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Marchetti M.C.,Syracuse Biomaterials Institute | Joanny J.F.,University Pierre and Marie Curie | Ramaswamy S.,Indian Institute of Science | Liverpool T.B.,University of Bristol | And 5 more authors.
Reviews of Modern Physics | Year: 2013

This review summarizes theoretical progress in the field of active matter, placing it in the context of recent experiments. This approach offers a unified framework for the mechanical and statistical properties of living matter: biofilaments and molecular motors in vitro or in vivo, collections of motile microorganisms, animal flocks, and chemical or mechanical imitations. A major goal of this review is to integrate several approaches proposed in the literature, from semimicroscopic to phenomenological. In particular, first considered are "dry" systems, defined as those where momentum is not conserved due to friction with a substrate or an embedding porous medium. The differences and similarities between two types of orientationally ordered states, the nematic and the polar, are clarified. Next, the active hydrodynamics of suspensions or "wet" systems is discussed and the relation with and difference from the dry case, as well as various large-scale instabilities of these nonequilibrium states of matter, are highlighted. Further highlighted are various large-scale instabilities of these nonequilibrium states of matter. Various semimicroscopic derivations of the continuum theory are discussed and connected, highlighting the unifying and generic nature of the continuum model. Throughout the review, the experimental relevance of these theories for describing bacterial swarms and suspensions, the cytoskeleton of living cells, and vibrated granular material is discussed. Promising extensions toward greater realism in specific contexts from cell biology to animal behavior are suggested, and remarks are given on some exotic active-matter analogs. Last, the outlook for a quantitative understanding of active matter, through the interplay of detailed theory with controlled experiments on simplified systems, with living or artificial constituents, is summarized. © 2013 American Physical Society. Source


Krishnan Y.,National Center for Biological science | Bathe M.,Massachusetts Institute of Technology
Trends in Cell Biology | Year: 2012

Recent advances in nucleic acid sequencing, structural, and computational technologies have resulted in dramatic progress in our understanding of nucleic acid structure and function in the cell. This knowledge, together with the predictable base-pairing of nucleic acids and powerful synthesis and expression capabilities now offers the unique ability to program nucleic acids to form precise 3D architectures with diverse applications in synthetic and cell biology. The unique modularity of structural motifs that include aptamers, DNAzymes, and ribozymes, together with their well-defined construction rules, enables the synthesis of functional higher-order nucleic acid complexes from these subcomponents. As we illustrate here, these highly programmable, smart complexes are increasingly enabling researchers to probe and program the cell in a sophisticated manner that moves well beyond the use of nucleic acids for conventional genetic manipulation alone. © 2012 Elsevier Ltd. Source


Saha S.,National Center for Biological science
Nature Nanotechnology | Year: 2015

The concentration of chloride ions in the cytoplasm and subcellular organelles of living cells spans a wide range (5–130 mM), and is tightly regulated by intracellular chloride channels or transporters. Chloride-sensitive protein reporters have been used to study the role of these chloride regulators, but they are limited to a small range of chloride concentrations and are pH-sensitive. Here, we show that a DNA nanodevice can precisely measure the activity and location of subcellular chloride channels and transporters in living cells in a pH-independent manner. The DNA nanodevice, called Clensor, is composed of sensing, normalizing and targeting modules, and is designed to localize within organelles along the endolysosomal pathway. It allows fluorescent, ratiometric sensing of chloride ions across the entire physiological regime. We used Clensor to quantitate the resting chloride concentration in the lumen of acidic organelles in Drosophila melanogaster. We showed that lumenal lysosomal chloride, which is implicated in various lysosomal storage diseases, is regulated by the intracellular chloride transporter DmClC-b. © 2015 Nature Publishing Group Source


Howes M.T.,University of Queensland | Mayor S.,National Center for Biological science | Parton R.G.,University of Queensland
Current Opinion in Cell Biology | Year: 2010

Eukaryotic cells deftly coordinate an array of endocytic pathways beyond the classical clathrin-mediated endocytic route. Although the existence of clathrin-independent endocytic pathways has been accepted for some time, only recently have tools been developed that specifically delineate their fine details, including molecular composition and ultrastructural morphology. Identification of the salient features of distinct pathways has concomitantly attributed them with specific roles during important cellular processes. Insight from model organisms confirms these roles and suggests maintenance of crucially adapted functions across species. Among other roles, clathrin-independent endocytosis has now been linked to plasma membrane repair, cellular spreading, cellular polarization, and modulation of intercellular signaling. The field is now primed to identify how these pathways function within physiologically relevant environments. © 2010 Elsevier Ltd. Source


Mayor S.,National Center for Biological science
Cell | Year: 2011

Caveolae are protein-driven membrane invaginations that regulate both the physical and chemical composition of the plasma membrane. Sinha et al. (2011) now show that caveolae are membrane reservoirs that are used to rapidly buffer against changes in membrane tension. © 2011 Elsevier Inc. Source

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