Biology subjects

Bakshi, A.

Publications and source records attributed to Bakshi, A..

16 recordsLinked to original sources

bioRxiv2026

Serine/Threonine phosphatase PP1 is a regulator of Notch signalling.

Cell diversity generation is cardinal to the development of the functional central nervous system. The Notch pathway plays an important role in neurogenesis, spanning cell fate determination, cell death, and neural stem cell (NSC) competence switching, and is therefore highly regulated within cells. While the phosphorylation-based regulation of the pathway and its associated kinases is known, few phosphatases have been identified to counterbalance these regulations. Protein Phosphatase 1 is a member of a Serine/Threonine family of phosphatases responsible for a large majority of dephosphorylation events in the cell. In this study, we identify PP1- and its regulatory subunit, PNUTS, as novel regulators of the Notch signalling pathway during Drosophila neurogenesis. We show that PP1-87B/PNUTS positively regulate Notch signalling by dephosphorylating a highly conserved Serine residue in Su(H) to restore its DNA binding activity and thereby activating Notch downstream targets during neurogenesis. This facilitates the execution of two distinct physiological events, NSC apoptosis and competence switching, in different regions of the Drosophila CNS. We find that this regulation of the Notch pathway is also extendable to another cellular context, epithelial wing disc tissue, and critically relies on the phosphatase activity of PP1. Given that we can rescue the Notch-dependent depletion phenotypes of PP1- using its human ortholog, we believe this regulation is likely to be conserved across species during development.

developmental biology↗

bioRxiv2026

Single-locus chromatin memory enables flexible spatial fate specification in the Drosophila visual system

Spatial patterning generates neuronal diversity by compartmentalizing progenitors into domains with distinct molecular identities. However, these patterning cues are often transient in neurogenic domains, raising the question of how spatial information can be preserved and how rigidly it constrains neuronal fates. Here we show that a single-locus chromatin memory in the Drosophila medulla enables spatial identity to be both faithfully executed and flexibly bypassed. Medulla progenitors are partitioned into three spatial domains marked by Vsx1, Optix and Bifid. Domain-resolved single-cell multiome profiling reveals that progenies from different neuroepithelial domains are nearly indistinguishable for both transcriptome and chromatin accessibility, although persistent, domain-specific accessibility is retained only at a single spatial-factor locus, either Vsx1/2 or Bifid. These same factors are absent when neuroepithelial cells are converted to neural stem cells but are re-expressed in postmitotic neurons to execute domain-specific fates. Because this bookmarking is so restricted, specific classes of neurons can skip the domain-specific re-expression program and default to a common ground state, adopting equivalent fates regardless of spatial origin. Other neurons reach the same domain-ignoring state by expressing Vsx1/2 through a program independent of their domain of origin. PRC2-mediated silencing restricts Vsx1 re-expression to its home domain, while temporal identity and Notch signaling in newborn neurons determine which neurons engage or bypass the spatial program. Thus, single-locus chromatin memory preserves spatial information without making it an obligatory determinant of every neuronal fate.

developmental biology↗

bioRxiv2025

Deep Learning for Sorghum Yield Forecasting using Uncrewed Aerial Systems and Lab-Derived Imagery

The AI revolution, advanced Graphics Processing Units (GPUs), and open-source platforms have enabled Machine Learning (ML) and Deep Learning (DL) algorithms to rapidly and accurately extract phenotypic features from Uncrewed Aerial System (UAS)-derived imagery. Such advancement leads to phenotypic digitization and sorghum yield forecasting. Yield analytics are critical for breeding programs to assess the genetics and breeding potential of genotypes to enhance cultivar development. This trial followed a three-replicated Randomized Complete Block Design (RCBD) with 36 diverse sorghum genotypes in 2023 at Ashland Bottoms, Kansas. The field images were captured 6 meters above using a DJI M300 drone equipped with the P1 sensor at 90{degrees}nadir and 45{degrees} oblique angles. This research trained YOLO and the Faster R-CNN (Detectron2) models to harness yield attributes from UAS field and lab images. The YOLO models outperformed the Faster R-CNN model in detecting sorghum panicles, achieving a mean average precision at 50% IoU (mAP@0.50) ranging from 0.92 to 0.98, compared to 0.61 to 0.89. Panicle detection from field imagery correlated at 0.86 with ground truth. Lab imagery analyses measured panicle size, seed counts, and seed area with correlation coefficients of 0.71, 0.95, and 0.25, respectively. Three machine learning models: Support Vector Regression (SVR), Decision Tree Regression (DTR), and Random Forest Regression (RFR) are used to predict yield with correlation coefficients of 0.58, 0.76, and 0.70, respectively. We observed that YOLO models are well-suited for extracting yield-attributing traits from images, which are then incorporated into ML regression models to improve yield prediction performance.

plant biology↗

bioRxiv2024

Defining focal neuroendocrine differentiation as a transcriptionally distinct form of prostate cancer pathology characterized by the expression of androgen receptors

BackgroundMen with neuroendocrine prostate cancer (NEPC) have a poor prognosis. NEPC is commonly diagnosed by immunohistochemical markers (CHGA, SYP and NCAM1) and genomic features (mutations in RB1, PTEN, TP53). But by pathology, NEPC tumours are variable, leading to a classification of NE subtypes such as small cell and large cell neuroendocrine carcinomas, focal neuroendocrine differentiation (Focal NED), and Amphicrine. We postulated the diversity observed in NEPC pathologies might arise from differences in transcriptional profiles and the aim of this study is to utilize single-cell RNA sequencing to define the transcriptional differences between NEPC subtype pathologies. MethodsGene expression profiles were obtained for 18,632 individual tumour cells from 9 patient-derived xenograft (PDX) models representing five distinct neuroendocrine pathologies of prostate cancer. Integration and clustering of cell-level data demarked transcriptionally distinct sub-populations of cells. Differential gene expression, gene set enrichment and transcriptional factor regulon analysis identified expression signatures unique to specific neuroendocrine pathologies. Copy-number estimated from expression data revealed the clonal structure of PDXs with mixed adenocarcinoma and neuroendocrine pathologies. ResultsSignificant differences were observed in the transcriptional profiles of NEPC pathology subtypes. Focal NED cells maintain AR signaling, similar to the amphicrine subtype but different from small and large cell carcinomas. Cellular sub-populations enriched for expression of KRAS, IL2-STAT5 and TNF-signaling genes were found in focal NED and amphicrine pathologies, but not in small or large cell carcinomas. In contrast, sub-populations enriched for the YAP, Myc and E2F pathways were detected in small cell, large cell and amphicrine tumours, but not in focal NED cells. Each pathology showed unique patterns of master regulator activity as well, further implicating focal NED as a transcriptionally distinct entity. Based on copy number alterations within PDXs of mixed pathology, focal NED cells showed little clonal divergence from neighboring adenocarcinoma cells, whereas cells with small cell neuroendocrine pathology were clonally distinct. ConclusionsNeuroendocrine prostate cancer subtypes can be identified by pathology and our study shows that transcriptional features identified by single-cell RNA-sequencing also distinguish neuroendocrine subtypes pathologies from each other. In particular, our data redefine focal neuroendocrine differentiation as a pathology expressing androgen receptors (AR), exhibiting its distinctive composition of transcriptionally unique sub-populations. These findings advocate for differences in the treatment of NEPC tumors, particularly those displaying focal NED.

cancer biology↗

bioRxiv2024

Visually Induced Involuntary Movements

Looking at a virtual 3D environment with structural features rotating at 60{degrees}/s in a head-mounted display soon elicits an illusion of self-rotation and displacement in the opposite direction. We explored in 75 s long trials the effects of visually induced self-rotation on the head, torso, and horizontally extended right arm of standing subjects. The degree of body and limb movement was contingent on whether the arm was extended out freely or pointing at a briefly proprioceptively specified target position, but did not depend on whether the hand held a rod or not. Most subjects in the Free condition showed significant unintentional arm deviations, which averaged approximately 55{degrees} in the direction opposite the induced illusory self-motion, and were more than 150{degrees} in some cases. In contrast, on average, the deviations in the Pointing condition were a quarter of those in the Free condition. Deviations of head and torso positions also occurred in all conditions. Total arm and head deviations were the sum of deviations of the arm and head with respect to the torso plus deviations of the torso with respect to space. When given a pointing target, subjects were largely able to detect and correct for arm and head deviations with respect to the torso but not for the parts of arm and head deviation that were due to deviations of the torso with respect to space. In all conditions, the arm, head, and torso deviations occurred before subjects began to experience compelling self-rotation and displacement. This is contrasted with the compensations for expected but absent Coriolis forces that are made when stationary subjects make reaching movements to targets during exposure to structured moving visual scenes. These compensations do not occur until subjects experience self-rotation and spatial displacement. These results have implications for vehicle control and maneuvering in environments that induce illusory motion and displacement, and in situations where there is motion in a large area of the visual field. The impact of these effects on joystick control is described and discussed. We also describe the subjective sense of ownership attributed to hand-held objects when experiencing illusory self-motion and displacement.

neuroscience↗

bioRxiv2023

In Silico Therapeutic Intervention on Cytokine Storm in COVID-19

The recent global COVID-19 outbreak, attributed by the World Health Organization to the rapid spread of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), underscores the need for an extensive exploration of virological intricacies, fundamental pathophysiology, and immune responses. This investigation is vital to unearth potential therapeutic avenues and preventive strategies. Our study delves into the intricate interaction between SARS-CoV-2 and the immune system, coupled with exploring therapeutic interventions to counteract dysfunctional immune responses like the cytokine storm (CS), a driver of disease progression. Understanding these immunological dimensions informs the design of precise multiepitopetargeted peptide vaccines using advanced immunoinformatics and equips us with tools to confront the cytokine storm. Employing a control theory-based approach, we scrutinize the perturbed behavior of key proteins associated with cytokine storm during COVID-19 infection. Our findings support ACE2 activation as a potential drug target for CS control and confirm AT1R inhibition as an alternative strategy. Leveraging deep learning, we identify potential drugs to individually target ACE2 and AT1R, with Lomefloxacin and Fostamatinib emerging as standout options due to their close interaction with ACE2. Their stability within the protein-drug complex suggests superior efficacy among many drugs from our deep-learning analysis. Moreover, there is a significant scope for optimization in fine-tuning protein-drug interactions. Strong binding alone may not be the sole determining factor for potential drugs; precise adjustments are essential. The application of advanced computational power offers novel solutions, circumventing time-consuming lab work. In scenarios necessitating both ACE2 and AT1R targeting, optimal drug combinations can be derived from our analysis of drug-drug interactions, as detailed in the manuscript.

bioinformatics↗

bioRxiv2023

Postural Stability During Illusory Self-Motion - Interactions of Vision and Touch

The role of vision in stabilizing balance has been studied exhaustively. Other studies have shown that non-supportive light touch of the fingertip with a surface also can significantly stabilize postural balance. We have studied how vision and cutaneous information jointly affect balance. We used a head-mounted display to simulate a virtual room that rotated about a vertical axis centered with the standing subjects z-axis. Subjects viewing the displays rotational displacement soon experienced self-motion and displacement. We assessed how the moving visual input destabilized posture and how it interacted with touch cues that stabilized posture. A novel result is how balance is influenced by the onset of visual motion and the illusion of self-rotation. We discovered that motion perceptions are coupled with stochastic aspects of balance. Changes in the perception of types of motion - none, environment-, and self-rotation - distinctively influence metrics that encode for the stochasticity of balance and do not influence those that filter the stochasticity out. We reconfirmed the significant effects of touch in stabilizing balance and discovered how it interacts with the visual perception of motion. We also found lingering effects of past motion perception, which keep influencing the stochasticity of balance even when visual motion is long stopped. Our findings provide insights into multisensory interaction effects in postural balance and suggest novel future research directions.

neuroscience↗

bioRxiv2022

mBAT-combo: a more powerful test to detect gene-trait associations from GWAS data

Gene-based association tests aggregate multiple SNP-trait associations into sets defined by gene boundaries. Since genes have a direct biological link to downstream function, gene-based test results are widely used in post-GWAS analysis. A common approach for gene-based tests is to combine SNPs associations by computing the sum of{chi} 2 statistics. However, this strategy ignores the directions of SNP effects, which could result in a loss of power for SNPs with masking effects (e.g., when the product of the effects of two SNPs and their linkage disequilibrium (LD) correlation is negative). Here, we introduce "mBAT-combo", a new set-based test that is better powered than other methods to detect multi-SNP associations in the context of masking effects. We validate the method through simulations and applications to real data. We find that of 35 blood and urine biomarker traits in the UK Biobank, 34 traits show evidence for masking effects in a total of 4,175 gene-trait pairs, indicating that masking effects in complex traits is common. We further validate the improved power of our method in height, body mass index and schizophrenia with different GWAS sample sizes and show that on average 95.7% of the genes detected only by mBAT-combo with smaller sample sizes can be identified by the single-SNP approach with larger sample sizes (average sample size increased by 1.7-fold). For instance, LRRC4B is significant only in our method for schizophrenia, which has been shown to play a role in presynaptic pathology using genetic fine-mapping and evidence-based synaptic annotations. As a more powerful gene-based method, mBAT-combo is expected to improve the downstream pathway analysis or tissue and cell-type enrichment analysis that takes genes identified from GWAS data as input to understand the biological mechanisms of the trait or disease. Despite our focus on genes in this study, the framework of mBAT-combo is general and can be applied to any set of SNPs to refine trait-association signals hidden in genomic regions with complex LD structures.

genetics↗

bioRxiv2022

Cytoplasmic divisions without nuclei

Cytoplasmic divisions have been commonly considered a sequel to nuclear divisions, even in the absence of DNA replication. Here we found in fruit fly embryos that the cytoplasm can compartmentalize and divide without nuclei. Our targeted screen for potential necessary and sufficient conditions revealed that, although the cytoplasmic compartments are tightly associated with centrosomes, they can form without astral microtubules and divide without centrioles. Although a focal pool of microtubules is necessary for maintaining cytoplasmic compartments, this is not sufficient for their initial formation. Actin filaments are similarly an essential component of cytoplasmic compartments; however, their myosin II-based contractility is unexpectedly dispensable for divisions. We show that the myosin II-based contractility is instead involved in regulating the pace of these divisions. Importantly, our results revealed that the cytoplasmic divisions without nuclei can occur in a periodic manner autonomously of the Cdk-Cyclin oscillator that normally drives the cell cycle. We demonstrate that such autonomy of cytoplasmic divisions is preserved even in normal development, where it is leveraged to extrude mitotically delayed nuclei from the blastoderm, protecting the synchrony of rapid nuclear divisions against local delays in mitotic entry. We propose that an active coordination between otherwise autonomous cycles of cytoplasmic and nuclear divisions acts as a quality control mechanism for genome integrity and partitioning in development.

cell biology↗

bioRxiv2020

Ethylene-triggered subcellular trafficking of CTR1 suppresses the response to ethylene gas

Ethylene gas controls plant growth and stress responses. Ethylene-exposed dark-grown seedlings exhibit dramatic growth reduction, yet the seedlings rapidly return to the basal growth rate when ethylene gas is removed. However, the underlying mechanism governing this reversible acclimation of dark-grown seedlings to ethylene remains enigmatic. Here, we report that ethylene triggers the translocation of the Raf-like protein kinase CONSTITUTIVE TRIPLE RESPONSE1 (CTR1), a negative regulator of ethylene signaling, from the endoplasmic reticulum to the nucleus. Nuclear-localized CTR1 stabilizes the ETHYLENE-INSENSITIVE3 (EIN3) transcription factor via interaction with the EIN3-BINDING F-box (EBF) proteins, thus enhancing the ethylene response and delaying growth recovery. These findings uncover a mechanism of the ethylene signaling pathway that links the spatiotemporal dynamics of cellular signaling components to organismal responses.

plant biology↗

bioRxiv2020

Ribosomal Protein Large subunit RPL6 modulates salt tolerance in rice

The extra-ribosomal functions of ribosomal proteins RPL6 and RPL23a in stress-responsiveness have emanated from our previous studies on activation tagged mutants of rice screened for water-use efficiency (Moin et al., 2016a). In the present study, we functionally validated the RPL6, a Ribosomal Protein Large subunit member for salt stress tolerance in rice. The overexpression of RPL6 resulted in tolerance to moderate (150 mM) to high (200 mM) levels of salt (NaCl) in rice. The transgenic rice plants expressing RPL6 constitutively showed better phenotypic and physiological responses with high quantum efficiency, accumulation of more chlorophyll and proline contents, and an overall increase in seed yield compared with the wild type in salt stress treatments. An iTRAQ-based comparative proteomic analysis revealed the high expression of about 333 proteins among the 4,378 DEPs in a selected overexpression line of RPL6 treated with 200 mM of NaCl. The functional analysis showed that these highly expressed proteins (HEPs) are involved in photosynthesis, ribosome and chloroplast biogenesis, ion transportation, transcription and translation regulation, phytohormone and secondary metabolite signal transduction. An in silico network analysis of HEPs predicted that RPL6 binds with translation-related proteins and helicases, which coordinately affects the activities of a comprehensive signaling network, thereby inducing tolerance and promoting growth and yield in response to salt stress. Our overall findings identified a novel candidate, RPL6 whose characterization contributed to the existing knowledge on the complexity of salt tolerance mechanism in plants.

plant biology↗

bioRxiv2020

Gain of function mutagenesis through activation tagging identifies XPB2 and SEN1 helicase genes as potential targets for drought stress tolerance in rice

We have earlier reported on the development of an activation tagged gain-of-function mutant population in an indica rice variety, BPT-5204 (Moin et al. 2016). Screening of these gain of function mutants for water-use efficiency (WUE) followed by physiological analyses revealed the activation of two helicases, ATP-dependent RNA (SEN1) and DNA (XPB2) encoding unwinding proteins in two different mutant lines. In the current study, we examined the roles of these genes in stable activation tagged mutants of rice for drought stress responses. Transcript profiling of SEN1 and XPB2 showed their significant up-regulation under various stresses (particularly ABA and PEG). The SEN1 and XPB2 tagged mutants exhibited reduced leaf wilting, improved revival efficiency, high chlorophyll and proline contents, profuse tillering, high quantum efficiency and yield-related traits in response to simulated drought (PEG) and hormone (ABA) treatments with respect to their controls. These observations were further validated under greenhouse conditions by periodic withdrawal of water. Germination of the seeds of these mutant lines indicates their ABA insensitivity under high ABA concentration. Also, the associated high up-regulation of stress-specific genes suggests that their drought tolerance might have been because of the coordinated expression of several stress responsive genes in these two mutants. Altogether, our results provided a firm basis for SEN1 and XPB2 as potential candidates for manipulation of drought tolerance and improving rice performance and yield under limited water conditions.

plant biology↗

bioRxiv2020

Target of Rapamycin: function in abiotic stress tolerance in Arabidopsis and its involvement in a possible cross-talk with ribosomal proteins

The Target of Rapamycin (TOR) protein kinase reprograms cellular metabolism under various environmental stresses. The overexpression of TOR in Arabidopsis resulted in increased plant growth including yield and biomass when compared with the wild type under both controlled and limited water conditions. In the present investigation, we report that Arabidopsis plants overexpressing TOR exhibited enhanced tolerance to the osmotic and salt stress treatments. Further to determine the role of TOR in abiotic stresses other than water limiting conditions, which were observed earlier in rice, we have treated high and medium TOR expressing Arabidopsis plants, ATR-1.4.27 and ATR-3.7.32 respectively, with stress-inducing chemical agents such as Mannitol (100 mM), NaCl (150 mM), Sorbitol (200 mM) and PEG (7%). Both the lines, ATR-1.4.27 and ATR-3.7.32 exhibited enhanced tolerance to these stresses. These lines also had increased proline and total chlorophyll contents under stress conditions compared with their corresponding WT counterparts. The upregulation of several osmotic stress inducible genes in Arabidopsis transgenic lines indicated the role of TOR in modulating multi-stress tolerance. In the present investigation, we have also analyzed the transcriptional upregulation of ribosomal protein large and small subunit (RPL and RPS) genes in AtTOR overexpressing rice transgenic lines, TR-2.24 and TR-15.1 generated earlier (Bakshi et al., 2017a), which indicated that TOR also positively regulates the transcription of ribosomal proteins (RP) along with the synthesis of rRNAs. Also, the observations from phosphoproteomic analysis in SALK lines of various Arabidopsis T-DNA insertion mutants of ribosomal proteins showed differential regulation in phosphorylation of p70kDa ribosomal protein S6K1 and comparative analysis of phosphorylation sites for RSK (Ribosomal S6 Kinases) in RPL6, RPL18, RPL23, RPL24 and RPS28C proteins of Arabidopsis, Interestingly, rice showed similarity in their peptide sequences and Ser/Thr positions. These results suggest that the phosphorylation of S6K1 is controlled by loss/ inhibition of ribosomal protein function to switch on/ off the translational regulation for balanced growth and the pathways of both RPs and TOR are interlinked in a cyclic manner via phosphorylation of S6K1 as a modulatory step.

plant biology↗

bioRxiv2019

Quantifying genetic heterogeneity between continental populations for human height and body mass index

Genome-wide association studies (GWAS) in samples of European ancestry have identified thousands of genetic variants associated with complex traits in humans. However, it remains largely unclear whether these associations can be used in non-European populations. Here, we seek to quantify the proportion of genetic variation for a complex trait shared between continental populations. We estimated the between-population correlation of genetic effects at all SNPs (rg) or genome-wide significant SNPs (rg(GWS)) for height and body mass index (BMI) in samples of European (EUR; n = 49,839) and African (AFR; n = 17,426) ancestry. The [Formula] between EUR and AFR was 0.75 (s. e. = 0.035) for height and 0.68 (s. e. = 0.062) for BMI, and the corresponding [Formula] was 0.82 (s. e. = 0.030) for height and 0.87 (s. e. = 0.064) for BMI, suggesting that a large proportion of GWAS findings discovered in Europeans are likely applicable to non-Europeans for height and BMI. There was no evidence that [Formula] differs in SNP groups with different levels of between-population difference in allele frequency or linkage disequilibrium, which, however, can be due to the lack of power.

genetics↗

bioRxiv2019

Neonatal genetics of gene expression reveal the origins of autoimmune and allergic disease risk

Chronic immune-mediated diseases of adulthood often originate in early childhood. To investigate genetic associations between neonatal immunity and disease, we collected cord blood samples from a birth cohort and mapped expression quantitative trait loci (eQTLs) in resting monocytes and CD4+ T cells as well as in response to lipopolysaccharide (LPS) or phytohemagglutinin (PHA) stimulation, respectively. Cis-eQTLs were largely specific to cell type or stimulation, and response eQTLs were identified for 31% of genes with cis-eQTLs (eGenes) in monocytes and 52% of eGenes in CD4+ T cells. We identified trans-eQTLs and mapped cis regulatory factors which act as mediators of trans effects. There was extensive colocalisation of causal variants for cell type- and stimulation-specific neonatal cis-eQTLs and those of autoimmune and allergic diseases, in particular CTSH (Cathepsin H) which showed widespread colocalisation across diseases. Mendelian randomisation showed causal neonatal gene transcription effects on disease risk for BTN3A2, HLA-C and many other genes. Our study elucidates the genetics of gene expression in neonatal conditions and cell types as well as the aetiological origins of autoimmune and allergic diseases.

genetics↗

bioRxiv2017

The CURE for Culturing Fastidious Microbes

Course-based Undergraduate Research Experiences (CUREs) expand the scientific educational benefits of research to large groups of students in a course setting. As part of an ongoing effort to integrate CUREs into first-year biology labs, we developed a microbiology CURE (mCURE) that uses a modified dilution-to-extinction high throughput culturing protocol for isolating abundant yet fastidious aquatic bacterioplankton during one semester. Students learn common molecular biology techniques like nucleic acid extraction, PCR, and molecular characterization; read and evaluate scientific literature; and receive training in scientific communication through written and oral exercises that incorporate social media elements. In the first three semesters, the mCUREs achieved similar cultivability success as implementation of the protocol in a standard laboratory setting. Our modular framework facilitates customization of the curriculum for use in multiple settings and we provide classroom exercises, assignments, assessment tools, and examples of student output to assist with implementation.

scientific communication and education↗