Ekta Makhija - Academia.edu (original) (raw)

Papers by Ekta Makhija

Biophysical Journal, 2015

of biological systems and have been applied for protein systems with small charge polarization. H... more of biological systems and have been applied for protein systems with small charge polarization. However, these means are not suitable to obtain the ensemble of histone tails in a form of a nucleosome, because strong electrostatic interactions between positively charged histone tails and negatively charged DNA compared with those in regular protein systems makes difficult to realize a sufficient sampling. Thus, we applied adaptive lambda square dynamics (ALSD) simulation we developed recently to investigate the conformations of H3 histone tails. ALSD dynamically scales the simulation parameters (charge, van der Walls and torsion energies) only for the histone tails during the simulations. This successfully sampled various histone tail conformations. In this poster, we introduce the ALSD simulation results and the differences in conformational ensembles between unmodified and acetylated H3 histone tails.

Journal of Cell Science, 2016

Biomimetic materials have long been the (he)art of bioengineering. They usually aim at mimicking ... more Biomimetic materials have long been the (he)art of bioengineering. They usually aim at mimicking in vivo conditions to allow in vitro culture, differentiation and expansion of cells. The past decade has witnessed a considerable amount of progress in soft lithography, bioinspired micro-fabrication and biochemistry, allowing the design of sophisticated and physiologically relevant micro-and nanoenvironments. These systems now provide an exquisite toolbox with which we can control a large set of physicochemical environmental parameters that determine cell behavior. Biofunctionalized surfaces have evolved from simple protein-coated solid surfaces or cellular extracts into nano-textured 3D surfaces with controlled rheological and topographical properties. The mechanobiological molecular processes by which cells interact and sense their environment can now be unambiguously understood down to the single-molecule level. This Commentary highlights recent successful examples where bio-functionalized substrates have contributed in raising and answering new questions in the area of extracellular matrix sensing by cells, cell-cell adhesion and cell migration. The use, the availability, the impact and the challenges of such approaches in the field of biology are discussed.

bioRxiv (Cold Spring Harbor Laboratory), May 30, 2022

A critical initial stage of skeletal morphogenesis involves formation of highly compact aggregate... more A critical initial stage of skeletal morphogenesis involves formation of highly compact aggregates of mesenchymal cells, known as mesenchymal condensations, appearing as regularly-spaced pattern of spots. Conventional computational models to understand their patterning have been based on chemotaxis, haptotaxis, and reaction-diffusion equations. In this work, we investigate the mesenchymal condensations from a different perspective, namely topological defects within liquid crystal-like pattern. Using bone marrow-derived mesenchymal stromal cells (bm-MSCs), we observed emergence of cellular swirls in confluent in-vitro cultures, followed by appearance of mesenchymal condensations at the centers of the selfassembled swirls. Specifically, the condensations appeared at the 'comet-like' (+1/2) and 'spiral-shaped' (+1) topological defect sites within the swirl pattern. Next, with the rationale that cellular swirls precede skeletal morphogenesis, and supported with the qualitative observation that swirl pattern-features are donor-specific, we probed the correlation between swirl pattern and the chondrogenic differentiation outcome of bm-MSCs. Towards this, we first generated and imaged cellular swirls systematically across 5 donors by controlling seeding density, culture vessel geometry, and culture duration. We observed that the swirl pattern features quantified as variance of coherency correlated strongly with the cartilage matrix proteins, sulfated glycosaminoglycan and collagen-II, quantified from the standard in-vitro chondrogenic differentiation assay. Our work shows that swirl-pattern quantification provides a novel and powerful tool to predict efficacy of bm-MSCs for in-vitro cartilage regeneration.

Journal of Visualized Experiments, Jun 2, 2019

Extracellular mechanical strain is known to elicit cell phenotypic responses and has physiologica... more Extracellular mechanical strain is known to elicit cell phenotypic responses and has physiological relevance in several tissue systems. To capture the effect of applied extracellular tensile strain on cell populations in vitro via biochemical assays, a device has previously been designed which can be fabricated simply and is small enough to fit inside tissue culture incubators, as well as on top of microscope stages. However, the previous design of the polydimethylsiloxane substratum did not allow high-resolution subcellular imaging via oil-immersion objectives. This work describes a redesigned geometry of the polydimethylsiloxane substratum and a customized imaging setup that together can facilitate highresolution subcellular imaging of live cells while under applied strain. This substratum can be used with the same, earlier designed device and, hence, has the same advantages as listed above, in addition to allowing high-resolution optical imaging. The design of the polydimethylsiloxane substratum can be improved by incorporating a grid which will facilitate tracking the same cell before and after the application of strain. Representative results demonstrate high-resolution time-lapse imaging of fluorescently labeled nuclei within strained cells captured using the method described here. These nuclear dynamics data give insights into the mechanism by which applied tensile strain promotes differentiation of oligodendrocyte progenitor cells.

Neuroscience Letters, 2020

Oligodendrocytes (OL) are a subset of glial cells in the central nervous system (CNS) comprising ... more Oligodendrocytes (OL) are a subset of glial cells in the central nervous system (CNS) comprising the brain and spinal cord. The CNS environment is defined by complex biochemical and biophysical cues during development and response to injury or disease. In the last decade, significant progress has been made in understanding some of the key biophysical factors in the CNS that modulate OL biology, including their key role in myelination of neurons. Taken together, those studies offer translational implications for remyelination therapies, pharmacological research, identification of novel drug targets, and improvements in methods to generate human oligodendrocyte progenitor cells (OPCs) and OLs from donor stem cells in vitro. This review summarizes current knowledge of how various physical and mechanical cues affect OL biology and its implications for disease, therapeutic approaches, and generation of human OPCs and OLs.

Mechanobiology in Health and Disease

Abstract Physical boundary conditions of the cell define its cytoskeletal organization and thus r... more Abstract Physical boundary conditions of the cell define its cytoskeletal organization and thus regulate the force balance on the nucleus. The boundary can be very precisely engineered by plating cells on micropatterned substrate of various geometries. Such modulations of cell shape and size impinge on nuclear morphology and dynamics. Understanding the regulation of nuclear dynamics is crucial for both physiological processes such as migration, wound healing, stem cell differentiation, and gene expression program and for disease conditions like cancer progression and laminopathies. In this chapter, we discuss the different types of nuclear dynamics, translation, rotation, and fluctuations of the nuclear envelope, forces contributing to such dynamics, and their implications in cell physiology.

Extracellular mechanical signals (EMS) can regulate nuclear morphology and chromatin dynamics via... more Extracellular mechanical signals (EMS) can regulate nuclear morphology and chromatin dynamics via the physical link from focal adhesions to chromatin via the cytoskeleton, linker proteins on the nuclear envelope and the nuclear lamina. However, how such force transmission from cytoskeleton to the nucleus is regulated by different EMS and their effect on nuclear and chromatin dynamics is not well understood. In the first project, using micropillar substrates and correlation analysis techniques, we measured the time scale at which nuclear and chromatin dynamics respond to traction forces at cell periphery in unperturbed cells. In the second project, using nuclear envelope fluctuations and heterochromatin dynamics as readout, we characterized how cytoskeletal forces alter depending on the EMS provided by micropatterned substrates. In the third project, we developed a technique to quantify chromatin dynamics and used it to study the effect of cytoskeletal perturbations on chromatin dynamics and binding of transcription regulators. Taken together, this work provides a quantitative understanding of the coupling between cellular mechanotransduction and nuclear and chromatin plasticity.

A critical initial stage of skeletal morphogenesis involves formation of highly compact aggregate... more A critical initial stage of skeletal morphogenesis involves formation of highly compact aggregates of mesenchymal cells, known as mesenchymal condensations, appearing as regularly-spaced pattern of spots. Conventional computational models to understand their patterning have been based on chemotaxis, haptotaxis, and reaction-diffusion equations. In this work, we investigate the mesenchymal condensations from a different perspective, namely topological defects within liquid crystal-like pattern. Using bone marrow-derived mesenchymal stromal cells (bm-MSCs), we observed emergence of cellular swirls in confluent in-vitro cultures, followed by appearance of mesenchymal condensations at the centers of the selfassembled swirls. Specifically, the condensations appeared at the ‘comet-like’ (+1/2) and ‘spiral-shaped’ (+1) topological defect sites within the swirl pattern. Next, with the rationale that cellular swirls precede skeletal morphogenesis, and supported with the qualitative observati...

Molecular and Cellular Mechanobiology, 2016

In this book chapter, we summarize the current fi ndings for the physical and chemical connection... more In this book chapter, we summarize the current fi ndings for the physical and chemical connections between the extracellular matrix (ECM) and 3D chromosome organization, which ultimately lead to modular gene regulation. An overview is fi rst provided to delineate the linkage between the nucleoskeleton and cytoskeleton through LINC complexes and on how this linkage regulates nuclear mechanotransduction. This involves alterations in nuclear morphology and dynamics, by reorganization of cytoskeletal network and actomyosin contractility in response to different ECM constraints. These external mechanical signals, once transduced to the nucleus, facilitate remodeling of chromatin dynamics, epigenetic landscape, and 3D chromosome organization. Finally, we present the role of cell geometric constraints on 3D chromosome organization for modulating gene expression. Extreme alterations in matrix signals could lead to a number of diseases, including fi brosis and cancer. In this context, analysis of nuclear mechanotransduction and genome regulation could provide a better understanding of tissue homeostasis.

According to a news release dated 16 April 2005, recent experimental data from JLAB, the Thomas J... more According to a news release dated 16 April 2005, recent experimental data from JLAB, the Thomas Jefferson National Accelerator facility in Newport News, Virginia, USA point to the absence of the pentaquark called Q+, at the place where it was expected. This surprising result due to the CLAS collaboration (where CLAS stands for the CEBAF Large Acceptance Spectrometer; CEBAF stands for the Continuous Electron Beam Accelerator Facility, which was the name of JLAB) contradicts the findings of several prior experiments, including some of its own, which indicated that at least one kind of pentaquark exists in the mass range 1525-1555 MeV/c2 (for a review, see Hicks1), while none of the experiments could definitively prove its existence. This recent experiment was based on a high energy photon beam on a liquid hydrogen target. It had considerably greater statistics; in fact, two orders of magnitude greater than a similar experiment in Germany carried out by the SAPHIR collaboration at the ...

According to a news release dated 16 April 2005, recent experimental data from JLAB, the Thomas J... more According to a news release dated 16 April 2005, recent experimental data from JLAB, the Thomas Jefferson National Accelerator facility in Newport News, Virginia, USA point to the absence of the pentaquark called Θ, at the place where it was expected. This surprising result due to the CLAS collaboration (where CLAS stands for the CEBAF Large Acceptance Spectrometer; CEBAF stands for the Continuous Electron Beam Accelerator Facility, which was the name of JLAB) contradicts the findings of several prior experiments, including some of its own, which indicated that at least one kind of pentaquark exists in the mass range 1525–1555 MeV/c (for a review, see Hicks), while none of the experiments could definitively prove its existence. This recent experiment was based on a high energy photon beam on a liquid hydrogen target. It had considerably greater statistics; in fact, two orders of magnitude greater than a similar experiment in Germany carried out by the SAPHIR collaboration at the ELS...

Neuroscience Letters, 2019

Oligodendrocytes (OL) are a subset of glial cells in the central nervous system (CNS) comprising ... more Oligodendrocytes (OL) are a subset of glial cells in the central nervous system (CNS) comprising the brain and spinal cord. The CNS environment is defined by complex biochemical and biophysical cues during development and response to injury or disease. In the last decade, significant progress has been made in understanding some of the key biophysical factors in the CNS that modulate OL biology, including their key role in myelination of neurons. Taken together, those studies offer translational implications for remyelination therapies, pharmacological research, identification of novel drug targets, and improvements in methods to generate human oligodendrocyte progenitor cells (OPCs) and OLs from donor stem cells in vitro. This review summarizes current knowledge of how various physical and mechanical cues affect OL biology and its implications for disease, therapeutic approaches, and generation of human OPCs and OLs.

Frontiers in Cellular Neuroscience, 2018

Mechanical and physical stimuli including material stiffness and topography or applied mechanical... more Mechanical and physical stimuli including material stiffness and topography or applied mechanical strain have been demonstrated to modulate differentiation of glial progenitor and neural stem cells. Recent studies probing such mechanotransduction in oligodendrocytes have focused chiefly on the biomolecular components. However, the cell-level biophysical changes associated with such responses remain largely unknown. Here, we explored mechanotransduction in oligodendrocyte progenitor cells (OPCs) during the first 48 h of differentiation induction by quantifying the biophysical state in terms of nuclear dynamics, cytoskeleton organization, and cell migration. We compared these mechanophenotypic changes in OPCs exposed to both chemical cues (differentiation factors) and mechanical cues (static tensile strain of 10%) with those exposed to only those chemical cues. We observed that mechanical strain significantly hastened the dampening of nuclear fluctuations and decreased OPC migration, consistent with the progression of differentiation. Those biophysical changes were accompanied by increased production of the intracellular microtubule network. These observations provide insights into mechanisms by which mechanical strain of physiological magnitude could promote differentiation of progenitor cells to oligodendrocytes via inducing intracellular biophysical responses over hours to days post induction.

Journal of Visualized Experiments, 2019

Journal of Visualized Experiments

Scientific reports, Jan 16, 2018

The synthesis of middle-to-late-replicating DNA can be affected independently of the rest of the ... more The synthesis of middle-to-late-replicating DNA can be affected independently of the rest of the genome by down-regulating the tumor suppressor PREP1 (PKNOX1). Indeed, DNA combing shows that PREP1 down-regulation affects DNA replication rate, increases the number of simultaneously firing origins and the asymmetry of DNA replication, leading to DNA damage. Genome-wide analysis of replication timing by Repli-seq shows that, upon PREP1 down-regulation, 25% of the genome is replicated earlier in the S-phase. The targeted DNA sequences correspond to Lamin-Associated Domains (LADs), and include late-replicating (LRRs) and temporal transition regions (TTRs). Notably, the distribution of PREP1 DNA binding sites and of its target genes indicates that DNA replication defects are independent of the overall PREP1 transcriptional activity. Finally, PREP1 down-regulation causes a substantial decrease in Lamin B1 levels. This suggests that DNA is released from the nuclear lamina earlier than in th...

Proceedings of the National Academy of Sciences, 2015

Significance Physical properties of the cell nucleus are important for various cellular functions... more Significance Physical properties of the cell nucleus are important for various cellular functions. However, the role of cell geometry and active cytoskeletal forces in regulating nuclear dynamics and chromatin dynamics is not well understood. Our results show cells with reduced matrix constraints have short actomyosin structures. These dynamic structures together with lower lamin A/C levels, resulting in softer nuclei, may provide the driving force for nuclear fluctuations. Furthermore, we observed increased dynamics of heterochromatin and telomere structures under such reduced cell–matrix interactions. We conclude that extracellular matrix signals alter cytoskeletal organization and lamin A/C expression levels, which together lead to nuclear and chromatin dynamics. These results highlight the importance of matrix constraints in regulating gene expression and maintaining genome integrity.

Frontiers in cellular neuroscience, 2017

Differentiation of oligodendrocyte progenitor cells (OPC) to oligodendrocytes and subsequent axon... more Differentiation of oligodendrocyte progenitor cells (OPC) to oligodendrocytes and subsequent axon myelination are critical steps in vertebrate central nervous system (CNS) development and regeneration. Growing evidence supports the significance of mechanical factors in oligodendrocyte biology. Here, we explore the effect of mechanical strains within physiological range on OPC proliferation and differentiation, and strain-associated changes in chromatin structure, epigenetics, and gene expression. Sustained tensile strain of 10-15% inhibited OPC proliferation and promoted differentiation into oligodendrocytes. This response to strain required specific interactions of OPCs with extracellular matrix ligands. Applied strain induced changes in nuclear shape, chromatin organization, and resulted in enhanced histone deacetylation, consistent with increased oligodendrocyte differentiation. This response was concurrent with increased mRNA levels of the epigenetic modifier histone deacetylase...

Journal of cell science, 2017

Biomimetic materials have long been the (he)art of bioengineering. They usually aim at mimicking ... more Biomimetic materials have long been the (he)art of bioengineering. They usually aim at mimicking in vivo conditions to allow in vitro culture, differentiation and expansion of cells. The past decade has witnessed a considerable amount of progress in soft lithography, bio-inspired micro-fabrication and biochemistry, allowing the design of sophisticated and physiologically relevant micro- and nano-environments. These systems now provide an exquisite toolbox with which we can control a large set of physicochemical environmental parameters that determine cell behavior. Bio-functionalized surfaces have evolved from simple protein-coated solid surfaces or cellular extracts into nano-textured 3D surfaces with controlled rheological and topographical properties. The mechanobiological molecular processes by which cells interact and sense their environment can now be unambiguously understood down to the single-molecule level. This Commentary highlights recent successful examples where bio-fun...

Biophysical Journal, 2015

of biological systems and have been applied for protein systems with small charge polarization. H... more of biological systems and have been applied for protein systems with small charge polarization. However, these means are not suitable to obtain the ensemble of histone tails in a form of a nucleosome, because strong electrostatic interactions between positively charged histone tails and negatively charged DNA compared with those in regular protein systems makes difficult to realize a sufficient sampling. Thus, we applied adaptive lambda square dynamics (ALSD) simulation we developed recently to investigate the conformations of H3 histone tails. ALSD dynamically scales the simulation parameters (charge, van der Walls and torsion energies) only for the histone tails during the simulations. This successfully sampled various histone tail conformations. In this poster, we introduce the ALSD simulation results and the differences in conformational ensembles between unmodified and acetylated H3 histone tails.

Journal of Cell Science, 2016

Biomimetic materials have long been the (he)art of bioengineering. They usually aim at mimicking ... more Biomimetic materials have long been the (he)art of bioengineering. They usually aim at mimicking in vivo conditions to allow in vitro culture, differentiation and expansion of cells. The past decade has witnessed a considerable amount of progress in soft lithography, bioinspired micro-fabrication and biochemistry, allowing the design of sophisticated and physiologically relevant micro-and nanoenvironments. These systems now provide an exquisite toolbox with which we can control a large set of physicochemical environmental parameters that determine cell behavior. Biofunctionalized surfaces have evolved from simple protein-coated solid surfaces or cellular extracts into nano-textured 3D surfaces with controlled rheological and topographical properties. The mechanobiological molecular processes by which cells interact and sense their environment can now be unambiguously understood down to the single-molecule level. This Commentary highlights recent successful examples where bio-functionalized substrates have contributed in raising and answering new questions in the area of extracellular matrix sensing by cells, cell-cell adhesion and cell migration. The use, the availability, the impact and the challenges of such approaches in the field of biology are discussed.

bioRxiv (Cold Spring Harbor Laboratory), May 30, 2022

A critical initial stage of skeletal morphogenesis involves formation of highly compact aggregate... more A critical initial stage of skeletal morphogenesis involves formation of highly compact aggregates of mesenchymal cells, known as mesenchymal condensations, appearing as regularly-spaced pattern of spots. Conventional computational models to understand their patterning have been based on chemotaxis, haptotaxis, and reaction-diffusion equations. In this work, we investigate the mesenchymal condensations from a different perspective, namely topological defects within liquid crystal-like pattern. Using bone marrow-derived mesenchymal stromal cells (bm-MSCs), we observed emergence of cellular swirls in confluent in-vitro cultures, followed by appearance of mesenchymal condensations at the centers of the selfassembled swirls. Specifically, the condensations appeared at the 'comet-like' (+1/2) and 'spiral-shaped' (+1) topological defect sites within the swirl pattern. Next, with the rationale that cellular swirls precede skeletal morphogenesis, and supported with the qualitative observation that swirl pattern-features are donor-specific, we probed the correlation between swirl pattern and the chondrogenic differentiation outcome of bm-MSCs. Towards this, we first generated and imaged cellular swirls systematically across 5 donors by controlling seeding density, culture vessel geometry, and culture duration. We observed that the swirl pattern features quantified as variance of coherency correlated strongly with the cartilage matrix proteins, sulfated glycosaminoglycan and collagen-II, quantified from the standard in-vitro chondrogenic differentiation assay. Our work shows that swirl-pattern quantification provides a novel and powerful tool to predict efficacy of bm-MSCs for in-vitro cartilage regeneration.

Journal of Visualized Experiments, Jun 2, 2019

Extracellular mechanical strain is known to elicit cell phenotypic responses and has physiologica... more Extracellular mechanical strain is known to elicit cell phenotypic responses and has physiological relevance in several tissue systems. To capture the effect of applied extracellular tensile strain on cell populations in vitro via biochemical assays, a device has previously been designed which can be fabricated simply and is small enough to fit inside tissue culture incubators, as well as on top of microscope stages. However, the previous design of the polydimethylsiloxane substratum did not allow high-resolution subcellular imaging via oil-immersion objectives. This work describes a redesigned geometry of the polydimethylsiloxane substratum and a customized imaging setup that together can facilitate highresolution subcellular imaging of live cells while under applied strain. This substratum can be used with the same, earlier designed device and, hence, has the same advantages as listed above, in addition to allowing high-resolution optical imaging. The design of the polydimethylsiloxane substratum can be improved by incorporating a grid which will facilitate tracking the same cell before and after the application of strain. Representative results demonstrate high-resolution time-lapse imaging of fluorescently labeled nuclei within strained cells captured using the method described here. These nuclear dynamics data give insights into the mechanism by which applied tensile strain promotes differentiation of oligodendrocyte progenitor cells.

Neuroscience Letters, 2020

Oligodendrocytes (OL) are a subset of glial cells in the central nervous system (CNS) comprising ... more Oligodendrocytes (OL) are a subset of glial cells in the central nervous system (CNS) comprising the brain and spinal cord. The CNS environment is defined by complex biochemical and biophysical cues during development and response to injury or disease. In the last decade, significant progress has been made in understanding some of the key biophysical factors in the CNS that modulate OL biology, including their key role in myelination of neurons. Taken together, those studies offer translational implications for remyelination therapies, pharmacological research, identification of novel drug targets, and improvements in methods to generate human oligodendrocyte progenitor cells (OPCs) and OLs from donor stem cells in vitro. This review summarizes current knowledge of how various physical and mechanical cues affect OL biology and its implications for disease, therapeutic approaches, and generation of human OPCs and OLs.

Mechanobiology in Health and Disease

Abstract Physical boundary conditions of the cell define its cytoskeletal organization and thus r... more Abstract Physical boundary conditions of the cell define its cytoskeletal organization and thus regulate the force balance on the nucleus. The boundary can be very precisely engineered by plating cells on micropatterned substrate of various geometries. Such modulations of cell shape and size impinge on nuclear morphology and dynamics. Understanding the regulation of nuclear dynamics is crucial for both physiological processes such as migration, wound healing, stem cell differentiation, and gene expression program and for disease conditions like cancer progression and laminopathies. In this chapter, we discuss the different types of nuclear dynamics, translation, rotation, and fluctuations of the nuclear envelope, forces contributing to such dynamics, and their implications in cell physiology.

Extracellular mechanical signals (EMS) can regulate nuclear morphology and chromatin dynamics via... more Extracellular mechanical signals (EMS) can regulate nuclear morphology and chromatin dynamics via the physical link from focal adhesions to chromatin via the cytoskeleton, linker proteins on the nuclear envelope and the nuclear lamina. However, how such force transmission from cytoskeleton to the nucleus is regulated by different EMS and their effect on nuclear and chromatin dynamics is not well understood. In the first project, using micropillar substrates and correlation analysis techniques, we measured the time scale at which nuclear and chromatin dynamics respond to traction forces at cell periphery in unperturbed cells. In the second project, using nuclear envelope fluctuations and heterochromatin dynamics as readout, we characterized how cytoskeletal forces alter depending on the EMS provided by micropatterned substrates. In the third project, we developed a technique to quantify chromatin dynamics and used it to study the effect of cytoskeletal perturbations on chromatin dynamics and binding of transcription regulators. Taken together, this work provides a quantitative understanding of the coupling between cellular mechanotransduction and nuclear and chromatin plasticity.

A critical initial stage of skeletal morphogenesis involves formation of highly compact aggregate... more A critical initial stage of skeletal morphogenesis involves formation of highly compact aggregates of mesenchymal cells, known as mesenchymal condensations, appearing as regularly-spaced pattern of spots. Conventional computational models to understand their patterning have been based on chemotaxis, haptotaxis, and reaction-diffusion equations. In this work, we investigate the mesenchymal condensations from a different perspective, namely topological defects within liquid crystal-like pattern. Using bone marrow-derived mesenchymal stromal cells (bm-MSCs), we observed emergence of cellular swirls in confluent in-vitro cultures, followed by appearance of mesenchymal condensations at the centers of the selfassembled swirls. Specifically, the condensations appeared at the ‘comet-like’ (+1/2) and ‘spiral-shaped’ (+1) topological defect sites within the swirl pattern. Next, with the rationale that cellular swirls precede skeletal morphogenesis, and supported with the qualitative observati...

Molecular and Cellular Mechanobiology, 2016

In this book chapter, we summarize the current fi ndings for the physical and chemical connection... more In this book chapter, we summarize the current fi ndings for the physical and chemical connections between the extracellular matrix (ECM) and 3D chromosome organization, which ultimately lead to modular gene regulation. An overview is fi rst provided to delineate the linkage between the nucleoskeleton and cytoskeleton through LINC complexes and on how this linkage regulates nuclear mechanotransduction. This involves alterations in nuclear morphology and dynamics, by reorganization of cytoskeletal network and actomyosin contractility in response to different ECM constraints. These external mechanical signals, once transduced to the nucleus, facilitate remodeling of chromatin dynamics, epigenetic landscape, and 3D chromosome organization. Finally, we present the role of cell geometric constraints on 3D chromosome organization for modulating gene expression. Extreme alterations in matrix signals could lead to a number of diseases, including fi brosis and cancer. In this context, analysis of nuclear mechanotransduction and genome regulation could provide a better understanding of tissue homeostasis.

According to a news release dated 16 April 2005, recent experimental data from JLAB, the Thomas J... more According to a news release dated 16 April 2005, recent experimental data from JLAB, the Thomas Jefferson National Accelerator facility in Newport News, Virginia, USA point to the absence of the pentaquark called Q+, at the place where it was expected. This surprising result due to the CLAS collaboration (where CLAS stands for the CEBAF Large Acceptance Spectrometer; CEBAF stands for the Continuous Electron Beam Accelerator Facility, which was the name of JLAB) contradicts the findings of several prior experiments, including some of its own, which indicated that at least one kind of pentaquark exists in the mass range 1525-1555 MeV/c2 (for a review, see Hicks1), while none of the experiments could definitively prove its existence. This recent experiment was based on a high energy photon beam on a liquid hydrogen target. It had considerably greater statistics; in fact, two orders of magnitude greater than a similar experiment in Germany carried out by the SAPHIR collaboration at the ...

According to a news release dated 16 April 2005, recent experimental data from JLAB, the Thomas J... more According to a news release dated 16 April 2005, recent experimental data from JLAB, the Thomas Jefferson National Accelerator facility in Newport News, Virginia, USA point to the absence of the pentaquark called Θ, at the place where it was expected. This surprising result due to the CLAS collaboration (where CLAS stands for the CEBAF Large Acceptance Spectrometer; CEBAF stands for the Continuous Electron Beam Accelerator Facility, which was the name of JLAB) contradicts the findings of several prior experiments, including some of its own, which indicated that at least one kind of pentaquark exists in the mass range 1525–1555 MeV/c (for a review, see Hicks), while none of the experiments could definitively prove its existence. This recent experiment was based on a high energy photon beam on a liquid hydrogen target. It had considerably greater statistics; in fact, two orders of magnitude greater than a similar experiment in Germany carried out by the SAPHIR collaboration at the ELS...

Neuroscience Letters, 2019

Oligodendrocytes (OL) are a subset of glial cells in the central nervous system (CNS) comprising ... more Oligodendrocytes (OL) are a subset of glial cells in the central nervous system (CNS) comprising the brain and spinal cord. The CNS environment is defined by complex biochemical and biophysical cues during development and response to injury or disease. In the last decade, significant progress has been made in understanding some of the key biophysical factors in the CNS that modulate OL biology, including their key role in myelination of neurons. Taken together, those studies offer translational implications for remyelination therapies, pharmacological research, identification of novel drug targets, and improvements in methods to generate human oligodendrocyte progenitor cells (OPCs) and OLs from donor stem cells in vitro. This review summarizes current knowledge of how various physical and mechanical cues affect OL biology and its implications for disease, therapeutic approaches, and generation of human OPCs and OLs.

Frontiers in Cellular Neuroscience, 2018

Mechanical and physical stimuli including material stiffness and topography or applied mechanical... more Mechanical and physical stimuli including material stiffness and topography or applied mechanical strain have been demonstrated to modulate differentiation of glial progenitor and neural stem cells. Recent studies probing such mechanotransduction in oligodendrocytes have focused chiefly on the biomolecular components. However, the cell-level biophysical changes associated with such responses remain largely unknown. Here, we explored mechanotransduction in oligodendrocyte progenitor cells (OPCs) during the first 48 h of differentiation induction by quantifying the biophysical state in terms of nuclear dynamics, cytoskeleton organization, and cell migration. We compared these mechanophenotypic changes in OPCs exposed to both chemical cues (differentiation factors) and mechanical cues (static tensile strain of 10%) with those exposed to only those chemical cues. We observed that mechanical strain significantly hastened the dampening of nuclear fluctuations and decreased OPC migration, consistent with the progression of differentiation. Those biophysical changes were accompanied by increased production of the intracellular microtubule network. These observations provide insights into mechanisms by which mechanical strain of physiological magnitude could promote differentiation of progenitor cells to oligodendrocytes via inducing intracellular biophysical responses over hours to days post induction.

Journal of Visualized Experiments, 2019

Journal of Visualized Experiments

Scientific reports, Jan 16, 2018

The synthesis of middle-to-late-replicating DNA can be affected independently of the rest of the ... more The synthesis of middle-to-late-replicating DNA can be affected independently of the rest of the genome by down-regulating the tumor suppressor PREP1 (PKNOX1). Indeed, DNA combing shows that PREP1 down-regulation affects DNA replication rate, increases the number of simultaneously firing origins and the asymmetry of DNA replication, leading to DNA damage. Genome-wide analysis of replication timing by Repli-seq shows that, upon PREP1 down-regulation, 25% of the genome is replicated earlier in the S-phase. The targeted DNA sequences correspond to Lamin-Associated Domains (LADs), and include late-replicating (LRRs) and temporal transition regions (TTRs). Notably, the distribution of PREP1 DNA binding sites and of its target genes indicates that DNA replication defects are independent of the overall PREP1 transcriptional activity. Finally, PREP1 down-regulation causes a substantial decrease in Lamin B1 levels. This suggests that DNA is released from the nuclear lamina earlier than in th...

Proceedings of the National Academy of Sciences, 2015

Significance Physical properties of the cell nucleus are important for various cellular functions... more Significance Physical properties of the cell nucleus are important for various cellular functions. However, the role of cell geometry and active cytoskeletal forces in regulating nuclear dynamics and chromatin dynamics is not well understood. Our results show cells with reduced matrix constraints have short actomyosin structures. These dynamic structures together with lower lamin A/C levels, resulting in softer nuclei, may provide the driving force for nuclear fluctuations. Furthermore, we observed increased dynamics of heterochromatin and telomere structures under such reduced cell–matrix interactions. We conclude that extracellular matrix signals alter cytoskeletal organization and lamin A/C expression levels, which together lead to nuclear and chromatin dynamics. These results highlight the importance of matrix constraints in regulating gene expression and maintaining genome integrity.

Frontiers in cellular neuroscience, 2017

Differentiation of oligodendrocyte progenitor cells (OPC) to oligodendrocytes and subsequent axon... more Differentiation of oligodendrocyte progenitor cells (OPC) to oligodendrocytes and subsequent axon myelination are critical steps in vertebrate central nervous system (CNS) development and regeneration. Growing evidence supports the significance of mechanical factors in oligodendrocyte biology. Here, we explore the effect of mechanical strains within physiological range on OPC proliferation and differentiation, and strain-associated changes in chromatin structure, epigenetics, and gene expression. Sustained tensile strain of 10-15% inhibited OPC proliferation and promoted differentiation into oligodendrocytes. This response to strain required specific interactions of OPCs with extracellular matrix ligands. Applied strain induced changes in nuclear shape, chromatin organization, and resulted in enhanced histone deacetylation, consistent with increased oligodendrocyte differentiation. This response was concurrent with increased mRNA levels of the epigenetic modifier histone deacetylase...

Journal of cell science, 2017

Biomimetic materials have long been the (he)art of bioengineering. They usually aim at mimicking ... more Biomimetic materials have long been the (he)art of bioengineering. They usually aim at mimicking in vivo conditions to allow in vitro culture, differentiation and expansion of cells. The past decade has witnessed a considerable amount of progress in soft lithography, bio-inspired micro-fabrication and biochemistry, allowing the design of sophisticated and physiologically relevant micro- and nano-environments. These systems now provide an exquisite toolbox with which we can control a large set of physicochemical environmental parameters that determine cell behavior. Bio-functionalized surfaces have evolved from simple protein-coated solid surfaces or cellular extracts into nano-textured 3D surfaces with controlled rheological and topographical properties. The mechanobiological molecular processes by which cells interact and sense their environment can now be unambiguously understood down to the single-molecule level. This Commentary highlights recent successful examples where bio-fun...