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https://www.readbyqxmd.com/read/27924725/anticancer-drug-targets-of-salvia-phytometabolites-chemistry-biology-and-omics
#1
Da-Cheng Hao, Guang-Bo Ge, Pei-Gen Xiao
Salvia displays diverse anticancer properties, which are attributable to their diterpene and phenolic contents. There is no comprehensive review on the anticancer diversity and molecular targets of Salvia components. We investigate the diversity and molecular targets of Salvia phytometabolites responsible for the prevention and treatment of cancer and sarcoma. Traditional therapeutic knowledge suggests that Salvia species can be used to develop anticancer drugs. Lots of concerns have been raised for tanshinone (Tan) IIA and cryptotanshinone...
December 7, 2016: Current Drug Targets
https://www.readbyqxmd.com/read/27918446/metabolomics-and-its-application-in-the-development-of-discovering-biomarkers-for-osteoporosis-research
#2
REVIEW
Huanhuan Lv, Feng Jiang, Daogang Guan, Cheng Lu, Baosheng Guo, Chileung Chan, Songlin Peng, Baoqin Liu, Wenwei Guo, Hailong Zhu, Xuegong Xu, Aiping Lu, Ge Zhang
Osteoporosis is a progressive skeletal disorder characterized by low bone mass and increased risk of fracture in later life. The incidence and costs associated with treating osteoporosis cause heavy socio-economic burden. Currently, the diagnosis of osteoporosis mainly depends on bone mineral density and bone turnover markers. However, these indexes are not sensitive and accurate enough to reflect the osteoporosis progression. Metabolomics offers the potential for a holistic approach for clinical diagnoses and treatment, as well as understanding of the pathological mechanism of osteoporosis...
December 2, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27917161/the-interaction-between-plants-and-bacteria-in-the-remediation-of-petroleum-hydrocarbons-an-environmental-perspective
#3
REVIEW
Panagiotis Gkorezis, Matteo Daghio, Andrea Franzetti, Jonathan D Van Hamme, Wouter Sillen, Jaco Vangronsveld
Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27916886/cyanobacteria-as-chassis-for-industrial-biotechnology-progress-and-prospects
#4
REVIEW
Lamya Al-Haj, Yuen Tin Lui, Raeid M M Abed, Mohamed A Gomaa, Saul Purton
Cyanobacteria hold significant potential as industrial biotechnology (IB) platforms for the production of a wide variety of bio-products ranging from biofuels such as hydrogen, alcohols and isoprenoids, to high-value bioactive and recombinant proteins. Underpinning this technology, are the recent advances in cyanobacterial "omics" research, the development of improved genetic engineering tools for key species, and the emerging field of cyanobacterial synthetic biology. These approaches enabled the development of elaborate metabolic engineering programs aimed at creating designer strains tailored for different IB applications...
November 30, 2016: Life
https://www.readbyqxmd.com/read/27914202/probiotic-roles-of-lactobacillus-spp-in-swine-insights-from-gut-microbiota
#5
REVIEW
Valerie Diane V Valeriano, Marilen P Balolong, Dae-Kyung Kang
The use of lactobacilli as probiotics in swine has been gaining attention due to their ability to improve growth performance and carcass quality, prevent gastrointestinal infection, and most importantly, their 'generally recognised as safe' status. Previous studies support the potential of lactobacilli to regulate host immune systems, enhance gut metabolic capacities, and maintain balance in the gut microbiota. Research on swine gut microbiota has revealed complex gut microbial community structure and showed the importance of Lactobacillus to the host's health...
December 3, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27912059/microbiota-diurnal-rhythmicity-programs-host-transcriptome-oscillations
#6
Christoph A Thaiss, Maayan Levy, Tal Korem, Lenka Dohnalová, Hagit Shapiro, Diego A Jaitin, Eyal David, Deborah R Winter, Meital Gury-BenAri, Evgeny Tatirovsky, Timur Tuganbaev, Sara Federici, Niv Zmora, David Zeevi, Mally Dori-Bachash, Meirav Pevsner-Fischer, Elena Kartvelishvily, Alexander Brandis, Alon Harmelin, Oren Shibolet, Zamir Halpern, Kenya Honda, Ido Amit, Eran Segal, Eran Elinav
The intestinal microbiota undergoes diurnal compositional and functional oscillations that affect metabolic homeostasis, but the mechanisms by which the rhythmic microbiota influences host circadian activity remain elusive. Using integrated multi-omics and imaging approaches, we demonstrate that the gut microbiota features oscillating biogeographical localization and metabolome patterns that determine the rhythmic exposure of the intestinal epithelium to different bacterial species and their metabolites over the course of a day...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27904969/metabolic-responses-and-omics-technologies-for-elucidating-the-effects-of-heat-stress-in-dairy-cows
#7
REVIEW
Li Min, Shengguo Zhao, He Tian, Xu Zhou, Yangdong Zhang, Songli Li, Hongjian Yang, Nan Zheng, Jiaqi Wang
Heat stress (HS) negatively affects various industries that rely on animal husbandry, particularly the dairy industry. A better understanding of metabolic responses in HS dairy cows is necessary to elucidate the physiological mechanisms of HS and offer a new perspective for future research. In this paper, we review the current knowledge of responses of body metabolism (lipid, carbohydrate, and protein), endocrine profiles, and bovine mammary epithelial cells during HS. Furthermore, we summarize the metabolomics and proteomics data that have revealed the metabolite profiles and differentially expressed proteins that are a feature of HS in dairy cows...
November 30, 2016: International Journal of Biometeorology
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#8
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J Colin Murrell, Josh D Neufeld, Marc G Dumont
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of (13)C, (18)O, or (15)N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27897000/identifying-cancer-specific-metabolic-signatures-using-constraint-based-models
#9
A Schultz, S Mehta, C W Hu, F W Hoff, T M Horton, S M Kornblau, A A Qutub
Cancer metabolism differs remarkably from the metabolism of healthy surrounding tissues, and it is extremely heterogeneous across cancer types. While these metabolic differences provide promising avenues for cancer treatments, much work remains to be done in understanding how metabolism is rewired in malignant tissues. To that end, constraint-based models provide a powerful computational tool for the study of metabolism at the genome scale. To generate meaningful predictions, however, these generalized human models must first be tailored for specific cell or tissue sub-types...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27895661/the-genome-conformation-as-an-integrator-of-multi-omic-data-the-example-of-damage-spreading-in-cancer
#10
Fabio Tordini, Marco Aldinucci, Luciano Milanesi, Pietro Liò, Ivan Merelli
Publicly available multi-omic databases, in particular if associated with medical annotations, are rich resources with the potential to lead a rapid transition from high-throughput molecular biology experiments to better clinical outcomes for patients. In this work, we propose a model for multi-omic data integration (i.e., genetic variations, gene expression, genome conformation, and epigenetic patterns), which exploits a multi-layer network approach to analyse, visualize, and obtain insights from such biological information, in order to use achieved results at a macroscopic level...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27891171/a-rapid-approach-to-investigate-spatiotemporal-distribution-of-phytohormones-in-rice
#11
Wen-Jing Cai, Tian-Tian Ye, Qing Wang, Bao-Dong Cai, Yu-Qi Feng
BACKGROUND: Phytohormones play crucial roles in almost all stages of plant growth and development. Accurate and simultaneous determination of multiple phytohormones enabled us to better understand the physiological functions and the regulatory networks of phytohormones. However, simultaneous determination of multiple phytohormones in plant is still a challenge due to their low concentrations, structural and chemical diversity, and complex matrix of plant tissues. Therefore, development of a simple and selective method for the simultaneous determination of multiple phytohormones is highly needed...
2016: Plant Methods
https://www.readbyqxmd.com/read/27890772/integrative-analysis-of-dna-methylation-and-gene-expression-in-butyrate-treated-cho-cells
#12
Anna Wippermann, Oliver Rupp, Karina Brinkrolf, Raimund Hoffrogge, Thomas Noll
The cellular mechanisms responsible for the versatile properties of CHO cells as the major production cell line for biopharmaceutical molecules are not entirely understood yet, although several 'omics' data facilitate the understanding of CHO cells and their reactions to environmental conditions. However, genome-wide studies of epigenetic processes such as DNA methylation are still limited. To prove the applicability and usefulness of integrating DNA methylation and gene expression data in a biotechnological context, we exemplarily analyzed the time course of cellular reactions upon butyrate addition in antibody-producing CHO cells by whole-genome bisulfite sequencing and CHO-specific cDNA microarrays...
November 24, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27885530/protein-secretion-in-gram-positive-bacteria-from-multiple-pathways-to-biotechnology
#13
Jozef Anné, Anastassios Economou, Kristel Bernaerts
A number of Gram-positive bacteria are important players in industry as producers of a diverse array of economically interesting metabolites and proteins. As discussed in this overview, several Gram-positive bacteria are valuable hosts for the production of heterologous proteins. In contrast to Gram-negative bacteria, proteins secreted by Gram-positive bacteria are released into the culture medium where conditions for correct folding are more appropriate, thus facilitating the isolation and purification of active proteins...
November 25, 2016: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/27884205/whole-genome-sequence-analysis-of-serum-amino-acid-levels
#14
Bing Yu, Paul S de Vries, Ginger A Metcalf, Zhe Wang, Elena V Feofanova, Xiaoming Liu, Donna Marie Muzny, Lynne E Wagenknecht, Richard A Gibbs, Alanna C Morrison, Eric Boerwinkle
BACKGROUND: Blood levels of amino acids are important biomarkers of disease and are influenced by synthesis, protein degradation, and gene-environment interactions. Whole genome sequence analysis of amino acid levels may establish a paradigm for analyzing quantitative risk factors. RESULTS: In a discovery cohort of 1872 African Americans and a replication cohort of 1552 European Americans we sequenced exons and whole genomes and measured serum levels of 70 amino acids...
November 24, 2016: Genome Biology
https://www.readbyqxmd.com/read/27879288/multi-omics-analysis-of-serum-samples-demonstrates-reprogramming-of-organ-functions-via-systemic-calcium-mobilization-and-platelet-activation-in-metastatic-melanoma
#15
Besnik Muqaku, Martin Eisninger, Samuel M Meier, Ammar Tahir, Tobias Prokop, Sebastian Haferkamp, Astrid Slany, Albrecht Reichle, Christopher Gerner
Pathophysiologies of cancer-associated syndroms such as cachexia are poorly understood and no routine biomarkers have been established, yet. Using shotgun proteomics, known marker molecules including PMEL, CRP, SAA and CSPG4 were found deregulated in patients with metastatic melanoma. Targeted analysis of 58 selected proteins with multiple reaction monitoring was applied for independent data verification. In three patients, two of which suffered from cachexia, a tissue damage signature was determined, consisting of nine proteins, PLTP, CD14, TIMP1, S10A8, S10A9, GP1BA, PTPRJ, CD44 and C4A, as well as increased levels of glycine and asparagine, and decreased levels of polyunsaturated phosphatidylcholine concentrations, as determined by targeted metabolomics...
November 22, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27878947/all-together-now-experimental-multispecies-biofilm-model-systems
#16
REVIEW
Chuan Hao Tan, Kai Wei Kelvin Lee, Mette Burmølle, Staffan Kjelleberg, Scott A Rice
Studies of microorganisms have traditionally focused on single species populations, which have greatly facilitated our understanding of the genetics and physiology that underpin microbial growth, adaptation and biofilm development. However, given that most microorganisms exist as multispecies consortia, the field is increasingly exploring microbial communities using a range of technologies traditionally limited to populations, including meta-omics based approaches and high resolution imaging. The experimental communities currently being explored range from relatively low diversity, e...
November 23, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27878342/breeding-approaches-and-genomics-technologies-to-increase-crop-yield-under-low-temperature-stress
#17
REVIEW
Uday Chand Jha, Abhishek Bohra, Rintu Jha
Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions. Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front...
November 22, 2016: Plant Cell Reports
https://www.readbyqxmd.com/read/27874080/integrated-omics-study-of-lipid-droplets-from-plasmodiophora-brassicae
#18
Kai Bi, Zhangchao He, Zhixiao Gao, Ying Zhao, Yanping Fu, Jiasen Cheng, Jiatao Xie, Daohong Jiang, Tao Chen
Plasmodiophora brassicae causes clubroot disease in cruciferous. In this report, lipid droplets were observed in the resting spores of P. brassicae. 295 lipid droplet-associated proteins were identified and categorized into nine groups. Transcriptome analysis of these proteins during three different zoosporic stages revealed differences in gene expression pattern. GO enrichment analysis revealed that these proteins associated with lipid droplets were mainly linked to biosynthesis and metabolism. GC-MS analysis revealed that lipid droplets contain seven types of free fatty acids: saturated fatty acids C16:0 and C18:0, and unsaturated fatty acids C18:1Δ9, C18:1Δ11, C18:2, C20:4 and C20:5...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27873024/p4%C3%A2-medicine-and-osteoporosis-a%C3%A2-systematic-review
#19
REVIEW
Klemen Kodrič, Klemen Čamernik, Darko Černe, Radko Komadina, Janja Marc
BACKGROUND: Osteoporosis is the most frequent bone metabolic disease. In order to improve early detection, prediction, prevention, diagnosis, and treatment of the disease, a new model of P4 medicine (personalized, predictive, preventive, and participatory medicine) could be applied. The aim of this work was to systematically review the publications of four different types of "omics" studies related to osteoporosis, in order to discover novel predictive, preventive, diagnostic, and therapeutic targets for better management of the geriatric population...
November 21, 2016: Wiener Klinische Wochenschrift
https://www.readbyqxmd.com/read/27872964/toward-sustainable-amino-acid-production
#20
Yoshihiro Usuda, Yoshihiko Hara, Hiroyuki Kojima
Because the global amino acid production industry has been growing steadily and is expected to grow even more in the future, efficient production by fermentation is of great importance from economic and sustainability viewpoints. Many systems biology technologies, such as genome breeding, omics analysis, metabolic flux analysis, and metabolic simulation, have been employed for the improvement of amino acid-producing strains of bacteria. Synthetic biological approaches have recently been applied to strain development...
November 22, 2016: Advances in Biochemical Engineering/biotechnology
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