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Genomics Medicine

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https://www.readbyqxmd.com/read/28938541/differential-expression-of-circulating-biomarkers-of-tumor-phenotype-and-outcomes-in-previously-treated-non-small-cell-lung-cancer-patients-receiving-erlotinib-vs-cytotoxic-chemotherapy
#1
Mary Jo Fidler, Casey Frankenberger, Richard Seto, Gabriela C Lobato, Cristina L Fhied, Selina Sayidine, Sanjib Basu, Mark Pool, Reem Karmali, Marta Batus, Wen-Rong Lie, David Hayes, Jehangir Mistry, Philip Bonomi, Jeffrey A Borgia
BACKGROUND: The objective of this study was to identify serum biomarkers capable of predicting clinical outcomes in previously-treated NSCLC patients with wild-type for EGFR activating mutations or insufficient tissue for mutation status determination. METHODS: Sixty-six Luminex immunoassays representative of biological themes that emerged from a re-analysis of transcriptome data from the Cancer Genome Atlas (TCGA) were evaluate against pretreatment serum specimens from previously-treated advanced NSCLC patients received either cytotoxic chemotherapy (n=32) or erlotinib (n=79)...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938417/new-perspectives-on-pheochromocytoma-and-paraganglioma-towards-a-molecular-classification
#2
Joakim Crona, David Taïeb, Karel Pacak
A new molecular biology based taxonomy has been proposed for pheochromocytoma and paraganglioma (PPGL). Data from the Cancer Genome Atlas revealed clinically relevant prognostic and predictive biomarkers and stratified PPGLs into three main clusters. Each subgroup has a distinct molecular-biochemical-imaging signature. Concurrently, new methods for biochemical analysis, functional imaging, and medical therapies have also become available. The research community now strives to match the cluster biomarkers with the most superior intervention...
August 4, 2017: Endocrine Reviews
https://www.readbyqxmd.com/read/28938122/genome-regulation-by-polycomb-and-trithorax-70-years-and-counting
#3
REVIEW
Bernd Schuettengruber, Henri-Marc Bourbon, Luciano Di Croce, Giacomo Cavalli
Polycomb (PcG) and Trithorax (TrxG) group proteins are evolutionarily conserved chromatin-modifying factors originally identified as part of an epigenetic cellular memory system that maintains repressed or active gene expression states. Recently, they have been shown to globally control a plethora of cellular processes. This functional diversity is achieved by their ability to regulate chromatin at multiple levels, ranging from modifying local chromatin structure to orchestrating the three-dimensional organization of the genome...
September 21, 2017: Cell
https://www.readbyqxmd.com/read/28934716/automatic-detection-of-micronuclei-by-cell-microscopic-image-processing
#4
Mohammad Taghi Bahreyni Toossi, Hosein Azimian, Omid Sarrafzadeh, Shokoufeh Mohebbi, Shokouhozaman Soleymanifard
With the development and applications of ionizing radiation in medicine, the radiation effects on human health get more and more attention. Ionizing radiation can lead to various forms of cytogenetic damage, including increased frequencies of micronuclei (MNi) and chromosome abnormalities. The cytokinesis block micronucleus (CBMN) assay is widely used method for measuring MNi to determine chromosome mutations or genome instability in cultured human lymphocytes. The visual scoring of MNi is time-consuming and scorer fatigue can lead to inconsistency...
August 12, 2017: Mutation Research
https://www.readbyqxmd.com/read/28934115/development-of-genome-wide-ssr-markers-from-angelica-gigas-nakai-using-next-generation-sequencing
#5
Jinsu Gil, Yurry Um, Serim Kim, Ok Tae Kim, Sung Cheol Koo, Chinreddy Subramanyam Reddy, Seong-Cheol Kim, Chang Pyo Hong, Sin-Gi Park, Ho Bang Kim, Dong Hoon Lee, Byung-Hoon Jeong, Jong-Wook Chung, Yi Lee
Angelica gigas Nakai is an important medicinal herb, widely utilized in Asian countries especially in Korea, Japan, and China. Although it is a vital medicinal herb, the lack of sequencing data and efficient molecular markers has limited the application of a genetic approach for horticultural improvements. Simple sequence repeats (SSRs) are universally accepted molecular markers for population structure study. In this study, we found over 130,000 SSRs, ranging from di- to deca-nucleotide motifs, using the genome sequence of Manchu variety (MV) of A...
September 21, 2017: Genes
https://www.readbyqxmd.com/read/28933478/natural-product-modulators-of-human-sensations-and-mood-molecular-mechanisms-and-therapeutic-potential
#6
REVIEW
Tomáš Pluskal, Jing-Ke Weng
Humans perceive physical information about the surrounding environment through their senses. This physical information is registered by a collection of highly evolved and finely tuned molecular sensory receptors. A multitude of bioactive, structurally diverse ligands have evolved in nature that bind these molecular receptors. The complex, dynamic interactions between the ligands and the receptors lead to changes in our sensory perception or mood. Here, we review our current knowledge of natural products and their derived analogues that interact specifically with human G protein-coupled receptors, ion channels, and nuclear hormone receptors to modulate the sensations of taste, smell, temperature, pain, and itch, as well as mood and its associated behaviour...
September 21, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28933079/-advance-in-transcriptomic-studies-of-ginseng-species
#7
Li-Qiu Zou, Xue-Jun Kuang, Ying Li, Chao Sun
There are many valuable medicinal plants in Ginseng genus belonging to Araliaceae. Among them, Panax ginseng, P. quinquefolium and P. notoginseng are the most famous species. With the development of next-generation sequencing (NGS) technologies, sequencing and analysis of transcriptomes have become powerful tools for discovery of novel genes, screening molecular markers and elucidation of specific biosynthetic pathway of secondary metabolites. Their transcriptomes provided abundant genes for further study on functional genomics...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28933076/-strategies-of-elucidation-of-biosynthetic-pathways-of-natural-products
#8
Li-Qiu Zou, Xue-Jun Kuang, Chao Sun, Shi-Lin Chen
Elucidation of the biosynthetic pathways of natural products is not only the major goal of herb genomics, but also the solid foundation of synthetic biology of natural products. Here, this paper reviewed recent advance in this field and put forward strategies to elucidate the biosynthetic pathway of natural products. Firstly, a proposed biosynthetic pathway should be set up based on well-known knowledge about chemical reactions and information on the identified compounds, as well as studies with isotope tracer...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28933074/-genomic-research-of-traditional-chinese-medicines-in-vivo-metabolism
#9
Shui-Ming Xiao, Rui Bai, Xiao-Yan Zhang
Gene is the base of in vivo metabolism and effectiveness for traditional Chinese medicines (TCM), and the gene expression, regulation and modification are used as the research directions to perform the TCM multi-component, multi-link and multi-target in vivo metabolism studies, which will improve the research on TCM metabolic proecess, effect target and molecular mechanism. Humans are superorganisms with 1% genes inherited from parents and 99% genes from various parts of the human body, mainly coming from the microorganisms in intestinal flora...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28933072/-metabolomics-research-of-medicinal-plants
#10
Li-Xin Duan, Yun-Tao Dai, Chao Sun, Shi-Lin Chen
Metabolomics is the comprehensively study of chemical processes involving small molecule metabolites. It is an important part of systems biology, and is widely applied in complex traditional Chinese medicine(TCM)system. Metabolites biosynthesized by medicinal plants are the effective basis for TCM. Metabolomics studies of medicinal plants will usher in a new period of vigorous development with the implementation of Herb Genome Program and the development of TCM synthetic biology. This manuscript introduces the recent research progresses of metabolomics technology and the main research contents of metabolomics studies for medicinal plants, including identification and quality evaluation for medicinal plants, cultivars breeding, stress resistance, metabolic pathways, metabolic network, metabolic engineering and synthetic biology researches...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28931564/towards-precision-medicine-for-hypertension-a-review-of-genomic-epigenomic-and-microbiomic-effects-on-blood-pressure-in-experimental-rat-models-and-humans
#11
REVIEW
Sandosh Padmanabhan, Bina Joe
Compelling evidence for the inherited nature of essential hypertension has led to extensive research in rats and humans. Rats have served as the primary model for research on the genetics of hypertension resulting in identification of genomic regions that are causally associated with hypertension. In more recent times, genome-wide studies in humans have also begun to improve our understanding of the inheritance of polygenic forms of hypertension. Based on the chronological progression of research into the genetics of hypertension as the "structural backbone," this review catalogs and discusses the rat and human genetic elements mapped and implicated in blood pressure regulation...
October 1, 2017: Physiological Reviews
https://www.readbyqxmd.com/read/28930608/anti-tick-vaccines-in-the-omics-era
#12
Manuel Rodriguez Valle, Felix D Guerrero
Tick vaccines have been available for more than 20 years. They are useful and effective control agents when used properly. However, no new products have emerged since the Bm86-based Gavac vaccine was commercialized. Acaricide resistance is a problem with no abatement in sight and anti-tick vaccines are likely to be relied upon even more in the coming years. As human medicine and plant agriculture has embraced the various Omics technologies, the search for anti-tick vaccines would be well served to follow; so that new vaccine antigens and adjuvants might be developed to assist tick control programs...
January 1, 2018: Frontiers in Bioscience (Elite Edition)
https://www.readbyqxmd.com/read/28929670/-herbgenomics
#13
Shi-Lin Chen, Jing-Yuan Song
Traditional Chinese medicine (TCM) has contributad greatly to improving human health. However, the biological characteristics and molecular mechanisms of TCM in the treatment of human diseases remain largely unknown. Genomics plays an important role in modern medicine and biology. Here, we introduce genomics and other related omics to the study of herbs to propose a new discipline, Herbgenomics, that aims to uncover the genetic information and regulatory networks of herbs and to clarify their molecular mechanisms in the prevention and treatment of human diseases...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28929311/tbi-rehabilomics-research-an-exemplar-of-a-biomarker-based-approach-to-precision-care-for-populations-with-disability
#14
REVIEW
Amy K Wagner
PURPOSE OF REVIEW: The purpose of this review is to summarize how "-omics" technologies can inform rehabilitation-relevant outcomes for a range of populations with neurologically related disability by including outcome metrics linked to the World Health Organization's International Classification of Functioning, Disability, and Health (WHO-ICF) domains of impairments in body function, activity limitations, and participation restrictions. RECENT FINDINGS: To date, nearly every area of medicine uses biomarkers in some capacity to aid in understanding how personal biology informs clinical care...
September 19, 2017: Current Neurology and Neuroscience Reports
https://www.readbyqxmd.com/read/28928972/screening-of-mutations-in-the-additional-sex-combs-like-1-transcriptional-regulator-tumor-protein-p53-and-kras-proto-oncogene-gtpase-nras-proto-oncogene-gtpase-genes-of-patients-with-myelodysplastic-syndrome
#15
Carolina Leite, Lucas Delmonico, Gilda Alves, Romario José Gomes, Mariana Rodrigues Martino, Aline Rodrigues da Silva, Aline Dos Santos Moreira, Maria Christina Maioli, Luciano Rios Scherrer, Elenice Ferreira Bastos, Roberto Irineu, Maria Helena Ornellas
Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal bone marrow disorders characterized by ineffective hematopoiesis, different degrees of cellular dysplasia, and increased risk of progression to acute myeloid leukemia. International Prognostic Scoring System is the gold standard for MDS classification; however, patients exhibiting different clinical behaviors often coexist in the same group, indicating that the currently available scoring systems are insufficient. The genes that have recently been identified as mutated in MDS, including additional sex combs like 1, transcriptional regulator (ASXL1), tumor protein p53 (TP53), and KRAS proto-oncogene and GTPase (KRAS)/NRAS proto-oncogene, GTPase (NRAS), may contribute to a more comprehensive classification, as well as to the prognosis and progression of the disease...
October 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28927991/deciphering-cell-intrinsic-properties-a-key-issue-for-robust-organoid-production
#16
REVIEW
Nathalie Picollet-D'hahan, Monika E Dolega, Delphine Freida, Donald K Martin, Xavier Gidrol
We highlight the disposition of various cell types to self-organize into complex organ-like structures without necessarily the support of any stromal cells, provided they are placed into permissive 3D culture conditions. The goal of generating organoids reproducibly and efficiently has been hampered by poor understanding of the exact nature of the intrinsic cell properties at the origin of organoid generation, and of the signaling pathways governing their differentiation. Using microtechnologies like microfluidics to engineer organoids would create opportunities for single-cell genomics and high-throughput functional genomics to exhaustively characterize cell intrinsic properties...
September 16, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28926565/a-snp-panel-and-online-tool-for-checking-genotype-concordance-through-comparing-qr-codes
#17
Yonghong Du, Joshua S Martin, John McGee, Yuchen Yang, Eric Yi Liu, Yingrui Sun, Matthias Geihs, Xuejun Kong, Eric Lingfeng Zhou, Yun Li, Jie Huang
In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade...
2017: PloS One
https://www.readbyqxmd.com/read/28925997/precision-annotation-of-digital-samples-in-ncbi-s-gene-expression-omnibus
#18
Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D Azad, Mohamad O Hadied, Shuaib Raza, Benjamin Abhishek Rayikanti, Bin Chen, Hyojung Paik, Dvir Aran, Jordan Spatz, Daniel Himmelstein, Maryam Panahiazar, Sanchita Bhattacharya, Marina Sirota, Mark A Musen, Atul J Butte
The Gene Expression Omnibus (GEO) contains more than two million digital samples from functional genomics experiments amassed over almost two decades. However, individual sample meta-data remains poorly described by unstructured free text attributes preventing its largescale reanalysis. We introduce the Search Tag Analyze Resource for GEO as a web application (http://STARGEO.org) to curate better annotations of sample phenotypes uniformly across different studies, and to use these sample annotations to define robust genomic signatures of disease pathology by meta-analysis...
September 19, 2017: Scientific Data
https://www.readbyqxmd.com/read/28924942/exploring-the-anti-proliferative-activity-of-pelargonium-sidoides-dc-with-in-silico-target-identification-and-network-pharmacology
#19
A S P Pereira, M J Bester, Z Apostolides
Pelargonium sidoides DC (Geraniaceae) is a medicinal plant indigenous to Southern Africa that has been widely evaluated for its use in the treatment of upper respiratory tract infections. In recent studies, the anti-proliferative potential of P. sidoides was shown, and several phenolic compounds were identified as the bioactive compounds. Little, however, is known regarding their anti-proliferative protein targets. In this study, the anti-proliferative mechanisms of P. sidoides through in silico target identification and network pharmacology methodologies were evaluated...
September 18, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/28923015/transcriptome-analysis-of-pseudostellaria-heterophylla-in-response-to-the-infection-of-pathogenic-fusarium-oxysporum
#20
Xianjin Qin, Hongmiao Wu, Jun Chen, Linkun Wu, Sheng Lin, Muhammad Umar Khan, Mohammad Reza Boorboori, Wenxiong Lin
BACKGROUND: Pseudostellaria heterophylla (P. heterophylla), a herbaceous perennial, belongs to Caryophyllaceae family and is one of the Chinese herbal medicine with high pharmacodynamic value. It can be used to treat the spleen deficiency, anorexia, weakness after illness and spontaneous perspiration symptoms. Our previous study found that consecutive monoculture of Pseudostellaria heterophylla could lead to the deterioration of the rhizosphere microenvironment. The specialized forms of pathogenic fungus Fusarium oxysporum f...
September 18, 2017: BMC Plant Biology
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