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Consumer genomics

Zhongqiu Chen, Wen Ling, Guangdong Shang
Pseudomonas putida KT2440 is a saprophytic, generally recognized as safe microorganism that plays important roles in the biodegradation and production of value-added chemicals. Chromosomal gene deletion of P. putida KT2440 usually involves time-consuming gene coning, conjugal transfer and counterselection. Recently, we developed a P. putida KT2440 markerless gene deletion method based on recombineering and Cre/loxP site-specific recombination. PCR-based λ Red recombineering circumvents the tedious cloning steps and is more amenable to high-throughput manipulation...
October 7, 2016: FEMS Microbiology Letters
Xingxing Dong, Xiaohong Wang, Xingchun Chen, Zhiyun Yan, Jing Cheng, Liangliang Gao, Yuan Liu, Jinquan Li
Staphylococcus aureus, a commensal and a pathogenic bacterium, causes a wide variety of diseases in humans and animals with a high impact on public health and the livestock industry. The risk of zoonotic transmission to humans highlights the need to understand the molecular ecology of S. aureus in foods. In this study, we obtained 25 S. aureus isolates from 39 crayfish samples in Hubei, China. PCR was applied for detection of presence of virulence and methicillin resistance genes in the pathogen genome. The result revealed that all of the 25 S...
October 19, 2016: Current Microbiology
Daniel Garrido, Santiago Ruiz-Moyano, Nina Kirmiz, Jasmine C Davis, Sarah M Totten, Danielle G Lemay, Juan A Ugalde, J Bruce German, Carlito B Lebrilla, David A Mills
The infant intestinal microbiota is often colonized by two subspecies of Bifidobacterium longum: subsp. infantis (B. infantis) and subsp. longum (B. longum). Competitive growth of B. infantis in the neonate intestine has been linked to the utilization of human milk oligosaccharides (HMO). However, little is known how B. longum consumes HMO. In this study, infant-borne B. longum strains exhibited varying HMO growth phenotypes. While all strains efficiently utilized lacto-N-tetraose, certain strains additionally metabolized fucosylated HMO...
October 19, 2016: Scientific Reports
Paul M Hime, Scott Hotaling, Richard E Grewelle, Eric M O'Neill, S Randal Voss, H Bradley Shaffer, David W Weisrock
Perhaps the most important recent advance in species delimitation has been the development of model-based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next-generation sequence datasets provides powerful insights into genome-wide patterns of divergence during speciation. However, applying complex models to large datasets is time consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of loci on species delimitation conclusions...
October 17, 2016: Molecular Ecology
Teresa Graziano, Angela Amoruso, Stefania Nicola, Francesca Deidda, Serena Allesina, Marco Pane, Pietro Piffanelli, Francesco Strozzi, Luca Mogna, Mario Del Piano
GOALS: The aim of the study was to unequivocally demonstrate the nontransmissibility of the genes mediating the resistance of the strain Bifidobacterium longum W11 (LMG P-21586) to rifaximin. BACKGROUND: Most antibiotic treatments can induce unfavorable side effects such as antibiotic-associated diarrhea, which is largely attributable to the disruption of the intestinal microbiota. The parallel intake of probiotic bacteria might reduce these events, even if with generally very poor results...
November 2016: Journal of Clinical Gastroenterology
June C Carroll, Tutsirai Makuwaza, Donna P Manca, Nicolette Sopcak, Joanne A Permaul, Mary Ann O'Brien, Ruth Heisey, Elizabeth A Eisenhauer, Julie Easley, Monika K Krzyzanowska, Baukje Miedema, Sandhya Pruthi, Carol Sawka, Nancy Schneider, Jonathan Sussman, Robin Urquhart, Catarina Versaevel, Eva Grunfeld
OBJECTIVE: To assess primary care providers' (PCPs') experiences with, perceptions of, and desired role in personalized medicine, with a focus on cancer. DESIGN: Qualitative study involving focus groups. SETTING: Urban and rural interprofessional primary care team practices in Alberta and Ontario. PARTICIPANTS: Fifty-one PCPs. METHODS: Semistructured focus groups were conducted and audiorecorded...
October 2016: Canadian Family Physician Médecin de Famille Canadien
A D Samarajeewa, J R Velicogna, J I Princz, R M Subasinghe, R P Scroggins, L A Beaudette
Silver nano-particles (AgNPs) are widely used in a range of consumer products as a result of their antimicrobial properties. Given the broad spectrum of uses, AgNPs have the potential for being released to the environment. As a result, environmental risks associated with AgNPs need to be assessed to aid in the development of regulatory guidelines. Research was performed to assess the effects of AgNPs on soil microbial activity and diversity in a sandy loam soil with an emphasis on using a battery of microbial tests involving multiple endpoints...
October 4, 2016: Environmental Pollution
Ankita Mishra, Anuradha Singh, Monica Sharma, Pankaj Kumar, Joy Roy
BACKGROUND: Starch is a major part of cereal grain. It comprises two glucose polymer fractions, amylose (AM) and amylopectin (AP), that make up about 25 and 75 % of total starch, respectively. The ratio of the two affects processing quality and digestibility of starch-based food products. Digestibility determines nutritional quality, as high amylose starch is considered a resistant or healthy starch (RS type 2) and is highly preferred for preventive measures against obesity and related health conditions...
October 6, 2016: BMC Plant Biology
Baptiste Mayjonade, Jérôme Gouzy, Cécile Donnadieu, Nicolas Pouilly, William Marande, Caroline Callot, Nicolas Langlade, Stéphane Muños
De novo sequencing of complex genomes is one of the main challenges for researchers seeking high-quality reference sequences. Many de novo assemblies are based on short reads, producing fragmented genome sequences. Third-generation sequencing, with read lengths >10 kb, will improve the assembly of complex genomes, but these techniques require high-molecular-weight genomic DNA (gDNA), and gDNA extraction protocols used for obtaining smaller fragments for short-read sequencing are not suitable for this purpose...
October 1, 2016: BioTechniques
Xueqiu Jian, Xiaoming Liu
In silico prediction methods have increasingly been valuable and popular in molecular biology, especially in human genetics, for deleteriousness prediction to filter and prioritize huge amounts of DNA variation identified by sequencing human genomes. There is a rich collection of available methods developed upon different levels/aspects of knowledge about how DNA variations affect gene expression. Given the fact that their predictions are not always consistent or even opposite of what was expected, using consensus prediction or majority vote among these methods is preferred to trusting any single one...
2017: Methods in Molecular Biology
Leila Syedmoradi, Fariba Esmaeili, Michael L Norton
DNA methylation, a stable and heritable covalent modification which mostly occurs in the context of a CpG dinucleotide, has great potential as a biomarker to detect disease, provide prognoses and predict therapeutic responses. It can be detected in a quantitative manner by many different approaches both genome-wide and at specific gene loci, in various biological fluids such as urine, plasma, and serum, which can be obtained without invasive procedures. The current, classical methods are effective in studying DNA methylation patterns, however, for the most part; they have major drawbacks such as expensive instruments, complicated and time consuming protocols as well as relatively low sensitivity, and high false positive rates...
October 17, 2016: Analyst
Marilyn C Cornelis, Tim Kacprowski, Cristina Menni, Stefan Gustafsson, Edward Pivin, Jerzy Adamski, Anna Artati, Chin B Eap, Georg Ehret, Nele Friedrich, Andrea Ganna, Idris Guessous, Georg Homuth, Lars Lind, Patrik K Magnusson, Massimo Mangino, Nancy L Pedersen, Maik Pietzner, Karsten Suhre, Henry Völzke, Murielle Bochud, Tim D Spector, Hans J Grabe, Erik Ingelsson
Caffeine is the most widely consumed psychoactive substance in the world and presents with wide interindividual variation in metabolism. This variation may modify potential adverse or beneficial effects of caffeine on health. We conducted a genome-wide association study (GWAS) of plasma caffeine, paraxanthine, theophylline, theobromine and paraxanthine/caffeine ratio among up to 9,876 individuals of European ancestry from six population-based studies. A single SNP at 6p23 (near CD83) and several SNPs at 7p21 (near AHR), 15q24 (near CYP1A2) and 19q13...
October 3, 2016: Human Molecular Genetics
Nadav Brandes, Dan Ofer, Michal Linial
Determining residue-level protein properties, such as sites of post-translational modifications (PTMs), is vital to understanding protein function. Experimental methods are costly and time-consuming, while traditional rule-based computational methods fail to annotate sites lacking substantial similarity. Machine Learning (ML) methods are becoming fundamental in annotating unknown proteins and their heterogeneous properties. We present ASAP (Amino-acid Sequence Annotation Prediction), a universal ML framework for predicting residue-level properties...
2016: Database: the Journal of Biological Databases and Curation
W Mazzucco, R Pastorino, T Lagerberg, M Colotto, E d'Andrea, C Marotta, C Marzuillo, P Villari, A Federici, W Ricciardi, S Boccia
BACKGROUND: A need for a governance of genomics in healthcare among European Union (EU) countries arose during an international meeting of experts on public health genomics (PHG). We have conducted a survey on existing national genomic policies in healthcare among Chief Medical Officers (CMOs) of the 28 EU member states, plus Norway. METHODS: A questionnaire was sent to CMOs after a meeting on the policy implications of PHG held during the Italian presidency of the Council of EU in 2014...
September 29, 2016: European Journal of Public Health
Nathaniel A Dyment, Xi Jiang, Li Chen, Seung-Hyun Hong, Douglas J Adams, Cheryl Ackert-Bicknell, Dong-Guk Shin, David W Rowe
There is an increasing need for efficient phenotyping and histopathology of a variety of tissues. This phenotyping need is evident with the ambitious projects to disrupt every gene in the mouse genome. The research community needs rapid and inexpensive means to phenotype tissues via histology. Histological analyses of skeletal tissues are often time consuming and semi-quantitative at best, regularly requiring subjective interpretation of slides from trained individuals. Here, we present a cryohistological paradigm for efficient and inexpensive phenotyping of mineralized tissues...
2016: Journal of Visualized Experiments: JoVE
Gunnar Völkel, Sebastian Wiese, Karlheinz Holzmann, Johann M Kraus, Fabian Schneider, Matthias Görlach, Hans A Kestler
MOTIVATION: Core service units have become an organisational hallmark in many research institutions world wide. Such service cores provide complex state-of-the-art technologies and expertise to the research community. Typically, a user delivers material or raw data to a core. The core defines work packages for ensuing analysis and returns results back to the user. This core activity can be quite complex and time consuming and usually does not communicate itself to the outside. Naturally, the user is highly interested to follow the progress of a project once handed over to the core unit...
2016: PloS One
Erika A Waters, Courtney Wheeler, Jada G Hamilton
Understanding that cancer is caused by both genetic and behavioral risk factors is an important component of genomic literacy. However, a considerable percentage of people in the United States do not endorse such multifactorial beliefs. Using nationally representative cross-sectional data from the U.S. Health Information National Trends Survey (N = 2,529), we examined how information seeking, information scanning, and key information-processing characteristics were associated with endorsing a multifactorial model of cancer causation...
2016: Journal of Health Communication
Emilia Niemiec, Pascal Borry, Wim Pinxten, Heidi Carmen Howard
Whole exome sequencing (WES) and whole genome sequencing (WGS) have become increasingly available in the research and clinical settings and are now also being offered by direct-to-consumer (DTC) genetic testing (GT) companies. This offer can be perceived as amplifying the already identified concerns regarding adequacy of informed consent (IC) for both WES/WGS and the DTC GT context. We performed a qualitative content analysis of Websites of four companies offering WES/WGS DTC regarding the following elements of IC: pre-test counseling, benefits and risks, and incidental findings (IFs)...
October 5, 2016: Human Mutation
J-M Drezen, J Gauthier, T Josse, A Bézier, E Herniou, E Huguet
Recent studies have highlighted that the accidental acquisition of DNA from other species by invertebrate genomes is much more common than originally thought. The transferred DNAs are of bacterial or eukaryote origin and in both cases the receiver species may end up utilising the transferred genes for its own benefit. Frequent contact with prokaryotic DNA from symbiotic endocellular bacteria may predispose invertebrates to incorporate this genetic material into their genomes. Increasing evidence also points to viruses as major players in transferring genes and mobile elements between the species they infect...
September 15, 2016: Journal of Invertebrate Pathology
Michael E Pyne, Xuejia Liu, Murray Moo-Young, Duane A Chung, C Perry Chou
Clostridium pasteurianum is emerging as a prospective host for the production of biofuels and chemicals, and has recently been shown to directly consume electric current. Despite this growing biotechnological appeal, the organism's genetics and central metabolism remain poorly understood. Here we present a concurrent genome sequence for the C. pasteurianum type strain and provide extensive genomic analysis of the organism's defence mechanisms and central fermentative metabolism. Next generation genome sequencing produced reads corresponding to spontaneous excision of a novel phage, designated φ6013, which could be induced using mitomycin C and detected using PCR and transmission electron microscopy...
2016: Scientific Reports
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