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Metabolism and RNA

Zhenzhong Zheng, Fan Zhang, Dengpeng Gao, Yujing Wu, Hao Wu
BACKGROUND: Cardiac microvascular endothelial cells is one of the key factors in the process of diabetic cardiomyopathy, a common chronic complication of diabetes. Fibrinogen-like protein 2 (FGL2) is linked to apoptosis, angiogenesis, and inflammatory response, all of which also occur in diabetes. Thus, we investigate the role of FGL 2 and other genes in the pathology of diabetic cardiomyopathy. METHODS: In the present study, we used high-throughput microarray to profile gene expression in rat myocardial microvascular endothelial cells (MMEC) with or without silencing the fgl2 gene and in different glucose environments...
August 11, 2018: Diabetes/metabolism Research and Reviews
F Nadiya, N Anjali, Jinu Thomas, A Gangaprasad, K K Sabu
Cardamom has long been used as a food flavoring agent and in ayurvedic medicines for mouth ulcers, digestive problems, and even depression. Extensive occurrence of pests and diseases adversely affect its cultivation and result in substantial reduction in total production and productivity. Numerous studies revealed the significant role of miRNAs in plant biotic stress responses. In the current study, miRNA profiling of cultivar and wild cardamom genotypes was performed using Ion Proton sequencer. We identified 161 potential miRNAs representing 42 families including monocot/tissue specific and 14 novel miRNAs in both genotypes...
August 11, 2018: Plant Biology
Jiyu Tong, Richard A Flavell, Hua-Bing Li
N6 -methyladenosine (m6 A) is the most common post-transcriptional RNA modification throughout the transcriptome, affecting fundamental aspects of RNA metabolism. m6 A modification could be installed by m6 A "writers" composed of core catalytic components (METTL3/METTL14/WTAP) and newly defined regulators and removed by m6 A "erasers" (FTO and ALKBH5). The function of m6 A is executed by m6 A "readers" that bind to m6 A directly (YTH domain-containing proteins, eIF3 and IGF2BPs) or indirectly (HNRNPA2B1)...
August 10, 2018: Frontiers of Medicine
Hanna Bragde, Ulf Jansson, Mats Fredrikson, Ewa Grodzinsky, Jan Söderman
Establishing a celiac disease (CD) diagnosis can be difficult, such as when CD-specific antibody levels are just above cutoff or when small intestinal biopsies show low-grade injuries. To investigate the biological pathways involved in CD and select potential biomarkers to aid in CD diagnosis, RNA sequencing of duodenal biopsies from subjects with either confirmed Active CD (n = 20) or without any signs of CD (n = 20) was performed. Gene enrichment and pathway analysis highlighted contexts, such as immune response, microbial infection, phagocytosis, intestinal barrier function, metabolism, and transportation...
August 10, 2018: Cellular and Molecular Life Sciences: CMLS
Kristina Keidel, Fabian Amman, Ilona Bibova, Jakub Drzmisek, Vladimir Benes, David Hot, Branislav Vecerek
Bordetella pertussis is the causative agent of human whooping cough (pertussis), a highly contagious respiratory disease which despite massive vaccination programs remains the major cause of infant morbidity and mortality. The requirement of the RNA chaperone Hfq for virulence of B. pertussis suggested that Hfq-dependent small regulatory RNAs are involved in the modulation of gene expression in this re-emerging pathogen. High through-put RNA sequencing revealed hundreds of putative non-coding RNAs including the RgtA sRNA...
August 10, 2018: RNA
Jiradej Makjaroen, Poorichaya Somparn, Kenneth Hodge, Witthaya Poomipak, Nattiya Hirankarn, Trairak Pisitkun
Interferon lambda (IFN-λ) is a relatively unexplored, yet promising anti-viral agent. IFN-λ has recently been tested in clinical trials of chronic hepatitis B virus infection (CHB), with the advantage that side effects may be limited compared with IFN-α, as IFN-λ receptors are found only in epithelial cells. To date, IFN-λ's downstream signaling pathway remains largely unelucidated, particularly via proteomics methods. Here, we report that IFN-λ3 inhibits HBV replication in HepG2.2.15 cells, reducing levels of both HBV transcripts and intracellular HBV DNA...
August 10, 2018: Molecular & Cellular Proteomics: MCP
Haojie Cao, Julio Villatoro-Hernandez, Ruud Detert Oude Weme, Elrike Frenzel, Oscar P Kuipers
Bacillus subtilis is extensively applied as a microorganism for the high-level production of heterologous proteins. Traditional strategies for increasing the productivity of this microbial cell factory generally focused on the targeted modification of rate-limiting components or steps. However, the longstanding problems of limited productivity of the expression host, metabolic burden and non-optimal nutrient intake, have not yet been completely solved to achieve significant production-strain improvements. To tackle this problem, we systematically rewired the regulatory networks of the global nitrogen and carbon metabolism by random mutagenesis of the pleiotropic transcriptional regulators CodY and CcpA, to allow for optimal nutrient intake, translating into significantly higher heterologous protein production yields...
August 7, 2018: Metabolic Engineering
Amy C Kelly, Kate E Smith, William G Purvis, Catherine G Min, Craig S Weber, Amanda M Cooksey, Craig Hasilo, Steven Paraskevas, Thomas M Suszynski, Bradley P Weegman, Miranda J Anderson, Leticia E Camacho, Robert C Harland, Tom Loudovaris, Jana Jandova, Diana S Molano, Nicholas D Price, Ivan G Georgiev, William E Scott, Derek Manas, James Shaw, Doug O'Gorman, Tatsuya Kin, Fiona M McCarthy, Gregory L Szot, Andrew M Posselt, Peter G Stock, Theodore Karatzas, William J Shapiro, Ronald M Lynch, Sean W Limesand, Klearchos K Papas
BACKGROUND: All human islets used in research and for the clinical treatment of diabetes are subject to ischemic damage during pancreas procurement, preservation, and islet isolation. A major factor influencing islet function is exposure of pancreata to cold ischemia during unavoidable windows of preservation by static cold storage (SCS). Improved preservation methods may prevent this functional deterioration. In the present study, we investigated whether pancreas preservation by gaseous oxygen perfusion (persufflation) better preserved islet function versus SCS...
August 8, 2018: Transplantation
Pasquale Filannino, Maria De Angelis, Raffaella Di Cagno, Giorgia Gozzi, Ylenia Riciputi, Marco Gobbetti
Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here, we demonstrated how L. plantarum regulates and shapes its transcriptome in response to contrasting habitats. Firstly, multivariate clustering analysis of transcriptional data (RNA-Seq), complemented with metabolomics and phenomics, grouped the strains according to the habitats of origin...
August 9, 2018: Environmental Microbiology
Mehtap Civelek, Jan-Frederik Mehrkens, Nora-Maria Carstens, Elena Fitzenberger, Uwe Wenzel
Autophagy of mitochondria, i.e., mitophagy, plays a crucial role in coping with stressors in the aging process, metabolic disturbances, and neurological disorders. Impairments of the process might consequently lead to enhanced accumulation of aged and aggregated proteins and reduced cellular integrity in response to stress. In the present study, we used the stress-sensitive mutant mev-1 of Caenorhabditis elegans to assess the effects of the knockdown of mitophagy relevant genes on survival under heat stress, the amount of autophagosomes, and on protein aggregation...
August 9, 2018: Molecular and Cellular Biochemistry
Susan E Liao, Yiwei Ai, Ryuya Fukunaga
Drosophila Blanks is a testes-specific RNA-binding protein required for post-meiotic spermiogenesis. However, Blanks's role in regulating RNA populations in the testes remains unknown. We performed small RNA and mRNA high-throughput sequencing in blanks mutant testes and controls. We identified two miRNAs, one siRNA, and hundreds of mRNAs that are significantly upregulated or downregulated in blanks mutant testes. Pathway analysis revealed that differentially expressed mRNAs are involved in catabolic and metabolic processes, anion and cation transport, mating, and reproductive behavior...
July 2018: Heliyon
Zheying Min, Qian Gao, Xiumei Zhen, Yong Fan, Tao Tan, Rong Li, Yue Zhao, Yang Yu
BACKGROUND: Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder that affects female fertility. However, with the lack of a corresponding research model, the pathology mechanism of PCOS is poorly understood. Induced pluripotent stem cell (iPSC) technology has been recognized as means to generate patient-specific stem cells for disease modeling. METHODS: The mRNA abundance of iPSCs was analyzed by RNA microarray and real-time polymerase chain reaction (RT-PCR)...
August 9, 2018: Stem Cell Research & Therapy
Hehai Pan, Adam Strickland, Vedavathi Madhu, Zariel I Johnson, Saswati N Chand, Jonathan R Brody, Andrzej Fertala, Zhaomin Zheng, Irving M Shapiro, Makarand V Risbud
Nucleus pulposus (NP) cells reside in the hypoxic niche of the intervertebral disc. Studies have demonstrated that RNA-binding protein HuR modulates hypoxic signaling in several cancers, however, its function in the disc is unknown. HuR did not show cytoplasmic translocation in hypoxia and evidenced levels of Hif-1α and HIF-targets in NP cells. RNA-Sequencing data revealed important extracellular matrix-related genes including several collagens, MMPs, aggrecan, Tgf-β3 and Sdc4 were regulated by HuR. Analysis of HuR-silenced NP cells confirmed that HuR maintained expression of these matrix genes...
August 6, 2018: Matrix Biology: Journal of the International Society for Matrix Biology
Jizhou Tang, Yuanxi Ding, Jing Nan, Xiangyu Yang, Liang Sun, Xiuyun Zhao, Ling Jiang
Huanglongbing (HLB) is the most serious disease affecting citrus production worldwide. No HLB-resistant citrus varieties exist. The HLB pathogen Candidatus Liberibacter asiaticus is nonculturable, increasing the difficulty of preventing and curing the disease. We successfully screened the biocontrol agent Bacillus GJ1 for the control of HLB in nursery-grown citrus plants. RNA sequencing (RNA-seq) of the transcriptome and isobaric tags for relative and absolute quantification of the proteome revealed differences in the detoxification responses of Bacillus GJ1-treated and -untreated Ca...
2018: PloS One
Patrick Leuthold, Matthias Schwab, Ute Hofmann, Stefan Winter, Steffen Rausch, Michael N Pollak, Jörg Hennenlotter, Jens Bedke, Elke Schaeffeler, Mathias Haag
Tissue analysis represents a powerful tool for the investigation of disease pathophysiology. However, the heterogeneous nature of tissue samples, in particular of neoplastic, may affect the outcome of such analysis and hence obscure interpretation of results. Thus comprehensive isolation and extraction of transcripts and metabolites from an identical tissue specimen would minimize variations and enable the economic use of biopsy material which is usually available in limited amounts. Here we demonstrate a fast and simple protocol for combined transcriptomics and metabolomics analysis in homogenates prepared from one single tissue sample...
August 9, 2018: Journal of Proteome Research
Cheryl M Immethun, Tae Seok Moon
Cyanobacteria are appealing hosts for green chemical synthesis due to their use of light and carbon dioxide. To optimize product yields and titers, specific and tunable regulation of the metabolic pathways is needed. Synthetic biology has increased and diversified the genetic tools available for biological process control. While early tool development focused on commonly used heterotrophs, there has been a recent expansion of tools for cyanobacteria. CRISPR-Cas9 has been used to edit the genome of cyanobacterial strains, while transcriptional regulation has been accomplished with CRISPR interference and RNA riboswitches...
2018: Advances in Experimental Medicine and Biology
Qi Zhang, Chen-Feng Wang, Yun-Kai Lv
Metal-organic frameworks (MOFs) as sensing materials have experienced explosive growth in recent years due to their intrinsic merits, such as structural diversity, high porosity, large surface area, extraordinary adsorption affinities, etc. Biomolecules such as DNA, protein, and vitamins play vital roles in metabolism. Moreover, the sensitive detection of biomolecules is of importance in the disease prevention and treatment. This review intends to provide an update on the recent progress in the detection of various biomolecules via MOF-based luminescent sensors...
August 9, 2018: Analyst
Boris V Krivoshiev, Gerrit T S Beemster, Katrien Sprangers, Bart Cuypers, Kris Laukens, Ronny Blust, Steven J Husson
The flame retardant, 9,10-dihydro-9-oxa-10-phosphaphenanthrene 10-oxide (DOPO), has been receiving great interest given its superior fire protection properties, and its predicted low level of persistence, bioaccumulation, and toxicity. However, empirical toxicological data that are essential for a complete hazard assessment are severely lacking. In this study, we attempted to identify the potential toxicological modes of action by transcriptome (RNA-seq) profiling of the human liver hepatocellular carcinoma cell line, HepG2...
May 8, 2018: Toxicology Research
Mark E Pepin, Chae-Myeong Ha, David K Crossman, Silvio H Litovsky, Sooryanarayana Varambally, Joseph P Barchue, Salpy V Pamboukian, Nikolaos A Diakos, Stavros G Drakos, Steven M Pogwizd, Adam R Wende
Ischemic cardiomyopathy (ICM) is the clinical endpoint of coronary heart disease and a leading cause of heart failure. Despite growing demands to develop personalized approaches to treat ICM, progress is limited by inadequate knowledge of its pathogenesis. Since epigenetics has been implicated in the development of other chronic diseases, the current study was designed to determine whether transcriptional and/or epigenetic changes are sufficient to distinguish ICM from other etiologies of heart failure. Specifically, we hypothesize that genome-wide DNA methylation encodes transcriptional reprogramming in ICM...
August 8, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
Anitha Sundararajan, Hallie S Rane, Thiruvarangan Ramaraj, Johnny Sena, Amy B Howell, Stella M Bernardo, Faye D Schilkey, Samuel A Lee
Candida albicans is one of the most common causes of hospital-acquired urinary tract infections (UTIs). However, azoles are poorly active against biofilms, echinocandins do not achieve clinically useful urinary concentrations, and amphotericin B exhibits severe toxicities. Thus, novel strategies are needed to prevent Candida UTIs, which are often associated with urinary catheter biofilms. We previously demonstrated that cranberry-derived proanthocyanidins (PACs) prevent C. albicans biofilm formation in an in vitro urinary model...
2018: PloS One
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