keyword
MENU ▼
Read by QxMD icon Read
search

genome scale model

keyword
https://www.readbyqxmd.com/read/28732234/computational-modelling-of-genome-scale-metabolic-networks-and-its-application-to-cho-cell-cultures
#1
REVIEW
Živa Rejc, Lidija Magdevska, Tilen Tršelič, Timotej Osolin, Rok Vodopivec, Jakob Mraz, Eva Pavliha, Nikolaj Zimic, Tanja Cvitanović, Damjana Rozman, Miha Moškon, Miha Mraz
Genome-scale metabolic models (GEMs) have become increasingly important in recent years. Currently, GEMs are the most accurate in silico representation of the genotype-phenotype link. They allow us to study complex networks from the systems perspective. Their application may drastically reduce the amount of experimental and clinical work, improve diagnostic tools and increase our understanding of complex biological phenomena. GEMs have also demonstrated high potential for the optimisation of bio-based production of recombinant proteins...
July 8, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28732187/do-genetic-markers-of-inflammation-modify-the-relationship-between-periodontitis-and-nonalcoholic-fatty-liver-disease-findings-from-the-ship-study
#2
A A Akinkugbe, C L Avery, A S Barritt, S R Cole, M Lerch, J Mayerle, S Offenbacher, A Petersmann, M Nauck, H Völzke, G D Slade, G Heiss, T Kocher, B Holtfreter
An association between periodontitis and nonalcoholic fatty liver disease (NAFLD) has been reported by experimental animal and epidemiologic studies. This study investigated whether circulating levels of serum C-reactive protein (CRP) and a weighted genetic CRP score representing markers of inflammatory burden modify the association between periodontitis and NAFLD. Data came from 2,481 participants of the Study of Health in Pomerania who attended baseline examination that occurred between 1997 and 2001. Periodontitis was defined as the percentage of sites (0%, <30%, ≥30%) with probing pocket depth (PD) ≥4 mm, and NAFLD status was determined using liver ultrasound assessment...
July 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28730487/a-methodology-for-comprehensive-analysis-of-toll-like-receptor-signaling-in-macrophages
#3
Marijke Koppenol-Raab, Aleksandra Nita-Lazar
A combination of high-throughput, multiplexed, quantitative methods with computational modeling and statistical approaches is required to obtain system-level understanding of biological function. Mass spectrometry (MS)-based proteomics has emerged as a preferred tool for the analysis of changes in protein abundance and their post-translational modification (PTM) levels at a global scale, comparable with genomic experiments and generating data suitable for use in mathematical modeling of signaling pathways. Here we describe a set of parallel bottom-up proteomic approaches to detect and quantify the global protein changes in total intracellular proteins, their phosphorylation, and the proteins released by active and passive secretion or shedding mechanisms (referred to as the secretome as reviewed in Makridakis and Vlahou, J Proteome 73:2291-2305, 2010) in response to the stimulation of Toll-like receptors (TLRs) with specific ligands in cultured macrophages...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28727789/lumpgem-systematic-generation-of-subnetworks-and-elementally-balanced-lumped-reactions-for-the-biosynthesis-of-target-metabolites
#4
Meric Ataman, Vassily Hatzimanikatis
In the post-genomic era, Genome-scale metabolic networks (GEMs) have emerged as invaluable tools to understand metabolic capabilities of organisms. Different parts of these metabolic networks are defined as subsystems/pathways, which are sets of functional roles to implement a specific biological process or structural complex, such as glycolysis and TCA cycle. Subsystem/pathway definition is also employed to delineate the biosynthetic routes that produce biomass building blocks. In databases, such as MetaCyc and SEED, these representations are composed of linear routes from precursors to target biomass building blocks...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28727725/redgem-systematic-reduction-and-analysis-of-genome-scale-metabolic-reconstructions-for-development-of-consistent-core-metabolic-models
#5
Meric Ataman, Daniel F Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis
Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions. However the complexity of these large metabolic networks often hinders their utility in various practical applications. Although reduced models are commonly used for modeling and in integrating experimental data, they are often inconsistent across different studies and laboratories due to different criteria and detail, which can compromise transferability of the findings and also integration of experimental data from different groups...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28724412/assessment-of-genome-annotation-using-gene-function-similarity-within-the-gene-neighborhood
#6
Se-Ran Jun, Intawat Nookaew, Loren Hauser, Andrey Gorin
BACKGROUND: Functional annotation of bacterial genomes is an obligatory and crucially important step of information processing from the genome sequences into cellular mechanisms. However, there is a lack of computational methods to evaluate the quality of functional assignments. RESULTS: We developed a genome-scale model that assigns Bayesian probability to each gene utilizing a known property of functional similarity between neighboring genes in bacteria. CONCLUSIONS: Our model clearly distinguished true annotation from random annotation with Bayesian annotation probability >0...
July 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28720699/cellular-trade-offs-and-optimal-resource-allocation-during-cyanobacterial-diurnal-growth
#7
Alexandra-M Reimers, Henning Knoop, Alexander Bockmayr, Ralf Steuer
Cyanobacteria are an integral part of Earth's biogeochemical cycles and a promising resource for the synthesis of renewable bioproducts from atmospheric CO2 Growth and metabolism of cyanobacteria are inherently tied to the diurnal rhythm of light availability. As yet, however, insight into the stoichiometric and energetic constraints of cyanobacterial diurnal growth is limited. Here, we develop a computational framework to investigate the optimal allocation of cellular resources during diurnal phototrophic growth using a genome-scale metabolic reconstruction of the cyanobacterium Synechococcus elongatus PCC 7942...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28718799/zebrafish-as-a-model-organism-for-the-development-of-drugs-for-skin-cancer
#8
REVIEW
Fatemeh Bootorabi, Hamed Manouchehri, Reza Changizi, Harlan Barker, Elisabetta Palazzo, Annalisa Saltari, Mataleena Parikka, Carlo Pincelli, Ashok Aspatwar
Skin cancer, which includes melanoma and squamous cell carcinoma, represents the most common type of cutaneous malignancy worldwide, and its incidence is expected to rise in the near future. This condition derives from acquired genetic dysregulation of signaling pathways involved in the proliferation and apoptosis of skin cells. The development of animal models has allowed a better understanding of these pathomechanisms, with the possibility of carrying out toxicological screening and drug development. In particular, the zebrafish (Danio rerio) has been established as one of the most important model organisms for cancer research...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28717047/annotated-draft-genome-assemblies-for-the-northern-bobwhite-colinus-virginianus-and-the-scaled-quail-callipepla-squamata-reveal-disparate-estimates-of-modern-genome-diversity-and-historic-effective-population-size
#9
David L Oldeschulte, Yvette A Halley, Miranda L Wilson, Eric K Bhattarai, Wesley Brashear, Joshua Hill, Richard P Metz, Charles D Johnson, Dale Rollins, Markus J Peterson, Derek M Bickhart, Jared E Decker, John F Sewell, Christopher M Seabury
Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail (Callipepla squamata) populations have suffered precipitous declines across most of their U.S. ranges. Illumina-based first- (v1.0) and second-generation (v2.0) draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 Mb and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥ 90% of the assembled genomes were captured within 1,313 and 8,990 scaffolds, respectively...
July 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28715411/a-curated-genome-scale-metabolic-model-of-bordetella-pertussis-metabolism
#10
Nick Fyson, Jerry King, Thomas Belcher, Andrew Preston, Caroline Colijn
The Gram-negative bacterium Bordetella pertussis is the causative agent of whooping cough, a serious respiratory infection causing hundreds of thousands of deaths annually worldwide. There are effective vaccines, but their production requires growing large quantities of B. pertussis. Unfortunately, B. pertussis has relatively slow growth in culture, with low biomass yields and variable growth characteristics. B. pertussis also requires a relatively expensive growth medium. We present a new, curated flux balance analysis-based model of B...
July 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28715400/a-novel-method-to-model-chronic-traumatic-encephalopathy-in-drosophila
#11
Mingkuan Sun, Liam L Chen
Chronic Traumatic Encephalopathy (CTE) is an established neurodegenerative disease that is closely associated with exposure to repetitive mild Traumatic Brain Injury (mTBI). The mechanisms responsible for its complex pathological changes remain largely elusive, despite a recent consensus to define the neuropathological criteria. Here, we describe a novel method to develop a model of CTE in Drosophila melanogaster (Drosophila ) in an attempt to identify the key genes and pathways that lead to the characteristic hyperphosphorylated tau accumulation and neuronal death in the brain...
July 4, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28712497/use-of-crispr-cas9-for-symbiotic-nitrogen-fixation-research-in-legumes
#12
Longlong Wang, Longxiang Wang, Yu Zhou, Deqiang Duanmu
Nitrogen-fixing rhizobia have established a symbiotic relationship with the legume family through more than 60 million years of evolution. Hundreds of legume host genes are involved in the SNF (symbiotic nitrogen fixation) process, such as recognition of the bacterial partners, nodulation signaling and nodule development, maintenance of highly efficient nitrogen fixation within nodules, regulation of nodule numbers, and nodule senescence. However, investigations of SNF-related gene functions and dissecting molecular mechanisms of the complicated signaling crosstalk on a genomic scale were significantly restricted by insufficient mutant resources of several representative model legumes...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28710451/selection-of-complementary-foods-based-on-optimal-nutritional-values
#13
Partho Sen, Adil Mardinogulu, Jens Nielsen
Human milk is beneficial for growth and development of infants. Several factors result in mothers ceasing breastfeeding which leads to introduction of breast-milk substitutes (BMS). In some communities traditional foods are given as BMS, in others they are given as complementary foods during weaning. Improper food selection at this stage is associated with a high prevalence of malnutrition in children under 5 years. Here we listed the traditional foods from four continents and compared them with human milk based on their dietary contents...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28710368/genome-wide-linkage-analysis-of-large-multiple-multigenerational-families-identifies-novel-genetic-loci-for-coronary-artery-disease
#14
Yang Guo, Fan Wang, Lin Li, Hanxiang Gao, Stephen Arckacki, Isabel Z Wang, John Barnard, Stephen Ellis, Carlos Hubbard, Eric J Topol, Qiuyun Chen, Qing K Wang
Coronary artery disease (CAD) is the leading cause of death, and genetic factors contribute significantly to risk of CAD. This study aims to identify new CAD genetic loci through a large-scale linkage analysis of 24 large and multigenerational families with 433 family members (GeneQuest II). All family members were genotyped with markers spaced by every 10 cM and a model-free nonparametric linkage (NPL-all) analysis was carried out. Two highly significant CAD loci were identified on chromosome 17q21.2 (NPL score of 6...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28706201/genotypic-variability-based-association-identifies-novel-non-additive-loci-dhcr7-and-irf4-in-sero-negative-rheumatoid-arthritis
#15
Wen-Hua Wei, Sebastien Viatte, Tony R Merriman, Anne Barton, Jane Worthington
Sero-negative rheumatoid arthritis (RA) is a highly heterogeneous disorder with only a few additive loci identified to date. We report a genotypic variability-based genome-wide association study (vGWAS) of six cohorts of sero-negative RA recruited in Europe and the US that were genotyped with the Immunochip. A two-stage approach was used: (1) a mixed model to partition dichotomous phenotypes into an additive component and non-additive residuals on the liability scale and (2) the Levene's test to assess equality of the residual variances across genotype groups...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28705224/more-than-just-a-gut-feeling-constraint-based-genome-scale-metabolic-models-for-predicting-functions-of-human-intestinal-microbes
#16
REVIEW
Kees C H van der Ark, Ruben G A van Heck, Vitor A P Martins Dos Santos, Clara Belzer, Willem M de Vos
The human gut is colonized with a myriad of microbes, with substantial interpersonal variation. This complex ecosystem is an integral part of the gastrointestinal tract and plays a major role in the maintenance of homeostasis. Its dysfunction has been correlated to a wide array of diseases, but the understanding of causal mechanisms is hampered by the limited amount of cultured microbes, poor understanding of phenotypes, and the limited knowledge about interspecies interactions. Genome-scale metabolic models (GEMs) have been used in many different fields, ranging from metabolic engineering to the prediction of interspecies interactions...
July 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28700664/systematic-screening-for-skin-hair-and-nail-abnormalities-in-a-large-scale-knockout-mouse-program
#17
John P Sundberg, Soheil S Dadras, Kathleen A Silva, Victoria E Kennedy, Gaven Garland, Stephen A Murray, Beth A Sundberg, Paul N Schofield, C Herbert Pratt
The International Knockout Mouse Consortium was formed in 2007 to inactivate ("knockout") all protein-coding genes in the mouse genome in embryonic stem cells. Production and characterization of these mice, now underway, has generated and phenotyped 3,100 strains with knockout alleles. Skin and adnexa diseases are best defined at the gross clinical level and by histopathology. Representative retired breeders had skin collected from the back, abdomen, eyelids, muzzle, ears, tail, and lower limbs including the nails...
2017: PloS One
https://www.readbyqxmd.com/read/28699633/reversal-of-cancer-gene-expression-correlates-with-drug-efficacy-and-reveals-therapeutic-targets
#18
Bin Chen, Li Ma, Hyojung Paik, Marina Sirota, Wei Wei, Mei-Sze Chua, Samuel So, Atul J Butte
The decreasing cost of genomic technologies has enabled the molecular characterization of large-scale clinical disease samples and of molecular changes upon drug treatment in various disease models. Exploring methods to relate diseases to potentially efficacious drugs through various molecular features is critically important in the discovery of new therapeutics. Here we show that the potency of a drug to reverse cancer-associated gene expression changes positively correlates with that drug's efficacy in preclinical models of breast, liver and colon cancers...
July 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/28696678/benchmarking-water-quality-from-wastewater-to-drinking-waters-using-reduced-transcriptome-of-human-cells
#19
Pu Xia, Xiaowei Zhang, Hanxin Zhang, Pingping Wang, Mingming Tian, Hongxia Yu
One of the major challenge in environmental science is how to monitor and assess the risk of complex environmental mixtures. In vitro bioassays with limited key toxicological endpoints have been shown to be suitable to evaluate mixtures of organic pollutants in wastewater and recycled water. Omics approaches such as transcriptomics can monitor biological effects at genome-scale. However, few studies have applied omics approach in the assessment of mixtures of organic micropollutants. Here, an omics approach was developed for profiling bioactivity of ten water samples ranging from wastewater to drinking water in human cells by a reduced human transcriptome (RHT) method and dose response modeling...
July 11, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28696435/a-direct-test-of-the-diathesis-stress-model-for-depression
#20
L Colodro-Conde, B Couvy-Duchesne, G Zhu, W L Coventry, E M Byrne, S Gordon, M J Wright, G W Montgomery, P A F Madden, S Ripke, L J Eaves, A C Heath, N R Wray, S E Medland, N G Martin
The diathesis-stress theory for depression states that the effects of stress on the depression risk are dependent on the diathesis or vulnerability, implying multiplicative interactive effects on the liability scale. We used polygenic risk scores for major depressive disorder (MDD) calculated from the results of the most recent analysis from the Psychiatric Genomics Consortium as a direct measure of the vulnerability for depression in a sample of 5221 individuals from 3083 families. In the same we also had measures of stressful life events and social support and a depression symptom score, as well as DSM-IV MDD diagnoses for most individuals...
July 11, 2017: Molecular Psychiatry
keyword
keyword
18458
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"