Biology subjects

Nagarajan, D.

Publications and source records attributed to Nagarajan, D..

13 recordsLinked to original sources

bioRxiv2026

Assessment of Microbial Consortia for Biogenic Mineralization Potential of Lead (Pb) using Microbiologically Induced Calcite Precipitation and Nitrate Reduction

Groundwater contamination by lead and nitrate exceeding the permissible limits of the World Health Organization (WHO) and the Bureau of Indian Standards (BIS) of 10 ppb lead and 45 to 50 ppm nitrate poses a severe health risk of systemic toxicity in humans and animals. Microbial nitrate reduction coupled with microbiologically induced calcite precipitation (MICP) proved to be a novel bioremediation strategy to transform soluble lead nitrate into insoluble lead biominerals. This study presents statistical optimization of operational parameters for nitrate reduction and co-precipitation of biogenic lead carbonate-calcium carbonate by nitrate-reducing bacterial consortia. The SEM, TEM with SEAD, and XRD analysis of the biomineral confirmed lead carbonate co-precipitation with CaCO3. A two-level factorial design was applied to screen significant variables and interactive factors that influence nitrate reduction and biomineral precipitation. The highest nitrate reduction, maximum ammonia production, and biogenic Pb-mineralization efficiency of > 90% were obtained at the optimum conditions (initial nitrate requirement of 600 ppm, temperature 37 oC, pH 8, and carbon content of 5.5 g/L) compared to those obtained under the common process parameters. ANOVA with a high correlation coefficient (R2 > 0.99) corroborated the linear model for the biogenic mineralization process. This study on the biogenic removal of Pb by nitrate-reducing bacterial consortia revealed possible opportunities for large-scale treatment of Pb-contaminated surface and subsurface water bodies.

microbiology↗

bioRxiv2026

Pyrogallol Modulates Abscopal Tumour and Gut Microbial Responses to Localized Irradiation in an Ehrlich Ascites Carcinoma Model

Radiotherapys clinical utility is often limited by radio-resistance, enterotoxicity, and intestinal dysbiosis. This study evaluated pyrogallol--a plant-derived vicinal trihydroxybenzene--as a dual-action radiosensitizer and mucosal protectant in an Ehrlich ascites carcinoma (EAC) BALB/c mouse model subjected to targeted LINAC irradiation (8 Gy). By combining transcriptomic profiling with whole-genome metagenomic sequencing, we interrogated the underlying host-microbiome interactions. Pyrogallol co-treatment significantly augmented radiotherapeutic efficacy, driving marked tumour regression through the upregulation of pro-apoptotic effectors (Bax, Casp3, Casp7) and p53-mediated tumour suppressors (Tp53, p21), alongside Bcl2 repression. Concurrently, pyrogallol blunted oncogenic progression by arresting proliferation (Cdk4, Pcna), inhibiting epithelial-mesenchymal transition (N-cadherin, vimentin), downregulating fibrotic remodelling (Tgf-{beta}, Col1A1, Fibronectin), and attenuating radiation-induced pro-inflammatory cytokine surges (Il-1, Il-6, Il-12). At the gut interface, radiation degraded colonization resistance by depleting homeostatic short-chain fatty acid producers and Clostridium scindens, while fuelling pathobiont blooms (Acinetobacter baumannii, Clostridioides difficile). Pyrogallol reversed this dysbiosis through a distinct ecological shift; despite a reduction in total species richness, the intestinal niche became dominated by the next-generation probiotic Parabacteroides distasonis ([~]94% relative abundance; Berger-Parker index: 0.94). Integrated Spearmans rank correlations demonstrated that host proliferative, EMT, fibrotic, and inflammatory markers aligned positively with pathobiont clusters (Bacteroides caecimuris, B. faecium, A. baumannii). Conversely, tumour regression and anti-inflammatory signatures correlated strongly with pathobiont restriction and P. distasonis enrichment. Overall, pyrogallol emerges as a compelling therapeutic adjuvant that synergistically enhances tumour radiosensitivity while remodelling the gut microbiome into a protective, anti-inflammatory state.

cancer biology↗

bioRxiv2026

Characterization of a novel soluble melanin secreted by Gliomastix polychroma

Melanin is a heterogeneous, amorphous biopolymer widely distributed in biological systems, yet most canonical forms are intrinsically insoluble. Soluble melanins are rare and remain poorly characterized, with pyomelanin and peptidomelanin representing the best-described fungal examples. Here, we report the isolation and characterization of a distinct, polyphyletic class of soluble melanin that we term `colloidal melanin'. This class of polymers was isolated from four different species of Ascomycetous fungi occupying varied environmental niches. Colloidal melanin was found to be phenolic and nitrogenous, with a low amino acid content. The polymers form particles with median diameters ranging from 79 to 127 nm, suggesting that small particle size may contribute to aqueous solubility via colloidal dispersion. Using chemical inhibition of melanin biosynthesis together with whole-genome sequencing, we show that colloidal melanin can be produced through multiple distinct biochemical pathways. Further, genes identified as involved in melanin biosynthesis across species do not share any detectable common ancestry, consistent with convergent evolution. Together, these findings identify a distinct class of soluble melanin that does not conform to existing soluble melanin classifications.

biochemistry↗

bioRxiv2024

Arid1b haploinsufficiency in cortical inhibitory interneurons causes cell-type-dependent changes in cellular and synaptic development

Autism spectrum disorder (ASD) presents with diverse cognitive and behavioral abnormalities beginning during early development. Although the neural circuit mechanisms remain unclear, recent work suggests pathology in cortical inhibitory interneurons (INs) plays a crucial role. However, we lack fundamental information regarding changes in the physiology of synapses to and from INs in ASD. Here, we used transgenic mice to conditionally knockout one copy of the high confidence ASD risk gene Arid1b from the progenitors of parvalbumin-expressing fast-spiking (PV-FS) INs and somatostatin-expressing non-fast-spiking (SST-NFS) INs. In brain slices, we performed paired whole-cell recordings between INs and excitatory projection neurons (PNs) to investigate changes in synaptic physiology. In neonates, we found reduced synaptic input to INs but not PNs, with a concomitant reduction in the frequency of spontaneous network events, which are driven by INs in immature circuits. In mature mice, we found a reduction in the number of PV-FS INs in cortical layers 2/3 and 5. However, changes in PV-FS IN synaptic physiology were cortical layer and PN cell-type dependent. In layer 5, synapses from PV-FS INs to subcortical-projecting PNs were weakened. In contrast, in layer 2/3, synapses to and from PV-FS INs and corticocortical-projecting PNs were strengthened, leading to enhanced feedforward inhibition of input from layer 4. Finally, we found a novel synaptic deficit among SST-NFS INs, in which excitatory synapses from layer 2/3 PNs failed to facilitate. Our data highlight that changes in unitary synaptic dynamics among INs in ASD depend on neuronal cell-type.

neuroscience↗

bioRxiv2024

Arid1b haploinsufficiency in pyramidal neurons causes cellular and circuit changes in neocortex but is not sufficient to produce behavioral or seizure phenotypes

Arid1b is a high confidence risk gene for autism spectrum disorder that encodes a subunit of a chromatin remodeling complex expressed in neuronal progenitors. Haploinsufficiency causes a broad range of social, behavioral, and intellectual disability phenotypes, including Coffin-Siris syndrome. Recent work using transgenic mouse models suggests pathology is due to deficits in proliferation, survival, and synaptic development of cortical neurons. However, there is conflicting evidence regarding the relative roles of excitatory projection neurons and inhibitory interneurons in generating abnormal cognitive and behavioral phenotypes. Here, we conditionally knocked out either one or both copies of Arid1b from excitatory projection neuron progenitors and systematically investigated the effects on intrinsic membrane properties, synaptic physiology, social behavior, and seizure susceptibility. We found that disrupting Arid1b expression in excitatory neurons alters their membrane properties, including hyperpolarizing action potential threshold; however, these changes depend on neuronal subtype. Using paired whole-cell recordings, we found increased synaptic connectivity rate between projection neurons. Furthermore, we found reduced strength of excitatory synapses to parvalbumin (PV)-expression inhibitory interneurons. These data suggest an increase in the ratio of excitation to inhibition. However, the strength of inhibitory synapses from PV interneurons to excitatory neurons was enhanced, which may rebalance this ratio. Indeed, Arid1b haploinsufficiency in projection neurons was insufficient to cause social deficits and seizure phenotypes observed in a preclinical germline haploinsufficient mouse model. Our data suggest that while excitatory projection neurons likely contribute to autistic phenotypes, pathology in these cells is not the primary cause.

neuroscience↗

bioRxiv2024

Improved prediction of stabilizing mutations in proteins by incorporation of mutational effects on ligand binding

While many computational methods accurately predict destabilizing mutations, identifying stabilizing mutations has remained a challenge, due to their relative rarity. We tested {Delta}{Delta}G0 predictions from computational predictors such as Rosetta, ThermoMPNN, RaSP, and DeepDDG, using eighty-two mutants of the bacterial toxin CcdB as a test case. On this dataset, the best computational predictor is ThermoMPNN which identifies stabilizing mutations with a precision of 68%. However, the average increase in Tm for these predicted mutations was only 1{degrees}C for CcdB, and predictions were poorer for a more challenging target, influenza neuraminidase. Using data from multiple previously described yeast surface display libraries and in vitro thermal stability measurements, we trained logistic regression models to identify stabilizing mutations with a precision of 90% and an average increase in Tm of 3{degrees}C for CcdB. When such libraries contain a population of mutants with significantly enhanced binding relative to the corresponding wild type, there is no benefit in using computational predictors. It is then possible to predict stabilizing mutations without any training, simply by examining the distribution of mutational binding scores. This avoids laborious steps of in vitro expression, purification, and stability characterization. When this is not the case, combining data from computational predictors with high-throughput experimental binding data enhances the prediction of stabilizing mutations. However, this requires training on stability data measured in vitro with known stabilized mutants. It is thus feasible to predict stabilizing mutations rapidly and accurately for any system of interest that can be subjected to a binding selection or screen.

biophysics↗

bioRxiv2024

Arktos: a simple tool for the design of polyhedral 1DNA nanostructures

DNA nanostructures are a class of self-assembling nanomaterials with a wide range of potential applications in biomedicine and nanotechnology. The history of DNA nanotechnology can be traced back to the 1980s with the development of simple DNA polyhedra using either human intuition or simple algorithms. Today the field is dominated by DNA origami constructs to such an extent that the original algorithms used to design non-origami nanostructures have been lost. In this work we describe Arktos: an algorithm developed to design simple DNA polyhedra without the use of DNA origami. Arktos designs sequences predicted to fold into a desired structure using simulated annealing optimization. As a proof-of-concept, we used Arktos to design a simple DNA tetrahedron. The generated oligonucleotide sequences were synthesized and experimentally validated via polyacrylamide gel electrophoresis, indicating that they fold into the desired structure. These results demonstrate that Arktos can be used to design custom DNA polyhedra as per the needs of the research community.

bioinformatics↗

bioRxiv2024

Satb2 regulates pyramidal cell differentiation and the development of feedforward inhibitory circuits in CA1 hippocampus

Pyramidal cells (PCs) in CA1 hippocampus can be classified by their radial position as deep or superficial and organize into subtype-specific circuits necessary for differential information processing. Specifically, superficial PCs receive fewer inhibitory synapses from parvalbumin (PV)-expressing interneurons than deep PCs, resulting in weaker feedforward inhibition of input from CA3 Schaffer collaterals. Using mice, we investigated mechanisms underlying PC differentiation and the development of this inhibitory circuit motif. We found that expression of the transcriptional regulator SATB2 is biased towards superficial PCs during early postnatal development and necessary to suppress PV+ interneuron synapse formation. In the absence of SATB2, the number of PV+ interneuron synaptic puncta surrounding superficial PCs increases during development to match deep PCs. This results in equivalent inhibitory current strength observed in paired whole-cell recordings, and equivalent feedforward inhibition of Schaffer collateral input. Thus, SATB2 is necessary for superficial PC differentiation and biased feedforward inhibition in CA1.

neuroscience↗

bioRxiv2023

Blueprinting expandable nanomaterials with standardized protein building blocks

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies in comparison has been much more complex, largely due to the irregular shapes of protein structures1. Here we describe extendable linear, curved, and angled protein building blocks, as well as inter-block interactions that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight "train track" assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not been previously possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank 3D canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to "back of an envelope" architectural blueprints.

biochemistry↗

bioRxiv2023

A complete morphological characterization of all life stages of the phorid fly M. scalaris

Megaselia scalaris, commonly known as the scuttle fly, is a cosmopolitan species in the family Phoridae. It is an easily cultured fly species that is an emerging model organism in the fields of genetics and developmental biology. Its affinity for carrion and its predictable life cycle makes it useful in the field of forensic science for estimating the post-mortem interval (PMI) of human remains. Cases of human myasis caused by M. scalaris have also been reported in the medical literature. Despite its ubiquitous prevalence and its relevance across multiple fields, its morphology has not been adequately characterized. Here, we report the complete morphological characterization of all lifestages of M. scalaris, ranging from egg to adult. Scanning electron microscopy has enabled us to uncover morphological features and developmental processes that have previously not been reported in the literature. Our data lays the groundwork for future genetic studies: a morphological characterization of the wild type must be performed before mutants displaying different phenotypes can be identified. In this vein, we also report the observation of a acephalic, or headless, adult phenotype whose study could yield insights into the process of cephalogenesis.

zoology↗

bioRxiv2021

Computational design of nanoscale rotational mechanics in de novo protein assemblies

Natural nanomachines like the F1/F0-ATPase contain protein components that undergo rotation relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here we explore the de novo construction of protein rotary machinery from designed axle and ring components. Using cryoelectron microscopy, we find that axle-ring systems assemble as designed and populate diverse rotational states depending on symmetry match or mismatch and the designed interface energy landscape. These mechanical systems with internal rotational degrees of freedom are a step towards the systematic design of genetically encodable nanomachines. One-Sentence SummaryComputationally designed self-assembling protein rotary machines sample internal degrees of freedom sculpted within the energy landscape.

synthetic biology↗

bioRxiv2019

A simple method to determine the elimination half-life of drugs displaying noncumulative toxicity

The pharmacokinetic characterization of a drug, especially the determination of its biological half-life, is an essential step during the early phases of drug development. An adequate half-life is amongst the many properties needed for selecting a drug candidate for clinical trials. Conversely, drug candidates possessing inadequate half-lives may be modified or eliminated from the drug discovery pipeline altogether. Several methods exist for determining the half-lives of drugs, namely HPLC, fluorescence assays, radioassays, radioimmunoassays, and elemental mass spectrometric assays. However, all these techniques are resource and labor-intensive, and cannot be used for the high-throughput half-life determination of hundreds of drug candidates. Here, we describe TOXHL: a simple technique to determine the half-lives of compounds displaying noncumulative toxicity. To calculate the half life, TOXHL only relies on the survival outcomes of three experiments performed on an animal model: an acute toxicity experiment, a cumulative toxicity experiment, and a multi-dose experiment at different dosing intervals. As a proof of concept, we use TOXHL to determine the peritoneal half-life of {Omega}76, an antimicrobial peptide. The half-life of {Omega}76 determined by TOXHL is in good agreement with results from a standard mass spectrometric method, validating this approach.

pharmacology and toxicology↗

bioRxiv2018

A uniform in vitro efficacy dataset to guide antimicrobial peptide design

Antimicrobial peptides are ubiquitous molecules that form the innate immune system of organisms across all kingdoms of life. Despite their prevalence and early origins, they continue to remain potent natural antimicrobial agents. Antimicrobial peptides are therefore promising drug candidates in the face of overwhelming multi-drug resistance to conventional antibiotics. Over the past few decades, thousands of antimicrobial peptides have been characterized in vitro, and their efficacy data is now available in a multitude of public databases. Computational antimicrobial peptide design attempts typically use such data. However, utilizing heterogenous data aggregated from different sources presents significant drawbacks. In this report, we present a uniform dataset containing 20 antimicrobial peptides assayed against 30 organisms spanning gram positive, gram negative, fungal, and mycobacterial origin. We draw inferences from the results of 600 individual MIC assays, and discuss what characteristics are essential for antimicrobial peptide efficacy. We expect our uniform dataset to be useful for future projects involving computational antimicrobial peptide design.

microbiology↗