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https://www.readbyqxmd.com/read/29222900/comparisons-of-proteomic-profiles-of-whey-protein-between-donor-human-milk-collected-earlier-than-3-months-and-6-months-after-delivery
#1
Won-Ho Hahn, Joon-Hwan Song, Jong-Bok Seo, Jung Eun Lee, Jeong-Sang Lee, Seunghyun Song, Joohyun Lee, Nam Mi Kang
BACKGROUND AND OBJECTIVES: Human milk has nutritional, protective, and developmental advantages for premature infants. However, proteomic information of low abundant protein of donor milk is insufficient. The purpose of this study is to analyze and compare the proteome of low abundant protein of donor milk obtained at different postpartum ages other than the colostrum. METHODS AND STUDY DESIGN: Donor breast milk from 12 healthy mothers was collected 15 days, 2 months and 6 months after delivery and stored by medically approved methods...
2018: Asia Pacific Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/29222764/optimization-of-multi-omic-genome-scale-models-methodologies-hands-on-tutorial-and-perspectives
#2
Supreeta Vijayakumar, Max Conway, Pietro Lió, Claudio Angione
Genome-scale metabolic models are valuable tools for assessing the metabolic potential of living organisms. Being downstream of gene expression, metabolism is increasingly being used as an indicator of the phenotypic outcome for drugs and therapies. We here present a review of the principal methods used for constraint-based modelling in systems biology, and explore how the integration of multi-omic data can be used to improve phenotypic predictions of genome-scale metabolic models. We believe that the large-scale comparison of the metabolic response of an organism to different environmental conditions will be an important challenge for genome-scale models...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222763/designing-optimized-production-hosts-by-metabolic-modeling
#3
Christian Jungreuthmayer, Matthias P Gerstl, David A Peña Navarro, Michael Hanscho, David E Ruckerbauer, Jürgen Zanghellini
Many of the complex and expensive production steps in the chemical industry are readily available in living cells. In order to overcome the metabolic limits of these cells, the optimal genetic intervention strategies can be computed by the use of metabolic modeling. Elementary flux mode analysis (EFMA) is an ideal tool for this task, as it does not require defining a cellular objective function. We present two EFMA-based methods to optimize production hosts: (1) the standard approach that can only be used for small and medium scale metabolic networks and (2) the advanced dual system approach that can be utilized to directly compute intervention strategies in a genome-scale metabolic model...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222761/coupling-fluxes-enzymes-and-regulation-in-genome-scale-metabolic-models
#4
Paul A Jensen
Genome-scale models have expanded beyond their metabolic origins. Multiple modeling frameworks are required to combine metabolism with enzymatic networks, transcription, translation, and regulation. Mathematical programming offers a powerful set of tools for tackling these "multi-modality" models, although special attention must be paid to the connections between modeling types. This chapter reviews common methods for combining metabolic and discrete logical models into a single mathematical programming framework...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222760/computational-prediction-of-synthetic-lethals-in-genome-scale-metabolic-models-using-fast-sl
#5
Karthik Raman, Aditya Pratapa, Omkar Mohite, Shankar Balachandran
In this chapter, we describe Fast-SL, an in silico approach to predict synthetic lethals in genome-scale metabolic models. Synthetic lethals are sets of genes or reactions where only the simultaneous removal of all genes or reactions in the set abolishes growth of an organism. In silico approaches to predict synthetic lethals are based on Flux Balance Analysis (FBA), a popular constraint-based analysis method based on linear programming. FBA has been shown to accurately predict the viability of various genome-scale metabolic models...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222758/differential-proteomics-based-on-2d-difference-in-gel-electrophoresis-and-tandem-mass-spectrometry-for-the-elucidation-of-biological-processes-in-antibiotic-producer-bacterial-strains
#6
Giuseppe Gallo, Andrea Scaloni
Proteomics based on 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) procedures can be considered a "gold standard" to determine quantitatively and comparatively protein abundances in cell extracts from different biological sources/conditions according to a gel-based approach. In particular, 2D-DIGE is used for protein specie separation, detection, and relative quantification, whenever tandem MS is used to obtain peptide sequence information that is managed according to bioinformatic procedures to identify the differentially represented protein species...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222757/rna-sequencing-and-analysis-in-microorganisms-for-metabolic-network-reconstruction
#7
Eva Pinatel, Clelia Peano
There is a strict interplay between metabolic networks and transcriptional regulation in bacteria; indeed, the transcriptome regulation, affecting the expression of large gene sets, can be used to predict the likely "on" or "off" state of metabolic genes as a function of environmental factors. Up to date, many bacterial transcriptomes have been studied by RNAseq, hundreds of experiments have been performed, and Giga bases of sequences have been produced. All this transcriptional information could potentially be integrated into metabolic networks in order to obtain a more comprehensive view of their regulation and to increase their prediction power...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222755/integrated-host-pathogen-metabolic-reconstructions
#8
Anu Raghunathan, Neema Jamshidi
The science and art of Genome scale metabolic network reconstructions have been explicitly documented in the literature for organisms across all the three kingdoms of life. Constraints-based models derived from such reconstructions have been used to assess metabolic phenotypes of their complex connections to genotype accurately. The problem of infectious disease is complex due to the multifactorial response of the host to the pathogen. Systems biology approaches and modeling allow one to study, understand, and predict emergent properties of such complex responses...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222750/the-fastcore-family-for-the-fast-reconstruction-of-compact-context-specific-metabolic-networks-models
#9
Maria Pires Pacheco, Thomas Sauter
The FASTCORE family is a family of algorithms that are mainly used to build context-specific models but can also be applied to other tasks such as gapfilling and consistency testing. The FASTCORE family has very low computational demands with running times that are several orders of magnitude lower than its main competitors. Furthermore, the models built by the FASTCORE family have a better resolution power (defined as the ability to capture metabolic variations between different tissues, cell types, or contexts) than models from other algorithms...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222749/the-mongoose-rational-arithmetic-toolbox
#10
Christopher Le, Leonid Chindelevitch
The modeling of metabolic networks has seen a rapid expansion following the complete sequencing of thousands of genomes. The constraint-based modeling framework has emerged as one of the most popular approaches to reconstructing and analyzing genome-scale metabolic models. Its main assumption is that of a quasi-steady-state, requiring that the production of each internal metabolite be balanced by its consumption. However, due to the multiscale nature of the models, the large number of reactions and metabolites, and the use of floating-point arithmetic for the stoichiometric coefficients, ensuring that this assumption holds can be challenging...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222457/a-control-analysis-perspective-on-katz-centrality
#11
Kieran J Sharkey
Methods for efficiently controlling dynamics propagated on networks are usually based on identifying the most influential nodes. Knowledge of these nodes can be used for the targeted control of dynamics such as epidemics, or for modifying biochemical pathways relating to diseases. Similarly they are valuable for identifying points of failure to increase network resilience in, for example, social support networks and logistics networks. Many measures, often termed 'centrality', have been constructed to achieve these aims...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222421/the-transcriptomic-signature-of-disease-development-and-progression-of-nonalcoholic-fatty-liver-disease
#12
Sophie Cazanave, Alexei Podtelezhnikov, Kristian Jensen, Mulugeta Seneshaw, Divya P Kumar, Hae-Ki Min, Prasanna K Santhekadur, Bubu Banini, Adolfo Gabriele Mauro, Abdul M Oseini, Robert Vincent, Keith Q Tanis, Andrea L Webber, Liangsu Wang, Pierre Bedossa, Faridoddin Mirshahi, Arun J Sanyal
A longitudinal molecular model of the development and progression of nonalcoholic fatty liver disease (NAFLD) over time is lacking. We have recently validated a high fat/sugar water-induced animal (an isogenic strain of C57BL/6 J:129S1/SvImJ mice) model of NAFLD that closely mimics most aspects of human disease. The hepatic transcriptome of such mice with fatty liver (8 weeks), steatohepatitis with early fibrosis (16-24 weeks) and advanced fibrosis (52 weeks) after initiation of the diet was evaluated and compared to mice on chow diet...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29221916/dna-methylation-signatures-at-endoplasmic-reticulum-stress-genes-are-associated-with-adiposity-and-insulin-resistance
#13
Omar Ramos-Lopez, Jose I Riezu-Boj, Fermin I Milagro, J Alfredo Martinez
A sustained activation of the unfolded protein response and the subsequent endoplasmic reticulum (ER) stress has been involved in the onset and severity of several metabolic diseases. The aim of this study was to analyze the association of DNA methylation signatures at ER stress genes with adiposity traits and related metabolic disorders. An epigenomic analysis within the Methyl Epigenome Network Association (MENA) project was conducted in an adult population (n=474). DNA methylation status in peripheral white blood cells was analyzed by a microarray approach...
November 28, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/29221790/fam3-gene-family-a-promising-therapeutical-target-for-nafld-and-type-2-diabetes
#14
REVIEW
Zhang Xiaoyan, Weili Yang, Junpei Wang, Yuhong Meng, Youfei Guan, Jichun Yang
Non-alcoholic fatty liver disease (NAFLD) and diabetes are severe public health issues worldwide. The Family with sequence similarity 3 (FAM3) gene family consists of four members designated as FAM3A, FAM3B, FAM3C and FAM3D, respectively. Recently, there had been increasing evidence that FAM3A, FAM3B and FAM3C are important regulators of glucose and lipid metabolism. FAM3A expression is reduced in the livers of diabetic rodents and NAFLD patients. Hepatic FAM3A restoration activates ATP-P2 receptor-Akt and AMPK pathways to attenuate steatosis and hyperglycemia in obese diabetic mice...
December 5, 2017: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/29220508/model-based-design-of-bistable-cell-factories-for-metabolic-engineering
#15
Shyam Srinivasan, William R Cluett, Radhakrishnan Mahadevan
Motivation: Metabolism can exhibit dynamic phenomena like bistability due to the presence of regulatory motifs like the positive feedback loop. As cell factories, microorganisms with bistable metabolism can have a high and a low product flux at the two stable steady states, respectively. The exclusion of metabolic regulation and network dynamics limits the ability of pseudo-steady state stoichiometric models to detect the presence of bistability, and reliably assess the outcomes of design perturbations to metabolic networks...
December 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29218953/-exploiture-and-application-of-an-internet-based-computation-platform-for-integrative-pharmacology-of-traditional-chinese-medicine
#16
Hai-Yu Xu, Zhen-Ming Liu, Yan Fu, Yan-Qiong Zhang, Jian-Jun Yu, Fei-Fei Guo, Shi-Huan Tang, Chuan-Yu Lv, Jin Su, Ru-Yi Cui, Hong-Jun Yang
Recently, integrative pharmacology(IP) has become a pivotal paradigm for the modernization of traditional Chinese medicines(TCM) and combinatorial drugs discovery, which is an interdisciplinary science for establishing the in vitro and in vivo correlation between absorption, distribution, metabolism, and excretion/pharmacokinetic(ADME/PK) profiles of TCM and the molecular networks of disease by the integration of the knowledge of multi-disciplinary and multi-stages. In the present study, an internet-based Computation Platform for IP of TCM(TCM-IP, www...
September 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29218114/comparative-transcriptome-analysis-of-the-global-circular-rnas-expression-profiles-between-shee-and-sheec-cell-lines
#17
Jiachun Sun, Xiaozhi Yuan, Xiangming Li, Dengkui Wang, Tanyou Shan, Wei Wang, Qiuyan Wan, Xinshuai Wang, Junqiang Yan, Shegan Gao
Esophageal squamous cell carcinoma (ESCC) is widely regarded as one of the most lethal types of cancer around the world. The fact that early detection of ESCC could dramatically improve the treatment outcome of the patients has sparked considerable interest in searching for reliable and accurate diagnostic biomarkers. Recently, circular RNAs (circRNA) have emerged as a new type of non-coding RNAs with significant RNase resistance, wide abundance and remarkable internal diversity. There is also increasing evidence suggesting that circRNAs could be implicated in the pathogenesis of cancer and other diseases...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/29216353/effects-of-sex-hormone-treatment-on-the-metabolic-syndrome-in-transgender-individuals-focus-on-metabolic-cytokines
#18
Matthias K Auer, Thomas Ebert, Maik Pietzner, Justine Defreyne, Johannes Fuss, Günter K Stalla, Guy T'Sjoen
Context: Hormone treatment (HT) in transgender persons affects many components of the metabolic syndrome (MS). Objective: To determine the role of direct hormonal effects, changes in metabolic cytokines and body composition on metabolic outcomes. Design, Setting, and Participants: 24 transwomen and 45 transmen from the European Network for the Investigation of Gender Incongruence (ENIGI) investigated at baseline and following 12 months of HT...
December 5, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29216278/systematic-integrative-analysis-of-gene-expression-identifies-hnf4a-as-the-central-gene-in-pathogenesis-of-non-alcoholic-steatohepatitis
#19
Cristina Baciu, Elisa Pasini, Marc Angeli, Katherine Schwenger, Jenifar Afrin, Atul Humar, Sandra Fischer, Keyur Patel, Johane Allard, Mamatha Bhat
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in the Western world, and encompasses a spectrum from simple steatosis to steatohepatitis (NASH). There is currently no approved pharmacologic therapy against NASH, partly due to an incomplete understanding of its molecular basis. The goal of this study was to determine the key differentially expressed genes (DEGs), as well as those genes and pathways central to its pathogenesis. We performed an integrative computational analysis of publicly available gene expression data in NASH from GEO (GSE17470, GSE24807, GSE37031, GSE89632)...
2017: PloS One
https://www.readbyqxmd.com/read/29215013/allosteric-pyruvate-kinase-based-logic-gate-synergistically-senses-energy-and-sugar-levels-in-mycobacterium-tuberculosis
#20
Wenhe Zhong, Liang Cui, Boon Chong Goh, Qixu Cai, Peiying Ho, Yok Hian Chionh, Meng Yuan, Abbas El Sahili, Linda A Fothergill-Gilmore, Malcolm D Walkinshaw, Julien Lescar, Peter C Dedon
Pyruvate kinase (PYK) is an essential glycolytic enzyme that controls glycolytic flux and is critical for ATP production in all organisms, with tight regulation by multiple metabolites. Yet the allosteric mechanisms governing PYK activity in bacterial pathogens are poorly understood. Here we report biochemical, structural and metabolomic evidence that Mycobacterium tuberculosis (Mtb) PYK uses AMP and glucose-6-phosphate (G6P) as synergistic allosteric activators that function as a molecular "OR logic gate" to tightly regulate energy and glucose metabolism...
December 7, 2017: Nature Communications
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