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https://www.readbyqxmd.com/read/28633641/expression-levels-of-atherosclerosis-associated-mir-143-and-mir-145-in-the-plasma-of-patients-with-hyperhomocysteinaemia
#1
Kejian Liu, Saiyare Xuekelati, Yue Zhang, Yin Yin, Yue Li, Rui Chai, Xinwei Li, Yi Peng, Jiangdong Wu, Xiaomei Guo
BACKGROUND: An elevated level of homocysteine (Hcy) in the blood is designated hyperhomocysteinaemia (Hhcy) and is regarded as a strong risk factor for the development of atherosclerosis (ATH), although the association remains controversial. Considered to be essential gene expression regulators, micro-RNAs (miRNAs) modulate cardiovascular disease development and thus can be regarded as potential biomarkers and therapeutic targets in atherosclerosis. The aim of the current study is to investigate the expression levels of atherosclerosis-associated miR-143 and miR-145 in Hhcy patients and predict the progress of atherosclerosis in Hhcy patients...
June 20, 2017: BMC Cardiovascular Disorders
https://www.readbyqxmd.com/read/28629934/recent-advances-in-leishmania-reverse-genetics-manipulating-a-manipulative-parasite
#2
REVIEW
Samuel M Duncan, Nathaniel G Jones, Jeremy C Mottram
In this review we describe the expanding repertoire of molecular tools with which to study gene function in Leishmania. Specifically we review the tools available for studying functions of essential genes, such as plasmid shuffle and DiCre, as well as the rapidly expanding portfolio of available CRISPR/Cas9 approaches for large scale gene knockout and endogenous tagging. We include detail on approaches that allow the direct manipulation of RNA using RNAi and protein levels via Tet or DiCre induced overexpression and destabilization domain mediated degradation...
June 16, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28618222/de-novo-biosynthesis-of-glutarate-via-%C3%AE-keto-acid-carbon-chain-extension-and-decarboxylation-pathway-in-escherichia-coli
#3
Jian Wang, Yifei Wu, Xinxiao Sun, Qipeng Yuan, Yajun Yan
Microbial based bioplastics are promising alternatives to petroleum based synthetic plastics due to their renewability and economic feasibility. Glutarate is one of the most potential building blocks for bioplastics. The recent biosynthetic routes for glutarate were mostly based on the L-lysine degradation pathway from Pseudomonas putida that required lysine either by feeding or lysine overproduction via genetic manipulations. Herein, we established a novel glutarate biosynthetic pathway by incorporation of a "+1" carbon chain extension pathway from α-ketoglutarate (α-KG) in combination with α-keto acid decarboxylation pathway in Escherichia coli...
June 15, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28614382/genome-wide-transposon-mutagenesis-of-proteus-mirabilis-essential-genes-fitness-factors-for-catheter-associated-urinary-tract-infection-and-the-impact-of-polymicrobial-infection-on-fitness-requirements
#4
Chelsie E Armbruster, Valerie Forsyth-DeOrnellas, Alexandra O Johnson, Sara N Smith, Lili Zhao, Weisheng Wu, Harry L T Mobley
The Gram-negative bacterium Proteus mirabilis is a leading cause of catheter-associated urinary tract infections (CAUTIs), which are often polymicrobial. Numerous prior studies have uncovered virulence factors for P. mirabilis pathogenicity in a murine model of ascending UTI, but little is known concerning pathogenesis during CAUTI or polymicrobial infection. In this study, we utilized five pools of 10,000 transposon mutants each and transposon insertion-site sequencing (Tn-Seq) to identify the full arsenal of P...
June 14, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28607498/male-factor-infertility-piwi-hiwi-miwi-essential-genes-for-effective-spermiogenesis
#5
Annette Fenner
No abstract text is available yet for this article.
June 13, 2017: Nature Reviews. Urology
https://www.readbyqxmd.com/read/28603666/in-silico-analysis-reveals-widespread-presence-of-three-gene-families-mapk-mapkk-and-mapkkk-of-the-mapk-cascade-from-crop-plants-of-solanaceae-in-comparison-to-the-distantly-related-syntenic-species-from-rubiaceae-coffee
#6
Hira Iftikhar, Nayab Naveed, Nasar Virk, Muhammad Faraz Bhatti, Fengming Song
Mitogen-activated protein kinases (MAPKs) are an important family of genes which play roles in vital plant processes, and they also help in coping against various kinds of environmental stresses including abiotic as well as biotic factors. The advancement of genomics calls for the annotation, identification, and detailed processing of the essential gene families in plants in order to provide insights into the importance of their central roles as well as for providing the basis for making their growth vigorous even under stressed conditions and, ultimately, to benefit from them by foreseeing the potential threats to their growth...
2017: PeerJ
https://www.readbyqxmd.com/read/28599096/proteases-as-antimalarial-targets-strategies-for-genetic-chemical-and-therapeutic-validation
#7
REVIEW
Edgar Deu
Malaria is a devastating parasitic disease affecting half of the world's population. The rapid emergence of resistance against new antimalarial drugs, including artemisinin-based therapies, has made the development of drugs with novel mechanisms of action extremely urgent. Proteases are enzymes proven to be well suited for target-based drug development due to our knowledge of their enzymatic mechanisms and active site structures. More importantly, Plasmodium proteases have been shown to be involved in a variety of pathways that are essential for parasite survival...
June 9, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28594867/gene-essentiality-conservation-index-and-co-evolution-of-genes-in-cyanobacteria
#8
Gopi Siva Sai Tiruveedula, Pramod P Wangikar
Cyanobacteria, a group of photosynthetic prokaryotes, dominate the earth with ~ 1015 g wet biomass. Despite diversity in habitats and an ancient origin, cyanobacterial phylum has retained a significant core genome. Cyanobacteria are being explored for direct conversion of solar energy and carbon dioxide into biofuels. For this, efficient cyanobacterial strains will need to be designed via metabolic engineering. This will require identification of target knockouts to channelize the flow of carbon toward the product of interest while minimizing deletions of essential genes...
2017: PloS One
https://www.readbyqxmd.com/read/28594177/a-versatile-toolbox-for-the-control-of-protein-levels-using-n-%C3%AE%C2%B5-acetyl-l-lysine-dependent-amber-suppression
#9
Wolfram Volkwein, Christopher Maier, Ralph Krafczyk, Kirsten Jung, Jürgen Lassak
The analysis of the function of essential genes in vivo depends on the ability to experimentally modulate levels of their protein products. Current methods to address this are based on transcriptional or post-transcriptional regulation of mRNAs but approaches based on the exploitation of translational regulation have so far been neglected. Here we describe a toolbox, based on amber suppression in the presence of Nε-acetyl-L-lysine (AcK), for translational tuning of protein output. We chose the highly sensitive luminescence system LuxCDABE as a reporter and incorporated a UAG stop codon into the gene for the reductase subunit LuxC...
June 8, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28589221/an-efficient-method-to-generate-conditional-knockout-cell-lines-for-essential-genes-by-combination-of-auxin-inducible-degron-tag-and-crispr-cas9
#10
Kohei Nishimura, Tatsuo Fukagawa
Generation of cells with a loss-of-function mutation in a gene (knockout cells) is a valuable technique for studying the function of a given gene product. However, if the product of the target gene is essential for cell viability, conditional knockout cell lines must be generated. Recently, as gene editing technology using CRISPR/Cas9 has developed, it has become possible to produce conditional knockout cell lines using this technique. However, to obtain final conditional knockout cell lines, it is necessary to perform several experiments with multiple complicated steps...
June 6, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28581500/hyperactivation-of-hush-complex-function-by-charcot-marie-tooth-disease-mutation-in-morc2
#11
Iva A Tchasovnikarova, Richard T Timms, Christopher H Douse, Rhys C Roberts, Gordon Dougan, Robert E Kingston, Yorgo Modis, Paul J Lehner
Dominant mutations in the MORC2 gene have recently been shown to cause axonal Charcot-Marie-Tooth (CMT) disease, but the cellular function of MORC2 is poorly understood. Here, through a genome-wide CRISPR-Cas9-mediated forward genetic screen, we identified MORC2 as an essential gene required for epigenetic silencing by the HUSH complex. HUSH recruits MORC2 to target sites in heterochromatin. We exploited a new method, differential viral accessibility (DIVA), to show that loss of MORC2 results in chromatin decompaction at these target loci, which is concomitant with a loss of H3K9me3 deposition and transcriptional derepression...
June 5, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28580727/integrative-gene-set-enrichment-analysis-utilizing-isoform-specific-expression
#12
Lie Li, Xinlei Wang, Guanghua Xiao, Adi Gazdar
Gene set enrichment analysis (GSEA) aims at identifying essential pathways, or more generally, sets of biologically related genes that are involved in complex human diseases. In the past, many studies have shown that GSEA is a very useful bioinformatics tool that plays critical roles in the innovation of disease prevention and intervention strategies. Despite its tremendous success, it is striking that conclusions of GSEA drawn from isolated studies are often sparse, and different studies may lead to inconsistent and sometimes contradictory results...
June 4, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28580003/rna-interference-a-novel-source-of-resistance-to-combat-plant-parasitic-nematodes
#13
REVIEW
Sagar Banerjee, Anamika Banerjee, Sarvajeet S Gill, Om P Gupta, Anil Dahuja, Pradeep K Jain, Anil Sirohi
Plant parasitic nematodes cause severe damage and yield loss in major crops all over the world. Available control strategies include use of insecticides/nematicides but these have proved detrimental to the environment, while other strategies like crop rotation and resistant cultivars have serious limitations. This scenario provides an opportunity for the utilization of technological advances like RNA interference (RNAi) to engineer resistance against these devastating parasites. First demonstrated in the model free living nematode, Caenorhabtidis elegans; the phenomenon of RNAi has been successfully used to suppress essential genes of plant parasitic nematodes involved in parasitism, nematode development and mRNA metabolism...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28576653/a-g-protein-coupled-chemokine-receptor-a-putative-insertion-site-for-a-multi-pathogen-recombinant-capripoxvirus-vaccine-strategy
#14
Catherine Cêtre-Sossah, Simon Dickmu, Olivier Kwiatek, Emmanuel Albina
Capripoxviruses (CaPVs) have been shown to be ideal viral vectors for the development of recombinant multivalent vaccines to enable delivery of immunogenic genes from ruminant pathogens. So far, the viral thymidine kinase (TK) gene is the only gene used to generate recombinants. A putative non-essential gene encoding a G-protein-coupled chemokine receptor subfamily homologue (GPCR) was targeted as an additional insertion site. Peste des petits ruminants (PPR) were chosen as a disease model. A new recombinant CaPV expressing the viral attachment hemagglutinin (H) of the PPR virus (PPRV) in the GPCR insertion site (rKS1-HPPR-GPCR) was generated in the backbone North African isolate KS1 strain of lumpy skin disease virus (LSDV)...
May 30, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28569133/defining-the-abc-of-gene-essentiality-in-streptococci
#15
Amelia R L Charbonneau, Oliver P Forman, Amy K Cain, Graham Newland, Carl Robinson, Mike Boursnell, Julian Parkhill, James A Leigh, Duncan J Maskell, Andrew S Waller
BACKGROUND: Utilising next generation sequencing to interrogate saturated bacterial mutant libraries provides unprecedented information for the assignment of genome-wide gene essentiality. Exposure of saturated mutant libraries to specific conditions and subsequent sequencing can be exploited to uncover gene essentiality relevant to the condition. Here we present a barcoded transposon directed insertion-site sequencing (TraDIS) system to define an essential gene list for Streptococcus equi subsp...
May 31, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28562614/properties-of-genes-essential-for-mouse-development
#16
Mitra Kabir, Ana Barradas, George T Tzotzos, Kathryn E Hentges, Andrew J Doig
Essential genes are those that are critical for life. In the specific case of the mouse, they are the set of genes whose deletion means that a mouse is unable to survive after birth. As such, they are the key minimal set of genes needed for all the steps of development to produce an organism capable of life ex utero. We explored a wide range of sequence and functional features to characterise essential (lethal) and non-essential (viable) genes in mice. Experimental data curated manually identified 1301 essential genes and 3451 viable genes...
2017: PloS One
https://www.readbyqxmd.com/read/28555625/co-infecting-microorganisms-dramatically-alter-pathogen-gene-essentiality-during-polymicrobial-infection
#17
Carolyn B Ibberson, Apollo Stacy, Derek Fleming, Justine L Dees, Kendra Rumbaugh, Michael S Gilmore, Marvin Whiteley
Identifying genes required by pathogens during infection is critical for antimicrobial development. Here, we use a Monte Carlo simulation-based method to analyse high-throughput transposon sequencing data to determine the role of infection site and co-infecting microorganisms on the in vivo 'essential' genome of Staphylococcus aureus. We discovered that co-infection of murine surgical wounds with Pseudomonas aeruginosa results in conversion of ∼25% of the in vivo S. aureus mono-culture essential genes to non-essential...
May 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28555054/knockdown-of-xbp1-by-rnai-in-mouse-granulosa-cells-promotes-apoptosis-inhibits-cell-cycle-and-decreases-estradiol-synthesis
#18
Nan Wang, Fan Zhao, Pengfei Lin, Guangle Zhang, Keqiong Tang, Aihua Wang, Yaping Jin
Granulosa cells are crucial for follicular growth, development, and follicular atresia. X-box binding protein 1 (XBP1), a basic region-leucine zipper protein, is widely involved in cell differentiation, proliferation, apoptosis, cellular stress response, and other signaling pathways. In this study, RNA interference, flow cytometry, western blot, real-time PCR, Cell Counting Kit (CCK8), and ELISA were used to investigate the effect of XBP1 on steroidogenesis, apoptosis, cell cycle, and proliferation of mouse granulosa cells...
May 29, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28550013/an-essential-regulatory-system-originating-from-polygenic-transcriptional-rewiring-of-phop-phoq-of-xanthomonas-campestris
#19
Bao-Yu Peng, Yue Pan, Ru-Jiao Li, Jin-Wei Wei, Fang Liang, Li Wang, Fang-Fang Wang, Wei Qian
How essential, regulatory genes originate and evolve is intriguing because mutations of these genes not only lead to lethality in organisms, but also have pleiotropic effects since they control the expression of multiple downstream genes. Therefore, the evolution of essential, regulatory genes is not only determined by genetic variations of their own sequences, but also by the biological function of downstream genes and molecular mechanisms of regulation. To understand the origin of essential, regulatory genes, experimental dissection of the complete regulatory cascade is needed...
May 26, 2017: Genetics
https://www.readbyqxmd.com/read/28547120/enzymatic-characterization-of-fructose-1-6-bisphosphatase-ii-from-francisella-tularensis-an-essential-enzyme-for-pathogenesis
#20
Hiten J Gutka, Nina M Wolf, Jasper Marc G Bondoc, Farahnaz Movahedzadeh
The glpX gene from Francisella tularensis encodes for the class II fructose 1,6-bisphosphatase (FBPaseII) enzyme. The glpX gene has been verified to be essential in F. tularensis, and the inactivation of this gene leads to impaired bacterial growth on gluconeogenic substrates. In the present work, we have complemented a ∆glpX mutant of Escherichia coli with the glpX gene of F. tularensis (FTF1631c). Our complementation work independently verifies that the glpX gene (FTF1631c) in F. tularensis is indeed an FBPase and supports the growth of the ΔglpX E...
May 25, 2017: Applied Biochemistry and Biotechnology
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