Showing papers in "Cell in 2016"

TL;DR: Data is reviewed supporting the diverse functional roles carried out by a major class of bacterial metabolites, the short-chain fatty acids (SCFAs), which affect various physiological processes and may contribute to health and disease.

TL;DR: Core stress-signaling pathways involve protein kinases related to the yeast SNF1 and mammalian AMPK, suggesting that stress signaling in plants evolved from energy sensing.

TL;DR: It is found that overall high mutational loads associate with improved survival, and tumors from responding patients are enriched for mutations in the DNA repair gene BRCA2, suggesting that attenuating the biological processes that underlie IPRES may improve anti-PD-1 response in melanoma and other cancer types.

TL;DR: This Review focuses on the context of tumor cells and their microenvironment, but similar results and challenges apply to all patho/physiological systems in which EV-mediated communication is proposed to take place.

TL;DR: It is reported herein that gut microbiota are required for motor deficits, microglia activation, and αSyn pathology, and suggested that alterations in the human microbiome represent a risk factor for PD.

TL;DR: It is concluded that transcript levels by themselves are not sufficient to predict protein levels in many scenarios and to thus explain genotype-phenotype relationships and that high-quality data quantifying different levels of gene expression are indispensable for the complete understanding of biological processes.

TL;DR: 3D culture technology allow embryonic and adult mammalian stem cells to exhibit their remarkable self-organizing properties, and the resulting organoids reflect key structural and functional properties of organs such as kidney, lung, gut, brain and retina, and hold promise to predict drug response in a personalized fashion.

TL;DR: Dietary fiber deprivation, together with a fiber-deprived, mucus-eroding microbiota, promotes greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium.

TL;DR: Evaluating mechanisms of mitochondrial function during tumorigenesis will be critical for the next generation of cancer therapeutics as multiple aspects of mitochondrial biology beyond bioenergetics support transformation.

TL;DR: The complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas were defined from The Cancer Genome Atlas and molecular profiles were used to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease.

TL;DR: A miniaturized spinning bioreactor (SpinΩ) is developed to generate forebrain-specific organoids from human iPSCs that recapitulate key features of human cortical development, including progenitor zone organization, neurogenesis, gene expression, and, notably, a distinct human-specific outer radial glia cell layer.

TL;DR: It is reported how cancer-driven alterations identified in 11,289 tumors from 29 tissues can be mapped onto 1,001 molecularly annotated human cancer cell lines and correlated with sensitivity to 265 drugs.

TL;DR: It is often presented as common knowledge that bacteria outnumber human cells by a ratio of at least 10:1, but it is found that the ratio is much closer to 1:1.

TL;DR: It is shown that subcompartments within the nucleolus represent distinct, coexisting liquid phases that may facilitate sequential RNA processing reactions in a variety of RNP bodies, and suggested that phase separation can give rise to multilayered liquids.

TL;DR: It is demonstrated that upon lipopolysaccharide stimulation, macrophages shift from producing ATP by oxidative phosphorylation to glycolysis while also increasing succinate levels, and repurpose mitochondria from ATP synthesis to ROS production in order to promote a pro-inflammatory state.

TL;DR: Gut microbes, through generation of trimethylamine N-oxide (TMAO), directly contribute to platelet hyperreactivity and enhanced thrombosis potential, revealing a previously unrecognized mechanistic link between specific dietary nutrients, gut microbes, platelet function, and thromBosis risk.

TL;DR: Evidence supporting a long, complex cellular phase consisting of feedback and feedforward responses of astrocytes, microglia, and vasculature is reviewed.

TL;DR: It is suggested that stress granules contain a stable core structure surrounded by a dynamic shell with assembly, disassembly, and transitions between the core and shell modulated by numerous protein and RNA remodeling complexes.

TL;DR: Perturb-seq as discussed by the authors combines single-cell RNA sequencing and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool.

TL;DR: A pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome is reported, which detect clinically relevant concentrations of Zika virus sequences and demonstrate specificity against closely related Dengue virus sequences.

TL;DR: DNA affinity purification sequencing (DAP-seq) is described, a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs and determined that >75% of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape.

TL;DR: A genome-wide association analysis in the UK Biobank and INTERVAL studies is performed, providing evidence of shared genetic pathways linking blood cell indices with complex pathologies, including autoimmune diseases, schizophrenia, and coronary heart disease and evidence suggesting previously reported population associations betweenBlood cell indices and cardiovascular disease may be non-causal.

TL;DR: This work provides a systematic methodology for achieving comprehensive molecular classification of neurons, identifies novel neuronal types, and uncovers transcriptional differences that distinguish types within a class.

TL;DR: Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

TL;DR: Nucleosome spacing inferred from cfDNA in healthy individuals correlates most strongly with epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA.

TL;DR: The data suggest that, by altering cristae morphology, fusion in TM cells configures electron transport chain (ETC) complex associations favoring oxidative phosphorylation (OXPHOS) and FAO, while fission in TE cells leads to cristsae expansion, reducing ETC efficiency and promoting aerobic glycolysis.

TL;DR: It is demonstrated that patients identified as non-responders to anti-CTLA-4 (ipilimumab) have tumors with genomic defects in IFN-γ pathway genes, demonstrating the importance of tumor genomic data, especially IFn-γ related genes, as prognostic information for patients selected to receive treatment with immune checkpoint therapy.

TL;DR: Elevating L-arginine levels induced global metabolic changes including a shift from glycolysis to oxidative phosphorylation in activated T cells and promoted the generation of central memory-like cells endowed with higher survival capacity and, in a mouse model, anti-tumor activity.

TL;DR: How new technologies can enable metabolic engineering to be scaled up to the industrial level, either by cutting off the lines of control for endogenous metabolism or by infiltrating the system with disruptive, heterologous pathways that overcome cellular regulation is discussed.

TL;DR: The current state of mass cytometry is reviewed, providing an overview of the instrumentation, its present capabilities, and methods of data analysis, as well as thoughts on future developments and applications.