Genomics and Traditional Indian Ayurvedic Medicine
01 Jan 2016-pp 271-292
TL;DR: Ayurgenomics is proposed as a novel approach for integration of Ayurveda into current medical practice to address the variability in therapeutic outcome as well as evolve preventive measures in health and disease.
Abstract: In the present times need is being felt for a change in paradigm from the current practice of modern medicine. This is not only to meet the challenges in diagnosis and treatment of chronic and complex diseases but also to address the variability in therapeutic outcome as well as evolve preventive measures in health and disease. The advent of genomics has provided a tremendous impetus to this area. However, there are a number of gaps before this is realized. Ayurveda, the ancient Indian system of predictive and personalized medicine still holds contemporary in the current era of P4 (predictive, preventive, personalized, and participatory) medicine and also has a promotive component. Ayurveda has documented methods for maintenance of health and personalized management of diseases. It is also widely practiced in most Indian communities despite sociocultural variations and many aspects for preventive health are also integrated into Indian traditional living. Despite this a large number of challenges exist in getting this system to mainstream and for its global acceptability. This review highlights some of these aspects and also proposes Ayurgenomics as a novel approach for integration of Ayurveda into current medical practice.
02 Dec 2014-The Biomedical & Life Sciences Collection
TL;DR: Why interactome networks are important to consider in biology, how they can be mapped and integrated with each other, what global properties are starting to emerge from interactome network models, and how these properties may relate to human disease are detailed.
Abstract: Complex biological systems and cellular networks may underlie most genotype to phenotype relationships. Here, we review basic concepts in network biology, discussing different types of interactome networks and the insights that can come from analyzing them. We elaborate on why interactome networks are important to consider in biology, how they can be mapped and integrated with each other, what global properties are starting to emerge from interactome network models, and how these properties may relate to human disease.
30 Nov 2020-Medicina-lithuania
TL;DR: The development of Ayurgenomics could greatly enrich P4 medicine by providing a clear theoretical understanding of the whole patient and a practical application of ancient and modern preventative and therapeutic practices to improve mental and physical health.
Abstract: Within the disciplines of modern medicine, P4 medicine is emerging as a new field which focuses on the whole patient. The development of Ayurgenomics could greatly enrich P4 medicine by providing a clear theoretical understanding of the whole patient and a practical application of ancient and modern preventative and therapeutic practices to improve mental and physical health. One of the most difficult challenges today is understanding the ancient concepts of Ayurveda in terms of modern science. To date, a number of researchers have attempted this task, of which one of the most successful outcomes is the creation of the new field of Ayurgenomics. Ayurgenomics integrates concepts in Ayurveda, such as Prakriti, with modern genetics research. It correlates the combination of three doshas, Vata, Pitta and Kapha, with the expression of specific genes and physiological characteristics. It also helps to interpret Ayurveda as an ancient science of epigenetics which assesses the current state of the doshas, and uses specific personalized diet and lifestyle recommendations to improve a patient's health. This review provides a current update of this emerging field.
01 Mar 2010-
Abstract: Drug discovery and development (very often unknowingly) is based on traditional and local knowledge about a species’ medical use or toxicological effects (both desired and undesired effects). The list of compounds ultimately derived from such knowledge is very long indeed and includes morphine, codeine, and aspirin to name just a few but also drugs licensed relatively recently like galanthamine and artemisinine. Here I review this link and – using examples of new drugs currently under development preclinically or in clinical trials – discuss how such new drugs have been ‘discovered’, or more precisely developed into a clinically used medication.
Massachusetts Institute of Technology1, Wellcome Trust Sanger Institute2, Washington University in St. Louis3, United States Department of Energy4, Baylor College of Medicine5, University of Texas Health Science Center at San Antonio6, Yeshiva University7, University of Texas Health Science Center at Houston8, Université Paris-Saclay9, National Institutes of Health10, Chinese Academy of Sciences11, Chinese National Human Genome Center12, Institute for Systems Biology13, Stanford University14, University of Oklahoma15, Max Planck Society16, Cold Spring Harbor Laboratory17, Case Western Reserve University18, Max Delbrück Center for Molecular Medicine19, University of California, Santa Cruz20, Thermo Fisher Scientific21, Trinity College, Dublin22, Weizmann Institute of Science23, University of Michigan24, University of Oxford25, University of Washington26, Keio University27, University of Texas Southwestern Medical Center28, Wellcome Trust29
15 Feb 2001-Nature
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Abstract: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
Celera Corporation1, University of California, Berkeley2, Pennsylvania State University3, Case Western Reserve University4, Johns Hopkins University School of Medicine5, Rockefeller University6, New England Biolabs7, California Institute of Technology8, Yale University9, Applied Biosystems10, Bar-Ilan University11, Pompeu Fabra University12
16 Feb 2001-Science
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Abstract: A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
01 Nov 2012-Nature
TL;DR: It is shown that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites.
Abstract: By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations.
28 Oct 2010-Nature
Abstract: The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10(-8) per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research.
Broad Institute1, Harvard University2, Howard Hughes Medical Institute3, University of Colorado Boulder4, Washington University in St. Louis5, J. Craig Venter Institute6, University of Maryland, Baltimore7, Baylor College of Medicine8, University of Guelph9, Massachusetts Institute of Technology10, Lawrence Berkeley National Laboratory11, University of California, San Francisco12, National Institutes of Health13, New York University14, Virginia Commonwealth University15, United States Department of Energy16, Los Alamos National Laboratory17, Procter & Gamble18, BioMérieux19, Cleveland Clinic20, Vrije Universiteit Brussel21, University of North Carolina at Charlotte22, University of Idaho23, Saint Louis University24, University of California, Los Angeles25, Marine Biological Laboratory26, University of Texas at Austin27, San Diego State University28, McGill University29, Cornell University30, University of Maryland, College Park31, University of Oklahoma32, University of Alabama at Birmingham33, Oak Ridge National Laboratory34, Indiana University35, Icahn School of Medicine at Mount Sinai36, University of Pennsylvania37, University of Michigan38, Michigan State University39, Harper University Hospital40, Johns Hopkins University41, Northwestern University42
14 Jun 2012-Nature
Abstract: The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.
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