Biology subjects

Shah, D.

Publications and source records attributed to Shah, D..

48 records · Page 3Linked to original sources

bioRxiv2020

Naphthalene monoimide derivative ameliorates amyloid burden and cognitive decline in a transgenic mouse model of Alzheimer's disease

Alzheimers disease (AD) is a major neurodegenerative disorder and the leading cause of dementia worldwide. Predominantly, misfolding and aggregation of amyloid-{beta} (A{beta}) peptides associated with multifaceted toxicity is the neuropathological hallmark of AD pathogenesis and thus, primary therapeutic target to ameliorate neuronal toxicity and cognitive deficits. Herein, we report the design, synthesis and evaluation of small molecule inhibitors with naphthalene monoimide scaffold to ameliorate in vitro and in vivo amyloid induced neurotoxicity. The detailed studies established TGR63 as the lead candidate to rescue neuronal cells from amyloid toxicity. The in silico studies showed disruption of salt bridges and intermolecular hydrogen bonding interactions within A{beta}42 fibrils by the interaction of TGR63, causing destabilization of A{beta}42 assembly. Remarkably, TGR63 treatment showed a significant reduction in cortical and hippocampal amyloid burden in the progressive stages of APP/PS1 AD mice brain. Various behavioral tests demonstrated rescued cognitive deficits. The excellent biocompatibility, BBB permeability and therapeutic efficacy to reduce amyloid burden make TGR63 a promising candidate for the treatment of AD.

neuroscience↗

bioRxiv2020

Robotic Assay for Drought (RoAD): An Automated Phenotyping System for Brassinosteroid and Drought Response

Brassinosteroids (BRs) are a group of plant steroid hormones involved in regulating growth, development, and stress responses. Many components of the BR pathway have previously been identified and characterized. However, BR phenotyping experiments are typically performed on petri plates and/or in a low-throughput manner. Additionally, the BR pathway has extensive crosstalk with drought responses, but drought experiments are time-consuming and difficult to control. Thus, we developed Robotic Assay for Drought (RoAD) to perform BR and drought response experiments in soil-grown Arabidopsis plants. RoAD is equipped with a bench scale, a precisely controlled watering system, an RGB camera, and a laser profilometer. It performs daily weighing, watering, and imaging tasks and is capable of administering BR response assays by watering plants with Propiconazole (PCZ), a BR biosynthesis inhibitor. We developed image processing algorithms for both plant segmentation and phenotypic trait extraction in order to accurately measure traits in 2-dimensional (2D) and 3-dimensional (3D) spaces including plant surface area, leaf length, and leaf width. We then applied machine learning algorithms that utilized the extracted phenotypic parameters to identify image-derived traits that can distinguish control, drought, and PCZ-treated plants. We carried out PCZ and drought experiments on a set of BR mutants and Arabidopsis accessions with altered BR responses. Finally, we extended the RoAD assays to perform BR response assays using PCZ in Zea mays (maize) plants. This study establishes an automated and non-invasive robotic imaging system as a tool to accurately measure morphological and growth-related traits of Arabidopsis and maize plants, providing insights into the BR-mediated control of plant growth and stress responses.

plant biology↗

bioRxiv2020

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Enhancer-promoter dynamics are crucial for the spatiotemporal control of gene expression, but it remains unclear whether these dynamics are controlled by chromatin regulators, such as the nucleosome remodelling and deacetylase (NuRD) complex. The NuRD complex binds to all active enhancers to modulate transcription and here we use Hi-C experiments to show that it blurs TAD boundaries and increases the proximity of intermediate-range (~1 Mb) genomic sequences and enhancer-promoter interactions. To understand whether NuRD alters the dynamics of 3D genome structure, we developed an approach to segment and extract key biophysical parameters from 3D single-molecule trajectories of the NuRD complex determined using live-cell imaging. Unexpectedly, this revealed that the intact NuRD complex decompacts chromatin structure and makes NuRD-bound enhancers move faster, increasing the overall volume of the nucleus that these key regulatory regions explore. Interestingly, we also uncovered a rare fast-diffusing state of NuRD bound enhancers that exhibits directed motion. The NuRD complex reduces the amount of time that enhancers remain in this fast-diffusing state, which we propose might otherwise re-organise enhancer-promoter proximity. Thus, we uncover an intimate connection between a chromatin remodeller and the spatial dynamics of the local regions of the genome to which it binds.

cell biology↗

bioRxiv2019

\"Viscotaxis\" - Directed Migration of Mesenchymal Stem Cells in Response to Loss Modulus Gradient

Directed cell migration in response to chemical and mechanical gradients plays a crucial role in physiological and pathological conditions. One such mechanical cues that is known to influences cell migration is the gradient of substrate elastic modulus (E). However, the elastic modulus alone cannot fully define the material properties of the cellular microenvironment, which often has both elastic and viscous characteristics. In this study, we investigated the influence of the gradient of viscous nature, as defined by loss modulus, G\", on cell migration. We cultured human mesenchymal stem cells (hMSCs) on a collagen-coated polyacrylamide gel with constant elastic property, as defined by the storage modulus G, but with the gradient of loss modulus G\". We found hMSCs to migrate from high to low loss modulus. We have termed this, thus far unreported, directional cellular migration as \"Viscotaxis\". We have confirmed uniform collagen density and constant storage modulus of the gel by fluorescence microscopy and atomic force microscopy to eliminate the possibilities of haptotaxis and durotaxis. We hypothesize that material creep in the high loss modulus region hinders the building up of the cellular traction, leading to a force asymmetry that drives the observed viscotaxis. To verify our hypothesis, we estimated the cellular traction on gels with high and low loss moduli. We indeed found that cells apply higher traction force on more elastic materials i.e. materials with low loss modulus. On the disruption of actomyosin contractility with myosin inhibitor blebbistatin and ROCK inhibitor Y27632, directional migration was lost. Further, we showed that cells can maintain a stable morphology on a low loss modulus substrate but due to its inability to build up stable cellular traction on a substrate with high loss modulus, the cell spreading remains in a dynamic state. Our findings in this paper highlight the importance of considering the viscous modulus while preparing stiffness-based substrates for the field of tissue engineering.

biophysics↗

bioRxiv2019

Antifungal potency and modes of action of a novel olive tree defensin against closely related ascomycete fungal pathogens

Antimicrobial peptides play a pivotal role in the innate immunity of plants. Defensins are cysteine-rich antifungal peptides with multiple mechanisms of action (MOA). A novel Oleaceae-specific defensin gene family was discovered in the genome sequences of the wild and cultivated species of a perennial olive tree, Olea europaea. Antifungal properties of an olive tree defensin OefDef1.1 were investigated against a necrotrophic ascomycete fungal pathogen Botrytis cinerea in vitro and in planta. OefDef1.1 displayed potent antifungal activity against this pathogen by rapidly permeabilizing the plasma membrane of the conidial and germling cells. Interestingly, it was translocated to the cytoplasm and induced reactive oxygen species in the germlings, but not in the conidia. In medium containing high concentrations of Na1+, antifungal activity of OefDef1.1 against B. cinerea was significantly reduced. In contrast, OefDef1.1_V1 variant in which the {gamma}-core motif of OefDef1.1 was replaced by that of a Medicago truncatula defensin MtDef4 displayed Na1+-tolerant antifungal activity and was more potent in reducing the virulence of B. cinerea in planta. OefDef1.1 also exhibited potent antifungal activity against three hemibiotrophic ascomycete pathogens Fusarium graminearum, F. oxysporum and F. virguliforme. Significant differences were observed among the four pathogens in their responses to OefDef1.1 in growth medium with or without the high concentrations of Na1+. The varied responses of closely related ascomycete pathogens to this defensin have implications for engineering disease resistance in plants.

plant biology↗

bioRxiv2019

Impact of Ferumoxytol Magnetic Resonance Imaging on the Rhesus Macaque Maternal-Fetal Interface

Ferumoxytol is a superparamagnetic iron oxide nanoparticle (SPION) used off-label as an intravascular magnetic resonance imaging (MRI) contrast agent. Additionally, ferumoxytol-uptake by macrophages facilitates detection of inflammatory sites by MRI through ferumoxytol-induced image contrast changes. Therefore, ferumoxytol-enhanced MRI holds great potential for assessing vascular function and inflammatory response, critical to determine placental health in pregnancy. This study sought to assess the fetoplacental unit and selected maternal tissues, pregnancy outcomes, and fetal well-being after ferumoxytol administration. In initial developmental studies, pregnant rhesus macaques were imaged with and without ferumoxytol administration. Pregnancies went to term with vaginal delivery and infants showed normal growth rates compared to control animals born the same year that did not undergo MRI. To determine the impact of ferumoxytol on the maternal-fetal interface, fetal well-being, and pregnancy outcome, four pregnant rhesus macaques at [~]100 gd (gestational day) underwent MRI before and after ferumoxytol administration. Collection of the fetoplacental unit and selected maternal tissues was performed 3-4 days following ferumoxytol administration. A control group that did not receive ferumoxytol or MRI was used for comparison. Iron levels in fetal and maternal-fetal interface tissues did not vary between groups. There was no significant difference in tissue histopathology with or without exposure to ferumoxytol, and no effect on placental hormone secretion. Together, these results suggest that the use of ferumoxytol and MRI in pregnant rhesus macaques will not introduce a detectable risk to the mother or fetus at the time of imaging or up to one year following normal vaginal delivery.\n\nSummary SentenceFerumoxytol magnetic resonance imaging for non-invasive pregnancy monitoring of the rhesus macaque does not impact histopathology or iron content of the maternal-fetal interface.

physiology↗

bioRxiv2019

Expression of ppsD, a gene involved in synthesis of Mycobacterium tuberculosis virulence factor PDIM, reflects treatment response in pulmonary tuberculosis patients

Drug resistant tuberculosis (TB) cases are primarily driven by transmission, however, treatment failure and acquisition of drug resistance are still significant issues in drug sensitive TB cases. Study of gene expression in Mycobacterium tuberculosis (Mtb) isolated from poor outcome patients may offer clues towards prediction of treatment response. In the current study, expression of five non-drug target genes (ppsD, embC, Rv1457c, Rv1687c and recB) previously identified to be associated with drug resistance was studied in clinical isolates from patients with different treatment outcomes to examine its correlation to treatment response and acquisition of drug resistance in Mtb. Our results show that expression of ppsD, a gene involved in synthesis of cell wall lipid PDIM, was significantly increased in patients who developed drug resistance during treatment and patients who were drug resistant at diagnosis. On the other hand in longitudinal isolates collected during treatment, ppsD expression decreased consistently in patients who responded to treatment and became culture negative, while it increased in patients who did not respond to treatment as indicated by their culture positive status towards the end of treatment. These results demonstrate that ppsD expression reflects treatment response in TB patients and hence can be potentially used as a marker for predicting treatment response. Additional longitudinal studies with a larger cohort of patients are required to establish application of ppsD expression as a marker of treatment response.

microbiology↗

bioRxiv2019

Common functional networks in the mouse brain revealed by multi-centre resting-state fMRI analysis

Preclinical applications of resting-state functional magnetic resonance imaging (rsfMRI) offer the possibility to non-invasively probe whole-brain network dynamics and to investigate the determinants of altered network signatures observed in human studies. Mouse rsfMRI has been increasingly adopted by numerous laboratories world-wide. Here we describe a multi-centre comparison of 17 mouse rsfMRI datasets via a common image processing and analysis pipeline. Despite prominent cross-laboratory differences in equipment and imaging procedures, we report the reproducible identification of several large-scale resting-state networks (RSN), including a murine default-mode network, in the majority of datasets. A combination of factors was associated with enhanced reproducibility in functional connectivity parameter estimation, including animal handling procedures and equipment performance. Our work describes a set of representative RSNs in the mouse brain and highlights key experimental parameters that can critically guide the design and analysis of future rodent rsfMRI investigations.

neuroscience↗

bioRxiv2019

β1 integrin is a sensor of blood flow direction

The ability of endothelial cells (EC) to sense blood flow direction is a critical determinant of vascular health and disease. Unidirectional flow induces EC alignment and vascular homeostasis, whereas bidirectional flow has pathophysiological effects. EC express several mechanoreceptors that can respond to fluid flow (shear stress) but the mechanism for sensing the direction of shearing force is poorly understood. We observed using in vitro flow systems and magnetic tweezers that {beta}1 integrin is a key sensor of force direction because it is activated by unidirectional but not bidirectional shearing forces. Consistently, {beta}1 integrin was essential for Ca2+ signalling and cell alignment in response to unidirectional but not bidirectional shear stress. {beta}1 integrin activation by unidirectional force was amplified in EC that were pre-sheared in the same direction, indicating that alignment and {beta}1 integrin activity has a feedforward interaction which is a hallmark of system stability. En face staining and EC-specific genetic deletion studies of the murine aorta revealed that {beta}1 integrin is activated and is essential for EC alignment at sites of unidirectional flow but is not activated at sites of bidirectional flow. In summary, {beta}1 integrin sensing of unidirectional force is a key mechanism for decoding blood flow mechanics to promote vascular homeostasis.\n\nSUMMARY STATEMENTWe demonstrate using flow systems, magnetic tweezers and knockout mice that {beta}1 integrin is a sensor of shear stress direction in endothelial cells. {beta}1 integrin is activated by unidirectional hemodynamic shear force leading to calcium signalling and cell alignment, but it is not activated by bidirectional force.

cell biology↗

bioRxiv2018

Bottom-up sensory processing can decrease activity and functional connectivity in the default mode like network in rats.

The default mode network is a large-scale brain network that is active during rest and internally focused states and deactivates as well as desynchronizes during externally oriented (top-down) attention demanding cognitive tasks. However, it is not sufficiently understood if unpredicted salient stimuli, able to trigger bottom-up attentional processes, could also result in similar reduction of activity and functional connectivity in the DMN. In this study, we investigated whether bottom-up sensory processing could influence the default mode like network (DMLN) in rats. DMLN activity was examined using block-design visual functional magnetic resonance imaging (fMRI) while its synchronization was investigated by comparing functional connectivity during a resting versus a continuously stimulated brain state by unpredicted light flashes. We demonstrated that activity in DMLN regions was decreased during visual stimulus blocks and increased during blanks. Furthermore, decreased inter-network functional connectivity between the DMLN and visual networks as well as decreased intra-network functional connectivity within the DMLN was observed during the continuous visual stimulation. These results suggest that triggering of bottom-up attention mechanisms in anesthetized rats can lead to a cascade similar to top-down orienting of attention in humans and is able to deactivate and desynchronize the DMLN.

neuroscience↗

bioRxiv2018

The autism and schizophrenia-associated protein CYFIP1 regulates bilateral brain connectivity

Copy-number variants of the CYFIP1 gene in humans have been linked to Autism and Schizophrenia, two neuropsychiatric disorders characterized by defects in brain connectivity. CYFIP1 regulates molecular events underlying post-synaptic functions. Here, we show that CYFIP1 plays an important role in brain functional connectivity and callosal functions. In particular, we find that Cyfip1 heterozygous mice have reduced brain functional connectivity and defects in white matter architecture, typically relating to phenotypes found in patients with Autism, Schizophrenia and other neuropsychiatric disorders. In addition, Cyfip1 deficient mice present deficits in the callosal axons, namely reduced myelination, altered pre-synaptic function, and impaired bilateral-connectivity related behavior. Altogether, our results show that Cyfip1 haploinsufficiency compromises brain connectivity and function, which might explain its genetic association to neuropsychiatric disorders.

neuroscience↗

bioRxiv2018

Unmodified, autologous adipose-derived regenerative cells improve cardiac function, structure and revascularization in a porcine model of chronic myocardial infarction

Numerous studies have investigated cell-based therapies for myocardial infarction (MI), with mixed results. In the present study the left anterior descending (LAD) artery of pigs was occluded for 180 min. Four weeks later, the mean left ventricular ejection fraction (LVEF) was shown to have been reduced to approximately 35%. At that time, 18x106 unmodified, autologous adipose-derived regenerative cells (UA-ADRCs) were delivered into the LAD vein (control: delivery of saline). Six weeks following UA-ADRCs/saline delivery, the mean LVEF had increased by 18% (p<0.01) after delivery of UA-ADRCs, but was unchanged after delivery of saline. This is among the best outcome ever reported in studies on porcine animal models of cell-based therapies for MI in which functional outcome was assessed with cardiac magnetic resonance imaging. The unique combination of the procedure used for isolating UA-ADRCs, the late cell delivery time and the uncommon cell delivery route applied in the present study may open new horizons for cell-based therapies for MI.

molecular biology↗