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Cell Systems

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https://www.readbyqxmd.com/read/28527885/maintenance-of-atp-homeostasis-triggers-metabolic-shifts-in-gas-fermenting-acetogens
#1
Kaspar Valgepea, Renato de Souza Pinto Lemgruber, Kieran Meaghan, Robin William Palfreyman, Tanus Abdalla, Björn Daniel Heijstra, James Bruce Behrendorff, Ryan Tappel, Michael Köpke, Séan Dennis Simpson, Lars Keld Nielsen, Esteban Marcellin
Acetogens are promising cell factories for producing fuels and chemicals from waste feedstocks via gas fermentation, but quantitative characterization of carbon, energy, and redox metabolism is required to guide their rational metabolic engineering. Here, we explore acetogen gas fermentation using physiological, metabolomics, and transcriptomics data for Clostridium autoethanogenum steady-state chemostat cultures grown on syngas at various gas-liquid mass transfer rates. We observe that C. autoethanogenum shifts from acetate to ethanol production to maintain ATP homeostasis at higher biomass concentrations but reaches a limit at a molar acetate/ethanol ratio of ∼1...
May 16, 2017: Cell Systems
https://www.readbyqxmd.com/read/28501650/prober-provides-a-general-toolkit-for-analyzing-sequencing-based-toeprinting-assays
#2
Bo Li, Akshay Tambe, Sharon Aviran, Lior Pachter
A number of sequencing-based transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and RNA modification. Although these assays survey a diverse set of epitranscriptomic marks, we use the term toeprinting assays since they share methodological similarities. Their interpretation is predicated on addressing a similar computational challenge: how to learn isoform-specific chemical modification profiles in the face of complex read multi-mapping...
May 9, 2017: Cell Systems
https://www.readbyqxmd.com/read/28365151/a-cell-surface-membrane-protein-signature-for-glioblastoma
#3
Dhimankrishna Ghosh, Cory C Funk, Juan Caballero, Nameeta Shah, Katherine Rouleau, John C Earls, Liliana Soroceanu, Greg Foltz, Charles S Cobbs, Nathan D Price, Leroy Hood
We present a systems strategy that facilitated the development of a molecular signature for glioblastoma (GBM), composed of 33 cell-surface transmembrane proteins. This molecular signature, GBMSig, was developed through the integration of cell-surface proteomics and transcriptomics from patient tumors in the REMBRANDT (n = 228) and TCGA datasets (n = 547) and can separate GBM patients from control individuals with a Matthew's correlation coefficient value of 0.87 in a lock-down test. Functionally, 17/33 GBMSig proteins are associated with transforming growth factor β signaling pathways, including CD47, SLC16A1, HMOX1, and MRC2...
March 28, 2017: Cell Systems
https://www.readbyqxmd.com/read/28365149/absolute-quantification-of-protein-and-mrna-abundances-demonstrate-variability-in-gene-specific-translation-efficiency-in-yeast
#4
Petri-Jaan Lahtvee, Benjamín J Sánchez, Agata Smialowska, Sergo Kasvandik, Ibrahim E Elsemman, Francesco Gatto, Jens Nielsen
Protein synthesis is the most energy-consuming process in a proliferating cell, and understanding what controls protein abundances represents a key question in biology and biotechnology. We quantified absolute abundances of 5,354 mRNAs and 2,198 proteins in Saccharomyces cerevisiae under ten environmental conditions and protein turnover for 1,384 proteins under a reference condition. The overall correlation between mRNA and protein abundances across all conditions was low (0.46), but for differentially expressed proteins (n = 202), the median mRNA-protein correlation was 0...
March 27, 2017: Cell Systems
https://www.readbyqxmd.com/read/28330614/a-predictive-3d-multi-scale-model-of-biliary-fluid-dynamics-in-the-liver-lobule
#5
Kirstin Meyer, Oleksandr Ostrenko, Georgios Bourantas, Hernan Morales-Navarrete, Natalie Porat-Shliom, Fabian Segovia-Miranda, Hidenori Nonaka, Ali Ghaemi, Jean-Marc Verbavatz, Lutz Brusch, Ivo Sbalzarini, Yannis Kalaidzidis, Roberto Weigert, Marino Zerial
Bile, the central metabolic product of the liver, is transported by the bile canaliculi network. The impairment of bile flow in cholestatic liver diseases has urged a demand for insights into its regulation. Here, we developed a predictive 3D multi-scale model that simulates fluid dynamic properties successively from the subcellular to the tissue level. The model integrates the structure of the bile canalicular network in the mouse liver lobule, as determined by high-resolution confocal and serial block-face scanning electron microscopy, with measurements of bile transport by intravital microscopy...
March 15, 2017: Cell Systems
https://www.readbyqxmd.com/read/28448797/the-single-cell-yin-and-yang-of-live-imaging-and-transcriptomics
#6
Michael Tsabar, Galit Lahav
A new approach to monitoring both signaling over time and a global gene expression profile from the same cell establishes a functional role for NF-κB dynamics in transcription.
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28448796/reconciling-epigenetic-memory-and-transcriptional-responsiveness
#7
Amanda G Fisher, Michael P H Stumpf, Matthias Merkenschlager
The molecular basis of cellular memory is important but poorly understood. Using estimates of histone dynamics, Martin Howard and colleagues construct a mathematical model that helps to explain both the stability and flexibility of Polycomb-mediated gene regulation in cellular memory.
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28448795/what-is-the-role-of-circuit-design-in-the-advancement-of-synthetic-biology-part-1
#8
(no author information available yet)
Enabling real-world applications and therapeutics.
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28448794/principles-of-systems-biology-no-16
#9
(no author information available yet)
This month: how T cells signal in binary (Vale), advances in interaction mapping (Greenleaf/Sabatini/Ahroni/Bodenmiller), single-cell RNA-seq (Suvà/Ramanathan/Marioni), and more (Hilvert/Wong/Chisholm).
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28448793/to-circuitry-and-beyond
#10
EDITORIAL
Ernesto Andrianantoandro
No abstract text is available yet for this article.
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28396000/measuring-signaling-and-rna-seq-in-the-same-cell-links-gene-expression-to-dynamic-patterns-of-nf-%C3%AE%C2%BAb-activation
#11
Keara Lane, David Van Valen, Mialy M DeFelice, Derek N Macklin, Takamasa Kudo, Ariel Jaimovich, Ambrose Carr, Tobias Meyer, Dana Pe'er, Stéphane C Boutet, Markus W Covert
Signaling proteins display remarkable cell-to-cell heterogeneity in their dynamic responses to stimuli, but the consequences of this heterogeneity remain largely unknown. For instance, the contribution of the dynamics of the innate immune transcription factor nuclear factor κB (NF-κB) to gene expression output is disputed. Here we explore these questions by integrating live-cell imaging approaches with single-cell sequencing technologies. We used this approach to measure both the dynamics of lipopolysaccharide-induced NF-κB activation and the global transcriptional response in the same individual cell...
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28365152/dynamic-gene-regulatory-networks-of-human-myeloid-differentiation
#12
Ricardo N Ramirez, Nicole C El-Ali, Mikayla Anne Mager, Dana Wyman, Ana Conesa, Ali Mortazavi
The reconstruction of gene regulatory networks underlying cell differentiation from high-throughput gene expression and chromatin data remains a challenge. Here, we derive dynamic gene regulatory networks for human myeloid differentiation using a 5-day time series of RNA-seq and ATAC-seq data. We profile HL-60 promyelocytes differentiating into macrophages, neutrophils, monocytes, and monocyte-derived macrophages. We find a rapid response in the expression of key transcription factors and lineage markers that only regulate a subset of their targets at a given time, which is followed by chromatin accessibility changes that occur later along with further gene expression changes...
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28365150/environment-tunes-propagation-of-cell-to-cell-variation-in-the-human-macrophage-gene-network
#13
Andrew J Martins, Manikandan Narayanan, Thorsten Prüstel, Bethany Fixsen, Kyemyung Park, Rachel A Gottschalk, Yong Lu, Cynthia Andrews-Pfannkoch, William W Lau, Katherine V Wendelsdorf, John S Tsang
Cell-to-cell variation in gene expression and the propagation of such variation (PoV or "noise propagation") from one gene to another in the gene network, as reflected by gene-gene correlation across single cells, are commonly observed in single-cell transcriptomic studies and can shape the phenotypic diversity of cell populations. While gene network "rewiring" is known to accompany cellular adaptation to different environments, how PoV changes between environments and its underlying regulatory mechanisms are less understood...
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28342718/noisy-response-to-antibiotic-stress-predicts-subsequent-single-cell-survival-in-an-acidic-environment
#14
Karin Mitosch, Georg Rieckh, Tobias Bollenbach
Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to "cross-protect" bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid...
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28342717/slow-chromatin-dynamics-allow-polycomb-target-genes-to-filter-fluctuations-in-transcription-factor-activity
#15
Scott Berry, Caroline Dean, Martin Howard
Genes targeted by Polycomb repressive complex 2 (PRC2) are regulated in cis by chromatin modifications and also in trans by diffusible regulators such as transcription factors. Here, we introduce a mathematical model in which transcription directly antagonizes Polycomb silencing, thereby linking these cis- and trans-regulatory inputs to gene expression. The model is parameterized by recent experimental data showing that PRC2-mediated repressive chromatin modifications accumulate extremely slowly. The model generates self-perpetuating, bistable active and repressed chromatin states that persist through DNA replication, thereby ensuring high-fidelity transmission of the current chromatin state...
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28330616/systematic-analysis-of-human-protein-phosphatase-interactions-and-dynamics
#16
Leena Yadav, Fitsum Tamene, Helka Göös, Audrey van Drogen, Riku Katainen, Ruedi Aebersold, Matthias Gstaiger, Markku Varjosalo
Coordinated activities of protein kinases and phosphatases ensure phosphorylation homeostasis, which, when perturbed, can instigate diseases, including cancer. Yet, in contrast to kinases, much less is known about protein phosphatase functions and their interactions and complexes. Here, we used quantitative affinity proteomics to assay protein-protein interactions for 54 phosphatases distributed across the three major protein phosphatase families, with additional analysis of their 12 co-factors. We identified 838 high-confidence interactions, of which 631, to our knowledge, have not been reported before...
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28330615/differential-aging-analysis-in-human-cerebral-cortex-identifies-variants-in-tmem106b-and-grn-that-regulate-aging-phenotypes
#17
Herve Rhinn, Asa Abeliovich
Human age-associated traits, such as cognitive decline, can be highly variable across the population, with some individuals exhibiting traits that are not expected at a given chronological age. Here we present differential aging (Δ-aging), an unbiased method that quantifies individual variability in age-associated phenotypes within a tissue of interest, and apply this approach to the analysis of existing transcriptome-wide cerebral cortex gene expression data from several cohorts totaling 1,904 autopsied human brain samples...
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28334575/cell-factory-engineering
#18
REVIEW
Anne Mathilde Davy, Helene Faustrup Kildegaard, Mikael Rørdam Andersen
Rational approaches to modifying cells to make molecules of interest are of substantial economic and scientific interest. Most of these efforts aim at the production of native metabolites, expression of heterologous biosynthetic pathways, or protein expression. Reviews of these topics have largely focused on individual strategies or cell types, but collectively they fall under the broad umbrella of a growing field known as cell factory engineering. Here we condense >130 reviews and key studies in the art into a meta-review of cell factory engineering...
March 22, 2017: Cell Systems
https://www.readbyqxmd.com/read/28334574/microscopy-meet-big-data
#19
Antony Orth, Diane Schaak, Ethan Schonbrun
The analysis of massive microscopy datasets using deep neural networks provides an alternative to molecular labeling to characterize cellular states.
March 22, 2017: Cell Systems
https://www.readbyqxmd.com/read/28334573/what-is-your-conceptual-definition-of-cell-type-in-the-context-of-a-mature-organism
#20
(no author information available yet)
No abstract text is available yet for this article.
March 22, 2017: Cell Systems
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