Feroz M. Hameed

National University of Singapore

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G. V. Shivashankar

ETH Zurich

Michael P. Sheetz

National University of Singapore

Gautam V. Soni

Raman Research Institute

Madan Rao

National Centre for Biological Sciences

Bo Yang

National University of Singapore

Nisha M. Ramdas

National University of Singapore

A. K. Raychaudhuri

Central Glass and Ceramic Research Institute

Boon Chuan Low

National University of Singapore

Shelly Kaushik

University of California, San Francisco

Haguy Wolfenson

Technion – Israel Institute of Technology

Cooperative Institutions

National University of Singapore

National Centre for Biological Sciences

Tata Institute of Fundamental Research

Raman Research Institute

S.N. Bose National Centre for Basic Sciences

Indian Institute of Science Bangalore

Centre National de la Recherche Scientifique

Institut Curie

Sorbonne Université

Sichuan University

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Dynamics of Passive and Active Particles in the Cell Nucleus

PLoS ONE (2012)

Feroz M. Hameed Madan Rao G. V. Shivashankar

Inspite of being embedded in a dense meshwork of nuclear chromatin, gene loci and large nuclear components are highly dynamic at C. To understand this apparent unfettered movement in an overdense environment, we study the dynamics of a passive micron size bead in live cell nuclei at two different temperatures ( and C) with and without external force. In the absence of a force, the beads are caged over large time scales. On application of a threshold uniaxial force (about 10 pN), the passive beads appear to hop between cages; this large scale movement is absent upon ATP-depletion, inhibition of chromatin remodeling enzymes and RNAi of lamin B1 proteins. Our results suggest that the nucleus behaves like an active solid with a finite yield stress when probed at a micron scale. Spatial analysis of histone fluorescence anisotropy (a measure of local chromatin compaction, defined as the volume fraction of tightly bound chromatin) shows that the bead movement correlates with regions of low chromatin compaction. This suggests that the physical mechanism of the observed yielding is the active opening of free-volume in the nuclear solid via chromatin remodeling. Enriched transcription sites at C also show caging in the absence of the applied force and directed movement beyond a yield stress, in striking contrast with the large scale movement of transcription loci at C in the absence of a force. This suggests that at physiological temperatures, the loci behave as active particles which remodel the nuclear mesh and reduce the local yield stress.

10.1371/journal.pone.0045843

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Citations (52)

Distinct levels in the nanoscale organization of DNA-histone complex revealed by its mechanical unfolding

Applied Physics Letters (2007)

Gautam V. Soni Loveleen K. Brar Feroz M. Hameed A. K. Raychaudhuri G. V. Shivashankar

Mechanical unfolding of nanoscale DNA-histone complex, using an atomic force microscope, shows a stepwise disassembly of histones from the nucleosome. A quantitative analysis of the rupture jump statistics and the length released per jump reveals insights into the possible histone contacts within the octamer complex. The measured ruptures correlate with the breakage of multiple contacts that stabilize the histone octamer. These results provide a mechanistic basis by which stepwise disassembly of histone proteins may result from an external force exerted by the adenosinetriphosphate (ATP) dependent chromatin remodeling machines to access regulatory sites on DNA.

Histone octamer

10.1063/1.2728031

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Citations (4)

Integrin adhesion drives the emergent polarization of active cytoskeletal stresses to pattern cell delamination

Proceedings of the National Academy of Sciences (2011)

C. Meghana Nisha M. Ramdas Feroz M. Hameed Madan Rao G. V. Shivashankar

Tissue patterning relies on cellular reorganization through the interplay between signaling pathways and mechanical stresses. Their integration and spatiotemporal coordination remain poorly understood. Here we investigate the mechanisms driving the dynamics of cell delamination, diversely deployed to extrude dead cells or specify distinct cell fates. We show that a local mechanical stimulus (subcellular laser perturbation) releases cellular prestress and triggers cell delamination in the amnioserosa during Drosophila dorsal closure, which, like spontaneous delamination, results in the rearrangement of nearest neighbors around the delaminating cell into a rosette. We demonstrate that a sequence of “emergent cytoskeletal polarities” in the nearest neighbors (directed myosin flows, lamellipodial growth, polarized actomyosin collars, microtubule asters), triggered by the mechanical stimulus and dependent on integrin adhesion, generate active stresses that drive delamination. We interpret these patterns in the language of active gels as asters formed by active force dipoles involving surface and body stresses generated by each cell and liken delamination to mechanical yielding that ensues when these stresses exceed a threshold. We suggest that differential contributions of adhesion, cytoskeletal, and external stresses must underlie differences in spatial pattern.

Cell polarity

Stimulus (psychology)

10.1073/pnas.1018652108

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Citations (37)

Probing structural stability of chromatin assembly sorted from living cells

Biochemical and Biophysical Research Communications (2009)

Feroz M. Hameed Gautam V. Soni H. Krishnamurthy G. V. Shivashankar

10.1016/j.bbrc.2009.05.086

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Citations (7)

Cells Sense Rigidity of their Micro-Environment by a Unique Force-Sensing Displacement Cassette

Biophysical Journal (2012)

Feroz M. Hameed Michael P. Sheetz

Rigidity (electromagnetism)

Pillar

10.1016/j.bpj.2011.11.3819

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Development of an optical tweezer combined with micromanipulation for DNA and protein nanobioscience

Current Science (2002)

Gautam V. Soni Feroz M. Hameed T. Roopa G. V. Shivashankar

We have constructed an optical tweezer using two lasers (830 nm and 1064 nm) combined with micropipette manipulation having sub-pN force sensitivity. Sample position is controlled within nanometer accuracy using XYZ piezo-electric stage. The position of the bead in the trap is monitored using single particle laser backscattering technique. The instrument is automated to operate in constant force, constant velocity or constant position measurement. We present data on single DNA force-extension, dynamics of DNA integration on membranes and optically trapped bead-cell interactions. A quantitative analysis of single DNA and protein mechanics, assembly and dynamics opens up new possibilities in nanobioscience.

Position (finance)

Constant (computer programming)

Bead

Nanometre

Source

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Citations (19)

Mechanosensing Controlled Directly by Tyrosine Kinases

Nano Letters (2016)

Bo Yang Zi Zhao Lieu Haguy Wolfenson Feroz M. Hameed Alexander D. Bershadsky

To understand how cells form tissues, we need to understand how the tyrosine kinases are involved in controlling cell mechanics, whether they act directly as parts of mechanosensing machines or indirectly. Cells test the critical parameter of matrix rigidity by locally contracting ("pinching") matrices and measuring forces, and the depletion of contractile units causes transformation. We report here that knocking down the receptor tyrosine kinases (RTKs), AXL, and ROR2, alters rigidity sensing and increases the magnitude or duration of local contraction events, respectively. Phospho-AXL and ROR2 localize to contraction units and bind major contractile components, tropomyosin 2.1 (AXL), myosin IIA (AXL), and filamin A (ROR2). At a molecular level, phosphorylated AXL localizes to active myosin filaments and phosphorylates tropomyosin at a tyrosine critical for adhesion formation. ROR2 binding of ligand is unnecessary, but binding filamin A helps function. Thus, AXL and ROR2 alter rigidity sensing and consequently morphogenic processes by directly controlling local mechanosensory contractions without ligands.

Tropomyosin

10.1021/acs.nanolett.6b02995

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Citations (83)

Micropillar displacements by cell traction forces are mechanically correlated with nuclear dynamics

Biochemical and Biophysical Research Communications (2015)

Qingsen Li Ekta Makhija Feroz M. Hameed G. V. Shivashankar

10.1016/j.bbrc.2015.04.041

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Cyclic stretching of soft substrates induces spreading and growth

Nature Communications (2015)

Yidan Cui Feroz M. Hameed Bo Yang Kyunghee Lee Catherine Pan

Abstract In the body, soft tissues often undergo cycles of stretching and relaxation that may affect cell behaviour without changing matrix rigidity. To determine whether transient forces can substitute for a rigid matrix, we stretched soft pillar arrays. Surprisingly, 1–5% cyclic stretching over a frequency range of 0.01–10 Hz caused spreading and stress fibre formation (optimum 0.1 Hz) that persisted after 4 h of stretching. Similarly, stretching increased cell growth rates on soft pillars comparative to rigid substrates. Of possible factors linked to fibroblast growth, MRTF-A (myocardin-related transcription factor-A) moved to the nucleus in 2 h of cyclic stretching and reversed on cessation; but YAP (Yes-associated protein) moved much later. Knockdown of either MRTF-A or YAP blocked stretch-dependent growth. Thus, we suggest that the repeated pulling from a soft matrix can substitute for a stiff matrix in stimulating spreading, stress fibre formation and growth.

Stress relaxation

Pillar

Matrix (chemical analysis)

10.1038/ncomms7333

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Citations (283)

Concerted modulation of paxillin dynamics at focal adhesions by deleted in liver cancer‐1 and focal adhesion kinase during early cell spreading

Cytoskeleton (2014)

Shelly Kaushik Archna Ravi Feroz M. Hameed Boon Chuan Low

Deleted in Liver Cancer‐1 (DLC1) is a RhoGTPase‐activating protein (GAP) and a tumor suppressor often downregulated in cancers. It is localized to the focal adhesions (FAs) and its absence leads to enhanced cell migration, invasion, and metastasis. Although DLC1 interacts with focal adhesion kinase (FAK), talin, and tensin, its role in focal adhesions dynamics remains unclear. We examined the effect of DLC1 in Human Foreskin Fibroblasts and determined its localization, dynamics and impact on paxillin by Fluorescence Recovery After Photobleaching at both nascent and mature focal adhesions. During early cell spreading, DLC1 is preferentially localized at the inner/mature adhesions whereas phosphorylated paxillin occupies the outer/nascent FAs. In addition, DLC1 downregulates paxillin turnover in a process, that does not require its GAP activity. Instead, it requires the presence of FAK. Acting in concert, both DLC1 and FAK could provide a unique spatio‐temporal mechanism to regulate paxillin function in tissue homeostasis. © 2014 Wiley Periodicals, Inc.

Paxillin

Tensin

Vinculin

PTK2

10.1002/cm.21201

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Citations (23)