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Gene expression microbiome

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https://www.readbyqxmd.com/read/28507320/the-microbiome-regulates-amygdala-dependent-fear-recall
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28464028/crude-oil-impairs-immune-function-and-increases-susceptibility-to-pathogenic-bacteria-in-southern-flounder
#10
Keith M Bayha, Natalie Ortell, Caitlin N Ryan, Kimberly J Griffitt, Michelle Krasnec, Johnny Sena, Thiruvarangan Ramaraj, Ryan Takeshita, Gregory D Mayer, Faye Schilkey, Robert J Griffitt
Exposure to crude oil or its individual constituents can have detrimental impacts on fish species, including impairment of the immune response. Increased observations of skin lesions in northern Gulf of Mexico fish during the 2010 Deepwater Horizon oil spill indicated the possibility of oil-induced immunocompromisation resulting in bacterial or viral infection. This study used a full factorial design of oil exposure and bacterial challenge to examine how oil exposure impairs southern flounder (Paralichthys lethostigma) immune function and increases susceptibility to the bacteria Vibrio anguillarum, a causative agent of vibriosis...
2017: PloS One
https://www.readbyqxmd.com/read/28462059/accumulation-and-expression-of-multiple-antibiotic-resistance-genes-in-arcobacter-cryaerophilus-that-thrives-in-sewage
#11
Jess A Millar, Rahul Raghavan
We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater...
2017: PeerJ
https://www.readbyqxmd.com/read/28456518/vaginal-ecosystem-modeling-of-growth-patterns-of-anaerobic-bacteria-in-microaerophilic-conditions
#12
Audrie A Medina-Colorado, Kathleen L Vincent, Aaron L Miller, Carrie A Maxwell, Lauren N Dawson, Trevelyn Olive, Elena V Kozlova, Marc M Baum, Richard B Pyles
The human vagina constitutes a complex ecosystem created through relationships established between host mucosa and bacterial communities. In this ecosystem, classically defined bacterial aerobes and anaerobes thrive as communities in the microaerophilic environment. Levels of CO2 and O2 present in the vaginal lumen are impacted by both the ecosystem's physiology and the behavior and health of the human host. Study of such complex relationships requires controlled and reproducible causational approaches that are not possible in the human host that, until recently, was the only place these bacterial communities thrived...
April 26, 2017: Anaerobe
https://www.readbyqxmd.com/read/28434033/the-gut-microbiome-as-a-target-for-prevention-and-treatment-of-hyperglycaemia-in-type-2-diabetes-from-current-human-evidence-to-future-possibilities
#13
REVIEW
Louise Brunkwall, Marju Orho-Melander
The totality of microbial genomes in the gut exceeds the size of the human genome, having around 500-fold more genes that importantly complement our coding potential. Microbial genes are essential for key metabolic processes, such as the breakdown of indigestible dietary fibres to short-chain fatty acids, biosynthesis of amino acids and vitamins, and production of neurotransmitters and hormones. During the last decade, evidence has accumulated to support a role for gut microbiota (analysed from faecal samples) in glycaemic control and type 2 diabetes...
April 22, 2017: Diabetologia
https://www.readbyqxmd.com/read/28431252/engineered-regulatory-systems-modulate-gene-expression-of-human-commensals-in-the-gut
#14
Bentley Lim, Michael Zimmermann, Natasha A Barry, Andrew L Goodman
The gut microbiota is implicated in numerous aspects of health and disease, but dissecting these connections is challenging because genetic tools for gut anaerobes are limited. Inducible promoters are particularly valuable tools because these platforms allow real-time analysis of the contribution of microbiome gene products to community assembly, host physiology, and disease. We developed a panel of tunable expression platforms for the prominent genus Bacteroides in which gene expression is controlled by a synthetic inducer...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28414763/enhanced-offspring-predisposition-to-steatohepatitis-with-maternal-high-fat-diet-is-associated-with-epigenetic-and-microbiome-alterations
#15
Umesh D Wankhade, Ying Zhong, Ping Kang, Maria Alfaro, Sree V Chintapalli, Keshari M Thakali, Kartik Shankar
OBJECTIVE: Non-alcoholic fatty liver disease (NAFLD) is an important co-morbidity associated with obesity and a precursor to steatohepatitis. However, the contributions of gestational and early life influences on development of NAFLD and NASH remain poorly appreciated. METHODS: Two independent studies were performed to examine whether maternal over-nutrition via exposure to high fat diet (HFD) leads to exacerbated hepatic responses to post-natal HFD and methionine choline deficient (MCD) diets in the offspring...
2017: PloS One
https://www.readbyqxmd.com/read/28404649/the-microbiome-in-respiratory-medicine-current-challenges-and-future-perspectives
#16
REVIEW
Rosa Faner, Oriol Sibila, Alvar Agustí, Eric Bernasconi, James D Chalmers, Gary B Huffnagle, Chaysavanh Manichanh, Philip L Molyneaux, Roger Paredes, Vicente Pérez Brocal, Julia Ponomarenko, Sanjay Sethi, Jordi Dorca, Eduard Monsó
The healthy lung has previously been considered to be a sterile organ because standard microbiological culture techniques consistently yield negative results. However, culture-independent techniques report that large numbers of microorganisms coexist in the lung. There are many unknown aspects in the field, but available reports show that the lower respiratory tract microbiota: 1) is similar in healthy subjects to the oropharyngeal microbiota and dominated by members of the Firmicutes, Bacteroidetes and Proteobacteria phyla; 2) shows changes in smokers and well-defined differences in chronic respiratory diseases, although the temporal and spatial kinetics of these changes are only partially known; and 3) shows relatively abundant non-cultivable bacteria in chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, cystic fibrosis and bronchiectasis, with specific patterns for each disease...
April 2017: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/28393904/transcriptomic-changes-in-an-animal-bacterial-symbiosis-under-modeled-microgravity-conditions
#17
Giorgio Casaburi, Irina Goncharenko-Foster, Alexandrea A Duscher, Jamie S Foster
Spaceflight imposes numerous adaptive challenges for terrestrial life. The reduction in gravity, or microgravity, represents a novel environment that can disrupt homeostasis of many physiological processes. Additionally, it is becoming increasingly clear that an organism's microbiome is critical for host health and examining its resiliency in microgravity represents a new frontier for space biology research. In this study, we examine the impact of microgravity on the interactions between the squid Euprymna scolopes and its beneficial symbiont Vibrio fischeri, which form a highly specific binary mutualism...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28386898/estrogen-receptor-beta-mediates-hepatotoxicity-induced-by-perfluorooctane-sulfonate-in-mouse
#18
Cheng Xu, Zhao-Yan Jiang, Qian Liu, Hui Liu, Aihua Gu
Perfluorooctane sulfonate (PFOS), an artificial fluorosurfactant and global contaminant, is used widely in various consumer products. In this study, we investigated the function of estrogen receptor β (ERβ) in PFOS-induced bile acid and cholesterol metabolism disorders and gut microbiome using ERβ knockout mice that were exposed to PFOS by gavage. Our results showed that a daily dose of 5 mg PFOS/kg significantly induced hydropic degeneration and vacuolation in hepatic cells, reduced bile acid, and cholesterol levels in liver tissue, and influenced the abundance and composition of gut microbiota...
April 7, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28384412/second-era-of-omics-in-caries-research-moving-past-the-phase-of-disillusionment
#19
M M Nascimento, E Zaura, A Mira, N Takahashi, J M Ten Cate
Novel approaches using OMICS techniques enable a collective assessment of multiple related biological units, including genes, gene expression, proteins, and metabolites. In the past decade, next-generation sequencing ( NGS) technologies were improved by longer sequence reads and the development of genome databases and user-friendly pipelines for data analysis, all accessible at lower cost. This has generated an outburst of high-throughput data. The application of OMICS has provided more depth to existing hypotheses as well as new insights in the etiology of dental caries...
April 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28374191/alternative-splicing-the-pledge-the-turn-and-the-prestige-the-key-role-of-alternative-splicing-in-human-biological-systems
#20
REVIEW
L M Gallego-Paez, M C Bordone, A C Leote, N Saraiva-Agostinho, M Ascensão-Ferreira, N L Barbosa-Morais
Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation...
April 3, 2017: Human Genetics
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