Use Of Genomic Techniques Research Articles

Nutrigenomics and nutrigenetics: Special emphasis on optimization of human health and animal performance

Environmental factors, food’s nutrients, and genetic makeup play an important role in phenotypic appearance of a trait via the principles of biological sciences. The nutritional genomics focuses on the interaction between bioactive food components and the genome, which includes nutrigenetics and nutrigenomics. The influence of nutrients on genes expression is called nutrigenomics, while the heterogeneous response of gene variants to dietary nutrients is called nutrigenetics. Nutrigenomics is providing the effects of ingested food’s nutrients on gene expression and gene regulation, i.e., diet-gene interaction in order to identify the dietetic components having beneficial or detrimental health effects. It elucidates that how DNA and genetic code influence the need for specific nutrients and also within specific quantities are required for maintaining good health throughout life. It is helpful to determine the personalized diet that means individual nutritional requirements based on the genetic makeup of the person as well as clarifies some etiological perspectives of chronic diseases like type-2 diabetes, cancer, obesity and cardiovascular diseases (CVD) because of associations between diet and chronic diseases. Rearing of farmed animals is a vital component of global food production systems, its impact on the environment, human health, animal welfare, and biodiversity is being increasingly challenged. Developments in genetic and genomic technologies have had a key role in improving the productivity of farmed animals for decades. The goal of discussing these issues is to get a better understanding of basic biological issues and to apply their knowledge to practical problems such as medicine, and improvement of animal performance. Therefore, this review article is focus on the role of genes and the use of genomic techniques in human health, as well as animals’ well-being and welfare.

RELEVANCE OF PHARMACOGEOMICS IN OVARIAN STIMULATION : A REVIEW

Genetic polymorphism is defined as the detection of a single genetic mutation in humans, and in addition each allele should occur at a rate of at least 1% of the population. Potential strategies for detecting various alleles related to specific diseases or responses to drug treatment include case-control studies in uninvolved and affected individuals or genome scanning techniques.Tailoring ovarian stimulation to the individual patient can be challenging because the ovarian response varies substantially between patients. Pharmacogenetics has emerged as a new area of research to improve the balance between desired and undesired actions of drugs, based upon the genetic predisposition of the individual patient. In summary, the use of genomic techniques may not be limited to the rapid and complete detection of drugs. The Ser680 in the gene FSH-receptor has been shown to cause low resistance and low response to FSH action in homozygous women (Ser680 / Ser680). The potential role of AMH in influencing the ovarian response in stimulation. Estrogen plays an important role in the development of secondary sex, fetal growth, the reproductive cycle, and the maintenance of pregnancy.

Genomics outperforms genetics to manage mistakes in fisheries stocking of threatened species

Hatchery production and fisheries stocking is a widespread and high profile management practice because it allows recreational fisheries to continue in threatened species. Human-mediated transfer of fish across the geographic boundaries of intraspecies lineages or closely related species can cause introgression and occasionally outbreeding depression. Hybridization can be difficult to detect due to limited morphological differences among close lineages and the relatively low power of traditional genetic datasets. Here we showcase the use of genomic techniques to detect admixture of the economically important and threatened golden perch (Macquaria ambigua) in the Murray-Darling Basin, southeast Australia. We detected admixture through a genome-wide dataset of 6,862 single nucleotide polymorphisms (SNPs) across 174 Murray-Darling sourced fish and 15 fish from each of two neighbouring basins: the Lake Eyre and Fitzroy basins. Individuals with partial ancestry from both neighboring basins were detected using genomics throughout the Murray-Darling, suggesting the release of individuals and introgression into the Murray-Darling Basin. Importantly, a traditional microsatellite dataset was unreliable for identifying admixed individuals. The SNP-detected admixed individuals were also found in Murray-Darling impoundments, where fish are solely sourced from government-managed hatcheries, suggesting that some broodstock in hatcheries might have non-endemic ancestry. Stocking programs for golden perch release over one million fingerlings each year, and so could impact the genetic variation in the wild. We advocate for using genomics to check the ancestry of broodstock and for increasing collaboration between managers and academics—as done here—to better integrate the power of genomics into biodiversity management and conservation.

Range-wide population genomics of the Mexican fruit fly: Toward development of pathway analysis tools.

Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California represent major threats to the agricultural systems of those regions. We developed a draft genome assembly for A. ludens, conducted range‐wide population genomics using restriction site‐associated DNA sequencing, and then developed and demonstrated a panel of highly differentiated diagnostic SNPs for source determination of intercepted flies in this system. Using 2,081 genomewide SNPs, we identified four populations across the range of A. ludens, corresponding to western Mexico, eastern Mexico/Texas, Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation present between clusters, particularly in Central America. From this population genomics framework, we developed a diagnostic panel of 28 highly differentiated SNPs that were able to recreate the genomewide population structure in this species. We demonstrated this panel on a set of test specimens, including specimens intercepted as part of regular trapping surveillance in Texas and California, and we were able to predict populations of origin for these specimens. This methodology presents a highly applied use of genomic techniques and can be implemented in any group of recurrently invading pests.

“From Large-Scale Collections to the Potential Use of Genomic Techniques for Supply of Drug Candidates”

The initial sources of compounds that on a small scale exhibited interesting biological activities were confined to medium (a few kilograms) to larger scale (up to 100 kilograms or more) of the nominal organism. Over the last 10 plus years, this paradigm has moved to semisynthesis, total synthesis (sometimes of simpler versions) and the use of genomic techniques both to identify the source and then to utilize the data in due course. Examples will range from the early days with the arabinose-containing nucleosides, didemnins, through the ecteinascidins and halichondrins, and then to more current molecules derived from dolastatins that are now used as “warheads.

Exploring public perceptions of solutions to tree diseases in the UK: Implications for policy-makers

Tree diseases are on the increase in many countries and the implications of their appearance can be political, as well as ecological and economic. Preventative policy approaches to tree diseases are difficult to formulate because dispersal pathways for pest and pathogens are numerous, poorly known and likely to be beyond human management control. Genomic techniques could offer the quickest and most predictable approach to developing a disease tolerant native ash.The population of European Ash (Fraxinus Excelsior) has suffered major losses in the last decade, due to the onset of Hymenoscyphus fraxineus (previously called Chalara Fraxinea) commonly known in the UK as ash dieback. This study presents evidence on the public acceptability of tree-breed solutions to the spread of Chalara, with the main aim to provide science and policy with an up-stream ‘steer’ on the likely public acceptability of different tree breeding solutions. The findings showed that whilst there was a firm anti-GM and ‘we shouldn’t tamper with nature’ attitude among UK publics, there was an equally firm and perhaps slightly larger pragmatic attitude that GM (science and technology) should be used if there is a good reason to do so, for example if it can help protect trees from disease and help feed the world. The latter view was significantly stronger among younger age groups (Millennials), those living in urban areas and when the (GM)modified trees were destined for urban and plantation, rather than countryside settings. Overall, our findings suggest that the UK government could consider genomic solutions to tree breeding with more confidence in the future, as large and influential publics appear to be relaxed about the use of genomic techniques to increase tolerance of trees to disease.

Genomic Approaches to Understanding Response and Resistance to Immunotherapy

Immunotherapy has led to a paradigm shift in the treatment of some malignancies, providing long-term, durable responses for patients with advanced cancers. However, such therapy has benefited only a subset of patients, with some patients failing to respond to treatment at all and others achieving a limited response followed by tumor progression. Understanding factors contributing to an effective response and further elucidating mechanisms of resistance will be crucial as these therapies are applied more broadly. Genomics-based approaches have significantly advanced the study of response and resistance to immunotherapy in general, and to immune checkpoint blockade more specifically. Here, we review how genomic and transcriptomic approaches have identified both somatic and germline positive correlates of response, including high mutational/neoantigen load and low intratumoral heterogeneity, among others. The genomic analysis of resistant tumors has additionally identified crucial factors involved in resistance to immune checkpoint blockade, including loss of PTEN and upregulation of other immune checkpoints. Overall, the continued use of genomic techniques at the point of care, combined with appropriate functional studies, would ideally lead to a better understanding of why certain patients respond to immune-based therapies, allowing clinicians to identify the subset of patients likely to benefit from such therapy, and potentially providing insight into how other therapies may be added in combination to increase the number of patients who may benefit from immunotherapy. Clin Cancer Res; 22(23); 5642-50. ©2016 AACR.

Evidence for and Against Genetic Predispositions to Acute and Chronic Altitude Illnesses.

MacInnis, Martin J., and Michael S. Koehle. Evidence for and against genetic predispositions to acute and chronic altitude illnesses. High Alt Med Biol. 17:281-293, 2016.-Humans exhibit marked variation in their responses to hypoxia, with susceptibility to acute and chronic altitude illnesses being a prominent and medically important example. Many have hypothesized that genetic differences are the cause of these variable responses to hypoxia; however, until recently, these hypotheses were based primarily on small (and sometimes anecdotal) reports pertaining to apparent differences in altitude illness susceptibility between populations, the notion that a history of altitude illness is indicative of subsequent risk, the heritability of hypoxia-related traits, and candidate gene association studies. In the past 5 years, the use of genomic techniques has helped bolster the claim that susceptibility to some altitude illnesses is likely the result of genetic variation. For each of the major altitude illnesses, we summarize and evaluate the evidence stemming from three important characteristics of a genetic trait: (1) individual susceptibility and repeatability across assessments, (2) biogeographical differences and familial aggregation, and (3) association(s) with genetic variants. Evidence to support a genetic basis for susceptibilities to acute mountain sickness (AMS) and high-altitude cerebral edema (HACE) is limited, owing partially to the subjective and unclear phenotype of AMS and the rarity and severity of HACE. In contrast, recent genomic studies have identified genes that influence susceptibility to high-altitude pulmonary edema, chronic mountain sickness, and high-altitude pulmonary hypertension. The collection of more individual, familial, and biogeographical susceptibility data should improve our understanding of the extent to which genetic variation contributes to altitude illness susceptibility, and genomic and molecular investigations have the potential to elucidate the mechanisms that underpin altitude illness susceptibility.

The metamorphosis of amphibian toxicogenomics.

Amphibians are important vertebrates in toxicology often representing both aquatic and terrestrial forms within the life history of the same species. Of the thousands of species, only two have substantial genomics resources: the recently published genome of the Pipid, Xenopus (Silurana) tropicalis, and transcript information (and ongoing genome sequencing project) of Xenopus laevis. However, many more species representative of regional ecological niches and life strategies are used in toxicology worldwide. Since Xenopus species diverged from the most populous frog family, the Ranidae, ~200 million years ago, there are notable differences between them and the even more distant Caudates (salamanders) and Caecilians. These differences include genome size, gene composition, and extent of polyploidization. Application of toxicogenomics to amphibians requires the mobilization of resources and expertise to develop de novo sequence assemblies and analysis strategies for a broader range of amphibian species. The present mini-review will present the advances in toxicogenomics as pertains to amphibians with particular emphasis upon the development and use of genomic techniques (inclusive of transcriptomics, proteomics, and metabolomics) and the challenges inherent therein.

Gene expression profiling: opening the black box of plant ecosystem responses to global change

AbstractThe use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Because the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical, and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the ‘black box’ of unknown mechanism. Various tools and approaches are available for assessing gene expression in model and nonmodel species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.

What is a virulence factor?

Bacterial virulence factors enable a host to replicate and disseminate within a host in part by subverting or eluding host defenses. The use of genomic techniques has led to the identification of new virulence factors that may serve as targets for new therapies. These putative virulence factors must be rigorously evaluated with in vitro and in vivo studies with an awareness of the technical limitations of each approach as well as an assessment of the prevalence of this factor in clinical bacterial isolates retrieved from appropriately controlled epidemiologic studies.

Intestinal Microbiota in Neonates and Preterm Infants: A Review

The fetal gastrointestinal tract is sterile until birth when microbes colonize the gastrointestinal tract, and a dense, complex microbiota develops. This enormous cell mass performs a variety of activities that affect both the intestinal and systemic physiology. The microbiota provides nutritional, metabolic, immunological, and protective functions. The neonatal gastrointestinal tract is an organ at risk. Increasing awareness that the human flora is a major factor in both health and disease has led to different strategies to manipulate the flora. Manipulation with prebiotics and probiotics has shown promising results although a better understanding of the gut bacterial colonization process is required before attempts to change the flora should be made. In this review, we summarize the data regarding developmental microbial ecology in the neonatal gastrointestinal tract, and the modulation of such microbiota. The discussion focuses on the control and manipulation of bacterial colonization in the neonatal gut for the prevention and treatment of bacterial intestinal disease in both in human infants and on animal models. Since the best available methodologies should be utilized in studies of nutritional sciences, a recapitulation of the latest techniques for the study of the gastrointestinal flora is presented. Future progress is likely to arise from the use of genomic techniques to track of dietinduced changes in microbiota. Keywords: Neonatal gastrointestinal tract, microbiota, colonization

Genomics as a probe for disease biology.

The use of genomic techniques has led to insights into the pathobiology of both common and uncommon diseases. This last installment in the Genomic Medicine series provides a number of examples of the ways in which genomics has served as a probe for disease biology.