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Molecular Systems Biology

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https://www.readbyqxmd.com/read/28916541/a-proteomic-atlas-of-insulin-signalling-reveals-tissue-specific-mechanisms-of-longevity-assurance
#1
Luke S Tain, Robert Sehlke, Chirag Jain, Manopriya Chokkalingam, Nagarjuna Nagaraj, Paul Essers, Mark Rassner, Sebastian Grönke, Jenny Froelich, Christoph Dieterich, Matthias Mann, Nazif Alic, Andreas Beyer, Linda Partridge
Lowered activity of the insulin/IGF signalling (IIS) network can ameliorate the effects of ageing in laboratory animals and, possibly, humans. Although transcriptome remodelling in long-lived IIS mutants has been extensively documented, the causal mechanisms contributing to extended lifespan, particularly in specific tissues, remain unclear. We have characterized the proteomes of four key insulin-sensitive tissues in a long-lived Drosophila IIS mutant and control, and detected 44% of the predicted proteome (6,085 proteins)...
September 15, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28835372/pervasive-coexpression-of-spatially-proximal-genes-is-buffered-at-the-protein-level
#2
Georg Kustatscher, Piotr Grabowski, Juri Rappsilber
Genes are not randomly distributed in the genome. In humans, 10% of protein-coding genes are transcribed from bidirectional promoters and many more are organised in larger clusters. Intriguingly, neighbouring genes are frequently coexpressed but rarely functionally related. Here we show that coexpression of bidirectional gene pairs, and closeby genes in general, is buffered at the protein level. Taking into account the 3D architecture of the genome, we find that co-regulation of spatially close, functionally unrelated genes is pervasive at the transcriptome level, but does not extend to the proteome...
August 23, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28827398/network-analyses-identify-liver-specific-targets-for-treating-liver-diseases
#3
Sunjae Lee, Cheng Zhang, Zhengtao Liu, Martina Klevstig, Bani Mukhopadhyay, Mattias Bergentall, Resat Cinar, Marcus Ståhlman, Natasha Sikanic, Joshua K Park, Sumit Deshmukh, Azadeh M Harzandi, Tim Kuijpers, Morten Grøtli, Simon J Elsässer, Brian D Piening, Michael Snyder, Ulf Smith, Jens Nielsen, Fredrik Bäckhed, George Kunos, Mathias Uhlen, Jan Boren, Adil Mardinoglu
We performed integrative network analyses to identify targets that can be used for effectively treating liver diseases with minimal side effects. We first generated co-expression networks (CNs) for 46 human tissues and liver cancer to explore the functional relationships between genes and examined the overlap between functional and physical interactions. Since increased de novo lipogenesis is a characteristic of nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC), we investigated the liver-specific genes co-expressed with fatty acid synthase (FASN)...
August 21, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28779005/improving-the-phenotype-predictions-of-a-yeast-genome-scale-metabolic-model-by-incorporating-enzymatic-constraints
#4
Benjamín J Sánchez, Cheng Zhang, Avlant Nilsson, Petri-Jaan Lahtvee, Eduard J Kerkhoven, Jens Nielsen
Genome-scale metabolic models (GEMs) are widely used to calculate metabolic phenotypes. They rely on defining a set of constraints, the most common of which is that the production of metabolites and/or growth are limited by the carbon source uptake rate. However, enzyme abundances and kinetics, which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance and turnover number...
August 3, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28743795/capturing-protein-communities-by-structural-proteomics-in-a-thermophilic-eukaryote
#5
Panagiotis L Kastritis, Francis J O'Reilly, Thomas Bock, Yuanyue Li, Matt Z Rogon, Katarzyna Buczak, Natalie Romanov, Matthew J Betts, Khanh Huy Bui, Wim J Hagen, Marco L Hennrich, Marie-Therese Mackmull, Juri Rappsilber, Robert B Russell, Peer Bork, Martin Beck, Anne-Claude Gavin
The arrangement of proteins into complexes is a key organizational principle for many cellular functions. Although the topology of many complexes has been systematically analyzed in isolation, their molecular sociology in situ remains elusive. Here, we show that crude cellular extracts of a eukaryotic thermophile, Chaetomium thermophilum, retain basic principles of cellular organization. Using a structural proteomics approach, we simultaneously characterized the abundance, interactions, and structure of a third of the C...
July 25, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28705884/quantitative-analysis-of-protein-interaction-network-dynamics-in-yeast
#6
Albi Celaj, Ulrich Schlecht, Justin D Smith, Weihong Xu, Sundari Suresh, Molly Miranda, Ana Maria Aparicio, Michael Proctor, Ronald W Davis, Frederick P Roth, Robert P St Onge
Many cellular functions are mediated by protein-protein interaction networks, which are environment dependent. However, systematic measurement of interactions in diverse environments is required to better understand the relative importance of different mechanisms underlying network dynamics. To investigate environment-dependent protein complex dynamics, we used a DNA-barcode-based multiplexed protein interaction assay in Saccharomyces cerevisiae to measure in vivo abundance of 1,379 binary protein complexes under 14 environments...
July 13, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28652282/biphasic-response-as-a-mechanism-against-mutant-takeover-in-tissue-homeostasis-circuits
#7
Omer Karin, Uri Alon
Tissues use feedback circuits in which cells send signals to each other to control their growth and survival. We show that such feedback circuits are inherently unstable to mutants that misread the signal level: Mutants have a growth advantage to take over the tissue, and cannot be eliminated by known cell-intrinsic mechanisms. To resolve this, we propose that tissues have biphasic responses in and the signal is toxic at both high and low levels, such as glucotoxicity of beta cells, excitotoxicity in neurons, and toxicity of growth factors to T cells...
June 26, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28596423/integration-of-over-9-000-mass-spectrometry-experiments-builds-a-global-map-of-human-protein%C3%A2-complexes
#8
Kevin Drew, Chanjae Lee, Ryan L Huizar, Fan Tu, Blake Borgeson, Claire D McWhite, Yun Ma, John B Wallingford, Edward M Marcotte
Macromolecular protein complexes carry out many of the essential functions of cells, and many genetic diseases arise from disrupting the functions of such complexes. Currently, there is great interest in defining the complete set of human protein complexes, but recent published maps lack comprehensive coverage. Here, through the synthesis of over 9,000 published mass spectrometry experiments, we present hu.MAP, the most comprehensive and accurate human protein complex map to date, containing > 4,600 total complexes, > 7,700 proteins, and > 56,000 unique interactions, including thousands of confident protein interactions not identified by the original publications...
June 8, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28495919/alternative-tsss-are-co-regulated-in-single-cells-in-the-mouse-brain
#9
Kasper Karlsson, Peter Lönnerberg, Sten Linnarsson
Alternative transcription start sites (TSSs) have been extensively studied genome-wide for many cell types and have been shown to be important during development and to regulate transcript abundance between cell types. Likewise, single-cell gene expression has been extensively studied for many cell types. However, how single cells use TSSs has not yet been examined. In particular, it is unknown whether alternative TSSs are independently expressed, or whether they are co-activated or even mutually exclusive in single cells...
May 11, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28490437/high-throughput-crispri-phenotyping-identifies-new-essential-genes-in-streptococcus-pneumoniae
#10
Xue Liu, Clement Gallay, Morten Kjos, Arnau Domenech, Jelle Slager, Sebastiaan P van Kessel, Kèvin Knoops, Robin A Sorg, Jing-Ren Zhang, Jan-Willem Veening
Genome-wide screens have discovered a large set of essential genes in the opportunistic human pathogen Streptococcus pneumoniae However, the functions of many essential genes are still unknown, hampering vaccine development and drug discovery. Based on results from transposon sequencing (Tn-seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting 348 potentially essential genes by CRISPR interference (CRISPRi) and show a growth phenotype for 254 of them (73%)...
May 10, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28468958/an-immediate-late-gene-expression-module-decodes-erk-signal-duration
#11
Florian Uhlitz, Anja Sieber, Emanuel Wyler, Raphaela Fritsche-Guenther, Johannes Meisig, Markus Landthaler, Bertram Klinger, Nils Blüthgen
The RAF-MEK-ERK signalling pathway controls fundamental, often opposing cellular processes such as proliferation and apoptosis. Signal duration has been identified to play a decisive role in these cell fate decisions. However, it remains unclear how the different early and late responding gene expression modules can discriminate short and long signals. We obtained both protein phosphorylation and gene expression time course data from HEK293 cells carrying an inducible construct of the proto-oncogene RAF By mathematical modelling, we identified a new gene expression module of immediate-late genes (ILGs) distinct in gene expression dynamics and function...
May 3, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28455349/a-notch-positive-feedback-in-the-intestinal-stem-cell-niche-is-essential-for-stem-cell-self-renewal
#12
Kai-Yuan Chen, Tara Srinivasan, Kuei-Ling Tung, Julio M Belmonte, Lihua Wang, Preetish Kadur Lakshminarasimha Murthy, Jiahn Choi, Nikolai Rakhilin, Sarah King, Anastasia Kristine Varanko, Mavee Witherspoon, Nozomi Nishimura, James A Glazier, Steven M Lipkin, Pengcheng Bu, Xiling Shen
The intestinal epithelium is the fastest regenerative tissue in the body, fueled by fast-cycling stem cells. The number and identity of these dividing and migrating stem cells are maintained by a mosaic pattern at the base of the crypt. How the underlying regulatory scheme manages this dynamic stem cell niche is not entirely clear. We stimulated intestinal organoids with Notch ligands and inhibitors and discovered that intestinal stem cells employ a positive feedback mechanism via direct Notch binding to the second intron of the Notch1 gene...
April 28, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28455348/a-spectrum-of-modularity-in-multi-functional-gene-circuits
#13
Alba Jiménez, James Cotterell, Andreea Munteanu, James Sharpe
A major challenge in systems biology is to understand the relationship between a circuit's structure and its function, but how is this relationship affected if the circuit must perform multiple distinct functions within the same organism? In particular, to what extent do multi-functional circuits contain modules which reflect the different functions? Here, we computationally survey a range of bi-functional circuits which show no simple structural modularity: They can switch between two qualitatively distinct functions, while both functions depend on all genes of the circuit...
April 27, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28442489/integrative-genomics-of-gene-and-metabolic-regulation-by-estrogen-receptors-%C3%AE-and-%C3%AE-and-their-coregulators
#14
Zeynep Madak-Erdogan, Tze-Howe Charn, Yan Jiang, Edison T Liu, John A Katzenellenbogen, Benita S Katzenellenbogen
No abstract text is available yet for this article.
April 25, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28438832/a-photoconversion-model-for-full-spectral-programming-and-multiplexing-of-optogenetic%C3%A2-systems
#15
Evan J Olson, Constantine N Tzouanas, Jeffrey J Tabor
Optogenetics combines externally applied light signals and genetically engineered photoreceptors to control cellular processes with unmatched precision. Here, we develop a mathematical model of wavelength- and intensity-dependent photoconversion, signaling, and output gene expression for our two previously engineered light-sensing Escherichia coli two-component systems. To parameterize the model, we develop a simple set of spectral and dynamical calibration experiments using our recent open-source "Light Plate Apparatus" device...
April 24, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28420678/automated-analysis-of-high-content-microscopy-data-with-deep-learning
#16
Oren Z Kraus, Ben T Grys, Jimmy Ba, Yolanda Chong, Brendan J Frey, Charles Boone, Brenda J Andrews
Existing computational pipelines for quantitative analysis of high-content microscopy data rely on traditional machine learning approaches that fail to accurately classify more than a single dataset without substantial tuning and training, requiring extensive analysis. Here, we demonstrate that the application of deep learning to biological image data can overcome the pitfalls associated with conventional machine learning classifiers. Using a deep convolutional neural network (DeepLoc) to analyze yeast cell images, we show improved performance over traditional approaches in the automated classification of protein subcellular localization...
April 18, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28373240/engineering-bacterial-thiosulfate-and-tetrathionate-sensors-for-detecting-gut-inflammation
#17
Kristina N-M Daeffler, Jeffrey D Galley, Ravi U Sheth, Laura C Ortiz-Velez, Christopher O Bibb, Noah F Shroyer, Robert A Britton, Jeffrey J Tabor
There is a groundswell of interest in using genetically engineered sensor bacteria to study gut microbiota pathways, and diagnose or treat associated diseases. Here, we computationally identify the first biological thiosulfate sensor and an improved tetrathionate sensor, both two-component systems from marine Shewanella species, and validate them in laboratory Escherichia coli Then, we port these sensors into a gut-adapted probiotic E. coli strain, and develop a method based upon oral gavage and flow cytometry of colon and fecal samples to demonstrate that colon inflammation (colitis) activates the thiosulfate sensor in mice harboring native gut microbiota...
April 3, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28348067/proteomics-and-integrative-omic-approaches-for-understanding-host-pathogen-interactions-and-infectious-diseases
#18
REVIEW
Pierre M Jean Beltran, Joel D Federspiel, Xinlei Sheng, Ileana M Cristea
Organisms are constantly exposed to microbial pathogens in their environments. When a pathogen meets its host, a series of intricate intracellular interactions shape the outcome of the infection. The understanding of these host-pathogen interactions is crucial for the development of treatments and preventive measures against infectious diseases. Over the past decade, proteomic approaches have become prime contributors to the discovery and understanding of host-pathogen interactions that represent anti- and pro-pathogenic cellular responses...
March 27, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28320772/mechanism-for-microbial-population-collapse-in-a-fluctuating-resource-environment
#19
Serdar Turkarslan, Arjun V Raman, Anne W Thompson, Christina E Arens, Mark A Gillespie, Frederick von Netzer, Kristina L Hillesland, Sergey Stolyar, Adrian López García de Lomana, David J Reiss, Drew Gorman-Lewis, Grant M Zane, Jeffrey A Ranish, Judy D Wall, David A Stahl, Nitin S Baliga
Managing trade-offs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. To investigate this hypothesis, we imposed a fluctuating environment that required the sulfate-reducer Desulfovibrio vulgaris to undergo repeated ecologically relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen-consuming Methanococcus maripaludis Strikingly, the microbial community became progressively less proficient at restoring the environmentally relevant physiological state after each perturbation and most cultures collapsed within 3-7 shifts...
March 20, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28302863/transfer-of-dysbiotic-gut-microbiota-has-beneficial-effects-on-host-liver-metabolism
#20
Simon Nicolas, Vincent Blasco-Baque, Audren Fournel, Jerome Gilleron, Pascale Klopp, Aurelie Waget, Franck Ceppo, Alysson Marlin, Roshan Padmanabhan, Jason S Iacovoni, François Tercé, Patrice D Cani, Jean-François Tanti, Remy Burcelin, Claude Knauf, Mireille Cormont, Matteo Serino
Gut microbiota dysbiosis has been implicated in a variety of systemic disorders, notably metabolic diseases including obesity and impaired liver function, but the underlying mechanisms are uncertain. To investigate this question, we transferred caecal microbiota from either obese or lean mice to antibiotic-free, conventional wild-type mice. We found that transferring obese-mouse gut microbiota to mice on normal chow (NC) acutely reduces markers of hepatic gluconeogenesis with decreased hepatic PEPCK activity, compared to non-inoculated mice, a phenotypic trait blunted in conventional NOD2 KO mice...
March 16, 2017: Molecular Systems Biology
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