Biology subjects

Datta, P.

Publications and source records attributed to Datta, P..

8 recordsLinked to original sources

bioRxiv2021

Characterisation of a novel ACE2-based therapeutic with enhanced rather than reduced activity against SARS-CoV2 variants

The human angiotensin-converting enzyme 2 acts as the host cell receptor for SARS-CoV-2 and the other members of the Coronaviridae family SARS-CoV-1 and HCoV-NL63. Here we report the biophysical properties of the SARS-CoV-2 spike variants D614G, B.1.1.7 and B.1.351 with affinities to the ACE2 receptor and infectivity capacity, revealing weaknesses in the developed neutralising antibody approaches. Furthermore, we report a pre-clinical characterisation package for a soluble receptor decoy engineered to be catalytically inactive and immunologically inert, with broad neutralisation capacity, that represents an attractive therapeutic alternative in light of the mutational landscape of COVID-19. This construct efficiently neutralised four SARS-CoV-2 variants of concern. The decoy also displays antibody-like biophysical properties and manufacturability, strengthening its suitability as a first-line treatment option in prophylaxis or therapeutic regimens for COVID-19 and related viral infections.

immunology↗

bioRxiv2021

Differential requirement of NPHP1 for compartmentalized protein localization during photoreceptor outer segment development and maintenance

Nephrocystin (NPHP1) is a ciliary transition zone protein and its ablation causes nephronophthisis (NPHP) with partially penetrant retinal dystrophy. However, the precise requirements of NPHP1 in photoreceptors are not well understood. Here, we characterize retinal degeneration in a mouse model of NPHP1 and show that NPHP1 is required to prevent infiltration of inner segment plasma membrane proteins into the outer segment during the photoreceptor maturation. We demonstrate that Nphp1 gene-trap mutant mice, which were previously described as null, are in fact hypomorphs due to the production of a small quantity of functional mRNAs derived from nonsense-associated altered splicing and skipping of two exons including the one harboring the gene-trap. In homozygous mutant animals, inner segment plasma membrane proteins such as syntaxin-3 (STX3), synaptosomal-associated protein 25 (SNAP25), and interphotoreceptor matrix proteoglycan 2 (IMPG2) accumulate in the outer segment when outer segments are actively elongating. This phenotype, however, is spontaneously ameliorated after the outer segment elongation is completed. Retinal degeneration also occurs temporarily during the photoreceptor maturation but stops afterward. We further show that Nphp1 genetically interacts with Cep290, another NPHP gene, and that a reduction of Cep290 gene dose results in retinal degeneration that continues until adulthood in Nphp1 mutant mice. These findings demonstrate that NPHP1 is required for the confinement of inner segment plasma membrane proteins during the outer segment development, but its requirement diminishes as photoreceptors mature. Our study also suggests that additional mutations in other NPHP genes may influence the penetrance of retinopathy in human NPHP1 patients.

neuroscience↗

bioRxiv2020

A vision prosthesis based on electrical stimulation of the primary visual cortex using epicortical microelectrodes

Prostheses that can restore limited vision in the profoundly blind have been under investigation for several decades. Studies using epicortical macroelectrodes and intracortical microelectrodes have validated that electrical stimulation of primary visual cortical can serve as the basis for a vision prosthesis. However, neither of these approaches has resulted in a clinically viable vision prosthesis. Epicortical macroelectrodes required high levels of electrical current to evoke visual percepts, while intracortical microelectrodes faced challenges with longevity and stability. We hypothesized that epicortical microelectrodes could evoke visual percepts at lower currents than macroelectrodes and provide improved longevity and stability compared with intracortical microelectrodes. To test this hypotheses we implanted epicortical microelectrode arrays over the primary visual cortex of a nonhuman primate. Electrical stimulation via this array was used to evaluate the ability of epicortical microstimulation to evoke differentiable visual percepts. Visual percepts were evoked using the epicortical microelectrode array, and at electrical currents notably lower than those required to evoke visual percepts on macroelectrode arrays. The electrical current thresholds for evoking visual percepts on the epicortical microelectrode array were consistent across multiple array implants and over several months. Normal vision of light perception was not impaired by multiple array implants or chronic electrical stimulation, demonstrating that no gross visual deficit resulted from the experiments. We specifically demonstrate that epicortical microelectrode interfaces can serve as the basis for a vision prosthesis and more generally may provide an approach to evoking perception in multiple sensory modalities. One Sentence SummaryElectrical stimulation of the brain via microelectrodes resting on the surface of primary visual cortex can evoke multiple differentiable visual percepts.

bioengineering↗

bioRxiv2020

Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History and Discovery of Novel Players

Bacterial phage shock protein (PSP) systems stabilize the bacterial cell membrane and protect against envelope stress. These systems have been associated with virulence, but despite their critical roles, PSP components are not well-characterized outside proteobacteria. Using comparative genomics and protein sequence-structure-function analyses, we systematically identified and analyzed PSP homologs, phyletic patterns, domain architectures, and gene neighborhoods. This approach underscored the evolutionary significance of the system, revealing that the core PspA gene (Snf7 in ESCRT outside bacteria) was present in the Last Universal Common Ancestor (LUCA), and that this ancestral functionality has since diversified into multiple novel, distinct PSP systems across life. Several novel partners of the PSP system were identified: (i) the Toastrack domain, likely facilitating assembly of sub-membrane stress-sensing and signaling complexes, (ii) the newly-defined HAAS-PadR-like transcriptional regulator pair system, and (iii) multiple independent associations with ATPase, CesT/Tir-like chaperone, and Band-7 domains in proteins thought to mediate sub-membrane dynamics. Our work also uncovered links between the PSP components and other domains, such as novel variants of SHOCT-like domains, suggesting roles in assembling membrane-associated complexes of proteins with disparate biochemical functions. Results are available at https://jravilab.org/psp. ImportancePhage shock proteins (PSP) are virulence-associated, cell membrane stress-protective systems. They have mostly been characterized in proteobacteria and firmicutes. We now show that PSP systems were present in the Last Universal Common Ancestor, and that homologs have evolved and diversified into newly identified functional contexts. Recognizing the conservation and evolution of PSP systems across bacterial phyla contributes to our understanding of stress response mechanisms in prokaryotes. Moreover, the newly discovered PSP modularity will likely prompt new studies of lineage-specific cell-envelope structures, lifestyles, and adaptation mechanisms. Finally, our results validate use of domain architecture and genetic context for discovery in comparative genomics.

evolutionary biology↗

bioRxiv2020

Hybrid Chemomechanical Promotion of PEDOT Adhesion onto Flexible Microelectrode Arrays for Chronic Neural Stimulation

Advances in neural prosthetic technologies demand ever increasing novelty in material composition to enhance the mechanical and electrochemical properties of existing microelectrode arrays. Conductive polymers present advantages such as mechanical flexibility, outstanding biocompatibility, remarkable electrical properties and, most of all, cellular agreement. However, for long-term chronic applications, they fall short in their electrochemical endurance and mechanical adhesion to their substrate materials. Multiple electrochemical approaches have been investigated to improve the adherence of Poly(3,4-ethylenedioxythiophene) (PEDOT) to underlying metallic thin films. In this work, an electrochemical treatment of diazonium salt on platinum microelectrodes is incorporated as an electrochemical adhesion promoter for PEDOT and it is further combined with using the highly microporous geometry of Platinum Grey (Pt-Grey); a technology developed by Second Sight Medical Products Inc (SSMP). The intertwined mechanical integration of Pt-Grey and PEDOT molecules together with the covalent binding agency of diazonium salt demostrate a composite coating technology with long-term stability of more than 452 days while providing >70x enhancement to the interfacial capacitive impedance.

bioengineering↗

bioRxiv2020

Chaperone-mediated stress-sensing in Mycobacterium tuberculosis enables fast activation and sustained response

Dynamical properties of gene-regulatory networks are tuned to ensure bacterial survival. In mycobacteria, MprAB-{sigma}E network responds to the presence of stressors, such as surfactants causing surface stress. Positive feedback loops in this network were previously predicted to cause hysteresis, i.e. different responses to identical stressor levels for pre-stressed and unstressed cells. Here we show that hysteresis does not occur in non-pathogenic Mycobacterium smegmatis but occurs in Mycobacterium tuberculosis. However, the observed rapid temporal response in M. tuberculosis is inconsistent with the model predictions. To reconcile these observations, we implement a recently proposed mechanism for stress-sensing: the release of MprB from the inhibitory complex with chaperone DnaK upon the stress exposure. Using modeling and parameter fitting, we demonstrate that this mechanism can accurately describe the experimental observations. Furthermore, we predict perturbations in DnaK expression that can strongly affect dynamical properties. Experiments with these perturbations agree with model predictions, confirming the role of DnaK in fast and sustained response. IMPORTANCEGene-regulatory networks controlling stress response in mycobacterial species have been linked to persistence switches enabling the bacterial dormancy within a host. However, the mechanistic basis of switching and stress sensing is not fully understood. In this paper, combining quantitative experiments and mathematical modeling, we uncover how interactions between two master regulators of stress response -- MprAB two-component system and alternative sigma factor{sigma} E - shape the dynamical properties of surface-stress network. The result show hysteresis (history dependence) in the response of pathogenic bacteria M. tuberculosis to surface stress and lack of the hysteresis in non-pathogenic M. smegmatis. Furthermore, to resolve the apparent contradiction between the existence of hysteresis and fast activation of the response, we utilize a recently proposed role of chaperone DnaK in stress-sensing. The results leads to a novel system-level understanding of bacterial stress-response dynamics.

systems biology↗

bioRxiv2020

Limited time window for retinal gene therapy in a preclinical model of ciliopathy

Retinal degeneration is a common clinical feature of ciliopathies, a group of genetic diseases linked to ciliary dysfunction, and gene therapy is an attractive treatment option to prevent vision loss. Although the efficacy of retinal gene therapy is well established by multiple proof-of-concept preclinical studies, its long-term effect, particularly when treatments are given at advanced disease stages, is controversial. Incomplete treatment and intrinsic variability of gene delivery methods may contribute to the variable outcomes. Here, we used a genetic rescue approach to "optimally" treat retinal degeneration at various disease stages and examined the long-term efficacy of gene therapy in a mouse model of ciliopathy. We used a Bardet-Biedl syndrome type 17 (BBS17) mouse model, in which the gene-trap that suppresses Bbs17 (also known as Lztfl1) expression can be removed by tamoxifen administration, restoring normal gene expression systemically. Our data indicate that therapeutic effects of retinal gene therapy decrease gradually as treatments are given at later stages. These results suggest the presence of limited time window for successful gene therapy in certain retinal degenerations. Our study also implies that the long-term efficacy of retinal gene therapy may depend on not only the timing of treatment but also other factors such as the function of mutated genes and residual activities of mutant alleles.

neuroscience↗

bioRxiv2019

CEP290 myosin-tail homology domain is essential for protein confinement between inner and outer segments in photoreceptors

Mutations in CEP290 cause various ciliopathies involving retinal degeneration. CEP290 proteins localize to the ciliary transition zone and are thought to act as a gatekeeper that controls ciliary protein trafficking. However, precise roles of CEP290 in photoreceptors and pathomechanisms of retinal degeneration in CEP290-associated ciliopathies are not sufficiently understood. Using Cep290 conditional mutant mice, in which the C-terminal myosin-tail homology domain is disrupted after the connecting cilium is assembled, we show that CEP290, more specifically the myosin-tail homology domain of CEP290, is essential for protein confinement between the inner and the outer segments. Inner segment plasma membrane proteins including STX3, SNAP25, and IMPG2 rapidly accumulate in the outer segment upon disruption of the myosin-tail homology domain. In contrast, localization of endomembrane proteins is not altered. Trafficking and confinement of most outer segment-resident proteins appear to be unaffected or only minimally affected in this mouse model. One notable exception is RHO, which exhibits severe mislocalization to inner segments from the initial stage of degeneration. Similar mislocalization phenotypes were observed in rd16 mice. These results suggest that failure of protein confinement at the connecting cilium and consequent accumulation of inner segment membrane proteins in the outer segment combined with insufficient RHO delivery is part of the disease mechanisms that cause retinal degeneration in CEP290-associated ciliopathies. Our study provides insights into the pathomechanisms of retinal degenerations associated with compromised ciliary gates.

cell biology↗