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Metabolome (0):
Recent article
Metabolome
Abstract
To elucidate the biosynthetic pathways for all proteinogenic amino acids in Xanthomonas campestris pv. campestris, this study combines results obtained by in silico genome analysis and by (13)C-NMR-based isotopologue profiling to provide a panoramic view on a substantial section of bacterial metaboli...
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PMID: 21853248
PDF is available here.
PDF is available here.
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Abstract
We evaluated a novel liquid chromatography tandem mass spectrometry (LC-MS/MS) method, which utilizes aTRAQ reagents, for amino acid analysis in urine. aTRAQ reagents tag the primary and secondary amino groups of amino acids. Internal standards for each amino acid are also labeled with a modified aT...
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PMID: 21852206
PDF is available here.
PDF is available here.
Abstract
Untargeted metabolomics on the plasma and urine from wild-type and organic anion transporter-1 (Oat1/Slc22a6) knockout mice identified a number of physiologically important metabolites, including several not previously linked to Oat1-mediated transport. Several, such as indoxyl sulfa...
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PMID: 21476605
PDF is available here.
PDF is available here.
Abstract
We characterized the genomic, metabolic, and physiological divergence of several inbred rat strains--Brown Norway, Lewis, Wistar Kyoto, Fisher (F344)--frequently used as healthy controls in genetic studies of the cardiometabolic syndrome. Hierarchical clustering of (1)H NMR-based metabolic profiles...
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PMID: 21322573
PDF is available here.
PDF is available here.
Abstract
We characterized the genomic, metabolic, and physiological divergence of several inbred rat strains--Brown Norway, Lewis, Wistar Kyoto, Fisher (F344)--frequently used as healthy controls in genetic studies of the cardiometabolic syndrome. Hierarchical clustering of (1)H NMR-based metabolic profiles...
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PMID: 21322573
PDF is available here.
PDF is available here.
Journal of Proteomics (74)4 2011
Abstract
We employ a comparative iTRAQ-coupled 2D LC-MS/MS system to analyze the protein profile of NPC cell line upon EBV infection. Based on the proteome data and Western blot validation, 12 proteins were found to be significantly up-regulated and associated with signal transduction, cytoskeleton formation...
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PMID: 21296196
PDF is available here.
PDF is available here.
Journal of Proteomics (74)4 2011
Abstract
We have utilized two cellular models of EOC, where transfer of normal chromosome 18 material into the EOC cell lines TOV-112D and TOV-21G induced in vitro and in vivo suppression of their tumourigenic phenotype. A combination of quantitative two-dimensional difference gel electrophoresis (2D-DIGE) a...
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PMID: 21237297
PDF is available here.
PDF is available here.
Abstract
We observed that mice deficient for RasGrf1(-/-) display an increase in average and most importantly, in maximal lifespan (20% higher than controls). This was not due to the role of Ras in cancer because tumor-free survival was also enhanced in these animals. Aged RasGrf1(-/-) displayed better motor...
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PMID: 21422498
PDF is available here.
PDF is available here.
Abstract
The aim of this study was to evaluate the effect of exenatide on fat deposition and a metabolic profile in patients with metabolic syndrome.
An uncontrolled, open clinical study was carried out in 10 patients with metabolic syndrome and without pharmacological treatme...
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PMID: 20874425
PDF is available here.
PDF is available here.
British Journal of Nutrition (105)1 2011
Abstract
Inter-individual response differences to vitamin D and Ca supplementation may be under genetic control through vitamin D and oestrogen receptor genes, which may influence their absorption and/or metabolism. Metabolomic studies on blood and urine from subjects supplemented with Ca and vitamin D revea...
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PMID: 20727239
PDF is available here.
PDF is available here.
Abstract
The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organ...
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PMID: 21569493
PDF is available here.
PDF is available here.
Abstract
HRMAS NMR is considered a valuable technique to obtain detailed metabolic profile of unprocessed tissues. To properly interpret the HRMAS metabolomic results, detailed information of the actual state of the sample inside the rotor is needed. MRM (Magnetic Resonance Microscopy) was applied for obtain...
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PMID: 20871822
PDF is available here.
PDF is available here.
Abstract
We derived fibroblast-like cells from two hiPS cell lines and show that their phenotypic properties and patterns of DNA methylation were similar to that of mature fibroblasts and to fibroblasts derived from hES cells. iPS-derived fibroblasts (iPDK) and their hES-derived counterparts (EDK) showed sim...
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PMID: 21386890
PDF is available here.
PDF is available here.
Abstract
We have utilized sensitive proteomic approaches to examine the impact of diurnal rhythms on the protein complement in Cyanothece 51142. We found that 250 proteins accounting for ∼5% of the predicted ORFs from the Cyanothece 51142 genome and 20% of proteins detected under alternating light/dark con...
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PMID: 21364985
PDF is available here.
PDF is available here.
Abstract
To date, studies on volatile metabolites in cereal grain have focused mainly on a single species. In this paper, results are presented of the analysis of volatile compounds in five cereal grain species (spring wheat, durum wheat, triticale, rye, oats and barley) based on representative sampling of a...
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PMID: 20730644
PDF is available here.
PDF is available here.
British Journal of Cancer (103)8 2010
Abstract
Human medulloblastomas exhibit diverse molecular pathology. Aberrant hedgehog signalling is found in 20-30% of human medulloblastomas with largely unknown metabolic consequences.
Transgenic mice over-expressing smoothened (SMO) receptor in granule cell precursors with high incidence of exophytic med...
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PMID: 20842126
PDF is available here.
PDF is available here.
Analytical Biochemistry (404)1 2010
Abstract
In this investigation, a gas chromatography/mass spectrometry (GC/MS)-based metabolomic protocol for adherent cell cultures was developed using statistical design of experiments. Cell disruption, metabolite extraction, and the GC/MS settings were optimized aiming at a gentle, unbiased, sensitive, an...
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PMID: 20417172
PDF is available here.
PDF is available here.
Abstract
High-throughput omics strategies delineate the molecular mechanism of toxicity, predict the toxicity of newer drugs and chemicals, and identify individuals at high risks on the basis of expression patterns of messenger ribonucleic acids, genes, and proteins, and detection of intermed...
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PMID: 20082572
PDF is available here.
PDF is available here.
Abstract
We employ metabolomics to re-examine the complete metabolic effects of the antibiotic trimethoprim in E. coli. In rich media, trimethoprim treatment causes thymineless death. In minimal media, in contrast, trimethoprim addition results in rapid stoppage of cell growth and stable cell stasis....
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PMID: 20553049
PDF is available here.
PDF is available here.
Xenobiotica (40)8 2010
Abstract
Difluprednate (DFBA; 6alpha,9-difluoro-11beta,17,21-trihydroxy-1,4-pregnadiene-3,20-dione 21-acetate 17-butyrate) is an effective anti-inflammatory agent derived from prednisolone. The present study aimed to evaluate the metabolite profile of DFBA in rabbit ocular tissues after instillation of DFBA...
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PMID: 20509750
PDF is available here.
PDF is available here.
Abstract
Male and female preimplantation mammalian embryos differ not only in their chromosomal complement, but in their proteome and subsequent metabolome. This phenomenon is due to a finite period during preimplantation development when both X chromosomes are active, between embryonic genome activation and...
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PMID: 20501630
PDF is available here.
PDF is available here.
Abstract
We investigated the remodeling of H3K27me3 in Bos taurus embryos obtained after in vitro fertilization (IVF) and SCNT. In this species, transfer-induced chromatin remodeling can be clearly separated from embryonic genome activation (EGA), which occurs at the 8-16-cell stage, and cloning by SCNT is 1...
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PMID: 20431250
PDF is available here.
PDF is available here.
Abstract
We have recently shown significant preventive benefit of methylseleninic acid (MSeA) and Se-methylselenocysteine (MSeC) in the transgenic adenocarcinoma mouse prostate (TRAMP) model by oral administration. The present work applied iTRAQ proteomic approach to profile protein changes of the TRAMP pros...
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PMID: 20647336
PDF is available here.
PDF is available here.
Plant Physiology (153)3 2010
Abstract
We selected five genes belonging to different functional classes that all positively affect leaf size when overexpressed: AVP1, GRF5, JAW, BRI1, and GA20OX1. We show that the increase in leaf area in these lines depended on leaf position and growth conditions and that all five lines affected leaf si...
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PMID: 20460583
PDF is available here.
PDF is available here.
Abstract
We show that amphioxus naturally produces TRIAC from its precursors T(3) and l-thyroxine (T(4)), supporting its possible role as the active TH in amphioxus larvae. In addition, we show that blocking TH production inhibits metamorphosis and that this effect is compensated by exogenous T(3), suggestin...
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PMID: 21558188
PDF is available here.
PDF is available here.
Analytical Biochemistry (401)2 2010
Abstract
We used complementary methods (e.g., gas chromatography and/or liquid chromatography coupled with mass spectrometry) to detect the highly chemically diverse groups of metabolites for a global insight into the intracellular metabolism of S. aureus.
Copyright (c) 2010 Elsevier Inc. All rights reserv...
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PMID: 20211591
PDF is available here.
PDF is available here.
Analytical Biochemistry (401)2 2010
Abstract
We describe an extremely time-effective microwave-assisted protocol for the commonly used methoxyamine and N-methyl-N-trimethylsilylfluoracetamide silylation method of primary metabolites. Our studies show that microwave irradiation can decrease the sample preparation time from approximately 120 min...
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PMID: 19397887
PDF is available here.
PDF is available here.
Abstract
We report the first lipidomic analysis of acute 2-week DHA dietary supplementation effects on the physiological state of 15 fatty-acid, N-acylethanolamine, and glycerol-ester endocannabinoid metabolome constituents in murine plasma and brain. The DHA-rich diet markedly elevated DHA, eicosapentaenoic...
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PMID: 20071693
PDF is available here.
PDF is available here.
Abstract
Cholesterol is the precursor of many compounds with functions in the physiology and metabolism of the organism. Methods for the multicomponent analysis of these compounds and their metabolites (metabolomics) are needed to improve our understanding of their roles in different species, organs, cells a...
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PMID: 20494115
PDF is available here.
PDF is available here.
Abstract
Parasitic infections cause a myriad of responses in their mammalian hosts, on immune as well as on metabolic level. A multiplex panel of cytokines and metabolites derived from four parasite-rodent models, namely, Plasmodium berghei-mouse, Trypanosoma brucei brucei-mouse, Schistosoma...
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PMID: 20092362
PDF is available here.
PDF is available here.
Abstract
We compared the serum metabolome and the lipidomes of serum, adipose tissue, and liver of conventionally raised (CONV-R) and germ-free mice. The serum metabolome of CONV-R mice was characterized by increased levels of energy metabolites, e.g., pyruvic acid, citric acid, fumaric acid, and malic acid,...
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PMID: 20040631
PDF is available here.
PDF is available here.
Fertility and Sterility (93)7 2010
Abstract
We performed a cross-sectional study and found that women with endometriosis had an increased low-density lipoprotein (LDL) and non-high-density lipoprotein (HDL) cholesterol levels compared with controls presumably without endometriosis.
Copyright 2010 American Society for Reproductive Medicine. P...
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PMID: 19969295
PDF is available here.
PDF is available here.
Animal Reproduction Science (119)1-2 2010
Abstract
These results in guanacos suggest a follicular wave pattern more similar to the llama (Lama glama) than previously described in other South American and Old World camelid species.
Copyright 2009. Published by Elsevier B.V....
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PMID: 20022436
PDF is available here.
PDF is available here.
Abstract
High temperature impairs grain filling by inhibiting the deposition of storage materials such as starch and protein. To comprehend its impact on grain filling metabolism in rice (Oryza sativa), levels of metabolites and transcripts related to central pathways of metabolism were simultaneously determ...
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PMID: 20304786
PDF is available here.
PDF is available here.
Abstract
We examined the effects of AOX deficiency on plant growth, gene expression of respiratory components and metabolic profiles under low-N stress, using an aox1a knockout transgenic line (aox1a) of Arabidopsis thaliana. We exposed wild-type (WT) and aox1a plants to low-N stress for 7 d and analyzed the...
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PMID: 20304787
PDF is available here.
PDF is available here.
Abstract
The effects of dark-induced stress on the evolution of the soluble metabolites present in senescent soybean (Glycine max L.) nodules were analysed in vitro using (13)C- and (31)P-NMR spectroscopy. Sucrose and trehalose were the predominant soluble storage carbons. During dark-induced stress, a decli...
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PMID: 20358222
PDF is available here.
PDF is available here.
Abstract
We describe a method, which is based on solid phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS) and which can be used for the profiling of microbial volatile organic compounds (MVOCs) in the headspace (HS) of cultures of filamentous fungi. The method comprises the...
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PMID: 20302890
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (135)5 2010
Abstract
We compared the gas chromatography-mass spectrometry (GC-MS) metabolite profiles of mouse tumour necrosis factor alpha (mTNF-alpha) secreting Streptomyces lividans TK24 to the non-secreting wild type and the wild type harbouring the empty pIJ486 plasmid by multi-block principal component analysis (P...
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PMID: 20419241
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (135)5 2010
Abstract
We compared extraction consistency of three homogenisation methods including manual ultrasonication, automatic homogenization with tissuelyser and their combination, and systematically optimised faecal metabolite extraction parameters, including the faeces-to-buffer ratio (W(f) : V(b)), extraction r...
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PMID: 20419252
PDF is available here.
PDF is available here.
Abstract
We have arrived where we are, and will spend more time ascertaining our place in the current biomedical community and our role in determining the future of personalized medicine. In the 1950s-1970s new tools were added to expand our ability to interrogate the metabolome and the result was an explosi...
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PMID: 20172755
PDF is available here.
PDF is available here.
Journal of Plant Research (123)3 2010
Abstract
We established a novel methodology, termed widely targeted metabolomics, which can generate thousands of metabolome data points in a high-throughput manner. We previously conducted a targeted metabolite analysis of large-scale Arabidopsis bioresources, namely transposon-tagged mutants and accessions...
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PMID: 20369372
PDF is available here.
PDF is available here.
Abstract
A targeted liquid chromatography/tandem mass spectrometry-based metabolomics type approach, employing a triple stage quadrupole mass spectrometer in the product ion scan and selected reaction monitoring modes, was established to profile 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), 2-amino-...
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PMID: 20192249
PDF is available here.
PDF is available here.
Plant Physiology (152)4 2010
Abstract
We studied the effects of NADK2 expression in rice by developing transgenic rice plants that constitutively expressed the Arabidopsis chloroplastic NADK gene (NK2 lines). NK2 lines showed enhanced activity of NADK and accumulation of the NADP(H) pool, while intermediates of NAD derivatives were unch...
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PMID: 20154096
PDF is available here.
PDF is available here.
Plant Physiology (152)4 2010
Abstract
We have expressed an Arabidopsis (Arabidopsis thaliana) transcription factor, AtMYB12, in tobacco (Nicotiana tabacum), which resulted in enhanced expression of genes involved in the phenylpropanoid pathway, leading to severalfold higher accumulation of flavonols. Global gene expression and limited m...
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PMID: 20190095
PDF is available here.
PDF is available here.
Abstract
We analyzed the effects of two key environmental variables, CO(2) and nitrogen, on leaf metabolite profiles, NAD status and the abundance of key transcripts involved in de novo NAD synthesis in wild-type (WT) Nicotiana sylvestris and the CMSII mutant that lacks respiratory complex I. High CO(2) and...
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PMID: 20182741
PDF is available here.
PDF is available here.
Clinical Cancer Research (16)7 2010
Abstract
These findings suggest the HNSCC degradome as a valuable source of diagnostic, predictive, and prognostic molecular markers for these malignant tumors.
Copyright 2010 AACR....
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PMID: 20305301
PDF is available here.
PDF is available here.
Abstract
Audio, Transactions of the IRE Professional Group on (Chapter 30) 2010
Abstract
Along with genes and proteins, metabolites play important roles in sustaining life. Their functions include "primary" functions in metabolism and energy storage, as well as "secondary" functions in cell-to-cell signaling, metal acquisition, and virulence. There remains much to be learned about the i...
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PMID: 20373502
PDF is available here.
PDF is available here.
Abstract
Plants must respond and adapt to abiotic stresses to survive in various environmental conditions. Plants have acquired various stress tolerance mechanisms, which are different processes involving physiological and biochemical changes that result in adaptive or morphological changes. Recent advances...
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PMID: 20080055
PDF is available here.
PDF is available here.
Planta Medica (76)4 2010
Abstract
We have shown that ECHINACEA preparations and some common alkylamides weakly inhibit several cytochrome P450 (CYP) isoforms, with considerable variation in potency. We now report a detailed analysis of six commercial ECHINACEA liquid preparations, with emphasis on the metabolomic characterisation of...
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PMID: 19790031
PDF is available here.
PDF is available here.
Physiological Genomics (41)1 2010
Abstract
We set out to better elucidate the function of PPARbeta/delta in liver by comparing the effect of PPARalpha and PPARbeta/delta deletion using whole genome transcriptional profiling and analysis of plasma and liver metabolites. In fed state, the number of genes altered by PPARalpha and PPARbeta/delta...
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PMID: 20009009
PDF is available here.
PDF is available here.
Abstract
We have used amino acid profiling, a noninvasive marker of developmental potential to compare the effect of sex on the metabolism of bovine blastocysts conceived in vivo and in vitro. Blastocysts were incubated individually for 24 hr in a close-to-physiological mixture of amino acids and the depleti...
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PMID: 20058302
PDF is available here.
PDF is available here.
Abstract
We provide an introduction and brief survey on the technological basis of targeted metabolomics in biomarker research, discuss various relevant analytical aspects in mass spectrometry including comparison to non-targeted approaches, effects of sample preparation, impact of sample stability, carryove...
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PMID: 20196726
PDF is available here.
PDF is available here.
Abstract
The Phenotype MicroArray (PM) technology was used to study the metabolic characteristics of 29 Salmonella strains belonging to seven serotypes of S. enterica spp. enterica. Strains of serotypes Typhimurium (six strains among definite phage types DTs 1, 40 and 104) and Agona (two stra...
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PMID: 20094898
PDF is available here.
PDF is available here.
Abstract
The present report discusses targeted and non-targeted approaches to monitor single nutrients and global metabolite profiles in nutritional research. Non-targeted approaches such as metabolomics allow for the global description of metabolites in a biological sample and combine an analytical platform...
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PMID: 19954566
PDF is available here.
PDF is available here.
Oncology Reports (23)2 2010
Abstract
Arsenic is well documented as a chemotherapeutic agent capable of inducing cell death; however, it is also considered as a human carcinogen. Although it has recently been shown that arsenite exposure can potentiate genotoxicity, little is known about its global effects exerted in cells at the proteo...
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PMID: 20043101
PDF is available here.
PDF is available here.
Molecular BioSystems (6)2 2010
Abstract
We report the development of a strategy for identifying drug targets by combined genome-scale metabolic network and essentiality analyses. First, a genome-scale metabolic network of A. baumannii AYE, a drug-resistant strain, was reconstructed based on its genome annotation data, and biochemical know...
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PMID: 20094653
PDF is available here.
PDF is available here.
Biotechnology Letters (32)2 2010
Abstract
We developed Streptomyces venezuelae YJ028 as an efficient heterologous host to increase the malonyl-CoA pool to be directed towards enhanced production of various polyketides. To probe the applicability of newly developed hosts in the heterologous production of polyketides, we expressed type III po...
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PMID: 19838628
PDF is available here.
PDF is available here.
Journal of Chromatography A (1217)3 2010
Abstract
An analytical platform comprising three LC-ESI-MS/MS methods is presented for qualitative and quantitative profiling of more than 200 intracellular metabolites. Employing a silica based zwitterionic stationary phase in the HILIC mode, in total 223 hydrophilic metabolites can be determined. In partic...
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PMID: 19954781
PDF is available here.
PDF is available here.
Clinical Cancer Research (16)2 2010
Abstract
Proteomic and validation immunohistochemical analyses revealed that alpha-defensins (DEFA) were overexpressed in tumors from patients with a pCR. Gene expression analysis revealed that MAP2, a microtubule-associated protein, had significantly higher levels of expression in patients achieving a pCR....
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PMID: 20068102
PDF is available here.
PDF is available here.