Biology subjects

Jana, A.

Publications and source records attributed to Jana, A..

10 recordsLinked to original sources

bioRxiv2026

Vibrio cholerae VgrG1-ACD Targets E. coli MreB and Regulates Cellular Morphology

Vibrio cholerae employs the Type VI Secretion System (T6SS) to outcompete neighboring bacteria and establish successful colonization within the polymicrobial gut. The T6SS effector VgrG1 contains a C-terminal Actin Crosslinking Domain (VgrG1-ACD), well known for irreversibly crosslinking eukaryotic actin to disrupt the host cytoskeleton. However, whether VgrG1-ACD also contributes directly to interbacterial competition has remained unexplored. Here, we identify a previously unrecognized bacterial target of VgrG1-ACD: MreB, the bacterial actin homolog essential for cell shape, cell wall synthesis, and cytoskeletal organization. We demonstrate that VgrG1-ACD specifically binds Escherichia coli MreB, resulting in pronounced morphological defects and impaired bacterial growth. Notably, unlike its activity toward mammalian actin, VgrG1-ACD targets MreB without crosslinking it, revealing a distinct mode of action. These findings expand the functional repertoire of VgrG1-ACD beyond host-directed virulence and uncover a dual-targeting strategy through which a single T6SS effector manipulates both mammalian actin and its bacterial homolog, likely enhancing V. cholerae fitness during interbacterial competition and host colonization.

microbiology↗

bioRxiv2025

Reversible superdeformability of hiPSC epithelial cortinoids

Epithelial cortinoids, fluid filled shells formed from induced pluripotent stem cells (iPSCs), must accommodate large deformations during growth and morphogenesis. Using inflation-deflation assays and high-resolution imaging, we find that these fluid-filled shells are weakly-pressurized and achieve extreme deformability through reversible soft modes of deformation accommodated by the cytoskeleton. We show that cytoskeletal elements such as actin localized along lateral cell edges undergo tilt and bend instabilities that buffer mechanical load by decoupling apico-basal stretching from lateral extension. These reversible instabilities act as elastic safety valves, permitting large shape changes without loss of epithelial hydraulic and topological integrity. A minimal theoretical and computational model demonstrates how tilt and bend reduce effective resistance to radial thinning and explains the observed pressure-strain softening. Thus, iPSC shells exploit reversible cytoskeletal instabilities as mechanical buffers, enabling robust tolerance of large deformations in developing epithelia.

biophysics↗

bioRxiv2024

Pheno-morphological screening and acoustic sorting of 3D multicellular aggregates using drop millifluidics

Three-dimensional multicellular aggregates like organoids and spheroids have become essential tools to study the biological mechanisms involved in the progression of diseases. In cancer research, they are now widely used as in vitro models for drug testing. However, their analysis still relies on tedious manual procedures, which hinders their routine use in large-scale biological assays. Here, we introduce a novel drop millifluidic approach to screen and sort large populations containing over one thousand multicellular aggregates. Our system utilizes real-time image processing to detect pheno-morphological traits in cellular aggregates. They are then encapsulated in millimetric drops, actuated on-demand using the acoustic radiation force. We demonstrate the performance of our system by sorting spheroids with uniform sizes from a heterogeneous population, and by isolating organoids from spheroids with different phenotypes. We anticipate that this work offers the potential to standardize drug testing on multicellular aggregates, which promises accelerated progress in biomedical research.

bioengineering↗

bioRxiv2024

Confinement in fibrous environments positions and orients mitotic spindles

Accurate positioning of the mitotic spindle within the rounded cell body is critical to physiological maintenance. Adherent mitotic cells encounter confinement from neighboring cells or the extracellular matrix (ECM), which can cause rotation of mitotic spindles and, consequently, titling of the metaphase plate (MP). To understand the positioning and orientation of mitotic spindles under confinement by fibers (ECM-confinement), we use flexible ECM-mimicking nanofibers that allow natural rounding of the cell body while confining it to differing levels. Rounded mitotic bodies are anchored in place by actin retraction fibers (RFs) originating from adhesion clusters on the ECM-mimicking fibers. We discover the extent of ECM-confinement patterns RFs in 3D: triangular and band-like at low and high confinement, respectively. A stochastic Monte-Carlo simulation of the centrosome (CS), chromosome (CH), membrane interactions, and 3D arrangement of RFs on the mitotic body recovers MP tilting trends observed experimentally. Our mechanistic analysis reveals that the 3D shape of RFs is the primary driver of the MP rotation. Under high ECM-confinement, the fibers can mechanically pinch the cortex, causing the MP to have localized deformations at contact sites with fibers. Interestingly, high ECM-confinement leads to low and high MP tilts, which mechanistically depend upon the extent of cortical deformation, RF patterning, and MP position. We identify that cortical deformation and RFs work in tandem to limit MP tilt, while asymmetric positioning of MP leads to high tilts. Overall, we provide fundamental insights into how mitosis may proceed in fibrous ECM-confining microenvironments in vivo.

biophysics↗

bioRxiv2024

zIncubascope: long-term quantitative imaging of multi-cellular assemblies inside an incubator

Recent advances in bioengineering have made it possible to develop increasingly complex biological systems to recapitulate organ functions as closely as possible in vitro. Monitoring the assembly and growth of multi-cellular aggregates, micro-tissues or organoids and extracting quantitative information is a crucial but challenging task required to decipher the underlying morphogenetic mechanisms. We present here an imaging platform designed to be accommodated inside an incubator which provides high-throughput monitoring of cell assemblies over days and weeks. We exemplify the capabilities of our system by investigating human induced pluripotent stem cells (hiPSCs) enclosed in spherical capsules, hiPSCs in tubular capsules and yeast cells in spherical capsules. Combined with a customized pipeline of image analysis, our solution provides insight into the impact of confinement on the morphogenesis of these self-organized systems.

bioengineering↗

bioRxiv2024

Gut feeling: host and habitat as drivers of the microbiome in blackbuck (Antilope cervicapra)

The gut microbiome can be shaped by both intrinsic host factors and extrinsic environmental factors. However, the relative importance of intrinsic and extrinsic factors in gut microbial composition has rarely been investigated, particularly for a single host across its natural range. Here, we characterise the gut microbiome of an endemic, endangered antelope, the blackbuck or Antilope cervicapra. We evaluated the influence of seven predictor variables, which were classified into intrinsic and extrinsic factors, on the gut microbiome. We determined which of these seven variables explains greater variation in the microbiome within (-diversity) and between ({beta}-diversity) the blackbuck host. We analysed the microbiome of 60 blackbuck hosts from ten different populations across India. We recorded 11800 unique OTUs across 30 known phyla and 2.9 million reads. We find an average of 2056 OTUs per individual, with firmicutes and bacteroidetes being the most dominant phyla. We find that nucleotide diversity (intrinsic), blackbuck population density (intrinsic), distance to human settlement (extrinsic), and anthropogenic land-use (extrinsic) explain within-host variation. In contrast, precipitation (extrinsic), nucleotide diversity, distance to human settlement, and anthropogenic land-use explain between-host variation. Overall, we also show that the genetic diversity of the host is more important than their environment for both within- and between-host variation in the microbiome, in blackbuck. Therefore, conservation efforts should be directed to not only preserve natural habitats but also increase the genetic pool of the blackbuck populations, which will positively impact their survival through diverse gut microbiomes.

ecology↗

bioRxiv2021

Mitotic Outcomes in Fibrous Environments

During mitosis, cells round up and generate outward forces to create space and orient the mitotic spindles. Here, using suspended ECM-mimicking nanofiber networks, we recapitulate in vivo adhesion organization and confinement to interrogate mitotic outcomes for various interphase cell shapes. Elongated cells attached to single fibers through two focal adhesion clusters (FACs) at their extremities result in perfect spherical mitotic cell bodies that undergo large 3D displacement while being held by retraction fibers. Increasing the number of parallel fibers increases cellular extremity FACs and retraction fiber-driven stability, leading to reduced 3D cell-body movement, metaphase plate rotations, and significantly faster division times. Interestingly, interphase kite shapes on a crosshatch pattern of four fibers undergo mitosis resembling single-fiber outcomes due to rounded bodies being primarily held in position by retraction fibers from two perpendicular suspended fibers. We develop a cortex-astral microtubule analytical friction and force model to capture retraction-fiber-driven stability of the metaphase plate rotations. We report that reduced orientational stability results in increased monopolar mitotic defects. In the case of cells attached to two parallel fibers, rounded mitotic cells can get confined between the suspended fibers, allowing estimation of the mitotic forces through measurement of the outward deflection of the fibers. Interestingly, confinement causes rotated mitotic spindles similar to those reported in dense tissues. Overall, we establish dynamics of mitosis in fibrous environments governed by fiber arrangement and architecture-driven differences in interphase cell shapes, adhesion geometries, and varying levels of mechanical confinement.

cell biology↗

bioRxiv2021

Sculpting rupture-free nuclear shapes in fibrous environments

Cytoskeleton-mediated force transmission regulates nucleus morphology. How nuclei shaping occurs in fibrous in vivo environments remains poorly understood. Here a suspended nanofiber assay of precisely-tunable (nm-m) diameters is used to quantify nucleus plasticity in fibrous environments mimicking the natural extracellular matrix. In contrast to the apical cap over the nucleus in cells on 2-dimensional surfaces, the cellular cytoskeleton of cells on fibers displays a uniform actin network caging the nucleus. The role of contractility-driven caging in sculpting nuclear shapes is investigated as cells spread on aligned single fibers, doublets, and multiple fibers of varying diameters. Cell contractility increases with fiber diameter due to increased focal adhesion clustering and density of actin stress fibers, which correlates with increased mechanosensitive transcription factor YAP translocation to the nucleus. Unexpectedly, large- and small-diameter fiber combinations lead to teardrop-shaped nuclei due to stress-fiber anisotropy across the cell. As cells spread on fibers, diameter-dependent invaginations that run the nucleuss length are formed at contact sites. The deepest and sharpest invaginations are insufficient to trigger nucleus rupture, often observed in 2D or confined systems. Overall, we describe the unknown adaptability of nuclei to fibrous environments and resultant sculpting of the nucleus shapes, with pathophysiological implications.

cell biology↗

bioRxiv2020

Effect of Lauric Acid on the Stability of Abeta-Oligomers

While Alzheimers disease is correlated with the presence of A{beta} fibrils in patient brains, the more likely agents are their precursors, soluble oligomers that may form pores or otherwise distort cell membranes. Using all-atom molecular dynamics simulation we study how presence of fatty acids such as lauric acid changes the stability of pore-forming oligomers built from three-stranded A{beta}42 chains. Such a change would alter the distribution of amyloids in the fatty-acid rich brain environment, and therefore could explain the lower polymorphism observed in A{beta}-fibrils derived from brains of patients with Alzheimers disease. We find that lauric acid stabilizes both ring-like and barrel-shaped models, with the effect being stronger for barrel-like models than for ring-like oligomers.

biophysics↗

bioRxiv2017

Shared High Value Research Resources: The CamCAN Human Lifespan Neuroimaging Dataset Processed on the Open Science Grid

The CamCAN Lifespan Neuroimaging Dataset [1,2], Cambridge (UK) Centre for Ageing and Neuroscience, was acquired and processed beginning in December, 2016. The referee consensus solver deployed to the Open Science Grid [3,4] was used for this task. The dataset includes demographic and screening measures, a high-resolution MRI scan of the brain, and whole-head magnetoencephalographic (MEG) recordings during eyes closed rest (560 sec), a simple task (540 sec), and passive listening/viewing (140 sec). The data were collected from 619 neurologically normal individuals, ages 18-87. The processed results from the resting recordings are completed and available for download at http://stash.osgconnect.net/+krieger/. These constitute {approx}1.7 TBytes of data including the location within the brain (1 mm resolution), time stamp (1 msec resolution), and 80 msec time course for each of 3.7 billion validated neuroelectric events, i.e. mean 6.1 million events for each of the 619 participants.\n\nThe referee consensus solver provides high yield (mean 11,000 neuroelectric currents/sec; standard deviation (sd): 3500/sec) high confidence (p < 10-12 for each identified current) measures of the neuroelectric currents whose magnetic fields are detected in the MEG recordings. We describe the solver, the implementation of the solver deployed on the Open Science Grid, the workflow management system, the opportunistic use of high performance computing (HPC) resources to add computing capacity to the Open Science Grid reserved for this project, and our initial findings from the recently completed processing of the resting recordings. This required {approx}14 million core hours, i.e. {approx}40 core hours per second of data.

neuroscience↗