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1.
DNA extraction for human microbiome studies: the issue of standardization.
Greathouse, KL, Sinha, R, Vogtmann, E
Genome biology. 2019;(1):212
Abstract
Among the laboratory and bioinformatic processing steps for human microbiome studies, a lack of consistency in DNA extraction methodologies is hindering the ability to compare results between studies and sometimes leading to errant conclusions. The purpose of this article is to highlight the issues related to DNA extraction methods and to suggest minimum standard requirements that should be followed to ensure consistency and reproducibility.
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2.
Functional genomics of dietary restriction and longevity in yeast.
Campos, SE, DeLuna, A
Mechanisms of ageing and development. 2019;:36-43
Abstract
Dietary restriction-limitation of calories or other specific nutrients in the diet-is the sole non-genetic intervention known to extend the lifespan of a wide range of model organisms from yeast to mammals. Cell biology studies on the responses to dietary restriction have provided important clues about the mechanisms of longevity; however, a comprehensive genome-wide description of lifespan by dietary restriction has been mostly absent. Large-scale genetic analysis in the budding yeast Saccharomyces cerevisiae offers a great opportunity to uncover the conserved systems-level mechanisms that give way to longevity in response to diet. Here, we review recent advances in high-throughput phenotyping of the replicative and chronological life spans of yeast cells, which have contributed to our understanding of longevity by dietary restriction and the cellular crosstalks of nutrient-sensing regulation.
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3.
Genebank genomics bridges the gap between the conservation of crop diversity and plant breeding.
Mascher, M, Schreiber, M, Scholz, U, Graner, A, Reif, JC, Stein, N
Nature genetics. 2019;(7):1076-1081
Abstract
Genebanks have the long-term mission of preserving plant genetic resources as an agricultural legacy for future crop improvement. Operating procedures for seed storage and plant propagation have been in place for decades, but there is a lack of effective means for the discovery and transfer of beneficial alleles from landraces and wild relatives into modern varieties. Here, we review the prospects of using molecular passport data derived from genomic sequence information as a universal monitoring tool at the single-plant level within and between genebanks. Together with recent advances in breeding methodologies, the transformation of genebanks into bio-digital resource centers will facilitate the selection of useful genetic variation and its use in breeding programs, thus providing easy access to past crop diversity. We propose linking catalogs of natural genetic variation and enquiries into biological mechanisms of plant performance as a long-term joint research goal of genebanks, plant geneticists and breeders.
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4.
Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective.
Muthamilarasan, M, Singh, NK, Prasad, M
Advances in genetics. 2019;:1-38
Abstract
For several decades, researchers are working toward improving the "major" crops for better adaptability and tolerance to environmental stresses. However, little or no research attention is given toward neglected and underutilized crop species (NUCS) which hold the potential to ensure food and nutritional security among the ever-growing global population. NUCS are predominantly climate resilient, but their yield and quality are compromised due to selective breeding. In this context, the importance of omics technologies namely genomics, transcriptomics, proteomics, phenomics and ionomics in delineating the complex molecular machinery governing growth, development and stress responses of NUCS is underlined. However, gaining insights through individual omics approaches will not be sufficient to address the research questions, whereas integrating these technologies could be an effective strategy to decipher the gene function, genome structures, biological pathways, metabolic and regulatory networks underlying complex traits. Given this, the chapter enlists the importance of NUCS in food and nutritional security and provides an overview of deploying omics approaches to study the NUCS. Also, the chapter enumerates the status of crop improvement programs in NUCS and suggests implementing "integrating omics" for gaining a better understanding of crops' response to abiotic and biotic stresses.
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5.
A Systems Biology Approach for Personalized Medicine in Refractory Epilepsy.
Naimo, GD, Guarnaccia, M, Sprovieri, T, Ungaro, C, Conforti, FL, Andò, S, Cavallaro, S
International journal of molecular sciences. 2019;(15)
Abstract
Epilepsy refers to a common chronic neurological disorder that affects all age groups. Unfortunately, antiepileptic drugs are ineffective in about one-third of patients. The complex interindividual variability influences the response to drug treatment rendering the therapeutic failure one of the most relevant problems in clinical practice also for increased hospitalizations and healthcare costs. Recent advances in the genetics and neurobiology of epilepsies are laying the groundwork for a new personalized medicine, focused on the reversal or avoidance of the pathophysiological effects of specific gene mutations. This could lead to a significant improvement in the efficacy and safety of treatments for epilepsy, targeting the biological mechanisms responsible for epilepsy in each individual. In this review article, we focus on the mechanism of the epilepsy pharmacoresistance and highlight the use of a systems biology approach for personalized medicine in refractory epilepsy.
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6.
Multi-omics and potential applications in wine production.
Sirén, K, Mak, SST, Fischer, U, Hansen, LH, Gilbert, MTP
Current opinion in biotechnology. 2019;:172-178
Abstract
The wine microbiome - that is the microbial communities associated with the fermentation of must, is one of the most important factors in transforming grapes to wine, including flavour and aroma. Recent developments in high throughput sequencing and other 'omics methodologies are rapidly changing the level and complexity of information that we are able to extract from the wine microbiome. This will significantly enhance not only our understanding of which microbes are present at the various stages of the grapevine growth and winemaking process, but also improve our understanding of the complex interactions between microbes, the substrate and environment, ultimately shaping wine production. In this perspective we describe the role and future potential of such techniques in wine production, and highlight the potential challenges that will be simultaneously faced.
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7.
Review: New sensors and data-driven approaches-A path to next generation phenomics.
Roitsch, T, Cabrera-Bosquet, L, Fournier, A, Ghamkhar, K, Jiménez-Berni, J, Pinto, F, Ober, ES
Plant science : an international journal of experimental plant biology. 2019;:2-10
Abstract
At the 4th International Plant Phenotyping Symposium meeting of the International Plant Phenotyping Network (IPPN) in 2016 at CIMMYT in Mexico, a workshop was convened to consider ways forward with sensors for phenotyping. The increasing number of field applications provides new challenges and requires specialised solutions. There are many traits vital to plant growth and development that demand phenotyping approaches that are still at early stages of development or elude current capabilities. Further, there is growing interest in low-cost sensor solutions, and mobile platforms that can be transported to the experiments, rather than the experiment coming to the platform. Various types of sensors are required to address diverse needs with respect to targets, precision and ease of operation and readout. Converting data into knowledge, and ensuring that those data (and the appropriate metadata) are stored in such a way that they will be sensible and available to others now and for future analysis is also vital. Here we are proposing mechanisms for "next generation phenomics" based on our learning in the past decade, current practice and discussions at the IPPN Symposium, to encourage further thinking and collaboration by plant scientists, physicists and engineering experts.
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8.
High-throughput phenotyping for crop improvement in the genomics era.
Mir, RR, Reynolds, M, Pinto, F, Khan, MA, Bhat, MA
Plant science : an international journal of experimental plant biology. 2019;:60-72
Abstract
Tremendous progress has been made with continually expanding genomics technologies to unravel and understand crop genomes. However, the impact of genomics data on crop improvement is still far from satisfactory, in large part due to a lack of effective phenotypic data; our capacity to collect useful high quality phenotypic data lags behind the current capacity to generate high-throughput genomics data. Thus, the research bottleneck in plant sciences is shifting from genotyping to phenotyping. This article review the current status of efforts made in the last decade to systematically collect phenotypic data to alleviate this 'phenomics bottlenecks' by recording trait data through sophisticated non-invasive imaging, spectroscopy, image analysis, robotics, high-performance computing facilities and phenomics databases. These modern phenomics platforms and tools aim to record data on traits like plant development, architecture, plant photosynthesis, growth or biomass productivity, on hundreds to thousands of plants in a single day, as a phenomics revolution. It is believed that this revolution will provide plant scientists with the knowledge and tools necessary for unlocking information coded in plant genomes. Efforts have been also made to present the advances made in the last 10 years in phenomics platforms and their use in generating phenotypic data on different traits in several major crops including rice, wheat, barley, and maize. The article also highlights the need for phenomics databases and phenotypic data sharing for crop improvement. The phenomics data generated has been used to identify genes/QTL through QTL mapping, association mapping and genome-wide association studies (GWAS) for genomics-assisted breeding (GAB) for crop improvement.
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9.
Furthering Precision Medicine Genomics With Healthy Living Medicine.
Standley, RA, Vega, RB
Progress in cardiovascular diseases. 2019;(1):60-67
Abstract
The Precision Medicine Initiative seeks to develop new approaches for disease treatment and prevention that considers the individual variation in genes, environment, and lifestyle for each person. To date, the focus has been on genetic drivers of disease risk and development but has now begun to incorporate lifestyle induced changes in phenotype to enhance treatments. Healthy Living Medicine is an emerging paradigm that focuses on moving more and sitting less, consuming a healthy diet, maintaining body weight and not smoking. A wealth of clinical trials has demonstrated the protective effects of high cardiorespiratory fitness, physical activity (PA), and exercise on all-cause mortality, and prevention of developing cardiovascular disease (CVD), obesity and type 2 diabetes (T2D). This review will summarize the impact of PA and exercise on modifying risk of disease from genetics in the general population and those with CVD, obesity and T2D.
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10.
Omics approaches to understand sourdough fermentation processes.
Weckx, S, Van Kerrebroeck, S, De Vuyst, L
International journal of food microbiology. 2019;:90-102
Abstract
The application of omics methodologies helps to further unravel sourdough fermentation processes. Of all methodologies applied, metagenetics is the most used one to analyse sourdoughs, allowing to elucidate their microbial structure, albeit that it is based on the sequencing of a very small part of whole-community DNA. Although shotgun metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics are very promising to analyse sourdough fermentations and the terminology is often used in a confusing way, they have not been fully used sensu stricto yet. For instance, up to now, metatranscriptomics is restricted to the use of a functional gene microarray for lactic acid bacteria. Further, meta-metabolomics often deals with metabolite target analysis of sourdough fermentation samples to determine the actual concentrations of residual substrates and metabolites produced as well as to list their volatilome solely. In contrast, genomics has been applied several times, albeit that the whole-genome sequence of only one yeast strain and of 41 lactic acid bacterial strains, originally isolated from sourdoughs, is available. However, the genomics data accessible in public databases should be considered with caution because of inaccurate gene annotations, due to automated annotation pipelines, thereby possibly overruling original, high-quality, well-curated gene annotations.