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https://www.readbyqxmd.com/read/28721208/new-perspectives-on-the-regulation-of-type-ii-inflammation-in-asthma
#1
REVIEW
Mireya Becerra-Díaz, Marsha Wills-Karp, Nicola M Heller
Asthma is a chronic inflammatory disease of the lungs which has been thought to arise as a result of inappropriately directed T helper type-2 (Th2) immune responses of the lungs to otherwise innocuous inhaled antigens. Current asthma therapeutics are directed towards the amelioration of downstream consequences of type-2 immune responses (i.e. β-agonists) or broad-spectrum immunosuppression (i.e. corticosteroids). However, few approaches to date have been focused on the primary prevention of immune deviation...
2017: F1000Research
https://www.readbyqxmd.com/read/28717593/short-reads-from-honey-bee-apis-sp-sequencing-projects-reflect-microbial-associate-diversity
#2
Michael Gerth, Gregory D D Hurst
High throughput (or 'next generation') sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and 'contaminating' material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome...
2017: PeerJ
https://www.readbyqxmd.com/read/28710295/relationships-between-gastrointestinal-microbiota-and-blood-group-antigens
#3
Anuhya Gampa, Phillip A Engen, Rima Shobar, Ece A Mutlu
FUT2 is a gene for a fucosyltransferase that encodes expression of ABO blood group antigens found on gastrointestinal mucosa and secretions. We hypothesized that the fecal microbiomes of healthy subjects, with blood group antigens A, B and O, have differing compositions. Thirty-three fecal and blood specimens from healthy subjects were analyzed for FUT2 genotype and the fecal microbiome was determined using 454 pyrosequencing. Our data shows that being a blood group secretor is associated with less diversity at higher orders of taxonomy; and the presence of blood group A antigens in the secretor subjects are associated with an expansion families of bacteria within the gut...
July 14, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28706193/polydextrose-changes-the-gut-microbiome-and-attenuates-fasting-triglyceride-and-cholesterol-levels-in-western-diet-fed-mice
#4
Ghulam Shere Raza, Heli Putaala, Ashley A Hibberd, Esa Alhoniemi, Kirsti Tiihonen, Kari Antero Mäkelä, Karl-Heinz Herzig
Obesity and dyslipidemia are hallmarks of metabolic and cardiovascular diseases. Polydextrose (PDX), a soluble fiber has lipid lowering effects. We hypothesize that PDX reduces triglycerides and cholesterol by influencing gut microbiota, which in turn modulate intestinal gene expression. C57BL/6 male mice were fed a Western diet (WD) ±75 mg PDX twice daily by oral gavage for 14 days. Body weight and food intake were monitored daily. Fasting plasma lipids, caecal microbiota and gene expression in intestine and liver were measured after 14 days of feeding...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28702033/how-streptomyces-anulatus-primes-grapevine-defenses-to-cope-with-gray-mold-a-study-of-the-early-responses-of-cell-suspensions
#5
Parul Vatsa-Portugal, Aziz Aziz, Marine Rondeau, Sandra Villaume, Hamid Morjani, Christophe Clément, Essaid Ait Barka
Gray mold, caused by Botrytis cinerea, is one of the most destructive diseases of grapevine and is controlled with an intense application of fungicides. As alternatives to chemicals, beneficial microbes may promote plant health by stimulating the plant's immune system. An actinomycete, Streptomyces anulatus S37, has been screened from the rhizosphere microbiome of healthy Vitis vinifera on the basis of its ability to promote grapevine growth and to induce resistance against various phytopathogens, including B...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28692535/effect-of-cmv-and-ebv-replication-on-intestinal-mucosal-gene-expression-and-microbiome-composition-of-hiv-infected-and-uninfected-individuals
#6
Sara Gianella, Antoine Chaillon, Ece A Mutlu, Phillip A Engen, Robin M Voigt, Ali Keshavarzian, John Losurdo, Prachi Chakradeo, Steven M Lada, Masato Nakazawa, Alan L Landay
BACKGROUND: HIV-infection is associated with dramatic changes in the intestinal mucosa. The impact of other viral pathogens is unclear. METHODS: Eighty biopsies from left and right colon (n=63) and terminal ileum (n = 17) were collected from 19 HIV-infected and 22 HIV-uninfected subjects. Levels of cytomegalovirus (CMV) and Epstein Barr Virus (EBV) DNA were measured by droplet-digital (dd)PCR. Mucosal gene expression was measured via multiplex-assay. Microbiome analysis was performed using bacterial 16S-rDNA-pyrosequencing...
July 7, 2017: AIDS
https://www.readbyqxmd.com/read/28691768/microbiome-inflammation-epigenetic-alterations-and-mental-diseases
#7
REVIEW
Reza Alam, Hamid M Abdolmaleky, Jin-Rong Zhou
Major mental diseases such as autism, bipolar disorder, schizophrenia, and major depressive disorder are debilitating illnesses with complex etiologies. Recent findings show that the onset and development of these illnesses cannot be well described by the one-gene; one-disease approach. Instead, their clinical presentation is thought to result from the regulative interplay of a large number of genes. Even though the involvement of many genes are likely, up regulating and activation or down regulation and silencing of these genes by the environmental factors play a crucial role in contributing to their pathogenesis...
July 10, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28686852/integrated-meta-omic-analyses-of-the-gastrointestinal-tract-microbiome-in-patients-undergoing-allogeneic-hematopoietic-stem-cell-transplantation
#8
Anne Kaysen, Anna Heintz-Buschart, Emilie E L Muller, Shaman Narayanasamy, Linda Wampach, Cédric C Laczny, Norbert Graf, Arne Simon, Katharina Franke, Jörg Bittenbring, Paul Wilmes, Jochen G Schneider
In patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), treatment-induced changes to the gastrointestinal tract (GIT) microbiome have been linked to adverse outcomes, most notably graft-versus-host disease (GvHD). However, it is presently unknown whether this relationship is causal or consequential. Here, we performed an integrated meta-omic analysis to probe deeper into the GIT microbiome changes, during allo-HSCT, and its accompanying treatments. We used 16S and 18S rRNA gene amplicon sequencing to resolve archaea, bacteria, and eukaryotes within the GIT microbiomes of 16 patients undergoing allo-HSCT for the treatment of hematologic malignancies...
June 20, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28680437/knots-untie-molecular-determinants-involved-in-knot-formation-induced-by-pseudomonas-savastanoi-in-woody-hosts
#9
REVIEW
Eloy Caballo-Ponce, Jesús Murillo, Marta Martínez-Gil, Alba Moreno-Pérez, Adrián Pintado, Cayo Ramos
The study of the molecular basis of tree diseases is lately receiving a renewed attention, especially with the emerging perception that pathogens require specific pathogenicity and virulence factors to successfully colonize woody hosts. Pathosystems involving woody plants are notoriously difficult to study, although the use of model bacterial strains together with genetically homogeneous micropropagated plant material is providing a significant impetus to our understanding of the molecular determinants leading to disease...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28675687/disruptive-physiology-olfaction-and-the-microbiome-gut-brain-axis
#10
John Bienenstock, Wolfgang A Kunze, Paul Forsythe
This review covers the field of olfaction and chemosensation of odorants and puts this information into the context of interactions between microbes and behaviour; the microbiome-gut-brain axis (MGBA). Recent emphasis has also been placed on the concept of the holobiome which states that no single aspect of an organism should be viewed separately and thus must include examination of their associated microbial populations and their influence. While it is known that the microbiome may be involved in the modulation of animal behaviour, there has been little systematized effort to incorporate into such studies the rapidly developing knowledge of the wide range of olfactory systems...
July 4, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/28673400/the-environment-epigenome-and-asthma
#11
REVIEW
Ivana V Yang, Catherine A Lozupone, David A Schwartz
Asthma prevalence has been on the increase, especially in North America compared with other continents. However, the prevalence of asthma differs worldwide, and in many countries the prevalence is stable or decreasing. This highlights the influence of environmental exposures, such as allergens, air pollution, and the environmental microbiome, on disease etiology and pathogenesis. The epigenome might provide the unifying mechanism that translates the influence of environmental exposures to changes in gene expression, respiratory epithelial function, and immune cell skewing that are hallmarks of asthma...
July 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28672212/elucidating-microbial-community-adaptation-to-anaerobic-co-digestion-of-fats-oils-and-grease-and-food-waste
#12
Yamrot M Amha, Pooja Sinha, Jewls Lagman, Matt Gregori, Adam L Smith
Despite growing interest in co-digestion and demonstrated process improvements (e.g., enhanced stability and biogas production), few studies have evaluated how co-digestion impacts the anaerobic digestion (AD) microbiome. Three sequential bench-scale respirometry experiments were conducted at thermophilic temperature (50 °C) with various combinations of primary sludge (PS); thickened waste activated sludge (TWAS); fats, oils, and grease (FOG); and food waste (FW). Two additional runs were then performed to evaluate microbial inhibition at higher organic fractions of FOG (30-60% volatile solids loading (VSL; v/v))...
June 23, 2017: Water Research
https://www.readbyqxmd.com/read/28658542/the-nutrition-gut-microbiome-physiology-axis-and-allergic-diseases
#13
REVIEW
Craig McKenzie, Jian Tan, Laurence Macia, Charles R Mackay
Dietary and bacterial metabolites influence immune responses. This raises the question whether the increased incidence of allergies, asthma, some autoimmune diseases, cardiovascular disease, and others might relate to intake of unhealthy foods, and the decreased intake of dietary fiber. In recent years, new knowledge on the molecular mechanisms underpinning a 'diet-gut microbiota-physiology axis' has emerged to substantiate this idea. Fiber is fermented to short chain fatty acids (SCFAs), particularly acetate, butyrate, and propionate...
July 2017: Immunological Reviews
https://www.readbyqxmd.com/read/28645180/alcohol-metabolism-and-oesophageal-cancer-a-systematic-review-of-the-evidence
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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