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Gene expression microbiome

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https://www.readbyqxmd.com/read/28645180/alcohol-metabolism-and-oesophageal-cancer-a-systematic-review-of-the-evidence
#1
Marco Matejcic, M J Gunter, Pietro Ferrari
Alcohol is a major risk factor for oesophageal squamous cell carcinoma (OSCC), the most prevalent histological subtype of oesophageal cancer (OC) worldwide. The metabolism of alcohol is regulated by specific enzymes whose activity and expression is influenced by genetic polymorphisms. We conducted a systematic review of current epidemiological evidence of the relationship between alcohol intake and OC risk, including the role of tobacco smoking and functional polymorphisms of dehydrogenases (ADHs) and aldehyde dehydrogenases (ALDHs)...
June 22, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28625995/novel-antibiotic-resistance-determinants-from-agricultural-soil-exposed-to-antibiotics-widely-used-in-human-medicine-and-animal-farming
#2
Calvin Ho-Fung Lau, Kalene van Engelen, Stephen Gordon, Justin Renaud, Edward Topp
Antibiotic resistance has emerged globally as one of the biggest threats to human and animal health. Although the excessive use of antibiotics is recognized for accelerating the selection for resistance, there is a growing body of evidence suggesting that natural environments are "hotspots" for the development of both ancient and contemporary resistance mechanisms. Given that pharmaceuticals can be entrained onto agricultural land through anthropogenic activities, this could be a potential driver for the emergence and dissemination of resistance in soil bacteria...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28621304/epigenetic-and-gene-expression-analysis-of-ankylosing-spondylitis-associated-loci-implicate-immune-cells-and-the-gut-in-the-disease-pathogenesis
#3
Z Li, K Haynes, D J Pennisi, L K Anderson, X Song, G P Thomas, T Kenna, P Leo, M A Brown
Ankylosing spondylitis (AS) is a common immune-mediated arthropathy primarily affecting the spine and pelvis. Most AS patients have subclinical intestinal inflammation, suggesting the gut microbiome and the immune response play a role in pathogenesis. Susceptibility to AS is primarily genetic, and at least 114 susceptibility variants have been identified to date. We applied bioinformatic methods utilizing epigenetic and gene and protein expression data to identify the cell types through which AS-associated variants operate...
June 15, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28605403/power-and-sample-size-calculations-for-high-throughput-sequencing-based-experiments
#4
Chung-I Li, David C Samuels, Ying-Yong Zhao, Yu Shyr, Yan Guo
Power/sample size (power) analysis estimates the likelihood of successfully finding the statistical significance in a data set. There has been a growing recognition of the importance of power analysis in the proper design of experiments. Power analysis is complex, yet necessary for the success of large studies. It is important to design a study that produces statistically accurate and reliable results. Power computation methods have been well established for both microarray-based gene expression studies and genotyping microarray-based genome-wide association studies...
June 9, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28589226/the-first-acidobacterial-laccase-like-multicopper-oxidase-revealed-by-metagenomics-shows-high-salt-and-thermo-tolerance
#5
Luka Ausec, Francesca Berini, Carmine Casciello, Mariana Silvia Cretoiu, Jan Dirk van Elsas, Flavia Marinelli, Ines Mandic-Mulec
Metagenomics is a powerful tool that allows identifying enzymes with novel properties from the unculturable component of microbiomes. However, thus far only a limited number of laccase or laccase -like enzymes identified through metagenomics has been subsequently biochemically characterized. This work describes the successful bio-mining of bacterial laccase-like enzymes in an acidic bog soil metagenome and the characterization of the first acidobacterial laccase-like multicopper oxidase (LMCO). LMCOs have hitherto been mostly studied in fungi and some have already found applications in diverse industries...
June 6, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28588643/molecular-cloning-expression-and-characterization-of-four-novel-thermo-alkaliphilic-enzymes-retrieved-from-a-metagenomic-library
#6
Mukil Maruthamuthu, Jan Dirk van Elsas
BACKGROUND: Enzyme discovery is a promising approach to aid in the deconstruction of recalcitrant plant biomass in an industrial process. Novel enzymes can be readily discovered by applying metagenomics on whole microbiomes. Our goal was to select, examine, and characterize eight novel glycoside hydrolases that were previously detected in metagenomic libraries, to serve biotechnological applications with high performance. RESULTS: Here, eight glycosyl hydrolase family candidate genes were selected from metagenomes of wheat straw-degrading microbial consortia using molecular cloning and subsequent gene expression studies in Escherichia coli...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28587312/molecular-typing-of-staphylococcus-aureus-isolated-from-patients-with-autosomal-dominant-hyper-ige-syndrome
#7
Inka Sastalla, Kelli W Williams, Erik D Anderson, Ian A Myles, Jensen D Reckhow, Marlene Espinoza-Moraga, Alexandra F Freeman, Sandip K Datta
Autosomal dominant hyper IgE syndrome (AD-HIES) is a primary immunodeficiency caused by a loss-of-function mutation in the Signal Transducer and Activator of Transcription 3 (STAT3). This immune disorder is clinically characterized by increased susceptibility to cutaneous and sinopulmonary infections, in particular with Candida and Staphylococcus aureus. It has recently been recognized that the skin microbiome of patients with AD-HIES is altered with an overrepresentation of certain Gram-negative bacteria and Gram-positive staphylococci...
June 6, 2017: Pathogens
https://www.readbyqxmd.com/read/28586253/characterization-of-recombinant-trypanosoma-brucei-gambiense-translationally-controlled-tumor-protein-rtbgtctp-and-its-interaction-with-glossina-midgut-bacteria
#8
Géraldine Bossard, Manon Bartoli, Marie-Laure Fardeau, Philippe Hozmuller, Bernard Ollivier, Anne Geiger
In humans, sleeping sickness (i.e. Human African Trypanosomiasis) is caused by the protozoan parasites Trypanosoma brucei gambiense (Tbg) in West and Central Africa, and T. b. rhodesiense in East Africa. We previously showed in vitro that Tbg is able to excrete/secrete a large number of proteins, including Translationally Controlled Tumour Protein (TCTP). Moreover, the tctp gene was previously described to be expressed in Tbg-infected flies. Aside from its involvement in diverse cellular processes, we have investigated a possible alternative role within the interactions occurring between the trypanosome parasite, its tsetse fly vector, and the associated midgut bacteria...
June 6, 2017: Gut Microbes
https://www.readbyqxmd.com/read/28572677/intraspecific-differences-in-molecular-stress-responses-and-coral-pathobiome-contribute-to-mortality-under-bacterial-challenge-in-acropora-millepora
#9
Rachel M Wright, Carly D Kenkel, Carly E Dunn, Erin N Shilling, Line K Bay, Mikhail V Matz
Disease causes significant coral mortality worldwide; however, factors responsible for intraspecific variation in disease resistance remain unclear. We exposed fragments of eight Acropora millepora colonies (genotypes) to putatively pathogenic bacteria (Vibrio spp.). Genotypes varied from zero to >90% mortality, with bacterial challenge increasing average mortality rates 4-6 fold and shifting the microbiome in favor of stress-associated taxa. Constitutive immunity and subsequent immune and transcriptomic responses to the challenge were more prominent in high-mortality individuals, whereas low-mortality corals remained largely unaffected and maintained expression signatures of a healthier condition (i...
June 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28561849/symbiosis-inspired-approaches-to-antibiotic-discovery
#10
REVIEW
Navid Adnani, Scott R Rajski, Tim S Bugni
Covering: 2010 up to 2017Life on Earth is characterized by a remarkable abundance of symbiotic and highly refined relationships among life forms. Defined as any kind of close, long-term association between two organisms, symbioses can be mutualistic, commensalistic or parasitic. Historically speaking, selective pressures have shaped symbioses in which one organism (typically a bacterium or fungus) generates bioactive small molecules that impact the host (and possibly other symbionts); the symbiosis is driven fundamentally by the genetic machineries available to the small molecule producer...
May 31, 2017: Natural Product Reports
https://www.readbyqxmd.com/read/28552621/intestinal-epithelial-sirtuin-1-regulates-intestinal-inflammation-during-aging-in-mice-by-altering-the-intestinal-microbiota
#11
Alicia S Wellman, Mallikarjuna R Metukuri, Nevzat Kazgan, Xiaojiang Xu, Qing Xu, Natalie S X Ren, Agnieszka Czopik, Michael T Shanahan, Ashley Kang, Willa Chen, M Andrea Azcarate-Peril, Ajay S Gulati, David C Fargo, Leonard Guarente, Xiaoling Li
BACKGROUND & AIMS: Intestinal epithelial homeostasis is maintained by complex interactions among epithelial cells, commensal gut microorganisms, and immune cells. Disruption of this homeostasis is associated with disorders such as inflammatory bowel disease, but the mechanisms of this process are not clear. We investigated how Sirtuin 1 (SIRT1), a conserved mammalian NAD(+)-dependent protein deacetylase, senses environmental stress to alter intestinal integrity. METHODS: We performed studies of mice with disruption of Sirt1 specifically in the intestinal epithelium (SIRT1 iKO, villin-Cre+, Sirt1(flox/flox) mice) and control mice (villin-Cre-, Sirt1(flox/flox)) on a C57BL/6 background...
May 25, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28507320/the-microbiome-regulates-amygdala-dependent-fear-recall
#12
A E Hoban, R M Stilling, G Moloney, F Shanahan, T G Dinan, G Clarke, J F Cryan
The amygdala is a key brain region that is critically involved in the processing and expression of anxiety and fear-related signals. In parallel, a growing number of preclinical and human studies have implicated the microbiome-gut-brain in regulating anxiety and stress-related responses. However, the role of the microbiome in fear-related behaviours is unclear. To this end we investigated the importance of the host microbiome on amygdala-dependent behavioural readouts using the cued fear conditioning paradigm...
May 16, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28496167/effect-of-trichoderma-harzianum-on-maize-rhizosphere-microbiome-and-biocontrol-of-fusarium-stalk-rot
#13
Kandasamy Saravanakumar, Yaqian Li, Chuanjin Yu, Qiang-Qiang Wang, Meng Wang, Jianan Sun, Jin-Xin Gao, Jie Chen
Fusarium stalk rot (FSR) caused by Fusarium graminearum (FG) significantly affects the productivity of maize grain crops. Application of agrochemicals to control the disease is harmful to environment. In this regard, use of biocontrol agent (BCA) is an alternative to agrochemicals. Although Trichoderma species are known as BCA, the selection of host-pathogen specific Trichoderma is essential for the successful field application. Hence, we screened a total of 100 Trichoderma isolates against FG, selected Trichoderma harzianum (CCTCC-RW0024) for greenhouse experiments and studied its effect on changes of maize rhizosphere microbiome and biocontrol of FSR...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28494786/compositionally-and-functionally-distinct-sinus-microbiota-in-chronic-rhinosinusitis-patients-have-immunological-and-clinically-divergent-consequences
#14
Emily K Cope, Andrew N Goldberg, Steven D Pletcher, Susan V Lynch
BACKGROUND: Chronic rhinosinusitis (CRS) is a heterogeneous disease characterized by persistent sinonasal inflammation and sinus microbiome dysbiosis. The basis of this heterogeneity is poorly understood. We sought to address the hypothesis that a limited number of compositionally distinct pathogenic bacterial microbiota exist in CRS patients and invoke discrete immune responses and clinical phenotypes in CRS patients. RESULTS: Sinus brushings from patients with CRS (n = 59) and healthy individuals (n = 10) collected during endoscopic sinus surgery were analyzed using 16S rRNA gene sequencing, predicted metagenomics, and RNA profiling of the mucosal immune response...
May 12, 2017: Microbiome
https://www.readbyqxmd.com/read/28494733/phage-mediated-gene-therapy
#15
Zeinab Hosseinidoust
Bacteriophages (bacterial viruses) have long been under investigation as vectors for gene therapy. Similar to other viral vectors, the phage coat proteins have evolved over millions of years to protect the viral genome from degradation post injection, offering protection for the valuable therapeutic sequence. However, what sets phage apart from other viral gene delivery vectors is their safety for human use and the relative ease by which foreign molecules can be expressed on the phage outer surface, enabling highly targeted gene delivery...
May 10, 2017: Current Gene Therapy
https://www.readbyqxmd.com/read/28489816/endothelial-tlr4-and-the-microbiome-drive-cerebral-cavernous-malformations
#16
Alan T Tang, Jaesung P Choi, Jonathan J Kotzin, Yiqing Yang, Courtney C Hong, Nicholas Hobson, Romuald Girard, Hussein A Zeineddine, Rhonda Lightle, Thomas Moore, Ying Cao, Robert Shenkar, Mei Chen, Patricia Mericko, Jisheng Yang, Li Li, Ceylan Tanes, Dmytro Kobuley, Urmo Võsa, Kevin J Whitehead, Dean Y Li, Lude Franke, Blaine Hart, Markus Schwaninger, Jorge Henao-Mejia, Leslie Morrison, Helen Kim, Issam A Awad, Xiangjian Zheng, Mark L Kahn
Cerebral cavernous malformations (CCMs) are a cause of stroke and seizure for which no effective medical therapies yet exist. CCMs arise from the loss of an adaptor complex that negatively regulates MEKK3-KLF2/4 signalling in brain endothelial cells, but upstream activators of this disease pathway have yet to be identified. Here we identify endothelial Toll-like receptor 4 (TLR4) and the gut microbiome as critical stimulants of CCM formation. Activation of TLR4 by Gram-negative bacteria or lipopolysaccharide accelerates CCM formation, and genetic or pharmacologic blockade of TLR4 signalling prevents CCM formation in mice...
May 10, 2017: Nature
https://www.readbyqxmd.com/read/28481971/bioinformatics-tools-for-quantitative-and-functional-metagenome-and-metatranscriptome-data-analysis-in-microbes
#17
Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma
Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota...
May 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28472674/saccharin-induced-liver-inflammation-in-mice-by-altering-the-gut-microbiota-and-its-metabolic-functions
#18
Xiaoming Bian, Pengcheng Tu, Liang Chi, Bei Gao, Hongyu Ru, Kun Lu
Maintaining the balance of the gut microbiota and its metabolic functions is vital for human health, however, this balance can be disrupted by various external factors including food additives. A range of food and beverages are sweetened by saccharin, which is generally considered to be safe despite controversial debates. However, recent studies indicated that saccharin perturbed the gut microbiota. Inflammation is frequently associated with disruptions of the gut microbiota. The aim of this study is to investigate the relationship between host inflammation and perturbed gut microbiome by saccharin...
May 1, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28471193/-molecular-pathology-of-colorectal-cancer-microsatellite-instability-the-detection-the-relationship-to-the-pathophysiology-and-prognosis
#19
V Brychtová, R Šefr, R Hrstka, P Vídeňská, B Bencsiková, B Hanáková, L Zdražilová Dubská, R Nenutil, E Budinská
BACKGROUND: Colorectal carcinoma (CRC) is third most common cancer worldwide with very heterogenous character. In most cases, it is caused by sporadic events leading to disruption of epithelial cells of the colon. The minority evolves from germline mutations associated with hereditary cancer syndromes. Mechanisms leading to mutations of oncogenes, tumour suppressors and genes of DNA repair mechanisms include: 1. chromosomal instability, 2. microsatellite instability and 3. CpG island methylator phenotype...
2017: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/28466260/autophagy-genes-of-host-responds-to-disruption-of-gut-microbial-community-by-antibiotics
#20
Sudha B Singh, Melissa Wilson, Nathaniel Ritz, Henry C Lin
BACKGROUND: Defective autophagic machinery, such as that in Crohn's disease patients homozygous for ATG16L1 risk allele, is associated with alteration of resident gut bacterial communities. However, whether or not host autophagy responds to changes in the resident gut microbial community is not known. Here, we investigated the effect of antibiotic-induced disruption of the gut microbiome (dysbiosis) on autophagy gene expression and the expression of antimicrobial peptides/protein (AMP) over time...
May 2, 2017: Digestive Diseases and Sciences
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