-dominated sorted genetic algorithm-II with response surface methodology, the key textured parameters are optimized. Local sensitivity analysis is used to evaluate the impact level of each parameter.

Findings

Spiral distribution of textures can effectively improve the lubrication performance of the thrust bearing compared with the linear distribution. The distribution with high amplitudes and high cycle numbers will weaken the spiral effect and destroy the high-pressure region. Through the multi-objective optimization of the textured structure and distribution parameters, the loading capacity demonstrates a 55.05per cent improvement compared to the basic model. Textured width is the most sensitive parameter for both loading capacity and friction force.

Originality/value

Present research provides a fundamental design guide for textured thrust bearings.