Biology subjects

Mahato, S.

Publications and source records attributed to Mahato, S..

4 recordsLinked to original sources

bioRxiv2025

Engineering Escherichia coli FAD synthetase for the biosynthesis of FAD nucleotide analogues results in aminoglycoside antibiotic tolerance

Cofactors such as flavin adenine dinucleotide (FAD), nicotinamide adenine dinucleotide, coenzyme A, and S-adenosylmethionine cofactors share a common adenosine moiety that is generally not considered to contribute directly to catalysis. In FAD biosynthesis, the adenosine group is installed by the flavin mononucleotide adenylyltransferase (FMNAT) domain of the bifunctional FAD synthetase using FMN and ATP. This study explores the nucleotide selectivity of the Escherichia coli FMNAT domain and physiological effects of FAD nucleotide analogues synthesized with cellular nucleotides other than ATP. First, we engineer the FAD synthetase enzyme at an active site loop to produce FAD nucleotide analogues. Chromosomal substitution of the wild-type E. coli FAD synthetase with the mutated version results in the intracellular synthesis of these noncanonical FAD nucleotide analogues and confers tolerance to aminoglycoside antibiotics. Upon investigating their potential downstream metabolic roles, we find that their biosynthesis perturbs cellular metabolism and they could bind to a range of E. coli enzymes. These findings validate the FMNAT domain loop as a viable site for cofactor engineering, with potential for synthetic biology applications. Finally, the observed correlation between FAD analogue production and increased tolerance to aminoglycosides reveals novel metabolic mechanisms underlying antibiotic sensitivity.

microbiology↗

bioRxiv2024

Dairy DigiD ~ A Deep Learning-Based, Non-Invasive Biometric Identification System for Dairy Cattle Using Detectron2

Precision livestock farming demands accurate and reliable individual animal identification for optimizing health monitoring, resource allocation, and overall herd productivity. Conventional identification methods--such as ear tagging and wearable sensors--are often invasive, potentially causing animal discomfort and affecting natural behaviors. To address these challenges, we introduce Dairy DigiD, a non-invasive biometric classification system for dairy cattle using facial image analysis. Leveraging deep learning and the Detectron2 framework, Dairy DigiD classifies cattle into four categories--young (<2 years), mature milking, pregnant, and old--using over 2,500 high-resolution facial images. A DenseNet121 model achieved a classification accuracy of 97%, showcasing its strong discriminative capability. Further, Detectron2 attained an average recall of 87% in category identification, an average precision of 96% in cattle detection, and an overall detection accuracy of 93%, demonstrating its robustness and adaptability to varied environmental conditions. Unlike traditional approaches that rely on fixed facial landmarks and can be sensitive to environmental variability, Dairy DigiDs flexible deep learning architecture enables stable and scalable facial feature extraction. This non-invasive method minimizes animal stress, enhances data integrity, and facilitates improved herd management and welfare monitoring. In comparison to existing convolutional neural network (CNN)-based strategies, Dairy DigiD exhibits superior adaptability to real-world farm conditions, including variable lighting and complex poses. This work highlights the potential of integrating advanced computer vision and deep learning methodologies into precision dairy farming, offering an ethically aligned, efficient, and scalable approach to modern livestock management.

animal behavior and cognition↗

bioRxiv2021

Generating and testing the efficacy of transgenic Cas9 in Tribolium castaneum

CRISPR/Cas9 genome editing has now expanded to many insect species, including Tribolium castaneum. However, compared to Drosophila melanogaster, the CRISPR toolkit of T. castaneum is limited. A particularly apparent gap is the lack of Cas9 transgenic animals, which generally offer higher editing efficiency. We address this by creating and testing transgenic beetles expressing Cas9. We generated two different constructs bearing basal heat shock promoter-driven Cas9, two distinct 3 UTRs, and one containing Cas9 fused to EGFP by a T2A peptide. For each construct, we were able to generate a line that is homozygous viable, though variable reductions in reproductive success with each construct were noted. Analyses of Cas9 activity in each transgenic line demonstrated that both designs are capable of inducing CRISPR-mediated changes in the genome in the absence of heat induction. Overall, these resources enhance the accessibility of CRISPR/Cas9 genome editing for the Tribolium research community and provide a benchmark against which to compare future transgenic Cas9 lines.

genetics↗

bioRxiv2018

A mosaic of independent innovations involving eyes shut are critical for the evolutionary transition from closed to open rhabdoms

A fundamental question in evolutionary biology is how developmental processes are modified to produce morphological innovations while abiding by functional constraints. Here we address this question by investigating the cellular mechanism responsible for the transition between fused and open rhabdoms in ommatidia of apposition compound eyes; a critical step required for the development of visual systems based on neural superposition. Utilizing Drosophila and Tribolium as representatives of fused and open rhabdom morphology respectively, we identified three changes required for this innovation to occur. First, the expression pattern of the extracellular matrix protein Eyes Shut (EYS) was co-opted and expanded from mechanosensory neurons to the photoreceptor cells in taxa with open rhabdoms. Second, EYS homologs in these taxa obtained a novel extension of the amino terminus leading to the internalization of a cleaved signal sequence. This amino terminus extension does not interfere with cleavage or function in mechanosensory neurons, but it does permit specific targeting of the EYS protein to the apical photoreceptor membrane. Finally, a specific interaction evolved between EYS and a subset of Prominin homologs that is required for the development of open, but not fused, rhabdoms. Together, our findings portray a case study wherein the evolution of a set of molecular novelties has precipitated the origin of an adaptive photoreceptor cell arrangement.\n\nAuthor SummaryUnderstanding how adaptive morphologies originate is a central question in evolutionary developmental biology. Once confined largely to arguments about the relative frequencies of protein coding vs. regulatory mutations, numerous studies have since revealed more complex interactions involving alterations in gene expression and novel protein-protein interactions as drivers of novel trait evolution. Our study exploits the genetic amenability of Drosophila and utilizes direct comparisons with Tribolium to define a set of cellular mechanisms necessary for the evolutionary transition from a fused (Tribolium) to an open (Drosophila) rhabdom. Our results depict an evolutionary transition involving both non-coding and coding changes that resulted in a novel visual architecture, permitting a subset of diurnal insects to diversify into niches characterized by low light.

evolutionary biology↗