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https://www.readbyqxmd.com/read/28918285/controlling-cell-volume-for-efficient-phb-production-by-halomonas
#1
Xiao-Ran Jiang, Zhi-Hao Yao, Guo-Qiang Chen
Bacterial morphology is decided by cytoskeleton protein MreB and cell division protein FtsZ encoded by essential genes mreB and ftsZ, respectively. Inactivating mreB and ftsZ lead to increasing cell sizes and cell lengths, respectively, yet seriously reduce cell growth ability. Here we develop a temperature-responsible plasmid expression system for compensated expression of relevant gene(s) in mreB or ftsZ disrupted recombinants H. campaniensis LS21, allowing mreB or ftsZ disrupted recombinants to grow normally at 30°C in a bioreactor for 12h so that a certain cell density can be reached, followed by 36h cell size expansions or cell shape elongations at elevated 37°C at which the mreB and ftsZ encoded plasmid pTKmf failed to replicate in the recombinants and thus lost themselves...
September 13, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28915706/the-role-of-autophagy-in-hepatocellular-carcinoma-friend-or-foe
#2
REVIEW
Lian Liu, Jia-Zhi Liao, Xing-Xing He, Pei-Yuan Li
Autophagy is an evolutionarily conserved lysosome-dependent catabolic process which degrades cell's components in order to recycle substrates to exert optimally and adapt to tough circumstances. It is a critical cellular homeostatic mechanism with stress resistance, immunity, antiaging, and pro-tumor or anti-tumor effects. Among these, the role of autophagy in cancer is the most eye-catching that is not immutable but dynamic and highly complex. Basal autophagy acts as a tumor suppressor by maintaining genomic stability in normal cells...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915237/dna-replication-stress-restricts-ribosomal-dna-copy-number
#3
Devika Salim, William D Bradford, Amy Freeland, Gillian Cady, Jianmin Wang, Steven C Pruitt, Jennifer L Gerton
Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen the yeast conditional temperature-sensitive mutant collection of essential genes...
September 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28904956/application-of-the-subtractive-genomics-and-molecular-docking-analysis-for-the-identification-of-novel-putative-drug-targets-against-salmonella-enterica-subsp-enterica-serovar-poona
#4
Tanvir Hossain, Mohammad Kamruzzaman, Talita Zahin Choudhury, Hamida Nooreen Mahmood, A H M Nurun Nabi, Md Ismail Hosen
The emergence of novel pathogenic strains with increased antibacterial resistance patterns poses a significant threat to the management of infectious diseases. In this study, we aimed at utilizing the subtractive genomic approach to identify novel drug targets against Salmonella enterica subsp. enterica serovar Poona strain ATCC BAA-1673. We employed in silico bioinformatics tools to subtract the strain-specific paralogous and host-specific homologous sequences from the bacterial proteome. The sorted proteome was further refined to identify the essential genes in the pathogenic bacterium using the database of essential genes (DEG)...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28901837/minimal-requirements-for-reverse-polymerization-and-trna-repair-by-trna-his-guanylyltransferase
#5
Riddhi Desai, Kunmo Kim, Hanna C Buechsenschuetz Allan W Chen, Yumin Bi, Mitchell R Mann, Matthew A Turk, Christina Z Chung, Ilka U Heinemann
tRNA(His) guanylyltransferase (Thg1) has unique reverse (3'-5') polymerase activity occurring in all three domains of life. Most eukaryotic Thg1 homologs are essential genes involved in tRNA(His) maturation. These enzymes normally catalyze a single 5' guanylation of tRNA(His) lacking the essential G(-1) identity element required for aminoacylation. Recent studies suggest that archaeal type Thg1, which includes most archaeal and bacterial Thg1 enzymes is phylogenetically distant from eukaryotic Thg1. Thg1 is evolutionarily related to canonical 5'-3' forward polymerases but catalyzes reverse 3'-5'polymerization...
September 13, 2017: RNA Biology
https://www.readbyqxmd.com/read/28900740/crispr-cas9-mediated-multiple-single-guide-rnas-potently-abrogate-pseudorabies-virus-replication
#6
Yan-Dong Tang, Ji-Ting Liu, Tong-Yun Wang, Ming-Xia Sun, Zhi-Jun Tian, Xue-Hui Cai
Pseudorabies virus (PRV) is a swine herpesvirus that causes significant morbidity and mortality in swine populations and has caused huge economic losses in the worldwide swine industry. Currently, there is no effective antiviral drug in clinical use for PRV infection; it is also difficult to eliminate PRV from infected swine. In our study, we set out to combat these swine herpesvirus infections by exploiting the CRISPR/Cas9 system. We designed 75 single guide RNAs (sgRNA) by targeting both essential and non-essential genes across the genome of PRV...
September 12, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28895127/evaluation-of-ccaat-enhancer-binding-protein-c-ebp-alpha-cebpa-and-runt-related-transcription-factor-1-runx1-expression-in-patients-with-de-novo-acute-myeloid-leukemia
#7
Fatemeh Salarpour, Kourosh Goudarzipour, Mohammad Hossein Mohammadi, Ahmad Ahmadzadeh, Sara Faraahi, Mehdi Allahbakhshian Farsani
The CCAAT/enhancer binding protein (C/EBP) alpha (CEBPA) and Runt-related transcription factor 1 (RUNX1) genes have been traditionally regarded as two essential genes involved in normal myeloid maturation. Although the link between mutations in these genes and the development of acute myeloid leukemia (AML) has been extensively documented, the ramifications of gene expression dysregulations of CEBPA and RUNX1 has drawn less attention. The present study investigated CEBPA and RUNX1 gene expression levels in 96 primary AML specimens against a normal control group by way of real-time RT-PCR...
September 11, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/28893188/developing-genome-reduced-pseudomonas-chlororaphis-strains-for-the-production-of-secondary-metabolites
#8
Xuemei Shen, Zheng Wang, Xianqing Huang, Hongbo Hu, Wei Wang, Xuehong Zhang
BACKGROUND: The current chassis organisms or various types of cell factories have considerable advantages and disadvantages. Therefore, it is necessary to develop various chassis for an efficient production of different bioproducts from renewable resources. In this context, synthetic biology offers unique potentialities to produce value-added products of interests. Microbial genome reduction and modification are important strategies for constructing cellular chassis and cell factories...
September 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28889175/expression-of-the-lef5-gene-from-spodoptera-exigua-multiple-nucleopolyhedrovirus-contributes-to-the-baculovirus-stability-in-cell-culture
#9
María Martínez-Solís, Agata K Jakubowska, Salvador Herrero
Baculoviruses are a broad group of viruses infecting insects, predominately of the order Lepidoptera. They are used worldwide as biological insecticides and as expression vectors to produce recombinant proteins. Baculoviruses replicate in their host, although several cell lines have been developed for in vitro replication. Nevertheless, replication of baculoviruses in cell culture involves the generation of defective viruses with a decrease in productivity and virulence. Transcriptional studies of the Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) and the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) infective process revealed differences in the expression patterns when the virus replicated under in vitro (Se301 cells) or in vivo (S...
September 9, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28888882/genome-wide-sequence-transposon-insertion-sites-and-analyze-the-essential-genes-of-brucella-melitensis
#10
Yanyan De, Congyue Dong, Yanyang Cao, Xiaolei Wang, Xiaowen Yang, Ning Wang, Cunrui Zhang, Zhen Wang, Yanli Lyu, Qingmin Wu
A transposon mutant library of B. melitensis NI including 32,640 transposon mutants was established. By sequencing the transposon insertion sites, 10,832 mutants were successfully defined for their insertion sites. Analysis of the mutants with defined transposon insertion sites (DTIS) indicated that the insertions were well spread through the two genomes. In addition, 948 genes with no detectable transposon insertions were taken as the candidate for identification of essential genes. In comparison with the Bacterial Database of Essential Genes and by using comparative genomics analysis, 183 potential essential genes of B...
September 6, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28888836/transcriptome-sequencing-and-characterization-of-symbiodinium-muscatinei-and-elliptochloris-marina-symbionts-found-within-the-aggregating-sea-anemone-anthopleura-elegantissima
#11
Jason C Macrander, James L Dimond, Brian L Bingham, Adam M Reitzel
There is a growing body of literature using transcriptomic data to study how tropical cnidarians and their photosynthetic endosymbionts respond to environmental stressors and participate in metabolic exchange. Despite these efforts, our understanding of how essential genes function to facilitate symbiosis establishment and maintenance remains limited. The inclusion of taxonomically and ecologically diverse endosymbionts will enhance our understanding of these interactions. Here we characterize the transcriptomes of two very different symbionts found within the temperate sea anemone Anthopleura elegantissima: the chlorophyte Elliptochloris marina and the dinoflagellate Symbiodinium muscatinei...
September 6, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28881838/prognostic-value-of-molecular-events-from-negative-surgical-margin-of-non-small-cell-lung-cancer
#12
Bangrong Cao, Lin Feng, Dan Lu, Yan Liu, Yu Liu, Suping Guo, Naijun Han, Xiangyang Liu, Yousheng Mao, Jie He, Shujun Cheng, Yanning Gao, Kaitai Zhang
It is hypothesized that the molecular status in negative surgical margin (NSM) is associated with prognosis of cancer patients. In this study, the prognostic relevance of Epithelial-to-Mesenchymal Transition (EMT) molecular events in NSMs in patients with NSCLC was investigated. EMT model was developed, in which the mesenchymal transition of human immortalized bronchial epithelial cell line was induced by TGF-beta1. Gene expression of EMT-induced cells and NSMs from 60 lung squamous cell carcinoma (SCC) patients was profiled by microarray and validated by quantitative RT-PCR...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28881634/heterogeneous-nuclear-ribonucleoprotein-hnrnp-l-promotes-dna-damage-induced-cell-apoptosis-by-enhancing-the-translation-of-p53
#13
Ji-Young Seo, Do-Yeon Kim, Seong-Hoon Kim, Hyo-Jin Kim, Hye Guk Ryu, Juhyun Lee, Kyung-Ha Lee, Kyong-Tai Kim
The tumor suppressor p53 is an essential gene in the induction of cell cycle arrest, DNA repair, and apoptosis. p53 protein is induced under cellular stress, blocking cell cycle progression and inducing DNA repair. Under DNA damage conditions, it has been reported that post-transcriptional regulation of p53 mRNA contributes to the increase in p53 protein level. Here we demonstrate that heterogeneous nuclear ribonucleoprotein (hnRNP) L enhances p53 mRNA translation. We found that hnRNP L is increased and binds to the 5'UTR of p53 mRNA in response to DNA damage...
August 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28875178/genetic-validation-of-leishmania-donovani-lysyl-trna-synthetase-shows-that-it-is-indispensable-for-parasite-growth-and-infectivity
#14
Sanya Chadha, N Arjunreddy Mallampudi, Debendra K Mohapatra, Rentala Madhubala
Leishmania donovani is a protozoan parasite that causes visceral leishmaniasis. Increasing resistance and severe side effects of existing drugs have led to the need to identify new chemotherapeutic targets. Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous and are required for protein synthesis. aaRSs are known drug targets for bacterial and fungal pathogens. Here, we have characterized and evaluated the essentiality of L. donovani lysyl-tRNA synthetase (LdLysRS). Two different coding sequences for lysyl-tRNA synthetases are annotated in the Leishmania genome database...
July 2017: MSphere
https://www.readbyqxmd.com/read/28873455/prediction-and-analysis-of-essential-genes-using-the-enrichments-of-gene-ontology-and-kegg-pathways
#15
Lei Chen, Yu-Hang Zhang, ShaoPeng Wang, YunHua Zhang, Tao Huang, Yu-Dong Cai
Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes...
2017: PloS One
https://www.readbyqxmd.com/read/28870810/analysis-of-an-acyl-coa-binding-protein-in-aspergillus-oryzae-that-undergoes-unconventional-secretion
#16
Hee Su Kwon, Kouhei Kawaguchi, Takashi Kikuma, Kaoru Takegawa, Katsuhiko Kitamoto, Yujiro Higuchi
Acyl-CoA binding protein (ACBP) plays important roles in the metabolism of lipids in eukaryotic cells. In the industrially important filamentous fungus Aspergillus oryzae, although we have previously demonstrated that the A. oryzae ACBP (AoACBP) localizes to punctate structures and exhibits long-range motility, which is dependent on autophagy-related proteins, the physiological role of AoACBP remains elusive. Here, we describe identification and characterization of another ACBP from A. oryzae; we named this ACBP as AoAcb2 and accordingly renamed AoACBP as AoAcb1...
September 1, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28865130/temperature-dependent-dynamic-control-of-the-tca-cycle-increases-volumetric-productivity-of-itaconic-acid-production-by-escherichia-coli
#17
Björn-Johannes Harder, Katja Bettenbrock, Steffen Klamt
Based on the recently constructed E. coli itaconic acid production strain ita23, we aimed to improve the productivity by applying a two-stage process strategy with decoupled production of biomass and itaconic acid. We constructed a strain ita32 (MG1655 ▵aceA ▵pta ▵pykF ▵pykA pCadCs), which, in contrast to ita23, has an active tricarboxylic acid (TCA) cycle and a fast growth rate of 0.52 h(-1) at 37°C, thus representing an ideal phenotype for the first stage, the growth phase. Subsequently we implemented a synthetic genetic control allowing the downregulation of the TCA cycle and thus the switch from growth to itaconic acid production in the second stage...
September 2, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28863367/monomeric-cocoa-catechins-enhance-%C3%AE-cell-function-by-increasing-mitochondrial-respiration
#18
Thomas J Rowley, Benjamin F Bitner, Jason D Ray, Daniel R Lathen, Andrew T Smithson, Blake W Dallon, Chase J Plowman, Benjamin T Bikman, Jason M Hansen, Melanie R Dorenkott, Katheryn M Goodrich, Liyun Ye, Sean F O'Keefe, Andrew P Neilson, Jeffery S Tessem
A hallmark of type 2 diabetes (T2D) is β-cell dysfunction and the eventual loss of functional β-cell mass. Therefore, mechanisms that improve or preserve β-cell function could be used to improve the quality of life of individuals with T2D. Studies have shown that monomeric, oligomeric and polymeric cocoa flavanols have different effects on obesity, insulin resistance and glucose tolerance. We hypothesized that these cocoa flavanols may have beneficial effects on β-cell function. INS-1 832/13-derived β-cells and primary rat islets cultured with a monomeric catechin-rich cocoa flavanol fraction demonstrated enhanced glucose-stimulated insulin secretion, while cells cultured with total cocoa extract and with oligomeric or polymeric procyanidin-rich fraction demonstrated no improvement...
July 27, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28856484/gene-disrupting-mutations-associated-with-regression-in-autism-spectrum-disorder
#19
Robin P Goin-Kochel, Sandy Trinh, Shelley Barber, Raphael Bernier
Approximately one-third of children with autism spectrum disorder (ASD) reportedly lose skills within the first 3 years, yet a causal mechanism remains elusive. Considering evidence of strong genetic effects for ASD and findings that distinct phenotypes in ASD associate with specific genetic events, we examined rates of parent-reported regression in the Simons Simplex Collection with likely gene disrupting mutations from five distinct classes: FMRP target genes, genes encoding chromatin modifiers, genes expressed preferentially in embryos, genes encoding postsynaptic density proteins, and essential genes...
August 30, 2017: Journal of Autism and Developmental Disorders
https://www.readbyqxmd.com/read/28851918/atp6ap2-ablation-in-adult-mice-impairs-viability-through-multiple-organ-deficiencies
#20
Olivia Wendling, Marie-France Champy, Solène Jaubert, Guillaume Pavlovic, Aline Dubos, Loic Lindner, Hugues Jacobs, Manuel Mark, Roy Combe, Isabelle Goncalves Da Cruz, Hervé Luche, John S Mudgett, Thomas Rosahl, Tania Sorg, Marie Malissen, Patrick T Reilly, Yann Hérault
ATP6AP2 codes for the (pro)renin receptor and is an essential component of vacuolar H+ ATPase. Activating (pro)renin for conversion of Angiotensinogen to Angiotensin makes ATP6AP2 attractive for drug intervention. Tissue-specific ATP6AP2 inactivation in mouse suggested a strong impact on various organs. Consistent with this, we found that embryonic ablation of Atp6ap2 resulted in both male hemizygous lethality and female haploinsufficiency. Next, we examined the phenotype of an induced inactivation in the adult animal, most akin to detect potential effect of functional interference of ATP6AP2 through drug therapy...
August 29, 2017: Scientific Reports
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