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Consumer genomics

Manuel Corpas, Nadezda V Kovalevskaya, Amanda McMurray, Fiona G G Nielsen
It is generally acknowledged that, for reproducibility and progress of human genomic research, data sharing is critical. For every sharing transaction, a successful data exchange is produced between a data consumer and a data provider. Providers of human genomic data (e.g., publicly or privately funded repositories and data archives) fulfil their social contract with data donors when their shareable data conforms to FAIR (findable, accessible, interoperable, reusable) principles. Based on our experiences via Repositive (https://repositive...
March 2018: PLoS Computational Biology
Germano Orrù, Mauro Giovanni Carta, Alessia Bramanti
Background: Several studies have shown that the Single Nucleotide Polymorphism (SNP) in the CACAN1C gene, rs1006737, is related to different mood disorder illnesses, such as bipolar disorder and schizophrenia. Current day molecular procedures for allele detection of this gene can be very expensive and time consuming. Hence, a sensitive and specific molecular procedure for detecting these mutations in a large number of subjects is desirable, especially for research groups who have no complex laboratory equipment...
2018: Clinical Practice and Epidemiology in Mental Health: CP & EMH
Moran N Cabili, Knox Carey, Stephanie O M Dyke, Anthony J Brookes, Marc Fiume, Francis Jeanson, Giselle Kerry, Alex Lash, Heidi Sofia, Dylan Spalding, Anne-Marie Tasse, Susheel Varma, Ravi Pandya
The volume of genomics and health data is growing rapidly, driven by sequencing for both research and clinical use. However, under current practices, the data is fragmented into many distinct datasets, and researchers must go through a separate application process for each dataset. This is time-consuming both for the researchers and the data stewards, and it reduces the velocity of research and new discoveries that could improve human health. We propose to simplify this process, by introducing a standard Library Card that identifies and authenticates researchers across all participating datasets...
March 14, 2018: Scientific Data
Wei Xiong, Luis H Reyes, William E Michener, Pin-Ching Maness, Katherine J Chou
Cellulose and hemicellulose are the most abundant components in plant biomass. A preferred Consolidated Bioprocessing (CBP) system is one which can directly convert both cellulose and hemicellulose into target products without adding the costly hydrolytic enzyme cocktail. In this work, the thermophilic, cellulolytic, and anaerobic bacterium, Clostridium thermocellum DSM 1313, was engineered to grow on xylose in addition to cellulose. Both xylA (encoding for xylose isomerase) and xylB (encoding for xylulokinase) genes from the thermophilic anaerobic bacterium Thermoanaerobacter ethanolicus were introduced to enable xylose utilization while still retaining its inherent ability to grow on 6-carbon substrates...
March 14, 2018: Biotechnology and Bioengineering
Anthony J Greenberg
Explosive growth in the amount of genomic data is matched by increasing power of consumer grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative samples from large data sets. I describe a fast and memory efficient implementation of an on-line sampling method developed for tape drives 30 years ago. Focusing on genotype files, I test the performance of this technique on modern solid-state and spinning hard drives, and show that it performs well compared to a simple sampling scheme...
March 12, 2018: G3: Genes—Genomes—Genetics
Bastian Vögeli, Sylvain Engilberge, Eric Girard, François Riobé, Olivier Maury, Tobias J Erb, Seigo Shima, Tristan Wagner
Many reactions within a cell are thermodynamically unfavorable. To efficiently run some of those endergonic reactions, nature evolved intermediate-channeling enzyme complexes, in which the products of the first endergonic reactions are immediately consumed by the second exergonic reactions. Based on this concept, we studied how archaea overcome the unfavorable first reaction of isoprenoid biosynthesis-the condensation of two molecules of acetyl-CoA to acetoacetyl-CoA catalyzed by acetoacetyl-CoA thiolases (thiolases)...
March 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
Lifeng Zhu, Qi Wu, Cao Deng, Mengjie Zhang, Chenglin Zhang, Hua Chen, Guoqing Lu, Fuwen Wei
Carnivorous members of the Carnivora reside at the apex of food chains and consume meat-only diets, rich in purine, fats and protein. Here, we aimed to identify potential adaptive evolutionary signatures compatible with high purine and fat metabolism based on analysis of host genomes and symbiotic gut microbial metagenomes. We found that the gut microbiomes of carnivorous Carnivora (e.g. Felidae, Canidae) clustered in the same clade, and other clades comprised omnivorous and herbivorous Carnivora (e.g. badgers, bears and pandas)...
March 12, 2018: Environmental Microbiology
Kazi Ada, Candy Chuah, Abu Bakar Abdul Majeed, Chiuan Herng Leow, Boon Huat Lim, Chiuan Yee Leow
Immunoinformatics plays a pivotal role in vaccine design, immunodiagnostic development, and antibody production. In the past, antibody design and vaccine development depended exclusively on immunological experiments which are relatively expensive and time-consuming. However, recent advances in the field of immunological bioinformatics have provided feasible tools which can be used to lessen the time and cost required for vaccine and antibody development. This approach allows the selection of immunogenic regions from the pathogen genomes...
March 12, 2018: Pathogens and Global Health
Jing-Jing Liu, Guo-Chang Zhang, In Iok Kong, Eun Ju Yun, Jia-Qi Zheng, Dae-Hyuk Kweon, Yong-Su Jin
The probiotic yeast Saccharomyces boulardii has been extensively studied for preventing and treating diarrheal diseases and is now commercially available in some countries. S. boulardii displays notable phenotypes, such as high optimal growth temperature, high tolerance against acidic conditions, and the inability to form ascospores, which differentiate S. boulardii from S. cerevisiae The majority of prior studies stated that S. boulardii exhibits sluggish or halted galactose utilization. Nonetheless, molecular mechanisms underlying inefficient galactose uptake have yet to be elucidated...
March 9, 2018: Applied and Environmental Microbiology
Astrid Nehlig
Most individuals adjust their caffeine intake according to the objective and subjective effects induced by the methylxanthine. However, to reach the desired effects, the quantity of caffeine consumed varies largely among individuals. It has been known for decades that the metabolism, clearance, and pharmacokinetics of caffeine is affected by many factors such as age, sex and hormones, liver disease, obesity, smoking, and diet. Caffeine also interacts with many medications. All these factors will be reviewed in the present document and discussed in light of the most recent data concerning the genetic variability affecting caffeine levels and effects at the pharmacokinetic and pharmacodynamic levels that both critically drive the level of caffeine consumption...
April 2018: Pharmacological Reviews
Allan Rd Nunes, Brenda Elen B Alves, Hannaly Wb Pereira, Yasmin M Nascimento, Ingryd C Morais, José Veríssimo Fernandes, Josélio Mg Araújo, Daniel Cf Lanza
BACKGROUND The genus Flavivirus includes a variety of medically important viruses, including dengue virus (DENV) and Zika virus (ZIKV), which are most prevalent in Brazil. Because the clinical profile of patients affected by different DENV serotypes or ZIKV may be similar, the development of new methods that facilitate a rapid and accurate diagnosis is crucial. OBJECTIVES The current study aimed to develop an improved reverse transcription-polymerase chain reaction (RT-PCR) protocol for universal detection of flaviviruses by using semi-nested primers that discriminate between DENV serotypes and ZIKV...
2018: Memórias do Instituto Oswaldo Cruz
Erica Ramos, Scott M Weissman
As the public's interest in genetics and genomics has increased, there has been corresponding and unprecedented growth in direct-to-consumer genetic testing (DTC-GT). Although regulatory concerns have limited true DTC-GT available without a physician order, the paradigm has shifted to a model of consumer-directed genetic testing (CD-GT) in which patients are researching testing options and requesting specific genetic testing from their health-care providers. However, many nongenetics health-care providers do not have the background, education, interest, or time to order and/or interpret typical clinical genetic testing, let alone DTC-GT...
March 7, 2018: American Journal of Medical Genetics. Part C, Seminars in Medical Genetics
M Saba Rahim, Himanshu Sharma, Afsana Parveen, Joy K Roy
Previously, association mapping (AM) methodology was used to unravel genetic complications in animal science by measuring the complex traits for candidate and non-candidate genes. Nowadays, this statistical approach is widely used to clarify the complexity in plant breeding program-based genome-wide breeding strategies, marker development, and diversity analysis. This chapter is particularly focused on methodologies with limitations and provides an overview of AM models and software used up to now. Association or linkage disequilibrium mapping has become a very popular method for discovering candidate and non-candidate genes and confirmation of quantitative trait loci (QTL) on various parts of the genome and in marker-assisted selection for breeding...
March 7, 2018: Advances in Biochemical Engineering/biotechnology
Abdul Rafay Khan, Muhammad Tariq Pervez, Masroor Ellahi Babar, Nasir Naveed, Muhammad Shoaib
Background: Current advancements in next-generation sequencing technology have made possible to sequence whole genome but assembling a large number of short sequence reads is still a big challenge. In this article, we present the comparative study of seven assemblers, namely, ABySS, Velvet, Edena, SGA, Ray, SSAKE, and Perga, using prokaryotic and eukaryotic paired-end as well as single-end data sets from Illumina platform. Results: Results showed that in case of single-end data sets, Velvet and ABySS outperformed in all the seven assemblers with comparatively low assembling time and high genome fraction...
2018: Evolutionary Bioinformatics Online
Johnny R Ramroop, Mark N Stein, Justin M Drake
Prostate cancer is the most common malignancy in men in the United States. While androgen deprivation therapy results in tumor responses initially, there is relapse and progression to metastatic castration-resistant prostate cancer. Currently, all prostate cancer patients receive essentially the same treatment, and there is a need for clinically applicable technologies to provide predictive biomarkers toward personalized therapies. Genomic analyses of tumors are used for clinical applications, but with a paucity of obvious driver mutations in metastatic castration-resistant prostate cancer, other applications, such as phosphoproteomics, may complement this approach...
2018: Frontiers in Oncology
Max Teplitski, Marcos de Moraes
Outbreaks of gastrointestinal illness, linked to the consumption of fruits, vegetables, and sprouts, continue to capture the attention of the general public and scientists. The recurrence of these outbreaks, despite heightened producer and consumer awareness, combined with improved sanitation protocols and technology, can be explained by the hypothesis that enteric pathogens, such as nontyphoidal Salmonella spp. and enterovirulent Escherichia coli, have evolved to exploit plants as alternative hosts. This review explores the genetic and genomic context for this hypothesis...
March 1, 2018: Trends in Microbiology
Jane Tiller, Paul Lacaze
The Internet currently enables unprecedented ease of access for direct-to-consumer (DTC) genetic testing, with saliva collection kits posted directly to consumer homes from anywhere in the world. This poses new challenges for local jurisdictions in regulating genetic testing, traditionally a tightly-regulated industry. Some Internet-based genetic tests have the capacity to cause significant confusion or harm to consumers who are unaware of the risks or potential variability in quality. The emergence of some online products of questionable content, unsupported by adequate scientific evidence, is a cause for concern...
2018: Frontiers in Public Health
C Randall Harrell, Valentin Djonov, Crissy Fellabaum, Vladislav Volarevic
The standard sterilization method for most medical devices over the past 40 years involves gamma irradiation. During sterilization, gamma rays efficiently eliminate microorganisms from the medical devices and tissue allografts, but also significantly change molecular structure of irradiated products, particularly fragile biologics such as cytokines, chemokines and growth factors. Accordingly, gamma radiation significantly alters biomechanical properties of bone, tendon, tracheal, skin, amnion tissue grafts and micronized amniotic membrane injectable products...
2018: International Journal of Medical Sciences
Ciara Staunton, Paulina Tindana, Melany Hendricks, Keymanthri Moodley
BACKGROUND: Genomic biobanking research is undergoing exponential growth in Africa raising a host of legal, ethical and social issues. Given the scientific complexity associated with genomics, there is a growing recognition globally of the importance of science translation and community engagement (CE) for this type of research, as it creates the potential to build relationships, increase trust, improve consent processes and empower local communities. Despite this level of recognition, there is a lack of empirical evidence of the practise and processes for effective CE in genomic biobanking in Africa...
February 27, 2018: BMC Medical Ethics
Célia Ventura, António Sousa-Uva, João Lavinha, Maria João Silva
The widespread application of carbon nanotubes (CNT) on industrial, biomedical, and consumer products can represent an emerging respiratory occupational hazard. Particularly, their similarity with the fiber-like shape of asbestos have raised a strong concern about their carcinogenic potential. Several in vitro and in vivo studies have been supporting this view by pointing to immunotoxic, cytotoxic and genotoxic effects of some CNT that may conduct to pulmonary inflammation, fibrosis, and bronchioloalveolar hyperplasia in rodents...
February 26, 2018: Environmental and Molecular Mutagenesis
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