bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competing endogenous RNA network: Potential entrants to gene editing in Hepatocellular Carcinoma Gene editing of ceRNA in Hepatocellular Carcinoma
Authors: Shafei Ayman El-Sayed , Matboli Marwa , Ali Mahmoud A. , Nagy Ziad , Reda Maged , Salah Mohamed , Hamdy Ahmed , Abdelgawad Mahmoud , Ashry Ahmed , Tarek Mohammad , Saber Osama , Azazy Ahmed , Mohamed Badr , Hassan Mohmed K. , El-Khazragy Nashwa , El-Khamisy Sherif 
Published: March 2018

AbstractBackgroundHepatocellular Carcinoma (HCC) is the leading cause of cancer deaths worldwide as well as in Egypt. We aimed to use Clustered Regulatory Interspaced Short Palindromic Repeats (CRISPR) gene editing technique to induce forced down-regulation of the circRNA which consequently modified miRNA expression in HepG2 cell line to prove the regulatory relationship between the RNA parts of an in silico-detected competing endogenous RNA network in HCCMethodWe first retrieved hsa_circ_0000064-miR-1285-TRIM2 mRNA from public microarray databases followed by in silico modelling to mimic the regulation kinetics of cirRNA associated ceRNA network. Secondly, we performed polymerase chain reaction (PCR)-based amplification of synthetic fragments, Gibson assembly of both CRISPR and non CRISPR based circuits, E-coli transformation, plasmid purification, HePG2 cell line transfection. Finally Expression levels of the chosen RNAs in hepatocellular carcinoma (HCC) cell line, HepG2, were examined by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and the cytotoxic effect was validated by viability assay.TRIM2 protein expression was proved by immunohistochemistry and flowcytometry.ResultsInduction of hsa_circ_0000064 into HepG2 cell line via CRISPR-and non-CRISPR mediated synthetic circuit resulted in statistically significant decrease in cell number and, then, cellular viability with marked increase in hsa_circ_0000064 and TRIM2 mRNA levels and concomitant decrease in miR-1285 expression in HepG2 cell line compared with control (p<0.0). Moreover exogenous expression of hsa_circ_0000064 in HepG2 cell line showed increased expression of the tumor suppressor protein, TRIM2.ConclusionsOur integrative approach, including in silico data analysis and experimental validation proved that CRISPR-mediated synthetic circuit-based overexpression of hsa_circ_0000064 was more efficient than conventional transient transfection, representing a promising therapeutic strategy for HCC.Data AvailabilityOur Data was made available online on the IGEM wiki of team AFCM-EGYPT:http://2017.igem.org/Team:AFCM-Egypt. Synthetic parts have been submitted to IGEM Parts Registry.Financial DisclosureThe project was funded by Armed Forces College of Medicine AFCM, Zewail City of Science and Technology, National Research Center NRC, VitaBiotics, PHARCO Pharmaceuticals, Sim Era and DANUB Paintings. IDT provided 20 kb of DNA synthesis. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Deciphering signaling specificity with interpretable deep neural networks
Authors: Luo Yunan , Ma Jianzhu , Liu Yang , Ye Qing , Ideker Trey , Peng Jian 
Published: March 2018

AbstractProtein kinase phosphorylation is a prevalent post-translational modification (PTM) regulating protein function and transmitting signals throughout the cell. Defective signal transductions, which are associated with protein phosphorylation, have been revealed to link to many human diseases, such as cancer. Defining the organization of the phosphorylation-based signaling network and, in particular, identifying kinase-specific substrates can help reveal the molecular mechanism of the signaling network. Here, we present DeepSignal, a deep learning framework for predicting the substrate specificity for kinase/SH2 sequences with or without mutations. Empowered by the memory and selection mechanism of recurrent neural network, DeepSignal can identify important specificity-defining residues to predict kinase specificity and changes upon mutations. Evaluated on several public benchmark datasets, DeepSignal significantly outperforms current methods on predicting substrate specificity on both kinase and SH2 domains. Further analysis in The Cancer Genome Atlas (TCGA) demonstrated that DeepSignal is able to aggregate mutations on both kinase/SH2 domains and substrates to quantify binding specificity changes, predict cancer genes related to signaling transduction, and identify novel perturbed pathways.AvailabilityImplementation of DeepSignal is athttps://github.com/luoyunan/DeepSignal
Characterisation of gut microbiota of farmed Chinook salmon using metabarcoding
Authors: Ciric Milica , Waite David , Draper Jenny , Jones John Brian 
Published: March 2018

ABSTRACTWith the growing importance of aquaculture worldwide, characterisation of the microbial flora of high-value aquaculture species and identification of gut flora shifts induced by changes in fish physiology or nutrition is of special interest.Here we report the first metabarcoding survey of the intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and intestinal samples, and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles.Over 1,000 operational taxonomic units (OTUs) were identified within the cohort, providing a first glimpse into the gut microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the familyVibrionaceae.This survey was performed amid a summer heat wave, during which the fish exhibited reduced feeding. Although the sampled fish appeared healthy, they had minimal intestinal content, and the observed intestinal flora may represent the microbiota of fasting and stressed fish. Limited comparison betweenMycoplasmaandVibriosequences from the Chinook salmon gut and published microbial sequences from the intestines of a variety of fish species (including Atlantic salmon) indicated that despite the starvation and temperature variations, the replacement ofVibriowithMycoplasmais occurring within expected ecological parameters and does not necessarily reflect colonisation by atypical microbes.DATA SUMMARYRaw sequences from Chinook salmon intestinal microbiome 16S survey generated on the Illumina platform are publically available through NCBI Sequence Read Archive (SRA) database:Bioproject PRJNA421844SRA study SRP134829https://www.ncbi.nlm.nih.gov/bioproject/PRJNA421844IMPACT STATEMENTAlthough 16S metabarcoding surveys are becoming routine, little is still known about the microbiota of fish. This is the first survey of the intestinal microbiota of Chinook salmon, a species native to the Pacific Northwest which is farmed in New Zealand and Chile. While most intestinal microbiota studies are performed on faecal material, we directly sampled the intestine epithelium and content.During the time of sampling, the farmed fish population was experiencing stress from a summer heat wave and had little intestinal content. Over 1,000 operational taxonomic units (OTUs) were identified within the intestines of the cohort, providing a first glimpse into the gut microbiota of farmed Chinook salmon.We believe this survey will be of interest not only to those interested in fish biology and aquaculture, but also as an addition to the ongoing debate in the literature on sampling and DNA extraction methods for challenging samples.
Cyclophilins A and B Oppositely Regulate Renal Tubular Epithelial Phenotype
Authors: Sarró Eduard , Durán Mónica , Rico Ana , Croatt Anthony J. , Nath Karl A. , Teresa Salcedo Maria , Gundelach Justin H. , Batlle Daniel , Bram Richard J. , Meseguer Anna 
Published: March 2018

AbstractCyclophilins (Cyp) are peptidil-prolyl-isomerases and the intracellular receptors for the immunosuppressant Cyclosporine-A (CsA), which produces epithelial-mesenchymal-transition (EMT) and renal tubule-interstitial fibrosis. Since CsA inhibits Cyp enzymatic activity, we hypothesized that Cyp could be involved in EMT and fibrosis. Here, we demonstrate that CypB is a critical regulator of tubule epithelial cell plasticity on the basis that: i) CypB silencing caused epithelial differentiation in proximal tubule-derived HK-2 cells, ii) CypB silencing prevented TGFβ-induced EMT in HK-2, and iii) CypB knockdown mice exhibited reduced UUO-induced inflammation and kidney fibrosis. By contrast, silencing of CypA induces a more undifferentiated phenotype and favors TGFβ effects. EMT mediators Slug and Snail were up-regulated in CypA-silenced cells, while in CypB silencing, Slug, but not Snail, was down-regulated; thus, reinforcing the role of Slug in kidney fibrosis. CypA regulates Slug through its PPIase activity whereas CypB depends on its ER location, where interacts with calreticulin, a calcium modulator which is involved in TGFβ signaling. In conclusion, this work uncovers new roles for CypA and CypB in modulating proximal tubular cell plasticity.
Discovery and Characterization of Novel Lignocellulose-Degrading Enzymes from the Porcupine Microbiome
Authors: Thornbury Mackenzie , Sicheri Jacob , Guinard Caroline , Mahoney David , Routledge Francis , Curry Matthew , Elaghil Mariam , Boudreau Nicholas , Tsai Angela , Slaine Patrick , Finlayson-Trick Emma , Getz Landon , Cook Jamie , Rohde John , McCormick Craig 
Published: March 2018

AbstractPlant cell walls are comprised of cellulose, hemicellulose, and lignin, collectively known as lignocellulose. Microorganisms degrade these components to liberate sugars to meet metabolic demands. Using a metagenomic sequencing approach, we previously demonstrated that the microbiome of the North American porcupine (Erethizon dorsatum) is replete with novel lignocellulose-degrading enzymes. Here, we report the identification, synthesis and partial characterization of four genes from the porcupine microbiome encoding putative novel lignocellulose-degrading enzymes, including a β-xylanase, endoxylanase, β-glucosidase, and an ⍺-L-arabinofuranosidase. These genes were identified via conserved catalytic domains associated with cellulose and hemicellulose degradation. We cloned the putative β-xylanase into the pET26b(+) plasmid, enabling inducible gene expression inEscherichia coli(E. coli) and periplasmic localization. We demonstrated IPTG-inducible accumulation of β-xylanase protein but failed to detect xylobiose degrading activity in a reporter assay. Alternative assays may be required to measure activity of this putative β-xylanase. In this report, we describe how a synthetic metagenomic pipeline can be used to identify novel microbial lignocellulose-degrading enzymes and take initial steps to introduce a hemicellulose-degradation pathway intoE. colito enable biofuel production from wood pulp feedstock.
Strong replicators associated with open chromatin are sufficient to establish an early replicating domain
Authors: Brossas Caroline , Chilaka Sabarinadh , Counillon Antonin , Laurent Marc , Goncalves Coralie , Duriez Bénédicte , Prioleau Marie-Noëlle 
Published: March 2018

AbstractVertebrate genomes replicate according to a precise temporal program strongly correlated with their organization into topologically associating domains. However, the molecular mechanisms underlying the establishment of early-replicating domains remain largely unknown. We defined two minimal cis-element modules containing a strong replication origin and chromatin modifier binding sites capable of shifting a targeted mid-late replicating region for earlier replication. When inserted side-by-side, these modules acted in cooperation, with similar effects on two late-replicating regions. Targeted insertions of these two modules at two chromosomal sites separated by 30 kb brought these two modules into close physical proximity and induced the formation of an early-replicating domain. Thus, combinations of strong origins and cis-elements capable of opening the chromatin structure are the basic units of early-replicating domains, and are absent from late-replicated regions. These findings are consistent with those of genome-wide studies mapping strong initiation sites and open chromatin marks in vertebrate genomes.
Porter 5: state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes
Authors: Torrisi Mirko , Kaleel Manaz , Pollastri Gianluca 
Published: March 2018

AbstractMotivationAlthough Secondary Structure Predictors have been developed for more than 60 years, current ab initio methods have still some way to go to reach their theoretical limits. Moreover, the continuous effort towards harnessing ever increasing data sets and more sophisticated, deeper Machine Learning techniques, has not come to an end.ResultsHere we present Porter 5, the last release of one of the best performing ab initio secondary structure predictor. Version 5 achieves 84% accuracy (84% SOV) when tested on 3 classes, and 73% accuracy (82% SOV) on 8 classes, on a large independent set, significantly outperforming all the most recent ab initio predictors we have tested.AvailabilityThe web and standalone versions of Porter5 are available at http://distilldeep.ucd.ie/porter.Contactname@bio.comSupplementary informationSupplementary data are available at Bioinformatics online.
Soil salinity inhibits plant shade avoidance
Authors: Hayes Scott , Tween Adrian Louis , van Gelderen Kasper , de Vries Michel , Prat Salomé , Schuurink Robert. C. , Testerink Christa , Pierik Ronald 
Published: March 2018

SummaryGlobal food production is set to keep increasing despite a predicted decrease in total arable land [1]. To achieve higher production, denser planting will be required on increasingly degraded soils. When grown in dense stands, crops elongate and raise their leaves in an effort to reach sunlight, a process termed shade-avoidance [2]. Shade is perceived by a reduction in the ratio of red (R) to (FR) light and results in the stabilisation of a class of transcription factors known as PHYTOCHROME INTERACTING FACTORs (PIFs) [3,4]. PIFs activate the expression of auxin biosynthesis genes [4,5] and enhance auxin sensitivity [6], which promotes cell wall loosening and drives elongation growth. Despite our molecular understanding of shade-induced growth, little is known about how this developmental programme is integrated with other environmental factors.Here we demonstrate that low levels of NaCl in soil strongly impair the ability of plants to respond to shade. This block is dependent upon abscisic acid (ABA) signalling and the canonical ABA signalling pathway. Low R:FR light enhances the expression of a positive regulator of the brassinosteroid (BR) signalling pathway, BRASSINOSTEROID SIGNALLING KINASE 5 (BSK5). We found that ABA inhibits BSK5 up-regulation and interferes with GSK3-like kinase inactivation by the BR pathway, thus leading to a suppression of PIF function. By demonstrating a link between the ABA and BR-signalling pathways this study provides an important step forward in our understanding of how environmental cues are integrated into plant development.
Mesenchymal stromal cell remodeling of a gelatin hydrogel microenvironment defines an artificial hematopoietic stem cell niche
Authors: Gilchrist Aidan E. , Lee Sunho , Hu Yuhang , Harley Brendan A.C. 
Published: March 2018

AbstractHematopoietic stem cells (HSCs) reside in the bone marrow within discrete niches defined by a complex milieu of external signals including biophysical cues, bound and diffusible biomolecules, and heterotypic cell-cell interactions. Recent studies have shown the importance of autocrine-mediated feedback of cell-secreted signals and the interplay between matrix architecture and biochemical diffusion on hematopoietic stem cell activity. Autocrine and paracrine signaling from HSCs and niche-associated mesenchymal stromal cells (MSCs) have both been suggested to support HSC maintenance in vivo and in vitro. Here we report the development of a library of methacrylamide-functionalized gelatin (GelMA) hydrogels to explore the balance between autocrine feedback and paracrine signals from co-encapsulated murine bone marrow MSCs on murine HSCs. The use of a degradable GelMA hydrogel enables the possibility for significant MSC-mediated remodeling, yielding dynamic shifts in the matrix environment surrounding HSCs. We identify a combination of an initially low-diffusivity hydrogel and a 1:1 HSPC:MSC seeding ratio as conducive to enhanced HSC population maintenance and quiescence. Further, gene expression and serial mechanical testing data suggests that MSC-mediated matrix remodeling is significant for the long-term HSC culture, reducing HSC autocrine feedback and potentially enhancing MSC-mediated signaling over 7-day culture in vitro. This work demonstrates the design of an HSC culture system that couples initial hydrogel properties, MSC co-culture, and concepts of dynamic reciprocity mediated by MSC remodeling to achieve enhanced HSC maintenance.One Sentence SummaryCoupling effects of hydrogel biotransport, heterotypic cell culture, and matrix remodeling enhances hematopoietic stem cell culture and quiescence.
A comprehensive toolkit to enable MinION sequencing in any laboratory
Authors: Schalamun Miriam , Kainer David , Beavan Eleanor , Nagar Ramawatar , Eccles David , Rathjen John P. , Lanfear Robert , Schwessinger Benjamin 
Published: March 2018

AbstractLong-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realising their full potential relies crucially on extracting high quality, high molecular weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which potentiates all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. One challenge of the MinION is that each group has to independently establish effective protocols for using the instrument, which can be time consuming and costly. Here we present a workflow and protocols that enabled us to establish MinION sequencing in our own laboratories, based on optimising DNA extractions from a challenging plant tissue as a case study. Following the workflow illustrated we were able to reliably and repeatedly obtain > 8.5 Gb of long read sequencing data with a mean read length of 13 kb and an N50 of 26 kb. Our protocols are open-source and can be performed in any laboratory without special equipment. We also illustrate some more elaborate workflows which can increase mean and average read lengths if this is desired. We envision that our workflow for establishing MinION sequencing, including the illustration of potential pitfalls, will be useful to others who plan to establish long-read sequencing in their own laboratories.
Cullin1 represses systematic inflammasome activation by binding and catalyzing NLRP3 ubiquitination
Authors: Wan Pin , Zhang Qi , Liu Weiyong , Jia Yaling , Wang Tianci , Wang Wenbiao , Pan Pan , Yang Ge , Xiang Qi , Huang Siyu , Yang Qingyu , Zhang Wei , Liu Fang , Wu Kailang , Liu Yingle , Wu Jianguo 
Published: March 2018

AbstractActivation of the NLRP3 inflammasome is a key process of host immune response, the first line of defense against cellular stresses and pathogen infections. However, excessive inflammasome activation damages the hosts, and thus it must be precisely controlled. The mechanism underlying the repression of systematic inflammasome activation remains largely unknown. This study reveals that CUL1, a key component of the SCF E3 ligase, plays a critical role in regulation of the inflammasome. CUL1 suppresses the inflammasome activation in HEK293T cells, inhibits endogenous NLRP3 in macrophages, and represses inflammatory responses in C57BL/6 mice. Under normal physiological conditions, CUL1 interacts with NLRP3 to disrupt the inflammasome assembly, and catalyzes NLRP3 ubiquitination to repress the inflammasome activation. In response to inflammatory stimuli, CUL1 disassociates from NLRP3 to release the repression of NLRP3 inflammasome activation. This work reveals a distinct mechanism underlying the repression of inflammasome activation under physiological conditions and the induction of inflammasome activation in response to inflammatory stimuli, and thus provides insights into the prevention and treatment of infectious and inflammatory diseases.
All-optical electrophysiology for high-throughput functional characterization of human iPSC-derived motor neuron model of ALS
Authors: Kiskinis Evangelos , Kralj Joel M. , Zou Peng , Weinstein Eli N. , Zhang Hongkang , Tsioras Konstantinos , Wiskow Ole , Ortega J. Alberto , Eggan Kevin , Cohen Adam E. 
Published: March 2018

AbstractHuman induced pluripotent stem cell (iPSC)-derived neurons are an attractive substrate for modeling disease, yet the heterogeneity of these cultures presents a challenge for functional characterization by manual patch clamp electrophysiology. Here we describe an optimized all-optical electrophysiology, “Optopatch”, pipeline for high-throughput functional characterization of human iPSC-derived neuronal cultures. We demonstrate the method in a human iPSC-derived motor neuron model of ALS. In a comparison of neurons with an ALS-causing mutation (SOD1 A4V) with their genome-corrected controls, the mutants showed elevated spike rates under weak or no stimulus, and greater likelihood of entering depolarization block under strong optogenetic stimulus. We compared these results to numerical simulations of simple conductance-based neuronal models and to literature results in this and other iPSC-based models of ALS. Our data and simulations suggest that deficits in slowly activating potassium channels may underlie the changes in electrophysiology in the SOD1 A4V mutation.