Biology subjects

Nair, G.

Publications and source records attributed to Nair, G..

14 recordsLinked to original sources

bioRxiv2026

CD47 blockade augments anti-GD2 driven phagocytosis in vitro but fails to improve in vivo efficacy in immune competent, chemoresistant neuroblastoma preclinical models

CD47 delivers a dominant "Dont Eat Me" signal that inhibits macrophage-mediated clearance of tumour cells. Using immune competent, chemoresistant neuroblastoma (NB) models, we tested a Fc-silent CD47 blocker (ALX301) with anti-GD2 antibody alone and in combination with a clinically aligned temozolomide/irinotecan chemoimmunotherapy backbone. Tumours expressed GD2 and CD47, and bound ALX301. In macrophage coculture assays, anti-GD2 antibody induced dose-dependent phagocytosis, whereas ALX301 or an anti-CD47 antibody alone did not. CD47 blockade in combination with a suboptimal concentration of anti-GD2 antibody showed an additive effect on phagocytosis in vitro. In vivo, however, ALX301 failed to improve tumour control or survival when added to anti-GD2 or to chemoimmunotherapy in two models. Toxicity was acceptable, showing only mild, expected red-cell changes without organ injury. This form of CD47 inhibition is therefore mechanistically active in vitro but insufficient to enhance anti-GD2 antibody-based therapy in immune competent mice bearing a chemoresistant NB, highlighting the potential need for myeloid-reprogramming partners.

immunology↗

bioRxiv2026

Drosophila pseudoobscura third chromosome inversion arrangements have sex-specific effects on life history traits

Chromosomal inversions can create polymorphic "supergenes" consisting of many alleles in linkage disequilibrium that affect constellations of traits. The coadaptation hypothesis supposes that many alleles within an inversion haplotype have synergistic epistatic interactions, which are maintained by suppressed recombination in inversion heterozygotes, heterozygote advantage, and context-dependent fitness effects. The fitness benefits of chromosomal inversions frequently arise from effects on life history syndromes, including ecotypes and reproductive strategies. Life history syndromes can also be caused by individual pleiotropic alleles in ways that resemble the effects of chromosomal inversions. It is therefore possible that the fitness effects of chromosomal inversions arise because of pleiotropic alleles and not coadaptation. These two hypotheses can be distinguished because pleiotropy predicts greater genetic correlations of traits than coadaptation. To test the coadaptation and pleiotropy hypotheses, we measured three life history traits (lifespan, development time, and body size) in Drosophila pseudoobscura with six different chromosomal inversion genotypes. We assayed males and females raised at multiple temperatures in order to expose phenotype variation. Temperature affected lifespan and development more than any other factor, but we also observed differences in mortality rates and development times that depended on chromosomal inversions and sex. Despite these context-dependent effects on life history traits, we failed to identify genetic correlations that would be evidence for pleiotropic alleles. Our results therefore suggest that the coadaptation hypothesis is better supported.

evolutionary biology↗

bioRxiv2025

High-throughput screening reveals diverse lambdoid prophage inducers

Prophages; dormant bacteriophage genomes integrated within the bacterial chromosome, play pivotal roles in shaping microbial communities when awakened. Our current understanding of prophage activation is largely shaped by a narrow set of traditional DNA-damaging inducers, such as mitomycin C and ciprofloxacin, which trigger the bacterial SOS response. This study employed high-throughput screening of 3,921 compounds to identify novel prophage inducers using model lambdoid prophage HK97. We identified multiple new inducers across diverse pharmacological classes, including dietary supplements and therapeutics. Despite the variety in compounds, all acted through SOS-dependent pathways. However, bleomycin, an antineoplastic antibiotic, demonstrated broad-spectrum and potent prophage induction exceeding standard inducers, with activity validated across multiple phages and bacterial hosts. These findings expand the repertoire of prophage inducers into commonly ingested xenobiotics, and introduce Bleomycin as a powerful, cost-effective tool for prophage research.

microbiology↗

bioRxiv2024

Metabolomic differentiation of amino acid profiles in adult deltamethrin-resistant Aedes albopictus (L.)

Understanding the susceptibility status of mosquitoes to insecticides is critical for effective decision making regarding the use or rotation of insecticides in control programs. In this study, we demonstrated the use of amino acid profiling for the detection of deltamethrin-resistant Aedes albopictus (L.). Mosquitoes collected in the field were first tested with WHO adulticide bioassay kits, and the amino acid profiles of the resistant mosquitoes were compared with the susceptible strain of Ae. albopictus. Samples were lyophilized and derived by silylation and then analyzed by gas chromatography-mass spectrometry (GC-MS). Using standardized, known concentrations of amino acids, we quantified the amino acids in both resistant and susceptible strains. An independent t-test was performed to compare the concentrations of each amino acid between strains. Logistic regression was then performed to assess the relationship between amino acid concentrations and susceptibility status of the mosquitoes. Our results showed that the amino acids in resistant mosquitoes differed significantly from those in susceptible mosquitoes, with the exception of serine. Further regression analysis showed that seven amino acids significantly predicted susceptibility, suggesting that they are suitable as biological indicators for rapid assessment of resistance status in field mosquitoes. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/604257v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@7c3c91org.highwire.dtl.DTLVardef@6c7ad1org.highwire.dtl.DTLVardef@1f36900org.highwire.dtl.DTLVardef@172b13d_HPS_FORMAT_FIGEXP M_FIG C_FIG Identification of deltamethrin-resistant mosquitoes based on differences in the amino acid profile: Deltamethrin-susceptible and -resistant mosquito strains were lyophilised and converted into esters by silylation, which were then analysed using a gas chromatography-mass spectrometer (GC-MS). The difference between susceptible and resistant could be classified by developing a classification model with logistic regression.

zoology↗

bioRxiv2024

Micro-plaque assays: A high-throughput method to detect, isolate, and characterize bacteriophages

The gold standard for the isolation and characterization of bacteriophages (phages), the plaque assay, has remained almost unchanged for over 100 years. The need for improvements to its scalability has been driven home by successes with personalized phage therapy requiring large phage libraries and rapid sensitivity testing. Using a robotic pinning platform, we miniaturized plaque assays from bacterial lawns to micro-colonies from 100 nl of inoculant, increasing throughput by >1000 fold without compromising sensitivity. A comparable manual workflow with one quarter the throughput maintained the same sensitivity. These micro-plaque assays can replace plaque assays as a new gold standard in phage biology. As proof of principle, we used our technique to isolate and de-replicate 21 unique Pseudomonas aeruginosa phages from a single environmental sample. We then demonstrated - using the same assay - that of 17 multi-drug resistant clinical P. aeruginosa strains, 15 were susceptible to infection by one or more of the 21 phages tested. Our method allows rapid isolation and de-replication of phages, as well as enabling screening of large phage libraries against bacterial isolates of interest.

microbiology↗

bioRxiv2024

Enhancer-targeted CRISPR-Activation Rescues Haploinsufficient Autism Susceptibility Genes

Autism Spectrum Disorder (ASD) is a highly heritable condition with diverse clinical presentations. Approximately 20% of ASDs genetic susceptibility is imparted by de novo mutations of major effect, most of which cause haploinsufficiency. We mapped enhancers of two high confidence autism genes - CHD8 and SCN2A and used CRISPR-based gene activation (CRISPR-A) in hPSC-derived excitatory neurons and cerebral forebrain organoids to correct the effects of haploinsufficiency, taking advantage of the presence of a wildtype allele of each gene and endogenous gene regulation. We found that CRISPR-A induced a sustained increase in CHD8 and SCN2A expression in neurons and organoids, with rescue of gene expression levels and mutation-associated phenotypes, including gene expression and physiology. These data support gene activation via targeting enhancers of haploinsufficient genes as a therapeutic intervention in ASD and other neurodevelopmental disorders.

neuroscience↗

bioRxiv2024

Microenvironment Shapes Cell State, Plasticity, and Heterogeneity of Small Cell Lung Cancer

Small-cell lung cancer (SCLC) is the most fatal form of lung cancer. Intra-tumoral heterogeneity, marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states, defines SCLC, but the drivers of SCLC plasticity are poorly understood. To map the landscape of SCLC tumor microenvironment (TME), we apply spatially resolved transcriptomics and quantitative mass spectrometry-based proteomics to metastatic SCLC tumors obtained via rapid autopsy. The phenotype and overall composition of non-malignant cells in the tumor microenvironment (TME) exhibits substantial variability, closely mirroring the tumor phenotype, suggesting TME-driven reprogramming of NE cell states. We identify cancer-associated fibroblasts (CAF) as a crucial element of SCLC TME heterogeneity, contributing to immune exclusion, and predicting exceptionally poor prognosis. Together, our work provides a comprehensive map of SCLC tumor and TME ecosystems, emphasizing their pivotal role in SCLCs adaptable nature, opening possibilities for re-programming the intercellular communications that shape SCLC tumor states.

cancer biology↗

bioRxiv2024

Postmortem MRI of Tissue Frozen at Autopsy

IntroductionPostmortem MRI provides insight into location of pathology within tissue blocks, enabling efficient targeting of histopathological studies. While postmortem imaging of fixed tissue is gaining popularity, imaging tissue frozen at the time of extraction is significantly more challenging. MethodsTissue integrity was examined using RNA integrity number (RIN), in mouse brains placed between -20 {degrees}C and 20 {degrees}C for up to 24 hours, to determine the highest temperature that could potentially be used for imaging without tissue degeneration. Human tissue frozen at the time of autopsy was sealed in a tissue chamber filled with 2-methylbutane to prevent contamination of the MRI components. The tissue was cooled to a range of temperatures in a 9.4T MRI using a recirculating aqueous ethylene glycol solution. MRI was performed using a magnetization-prepared rapid gradient echo (MPRAGE) sequence with inversion time of 1400 ms to null the signal from 2-methylbutane bath, isotropic resolution between 0.3-0.4 mm, and scan time of about 4 hours was used to study the anatomical details of the tissue block. Results and DiscussionA temperature of -7 {degrees}C was chosen for imaging as it was below the highest temperature that did not show significant RIN deterioration for over 12 hours, at the same time gave robust imaging signal and contrast between brain tissue types. Imaging performed on various human tissue blocks revealed good gray-white matter contrast and revealing subpial, subcortical, and deep white matter lesions typical of multiple sclerosis enabling further spatially targeted studies. ConclusionHere, we describe a new method to image cold tissue, while maintaining tissue integrity and biosafety during scanning. In addition to improving efficiency of downstream processes, imaging tissue at sub-zero temperatures may also improve our understanding of compartment specificity of MRI signal.

bioengineering↗

bioRxiv2023

BundleCleaner: Unsupervised Denoising and Subsampling of Diffusion MRI-Derived Tractography Data

We present BundleCleaner, an unsupervised multi-step frame-work that can filter, denoise and subsample bundles derived from diffusion MRI-based whole-brain tractography. Our approach considers both the global bundle structure and local streamline-wise features. We apply BundleCleaner to bundles generated from single-shell diffusion MRI data in an independent clinical sample of older adults from India using probabilistic tractography and the resulting cleaned bundles can better align with the atlas bundles with reduced overreach. In a downstream tractometry analysis, we show that the cleaned bundles, represented with less than 20% of the original set of points, can robustly localize along-tract microstructural differences between 32 healthy controls and 34 participants with Alzheimers disease ranging in age from 55 to 84 years old. Our approach can help reduce memory burden and improving computational efficiency when working with tractography data, and shows promise for large-scale multi-site tractometry.

neuroscience↗

bioRxiv2023

Deconfounded Dimension Reduction via Partial Embeddings

Dimension reduction tools preserving similarity and graph structure such as t-SNE and UMAP can capture complex biological patterns in high-dimensional data. However, these tools typically are not designed to separate effects of interest from unwanted effects due to confounders. We introduce the partial embedding (PARE) framework, which enables removal of confounders from any distance-based dimension reduction method. We then develop partial t-SNE and partial UMAP and apply these methods to genomic and neuroimaging data. Our results show that the PARE framework can remove batch effects in single-cell sequencing data as well as separate clinical and technical variability in neuroimaging measures. We demonstrate that the PARE framework extends dimension reduction methods to highlight biological patterns of interest while effectively removing confounding effects.

neuroscience↗

bioRxiv2022

Inter-scanner brain MRI volumetric biases persist even in a harmonized multi-subject study of multiple sclerosis

Background/PurposeMulticenter study designs involving a variety of MRI scanners have become increasingly common. However, these present the issue of biases in image-based measures due to scanner or site differences. To assess these biases, we imaged 11 volunteers with multiple sclerosis (MS) with scan and rescan data at 4 sites. Materials and MethodsImages were acquired on Siemens or Philips scanners at 3-tesla. Automated white matter lesion detection and whole brain, gray and white matter, and thalamic volumetry were performed, as well as expert manual delineations of T1 and T2 (FLAIR) lesions. Random effect and permutation-based nonparametric modeling was performed to assess differences in estimated volumes within and across sites. ResultsRandom effect modeling demonstrated model assumption violations for most comparisons of interest. Non-parametric modeling indicated that site explained > 50% of the variation for most estimated volumes. This expanded to > 75% when data from both Siemens and Philips scanners were included. Permutation tests revealed significant differences between average inter- and intra-scanner differences in most estimated brain volumes (P < .05). The automatic activation of spine coil elements during some acquisitions resulted in a shading artifact in these images. Permutation tests revealed significant differences between thalamic volume measurements from acquisitions with and without this artifact. ConclusionDifferences in brain volumetry persisted across MR scanners despite protocol harmonization. These differences were not well explained by variance component modeling; however, statistical innovations for mitigating inter-scanner differences show promise in reducing biases in multi-center studies of MS.

neuroscience↗

bioRxiv2021

Resting state functional connectivity in relapsing remitting multiple sclerosis with mild disability - a data driven, whole brain multivoxel pattern analysis study

BackgroundMultivoxel pattern analysis (MVPA) has emerged as a powerful unbiased approach for generating seed regions of interest (ROIs) in resting-state functional connectivity (RSFC) analysis in a data-driven manner. Studies exploring RSFC in multiple sclerosis have produced diverse and often incongruent results. ObjectivesThe aim of the present study was to investigate RSFC differences between persons with relapsing-remitting multiple sclerosis (RRMS) and healthy controls (HC). MethodsWe performed a whole-brain connectome-wide MVPA in 50 RRMS patients with expanded disability status scale [≤]4 and 50 age and gender-matched HCs. ResultsSignificant group differences were noted in RSFC in three clusters distributed in the following regions; anterior cingulate gyrus, right middle frontal gyrus, and frontal medial cortex. Whole-brain seed-to-voxel RSFC characterization of these clusters as seed ROIs revealed network-specific abnormalities, specifically in the anterior cingulate cortex and the default mode network. ConclusionsThe network-wide RSFC abnormalities we report agree with the previous findings in RRMS, the cognitive and clinical implications of which are discussed herein. IMPACT STATEMENTThis study investigated resting state functional connectivity (RSFC) in relapsing remitting multiple sclerosis (RRMS) persons with mild disability (expanded disability status scale [≤]4). Whole-brain connectome-wide multivoxel pattern analysis (MVPA) was used for assessing RSFC. Compared to healthy controls (HC), we were able to identify three regions of interest for significant differences in connectivity patterns, which were then extracted as a mask for whole-brain seed-to-voxel analysis. A reduced connectivity was noted in the RRMS group, particularly in the anterior cingulate cortex and the default mode network regions, providing insights into the RSFC abnormalities in RRMS.

neuroscience↗

bioRxiv2021

Imaging Multiple Sclerosis Pathology at 160μm Isotropic Resolution by Human Whole-Brain Ex Vivo Magnetic Resonance Imaging at 3T

Postmortem magnetic resonance imaging (MRI) of the fixed healthy and diseased human brain facilitates spatial resolutions and image quality that is not achievable with in vivo MRI scans. Though challenging - and almost exclusively performed at 7T field strength - depicting the tissue architecture of the entire brain in fine detail is invaluable since it enables the study of neuroanatomy and uncovers important pathological features in neurological disorders. The objectives of the present work were (i) to develop a 3D isotropic ultra-high-resolution imaging approach for human whole-brain ex vivo acquisitions working on a standard clinical 3T MRI system, and (ii) to explore the sensitivity and specificity of this concept for specific pathoanatomical features of multiple sclerosis. The reconstructed images demonstrate unprecedented resolution and soft tissue contrast of the diseased human brain at 3T, thus allowing visualization of sub-millimetric lesions in the different cortical layers and in the cerebellar cortex, as well as unique cortical lesion characteristics such as the presence of incomplete / complete iron rims, and patterns of iron accumulation. Further details such as the subpial molecular layer, the line of Gennari, and some intrathalamic nuclei are also well distinguishable.

neuroscience↗

bioRxiv2017

An automated statistical technique for counting distinct multiple sclerosis lesions can recover aspects of lesion history and provide relevant disease information

BackgroundLesion load is a common biomarker in multiple sclerosis, yet it has historically shown modest associations with clinical outcomes. Lesion count, which encapsulates the natural history of lesion formation and is thought to provide complementary information, is difficult to assess in patients with confluent (i.e. spatially overlapping) lesions. We introduce a statistical technique for cross-sectionally counting pathologically distinct lesions.\n\nMethodsMRI is used to assess the probability of lesion at each location. The texture of this map is quantified using a novel technique, and clusters resembling the center of a lesion are counted.\n\nResultsValidity was demonstrated by comparing the proposed count to a gold-standard count in 60 subjects observed longitudinally. The counts were highly correlated (r = .97, p < .001) and not significantly different (t59 = -0.83, p > .40). Reliability was determined using 14 scans of a clinically stable subject acquired at 7 sites, and variability of lesion count was equivalent to that of lesion load. Accounting for lesion load and age, lesion count was negatively associated (t58 = -2.73, p < .01) with the Expanded Disability Status Scale (EDSS). Average lesion size had a higher association with EDSS (r =.35, p < .01) than lesion load (r = .10, p > .40) or lesion count (r = -.12, p > .30) alone.\n\nConclusionThese findings demonstrate that it is possible to recover important aspects of the natural history of lesion formation without longitudinal data, and suggest that lesion size provides complementary information about disease.\n\nGrant SupportThe project described was supported in part by the NIH grants R01 NS085211, R21 NS093349, and R01 NS094456 from the National Institute of Neurological Disorders and Stroke (NINDS). The study was also supported by the Intramural Research Program of NINDS and the Race to Erase MS Foundation. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies.

neuroscience↗