Cellular network

Microbiota regulate intestinal physiology by modifying host gene expression along the length of the intestine, but the underlying regulatory mechanisms remain unresolved. Transcriptional specificity occurs through interactions between transcription factors (TFs) and cis-regulatory regions (CRRs) characterized by nucleosome-depleted accessible chromatin. We profiled transcriptome and accessible chromatin landscapes in intestinal epithelial cells (IECs) from mice reared in the presence or absence of microbiota...

Theoretical ideas have played a profound role in the development of idiotypic network theory. Mathematical models can help in the precise translation of speculative ideas into quantitative predictions. They can also help establish general principles and frameworks for thinking. Using the idea of shape space, criteria were introduced for evaluating the completeness and overlap in the antibody repertoire. Thinking about the distribution of clones in shape space naturally leads to considerations of stability and controllability...

Tissue-resident macrophages are highly heterogeneous in terms of their functions and phenotypes as a consequence of adaptation to different tissue environments. Local tissue-derived signals are thought to control functional polarization of resident macrophages; however, the identity of these signals remains largely unknown. It is also unknown whether functional heterogeneity is a result of irreversible lineage-specific differentiation or a consequence of continuous but reversible induction of diverse functional programs...

Quantitative views of cellular functions require precise measures of rates of biomolecule production, especially proteins-the direct effectors of biological processes. Here, we present a genome-wide approach, based on ribosome profiling, for measuring absolute protein synthesis rates. The resultant E. coli data set transforms our understanding of the extent to which protein synthesis is precisely controlled to optimize function and efficiency. Members of multiprotein complexes are made in precise proportion to their stoichiometry, whereas components of functional modules are produced differentially according to their hierarchical role...

To understand regulatory systems, it would be useful to uniformly determine how different components contribute to the expression of all other genes. We therefore monitored mRNA expression genome-wide, for individual deletions of one-quarter of yeast genes, focusing on (putative) regulators. The resulting genetic perturbation signatures reflect many different properties. These include the architecture of protein complexes and pathways, identification of expression changes compatible with viability, and the varying responsiveness to genetic perturbation...

BACKGROUND: In multicellular organisms, an intercellular signaling network communicates information from the environment or distant tissues to defined target cells. Intercellular signaling (mostly mediated by hormones) can affect the metabolic state and the gene expression program of target cells, thereby coordinating development, homeostasis of the organism and its reactions to external stimuli. Knowledge of the components of the intercellular signaling (specifically: the endocrine) network and their relations is an important, though so far a largely neglected part of systems biology...

Axon regeneration after damage is widespread in the animal kingdom, and the nematode Caenorhabditis elegans has recently emerged as a tractable model in which to study the genetics and cell biology of axon regrowth in vivo. A key early step in axon regrowth is the conversion of part of a mature axon shaft into a growth cone-like structure, involving coordinated alterations in the microtubule, actin, and neurofilament systems. Recent attention has focused on microtubule dynamics as a determinant of axon-regrowth ability in several organisms...

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We describe a mathematical model and Monte Carlo (MC) simulation of viral evolution during acute infection. We consider both synchronous and asynchronous processes of viral infection of new target cells. The model enables an assessment of the expected sequence diversity in new HIV-1 infections originating from a single transmitted viral strain, estimation of the most recent common ancestor (MRCA) of the transmitted viral lineage, and estimation of the time to coalesce back to the MRCA. We also calculate the probability of the MRCA being the transmitted virus or an evolved variant...

This article introduces generalization of the action potential spreading model which considers generation of the action potential in each segment of the nerve fiber. Behavior of the impulse signal waveform during the propagation process was analyzed. A mechanism of distributed generation of the charge in nerve fiber results in decrease of phase velocity of signal spreading rate. Amplitude of the action potential decreases and pulse width increases in the action potential propagation process.

From the cell cytoskeleton to connective tissues, fibrous networks are ubiquitous in metazoan life as the key promoters of mechanical strength, support and integrity. In recent decades, the application of physics to biological systems has made substantial strides in elucidating the striking mechanical phenomena observed in such networks, explaining strain stiffening, power law rheology and cytoskeletal fluidisation - all key to the biological function of individual cells and tissues. In this review we focus on the current progress in the field, with a primer into the basic physics of individual filaments and the networks they form...