Amlan Barai

• PhD
• Postdoctoral Scientist at Institut Jacques Monod

Live imaging of microtubules (MTs) allows obtaining mechanistic insights into cell division. In literature, mitotic spindle dynamics have been investigated in mammalian systems largely focusing on established cell lines. Here, we describe a detailed protocol that investigates MT dynamics during cell division in a 3D mouse intestinal organoid model...

Majority of the eukaryotic cell surface is decorated with a layer of membrane attached polysaccharides and glycoproteins collectively referred to as the glycocalyx. While formation of a bulky glycocalyx has been associated with cancer progression, the mechanisms by which the glycocalyx regulates cancer invasiveness is incompletely understood. We ad...

Epithelial tissues serve as physical barriers against various external pressures yet remarkably maintain structural stability. Various cellular apparatus including bicellular junction and actomyosin network contribute to the epithelial integrity, packing and remodelling. Although their role in morphogenetic and mechanical processes have been extens...

Majority of the eukaryotic cell surface is decorated with a layer of membrane attached polysaccharides and glycoproteins collectively referred to as the glycocalyx. While formation of a bulky glycocalyx has been associated with cancer progression, the mechanisms by which the glycocalyx regulates cancer invasiveness is incompletely understood. We ad...

Planar spindle orientation is critical for epithelial tissue organization and is generally instructed by the long cell-shape axis or cortical polarity domains. We introduced mouse intestinal organoids in order to study spindle orientation in a monolayered mammalian epithelium. Although spindles were planar, mitotic cells remained elongated along th...

Mimivirus and Marseillevirus infections of Acanthamoeba castellanii, like most other viral infections, induce cytopathic effects (CPE). The details of how they bring about CPE and to what extent and how they modify the host cytoskeletal network are unclear. In this study, we compared the rearrangement of the host cytoskeletal network induced by Mim...

Fabrication of nanoscale DNA devices to generate 3D nano-objects with precise control of shape, size, and presentation of ligands has shown tremendous potential for therapeutic applications. The interactions between the cell membrane and different topologies of 3D DNA nanostructures are crucial for designing efficient tools for interfacing DNA devi...

The mechanisms by which the mechanoresponsive actin crosslinking protein α-actinin-4 (ACTN4) regulates cell motility and invasiveness remains incompletely understood. Here we show that in addition to regulating protrusion dynamics and focal adhesion formation, ACTN4 transcriptionally regulates expression of non-muscle myosin IIB (NMM IIB), which is...

Fabrication of nanoscale DNA devices to generate 3D nano-objects with precise control of shape, size, and presentation of ligands has shown tremendous potential for therapeutic applications. The interactions between different topologies of 3D DNA nanostructures and the cell membranes are crucial for designing efficient tools for interfacing DNA dev...

In comparison to synthetic hydrogels where ligand density and stiffness can be independently tuned, cell responses are expected to deviate on native biopolymer networks where ligand density and stiffness are coupled. Here we probe the tensional homeostasis of fibroblasts on methacrylated gelatin (GelMA) gels, which are widely used in tissue enginee...

Quantification of nuclear stiffness is challenging for cells encapsulated within a 3D extracellular matrix (ECM). Here, we describe an experimental setup for measuring microenvironment-dependent tuning of nuclear stiffness using an atomic force microscope (AFM). In our setup, ECM-coated polyacrylamide hydrogels mimic the stiffness of the microenvir...

Phenotypic heterogeneity is increasingly appreciated to confer several advantages to cancer progression and drug resistance. Here we probe the collective importance of heterogeneity in cell size and deformability in breast cancer invasion. A computational model of invasion of a heterogeneous cell aggregate predicts that combined heterogeneity in ce...

The mechanisms by which the mechanoresponsive actin crosslinking protein 𝛼-actinin-4 (ACTN4) regulates cell motility and invasiveness remains incompletely understood. Here we show that in addition to regulating protrusion dynamics and focal adhesion formation, ACTN4 transcriptionally regulates expression of non-muscle myosin IIB (NMM IIB), which is...

Substantial number of breast cancer (BC) patients undergoing radiation therapy (RT) develop local recurrence over time. During RT therapy, cells can gradually acquire resistance implying adaptive radioresistance. Here we probe the mechanisms underlying this acquired resistance by first establishing radioresistant lines using ZR-75-1 and MCF-7 BC ce...

Large nuclear deformations during migration through confined spaces have been associated with nuclear membrane rupture and DNA damage. However, the stresses associated with nuclear damage remain unclear. Here, using a quasi-static plane strain finite element model, we map evolution of nuclear shape and stresses during confined migration of a cell t...

Large nuclear deformations during migration through confined spaces have been associated with nuclear membrane rupture and DNA damage. However, the stresses associated with nuclear damage remain unclear. Here, using a quasi-static plane strain finite element model, we map evolution of nuclear shape and stresses during confined migration of a cell t...

Collagens are the most abundant proteins in the animal kingdom. They form the structural framework of connective tissues such as bones, tendons and skin, and play important biomechanical role in supporting tissue functions. The preservation of collagen in deep time is a topic of intense debate. Here we provide indisputable evidence for the presence...

During amoeboidal migration, cancer cells migrate in a protease-independent manner by squeezing through pre-existing gaps in the extracellular matrix (ECM). However, the extent to which cells alter their physical properties in order to sustain this mode of migration remains unclear. Here, we address this question by documenting biophysical changes...

Statement of significance: It is increasingly understood that cells migrate in vivo through confining spaces which typically occur as pores in the matrix and through naturally occurring interfaces that exist between neighbouring ECM fibers, or between the stroma and the vasculature. Such interfaces are also created when treating wounds on the skin...

Invadopodia are micron-sized invasive structures that mediate extracellular matrix (ECM) degradation through a combination of membrane-bound and soluble matrix metalloproteinases (MMPs). However, how such localized degradation is converted into pores big enough for cancer cells to invade, and the relative contributions of membrane-bound versus solu...

The failure of chemotherapeutic drugs in treatment of various cancers is attributed to the acquisition of drug resistance. However, the migration mechanisms of drug-resistant cancer cells remain incompletely understood. Here we address this question from a biophysical perspective by mapping the phenotypic alterations in ovarian cancer cells (OCCs)...

Cancer invasion through dense extracellular matrices (ECMs) is mediated by matrix metalloproteinases (MMPs) which degrade the ECM thereby creating paths for migration. However, how this degradation influences the phenotype of cancer cells is not fully clear. Here we address this question by probing the function of MMPs in regulating biophysical pro...

Acquired radioresistance accompanied with increased metastatic potential is a major hurdle in effective radiotherapy of breast cancers. However, the nature of their inter-dependence and the underlying mechanism remains largely intangible. By employing radioresistant (RR) cell lines, we herein demonstrate that MCF-7 RR cells display phenotypic and m...

In light of the literature, in this hypothesis, we aimed to settle up an experimental procedure and possible mechanism for bacteremia induced disseminated intravascular coagulation via QA.Bacteremia resulting in sepsis and disseminated intravascular coagulation (DIC) are known for thrombosis and coagulopathy. DIC, which results in simultaneous acti...

In light of the literature, in this hypothesis, we aimed to settle up an experimental procedure and possible mechanism for bacteremia induced disseminated intravascular coagulation via QA.Bacteremia resulting in sepsis and disseminated intravascular coagulation (DIC) are known for thrombosis and coagulopathy. DIC, which results in simultaneous acti...

For maintaining pluripotency, mouse embryonic stem cells (mESCs) are typically grown on mitotically inactivated mouse embryonic fibroblasts (MEFs). While the role of MEF conditioned media (MEFCM) and leukemia inhibitory factor (LIF) in regulating mESC pluripotency has led to culturing of mESCs on LIF/MEFCM supplemented gelatin-coated substrates, th...