Department of Bioscience and Bioengineering

The availability of safe drinking water in non-networked rural areas and disaster-affected zones is dependent on point-of-use water filters. This study describes the design and performance assessment of a personal portable ceramic water filter named “sip-up.” Four sample variants were made using clay, exfoliated graphite (EG), and sawdust as raw materials. Samples were made using a mold to ensure uniformity and sintered at 850 °C. The experimental results showed that the sample containing the maximum amount of sawdust had the highest porosity of 36.07 ± 1.8%, providing an average flow rate of 0.61 ml/min in passive mode. The average pore size radius of all variants varied in the range of 1–10 nm, classifying the material as having a mesoporous structure. Compressive test results indicate that the addition of an organic additive (sawdust) decreases the compressive strength of filters as compared to non-organic additives. It has been observed that the addition of EG to clay does not significantly improve water filtration parameters as compared to samples containing only sawdust and clay. However, due to the smaller pore size, samples containing EG performed better in E. coli removal as compared to sawdust-containing samples. The final prototype can act as a single-use personal water filtration device that can be inserted into any commercial water bottle, making it an affordable and effective solution for hikers, travelers, and natural disasters such as floods and cyclones.

The AXXXA and GXXXG motifs are frequently observed in helices, especially in membrane proteins. The motif GXXXG is known to stabilize helix-helix association in membrane proteins via CαH[sbnd]O bonding. AXXXA sequence motif additionally stabilizes the folded state of proteins. We found 27,000 and 18,000 occurrences of AXXXA and GXXXG motifs in a non-redundant set of 6000 obligate homodimeric (OD) complexes. Interestingly, this is less pronounced in transient homodimers (TD) and heterodimers (HetD). On average each obligate homodimer contains four AXXXA motifs, it is 2 and 3.5 for HetD and TD, respectively. Focusing on the binding surface it is seen that 27 % of the ODs contain at least one AXXXA motif at the interface, whereas it is 17 % and 15 % for HetD and TD respectively. AXXXA predominantly stabilizes the OD quaternary structure via the side chain Cβ[sbnd]Cβ interactions. This interaction is energetically favorable and is found to be a major driving force for OD quaternary structure stability. Cβ-Cβ interactions are observed ∼6 times higher than the known CαH[sbnd]O interaction for helix-helix stabilization. Two additional new interactions of Cβ[sbnd]O and O[sbnd]O are observed at the AXXXA containing interface regions. The occurrence of the motif gets drastically reduced if any of the terminal Ala residues are replaced by Gly. Our findings show the importance of AXXXA in providing stability to the quaternary structure through specific hydrophobic interactions and the specificity of the Ala residue at motif termini. The knowledge gained can be used for designing synthetic proteins of improved stability and for designing peptide-based therapeutics.

The self-assembly of lipopeptide (peptide amphiphile) molecules bearing single linear lipid chains has been widely studied, as has their diverse range of bioactivities. Here, we introduce lipopeptides bearing one or two cycloalkane chains (cycloheptadecyl or cyclododecyl) conjugated to the collagen-stimulating pentapeptide KTTKS used in Matrixyl formulations. The self-assembly of all four molecules is probed using fluorescence probe measurements to detect the critical aggregation concentration (CAC), and cryogenic-TEM and small-angle X-ray scattering (SAXS) to image the nanostructure. The peptide conformation is studied using circular dichroism (CD) and FTIR spectroscopies. All the cycloalkane lipopeptides show excellent compatibility with dermal fibroblasts. The compounds bearing one or two cyclododecyl chains (denoted as DKT and DDKT, respectively) show wound healing in diabetic rats, the improvement being markedly enhanced for DDKT. Interestingly, the revival of hair follicles and blood vessels in the dermis were observed, which are the critical markers of effective wound repair. Analysis of H&E-stained tissue images (from a rat model) shows that the rat groups treated with DDKT and DKT displayed a significantly increased amount of regenerated hair follicles, indicating a faster healing process for DDKT compared to the control group. Collagen deposition was also enhanced, especially for DDKT, and by day 20, the DDKT-treated groups had developed a dense collagen network accompanied by a regenerated epidermis. At the same time, the number of blood vessels in DDKT-treated diabetic wounds was significantly higher than in control groups and neovascularization was substantially enhanced, as assayed using α-SMA (a marker for vascular smooth muscle cells) and CD31 (a marker specific to vascular endothelial cells). These results suggest that the lead lipopeptide DDKT exhibits a remarkable pro-vascularization capability and shows great promise for future application as a wound-healing biomaterial.

Mendelian randomization (MR) is an emerging tool for inferring causality in genetic epidemiology. MR studies suffer bias from weak genetic instrument variables (IVs) and horizontal pleiotropy. We introduce a robust integrative framework strictly adhering with STROBE-MR guidelines to improve causality inference through MR studies. We implemented novel t-statistics-based criteria to improve the reliability of selected IVs followed by various MR methods. Further, we include sensitivity analyses to remove horizontal-pleiotropy bias. For functional validation, we perform enrichment analysis of identified causal SNPs. We demonstrate effectiveness of our proposed approach on 5 different MR datasets selected from diverse populations. Our pipeline outperforms its counterpart MR analyses using default parameters on these datasets. Notably, we found a significant association between total cholesterol and coronary artery disease (P = 1.16 × 10−71) in a single-sample dataset using our pipeline. Contrarily, this same association was deemed ambiguous while using default parameters. Moreover, in a two-sample dataset, we uncover 13 new causal SNPs with enhanced statistical significance (P = 1.06 × 10−11) for liver-iron-content and liver-cell-carcinoma. Likewise, these SNPs remained undetected using the default parameters (P = 7.58 × 10−4). Furthermore, our analysis confirmed previously known pathways, such as hyperlipidemia in heart diseases and gene ME1 in liver cancer. In conclusion, we propose a robust and powerful framework to infer causality across diverse populations and easily adaptable to different diseases.

The brain is an incredibly complex structure that consists of millions of neural networks. In developmental and cellular neuroscience, probing the highly complex dynamics of the brain remains a challenge. Furthermore, deciphering how several cues can influence neuronal growth and its interactions with different brain cell types (such as astrocytes and microglia) is also a formidable task. Traditional in vitro macroscopic cell culture techniques offer simple and straightforward methods. However, they often fall short of providing insights into the complex phenomena of neuronal network formation and the relevant microenvironments. To circumvent the drawbacks of conventional cell culture methods, recent advancements in the development of microfluidic device-based microplatforms have emerged as promising alternatives. Microfluidic devices enable precise spatiotemporal control over compartmentalized cell cultures. This feature facilitates researchers in reconstituting the intricacies of the neuronal cytoarchitecture within a regulated environment. Therefore, in this review, we focus primarily on modeling neuronal development in a microfluidic device and the various strategies that researchers have adopted to mimic neurogenesis on a chip. Additionally, we have presented an overview of the application of brain-on-chip models for the recapitulation of the blood-brain barrier and neurodegenerative diseases, followed by subsequent high-throughput drug screening. These lab-on-a-chip technologies have tremendous potential to mimic the brain on a chip, providing valuable insights into fundamental brain processes. The brain-on-chip models will also serve as innovative platforms for developing novel neurotherapeutics to address several neurological disorders.

New therapeutic leads are in global demand against multiple drug-resistant Staphylococcus aureus, as presently there is no drug of choice left to treat this pathogen. In the present work, we have designed, synthesized, and in vitro validated dimedone-coupled 2,3-dihydrofuran (DDHF)-based inhibitor scaffolds against Staphylococcal thioredoxin reductase (SaTR), a pivotal drug target enzyme of Gram-positive pathogens. Accordingly, a green multicomponent method that is both efficient and one pot has been optimized to synthesize DDHF derivatives. The synthesized DDHF derivatives were found to inhibit a purified SaTR enzyme. The best inhibitor derivative, DDHF20, inhibits SaTR as a competitive inhibitor for the NADPH binding site at low micromolar concentrations. DDHF20-capped silver nanoparticles are synthesized and characterized, and their bactericidal property has been checked in vitro. Furthermore, detailed in silico-based structure-guided functional studies have been carried out to uncover the plausible mode of action of DDHF20 as a potential anti-Staphylococcal therapeutic lead.

Efficiently mapping of cell types in situ remains a major challenge in spatial transcriptomics. Most spot deconvolution tools ignore spatial coordinate information and perform extremely slow on large datasets. Here, we introduce SpatialPrompt, a spatially aware and scalable tool for spot deconvolution and domain identification. SpatialPrompt integrates gene expression, spatial location, and single-cell RNA sequencing (scRNA-seq) dataset as reference to accurately infer cell-type proportions of spatial spots. SpatialPrompt uses non-negative ridge regression and graph neural network to efficiently capture local microenvironment information. Our extensive benchmarking analysis on Visium, Slide-seq, and MERFISH datasets demonstrated superior performance of SpatialPrompt over 15 existing tools. On mouse hippocampus dataset, SpatialPrompt achieves spot deconvolution and domain identification within 2 minutes for 50,000 spots. Overall, domain identification using SpatialPrompt was 44 to 150 times faster than existing methods. We build a database housing 40 plus curated scRNA-seq datasets for seamless integration with SpatialPrompt for spot deconvolution.

A sensitive and rapid electrochemical sensor has been developed to detect Escherichia coli (E. coli) bacteria that is crucial for ensuring safe drinking water. E. coli significantly contributes to waterborne contamination, driven by overexploitation and insufficient cleanliness around water bodies. This work incorporates synthesis and characterization of graphene oxide (GO), sensor preparation, and sensor testing in the presence of varying E. coli dilutions via H2O2 decomposition. GO is used as a sensing layer and drop casted on the working electrode of screen printed electrode (SPE). The sensor is exposed to different bacterial solutions using varied bacterial concentrations and fixed percent solution of H2O2. The interface of GO and bacterial solution results in a change in potential. The cross-sensitivity tests have also been performed in the presence of chemical compounds found in wastewater samples, Pseudomonas aeruginosa and Citrobacter youngae. The sensor demonstrates a detection limit of 2.8 CFU/mL, with a sensitivity of 5.1 mV-mL/CFU, fast response time and excellent repeatability when tested with E. coli. Its performance has also been assessed by comparing the sensing results for regular tap water, reverse osmosis (RO) water, and deionized water samples. This work paves the way for developing a chip-based system to detect E. coli in water.

Reduced graphene oxide (rGO) is a potential biomaterial for tissue engineering, photothermal therapy, and drug delivery. However, the hydrophobic nature of rGO results in poor dispersibility in a physiologically relevant aqueous environment, limiting its biomedical applications. To surmount this problem, here, we have developed a silanized derivative of reduced graphene oxide (rSiGO) using 3-Aminopropyl) triethoxysilane and evaluated its impact on [I] stability of rGO in different aqueous solvents, [ii] drug loading capacities, and [iii] biocompatibility. The physico-chemical characterization suggested that silanization alters the 2D carbon skeleton of rGO to a certain extent and improves its aqueous dispersibility and drug-loading capacity. The in vitro cytocompatibility study showed that rSiGO was compatible with the human dermal fibroblasts and murine fibroblast cell lines. It was also found that rSiGO possesses a higher loading capacity for hydrophilic drugs than rGO. The drug-loaded rSiGO showed higher cytotoxicity against hepatocarcinoma cells by inducing intracellular reactive oxygen species production, apoptosis, and nuclear fragmentation. In vivo systemic toxicity studies in mice showed that the rSiGO is nontoxic at the tested concentration. These results clearly showed that silanization improves the aqueous dispersibility, drug loading capacity, and biocompatibility of rGO making it a better candidate for various biomedical applications.

Cisplatin (CDDP) is an FDA-approved chemotherapeutic drug used for treating various solid tumors. Despite of its effectiveness towards chemotherapy, it faces several challenges, such as multi-drug resistance (MDR) and significant damage to the normal tissues. To address these challenges, various nanoformulations were developed to improve the delivery and safety of CDDP. One of the limitation in these CDDP loaded nanoformulations is that the effective CDDP loading concentrations are very poor. Therefore, this leaves a grand challenge to develop an effective strategy to carry higher concentrations of CDDP molecules, and also simultaneously exhibit very unique properties. Herein, we have developed an one-pot synthesis of Cisplatin encapsulated Plasmonic blackbody (CiP), which offers a double play for near infrared (NIR) light activatable chemo-photothermal therapy in destructing cancer cells as well as mediate catalytic reduction of 4-nitrophenol (4-NP). The CiP nanoformulation exhibits superior light absorbing capabilities in the NIR region with an appreciable photothermal conversion efficiency of 41 %. Further, NIR light activatable combinatorial therapeutic approach of CiP was demonstrated against ovarian cancer cells and as a catalyst for the reduction of model pollutant 4-nitrophenol. Our findings highlight the potential of CiP as a versatile platform for light-activated combinatorial cancer therapy and environmental pollutant remediation.