keyword
MENU ▼
Read by QxMD icon Read
search

Gene expression microbiome

keyword
https://www.readbyqxmd.com/read/27896820/ppar%C3%AE-targeted-oral-cancer-treatment-and-additional-utility-of-genomics-analytic-techniques
#1
Nathan Handley, Jacob Eide, Randall Taylor, Beverly Wuertz, Patrick Gaffney, Frank Ondrey
OBJECTIVE: Peroxisome proliferator-activated receptor γ (PPARγ) agonists have been shown to have anti-proliferative, anti-angiogenic, and proapoptotic effects, leading to interest in their use as cancer therapeutics. Pioglitazone, a U.S. Food and Drug Administration-approved type II diabetes medication and PPARγ agonist, may have a role in adjuvant head-and-neck squamous cell carcinoma treatment or prevention. Therefore, the purpose of this study was: 1) to treat oral cavity cancer cells with the PPARγ activator, pioglitazone, to analyze gene expression changes; and 2) to compare those changes with our preexisting genomic data for development of hypothesis-driven additional basic and clinical studies...
November 29, 2016: Laryngoscope
https://www.readbyqxmd.com/read/27892926/dual-specificity-phosphatase-6-deficiency-regulates-gut-microbiome-and-transcriptome-response-against-diet-induced-obesity-in-mice
#2
Jhen-Wei Ruan, Sarah Statt, Chih-Ting Huang, Yi-Ting Tsai, Cheng-Chin Kuo, Hong-Lin Chan, Yu-Chieh Liao, Tse-Hua Tan, Cheng-Yuan Kao
The gut microbiota plays profound roles in host metabolism and the inflammatory response associated with the development of obesity. Dusp6-deficient mice have been shown to be resistant to diet-induced obesity, but the mechanism behind this remains unclear. 16S ribosomal RNA gene analysis demonstrated that dusp6-deficient mice harbour unique gut microbiota with resistance to diet-induced-obesity-mediated alteration of the gut microbiome. Using a germ-free mouse model, we found that faecal/gut microbiota derived from dusp6-deficient mice significantly increased energy expenditure and reduced weight gain in recipient wild-type mice fed on a high-fat diet...
November 28, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27871908/acetylated-deoxycholic-dca-and-cholic-ca-acids-are-potent-ligands-of-pregnane-x-pxr-receptor
#3
Alejandro Carazo, Lucie Hyrsova, Jan Dusek, Hana Chodounska, Alzbeta Horvatova, Karel Berka, Vaclav Bazgier, Hongying Gan-Schreier, Waleé Chamulitrat, Eva Kudova, Petr Pavek
The Pregnane X (PXR), Vitamin D (VDR) and Farnesoid X (FXR) nuclear receptors have been shown to be receptors of bile acids controlling their detoxification or synthesis. Chenodeoxycholic (CDCA) and lithocholic (LCA) acids are ligands of FXR and VDR, respectively, whereas 3-keto and acetylated derivates of LCA have been described as ligands for all three receptors. In this study, we hypothesized that oxidation or acetylation at position 3, 7 and 12 of bile acids DCA (deoxycholic acid), LCA, CA (cholic acid), and CDCA by detoxification enzymes or microbiome may have an effect on the interactions with bile acid nuclear receptors...
November 18, 2016: Toxicology Letters
https://www.readbyqxmd.com/read/27871240/abo-antigen-and-secretor-statuses-are-not-associated-with-gut-microbiota-composition-in-1-500-twins
#4
Emily R Davenport, Julia K Goodrich, Jordana T Bell, Tim D Spector, Ruth E Ley, Andrew G Clark
BACKGROUND: Host genetics is one of several factors known to shape human gut microbiome composition, however, the physiological processes underlying the heritability are largely unknown. Inter-individual differences in host factors secreted into the gut lumen may lead to variation in microbiome composition. One such factor is the ABO antigen. This molecule is not only expressed on the surface of red blood cells, but is also secreted from mucosal surfaces in individuals containing an intact FUT2 gene (secretors)...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27853522/recent-advances-in-entamoeba-biology-rna-interference-drug-discovery-and-gut-microbiome
#5
REVIEW
Pedro Morgado, Dipak Manna, Upinder Singh
In recent years, substantial progress has been made in understanding the molecular and cell biology of the human parasite Entamoeba histolytica, an important pathogen with significant global impact. This review outlines some recent advances in the Entamoeba field in the last five years, focusing on areas that have not recently been discussed in detail: (i) molecular mechanisms regulating parasite gene expression, (ii) new efforts at drug discovery using high-throughput drug screens, and (iii) the effect of gut microbiota on amoebiasis...
2016: F1000Research
https://www.readbyqxmd.com/read/27829448/the-bronchial-epithelial-cell-bacterial-microbiome-and-host-response-in-patients-infected-with-human-immunodeficiency-virus
#6
Marc A Sze, Stella Xu, Janice M Leung, Emily A Vucic, Tawimas Shaipanich, Aida Moghadam, Marianne Harris, Silvia Guillemi, Sunita Sinha, Corey Nislow, Darra Murphy, Cameron Hague, Jonathon Leipsic, Stephen Lam, Wan Lam, Julio S Montaner, Don D Sin, S F Paul Man
BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is an important comorbidity in patients living with human immunodeficiency virus (HIV). Previous bacterial microbiome studies have shown increased abundance of specific bacterium, like Tropheryma whipplei, and no overall community differences. However, the host response to the lung microbiome is unknown in patients infected with HIV. METHODS: Two bronchial brush samples were obtained from 21 HIV-infected patients...
November 9, 2016: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/27825829/metagenomics-probing-pollutant-fate-in-natural-and-engineered-ecosystems
#7
REVIEW
Emna Bouhajja, Spiros N Agathos, Isabelle F George
Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field...
November 5, 2016: Biotechnology Advances
https://www.readbyqxmd.com/read/27822530/moleculo-long-read-sequencing-facilitates-assembly-and-genomic-binning-from-complex-soil-metagenomes
#8
Richard Allen White, Eric M Bottos, Taniya Roy Chowdhury, Jeremy D Zucker, Colin J Brislawn, Carrie D Nicora, Sarah J Fansler, Kurt R Glaesemann, Kevin Glass, Janet K Jansson
Soil metagenomics has been touted as the "grand challenge" for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87...
May 2016: MSystems
https://www.readbyqxmd.com/read/27809786/analysis-of-gene-expression-in-the-midgut-of-bombyx-mori-during-the-larval-molting-stage
#9
Bing Yang, Wuren Huang, Jie Zhang, Qiuyun Xu, Shoulin Zhu, Qiaoli Zhang, Brenda T Beerntsen, Hongsheng Song, Erjun Ling
BACKGROUND: Insects can be models for understanding human intestinal infection and pathology. Molting, a special period during which the old insect cuticle is shed and a new one is produced, is crucial for insect development. Holometabolous insects may experience several larva-to-larva moltings to become larger, a pupal molt and adult eclosion to become adults. During the larval molts, they stop feeding and become quiescent. Although the molting larvae become quiescent, it is not known if changes in microbiome, physiology, development and immunity of midguts occur...
November 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27807042/mice-fed-a-high-fat-diet-supplemented-with-resistant-starch-display-marked-shifts-in-the-liver-metabolome-concurrent-with-altered-gut-bacteria
#10
Dorothy A Kieffer, Brian D Piccolo, Maria L Marco, Eun Bae Kim, Michael L Goodson, Michael J Keenan, Tamara N Dunn, Knud Erik Bach Knudsen, Roy J Martin, Sean H Adams
BACKGROUND: High-amylose-maize resistant starch type 2 (HAMRS2) is a fermentable dietary fiber known to alter the gut milieu, including the gut microbiota, which may explain the reported effects of resistant starch to ameliorate obesity-associated metabolic dysfunction. OBJECTIVE: Our working hypothesis was that HAMRS2-induced microbiome changes alter gut-derived signals (i.e., xenometabolites) reaching the liver via the portal circulation, in turn altering liver metabolism by regulating gene expression and other pathways...
November 2, 2016: Journal of Nutrition
https://www.readbyqxmd.com/read/27801835/dietary-gluten-induced-gut-dysbiosis-is-accompanied-by-selective-upregulation-of-micrornas-with-intestinal-tight-junction-and-bacteria-binding-motifs-in-rhesus-macaque-model-of-celiac-disease
#11
Mahesh Mohan, Cheryl-Emiliane T Chow, Caitlin N Ryan, Luisa S Chan, Jason Dufour, Pyone P Aye, James Blanchard, Charles P Moehs, Karol Sestak
The composition of the gut microbiome reflects the overall health status of the host. In this study, stool samples representing the gut microbiomes from 6 gluten-sensitive (GS) captive juvenile rhesus macaques were compared with those from 6 healthy, age- and diet-matched peers. A total of 48 samples representing both groups were studied using V4 16S rRNA gene DNA analysis. Samples from GS macaques were further characterized based on type of diet administered: conventional monkey chow, i.e., wheat gluten-containing diet (GD), gluten-free diet (GFD), barley gluten-derived diet (BOMI) and reduced gluten barley-derived diet (RGB)...
October 28, 2016: Nutrients
https://www.readbyqxmd.com/read/27795980/functional-characterization-of-inflammatory-bowel-disease-associated-gut-dysbiosis-in-gnotobiotic-mice
#12
Hiroko Nagao-Kitamoto, Andrew B Shreiner, Merritt G Gillilland, Sho Kitamoto, Chiharu Ishii, Akiyoshi Hirayama, Peter Kuffa, Mohamad El-Zaatari, Helmut Grasberger, Anna M Seekatz, Peter D R Higgins, Vincent B Young, Shinji Fukuda, John Y Kao, Nobuhiko Kamada
BACKGROUND & AIMS: Gut dysbiosis is closely involved in the pathogenesis of inflammatory bowel disease (IBD). However, it remains unclear whether IBD-associated gut dysbiosis contributes to disease pathogenesis or is merely secondary to intestinal inflammation. We established a humanized gnotobiotic (hGB) mouse system to assess the functional role of gut dysbiosis associated with 2 types of IBD: Crohn's disease (CD) and ulcerative colitis (UC). METHODS: Germ-free mice were colonized by the gut microbiota isolated from patients with CD and UC, and healthy controls...
July 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/27793585/methodologies-for-probing-the-metatranscriptome-of-grassland-soil
#13
Aaron Garoutte, Erick Cardenas, James Tiedje, Adina Howe
Metatranscriptomics provides an opportunity to identify active microbes and expressed genes in complex soil communities in response to particular conditions. Currently, there are a limited number of soil metatranscriptome studies to provide guidance for using this approach in this challenging matrix. Hence, we evaluated the technical challenges of applying soil metatranscriptomics to a highly diverse, low activity natural system. We used a non-targeted rRNA removal approach, duplex nuclease specific (DSN) normalization, to generate a metatranscriptomic library from field collected soil supporting a perennial grass, Miscanthus x giganteus (a biofuel crop), and evaluated its ability to provide insight into its active community members and their expressed protein-coding genes...
October 25, 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27790229/killing-two-birds-with-one-stone-natural-rice-rhizospheric-microbes-reduce-arsenic-uptake-and-blast-infections-in-rice
#14
Venkatachalam Lakshmanan, Jonathon Cottone, Harsh P Bais
Our recent work has shown that a rice thizospheric natural isolate, a Pantoea sp (hereafter EA106) attenuates Arsenic (As) uptake in rice. In parallel, yet another natural rice rhizospheric isolate, a Pseudomonas chlororaphis (hereafter EA105), was shown to inhibit rice blast pathogen Magnaporthe oryzae. Considering the above, we envisaged to evaluate the importance of mixed stress regime in rice plants subjected to both As toxicity and blast infections. Plants subjected to As regime showed increased susceptibility to blast infections compared to As-untreated plants...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27785786/the-genetic-background-of-inflammatory-bowel-disease-from-correlation-to-causality
#15
REVIEW
Werna T C Uniken Venema, Michiel D Voskuil, Gerard Dijkstra, Rinse K Weersma, Eleonora A M Festen
Recent studies have greatly improved our insight into the genetic background of Inflammatory Bowel Disease (IBD). New high throughput technologies and large-scale international collaborations have contributed to the identification of 200 independent genetic risk loci for IBD. However, in most of these loci it is unclear which gene conveys the risk for IBD. More importantly, it is unclear which variant within or near the gene is causal to the disease. Using targeted GWAS, imputation, re-sequencing of risk loci and in silico fine-mapping of densely typed loci, several causal variants have been identified in IBD risk genes, and various pathological pathways have been uncovered...
October 26, 2016: Journal of Pathology
https://www.readbyqxmd.com/read/27782139/antibiotic-mediated-gut-microbiome-perturbation-accelerates-development-of-type-1-diabetes-in-mice
#16
Alexandra E Livanos, Thomas U Greiner, Pajau Vangay, Wimal Pathmasiri, Delisha Stewart, Susan McRitchie, Huilin Li, Jennifer Chung, Jiho Sohn, Sara Kim, Zhan Gao, Cecily Barber, Joanne Kim, Sandy Ng, Arlin B Rogers, Susan Sumner, Xue-Song Zhang, Ken Cadwell, Dan Knights, Alexander Alekseyenko, Fredrik Bäckhed, Martin J Blaser
The early life microbiome plays important roles in host immunological and metabolic development. Because the incidence of type 1 diabetes (T1D) has been increasing substantially in recent decades, we hypothesized that early-life antibiotic use alters gut microbiota, which predisposes to disease. Using non-obese diabetic mice that are genetically susceptible to T1D, we examined the effects of exposure to either continuous low-dose antibiotics or pulsed therapeutic antibiotics (PAT) early in life, mimicking childhood exposures...
August 22, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27760570/rumen-metagenome-and-metatranscriptome-analyses-of-low-methane-yield-sheep-reveals-a-sharpea-enriched-microbiome-characterised-by-lactic-acid-formation-and-utilisation
#17
Janine Kamke, Sandra Kittelmann, Priya Soni, Yang Li, Michael Tavendale, Siva Ganesh, Peter H Janssen, Weibing Shi, Jeff Froula, Edward M Rubin, Graeme T Attwood
BACKGROUND: Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts...
October 19, 2016: Microbiome
https://www.readbyqxmd.com/read/27748750/discovery-of-mrsa-active-antibiotics-using-primary-sequence-from-the-human-microbiome
#18
John Chu, Xavier Vila-Farres, Daigo Inoyama, Melinda Ternei, Louis J Cohen, Emma A Gordon, Boojala Vijay B Reddy, Zachary Charlop-Powers, Henry A Zebroski, Ricardo Gallardo-Macias, Mark Jaskowski, Shruthi Satish, Steven Park, David S Perlin, Joel S Freundlich, Sean F Brady
Here we present a natural product discovery approach, whereby structures are bioinformatically predicted from primary sequence and produced by chemical synthesis (synthetic-bioinformatic natural products, syn-BNPs), circumventing the need for bacterial culture and gene expression. When we applied the approach to nonribosomal peptide synthetase gene clusters from human-associated bacteria, we identified the humimycins. These antibiotics inhibit lipid II flippase and potentiate β-lactam activity against methicillin-resistant Staphylococcus aureus in mice, potentially providing a new treatment regimen...
December 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27729904/functional-characteristics-of-the-gut-microbiome-in-c57bl-6-mice-differentially-susceptible-to-plasmodium-yoelii
#19
Joshua M A Stough, Stephen P Dearth, Joshua E Denny, Gary R LeCleir, Nathan W Schmidt, Shawn R Campagna, Steven W Wilhelm
C57BL/6 mice are widely used for in vivo studies of immune function and metabolism in mammals. In a previous study, it was observed that when C57BL/6 mice purchased from different vendors were infected with Plasmodium yoelii, a causative agent of murine malaria, they exhibited both differential immune responses and significantly different parasite burdens: these patterns were reproducible when gut contents were transplanted into gnotobiotic mice. To gain insight into the mechanism of resistance, we removed whole ceca from mice purchased from two vendors, Taconic Biosciences (low parasitemia) and Charles River Laboratories (high parasitemia), to determine the combined host and microflora metabolome and metatranscriptome...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27720237/novel-volatiles-of-skin-borne-bacteria-inhibit-the-growth-of-gram-positive-bacteria-and-affect-quorum-sensing-controlled-phenotypes-of-gram-negative-bacteria
#20
Marie Chantal Lemfack, Srinivasa Rao Ravella, Nicola Lorenz, Marco Kai, Kirsten Jung, Stefan Schulz, Birgit Piechulla
The skin microbiota is import for body protection. Here we present the first comprehensive analysis of the volatile organic compound (VOC) profiles of typical skin-resident corynebacterial and staphylococcal species. The VOC profile of Staphylococcus schleiferi DSMZ 4807 was of particular interest as it is dominated by two compounds, 3-(phenylamino)butan-2-one and 3-(phenylimino)butan-2-one (schleiferon A and B, respectively). Neither of these has previously been reported from natural sources. Schleiferon A and B inhibited the growth of various Gram-positive species and affected two quorum-sensing-dependent phenotypes - prodigiosin accumulation and bioluminescence - of Gram-negative bacteria...
December 2016: Systematic and Applied Microbiology
keyword
keyword
55403
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"