Biology subjects

Varma, A.

Publications and source records attributed to Varma, A..

9 recordsLinked to original sources

bioRxiv2026

Generation of a transgenic cephalopod

Coleoid cephalopods (cuttlefish, octopus, and squid) are marine mollusks with elaborate nervous systems that support a diverse repertoire of complex behaviors. These include the neural control of the color, pattern, and texture of the skin, facilitating both adaptive camouflage and innate patterning that may reflect internal state. The development of transgenic cephalopods expressing fluorescent proteins, optogenetic actuators, and reporters of neural activity would contribute a new and important technology to cephalopod biology. The generation of transgenic cephalopods, however, has remained a major challenge. Here, we report the development of stable transgenic dwarf cuttlefish (Ascarosepion bandense) expressing ubiquitous nuclear-localized mScarlet, a red fluorescent protein. We evaluated multiple strategies for transgenesis, and established cuttlefish lines using both CRISPR and the transposons Sleeping Beauty and Minos. The stable expression of transgenes enabled live imaging of cell dynamics during embryonic development. The Minos transposon emerged as the most efficient transgenesis strategy and is adaptable to promoters and transgenes of choice. These strategies now enable the generation of diverse genetic tools for mechanistic studies of cephalopod biology.

genetics↗

bioRxiv2026

Systemic hypoxia drives glycogen-fueled progression of lung adenocarcinoma

In advanced stages, lung adenocarcinoma obstructs airways and disrupts ventilation-perfusion relationships in the lung, causing systemic hypoxemia and enabling a feed-forward loop that accelerates malignancy. Systemic hypoxemia is also experienced due to common respiratory comorbidities such as chronic obstructive pulmonary disease (COPD) and obstructive sleep apnea (OSA), potentially accelerating malignancy. In a statewide electronic health record network, pre-existing COPD (598 matched pairs) or sleep apnea (235 matched pairs) independently predicted worse survival following incident lung cancer diagnosis. Since the mechanistic basis of the link between malignancy and hypoxia is not well understood, we created systemic hypoxia in KrasLSL-G12D/+;Trp53fl/fl (KP) mice by delivering low inspired oxygen concentrations (8% inspired oxygen; 8 h daily). Hypoxia nearly doubled tumor multiplicity and selectively remodeled cancer central carbon metabolism. Spatially resolved metabolomics revealed marked tumor-compartment glycogen accumulation, elevated tricarboxylic-acid cycle intermediates, and depleted glycolytic pools. Quantitative proteomics across cellular models and autochthonous tumors demonstrated that systemic hypoxia drives glycogen mobilization selectively through the lysosomal enzyme acid -glucosidase (GAA). Tumor-cell-autonomous deletion of GAA eliminated the hypoxia-driven growth advantage and disrupted downstream anabolic biosynthetic pathways. Thus, systemic hypoxia drives lung adenocarcinoma expansion by mobilizing lysosomal glycogen reserves through GAA to sustain proliferative growth.

cancer biology↗

bioRxiv2025

Sex-Stratified Transcriptomic Meta-Analysis of Alzheimer's Disease Reveal Brain Region and Sex Specific Dysregulation

ObjectiveAlzheimer disease (AD) is a neurodegenerative disorder leading to cognitive decline. Despite growing recognition of sex differences in epidemiology, symptomatology, and clinical outcomes of AD, the molecular mechanisms underlying these variations remain poorly defined. We performed transcriptome association studies of AD aiming to identify sex-specific and sex-dependent transcriptomic profiles that could provide insights into the molecular mechanisms underlying sex differences in AD pathogenesis. MethodsWe conducted a meta-analysis of bulk-RNAseq data derived from human postmortem brain studies. Specifically, we analyzed gene expression differences between individuals diagnosed with AD and non-cognitively impaired (NCI) individuals across two key brain regions: the prefrontal cortex and the temporal lobe. We performed stratified differential expression analyses separately in males and females, alongside combined analyses across sexes. Additionally, we assessed the data in relation to known AD genes, proteomic studies, and drug repurposing opportunities. ResultsBeyond the genes commonly dysregulated across both sexes, our meta-analyses identified multiple differentially expressed genes (DEGs) between AD and NCI that are either altered in only one sex or show different effects between sexes. Some genes are known AD genes from genetic studies, but others are novel. Correlation with proteomic data suggests that these transcriptional differences have functional significance, potentially contributing to the biological mechanisms underlying sex differences observed in AD. Finally, we identify drug compounds that are potential candidates for treatment. InterpretationOur findings enhance our understanding of sex-related differences in disease etiology and progression, and underscore the importance of incorporating sex as a critical variable in transcriptomic studies of AD. These insights help pave the way for more precise, personalized medicine approaches that account for sex-specific molecular mechanisms.

molecular biology↗

bioRxiv2025

Temporal integration and active sensing of light in planarians

Animal light sensing and processing are intimately connected to the design of the sensory apparatus, with eye-design a subject of longstanding interest. Understanding animal response to stimuli can elucidate the nature of neural-processing encoded within the photosensory system, tuned to the specific eye-design. Planarians show exquisite photosensitivity and remarkably diverse light-induced behaviors. Further, they are bilaterally-symmetric and possess prototypic cup-shaped eyes, considered an important landmark in eye evolution. Here, using quantitative analysis of behaviour, we address planarian photo-response to distinct presentation of light gradients. Notably, we find that as the nature and presentation of gradients are altered, planarians switch their navigation strategies. When subjected to side-illumination, planarians display negative-phototaxis with a predominantly angular trajectory which presumably allows the animal to maintain the intensity difference between their two eyes for orientation during taxis. However, when subjected to top illumination where light intensity difference between the two eyes would be minimal, animals are still negatively phototactic but the dominant trajectories tend to be directly away from light. Apart from spatial light-intensity sensing, planarians also appear capable of temporal light sensing; confirmed by their response to a spatially-uniform light source with intensity modified over time. Crucially data show that planarians may be using spatial and temporal light sensing to differing degrees depending on the stimuli. Further, when subjected to light illumination from below, planarians fully switch orientation and go belly-up, indicating an active sampling of light distinct from photo-aversive behaviour. Overall, our results show planarian light-sensing to be multilayered, dependent on distinct, highly plastic sensory strategies and beyond basic photo-aversive behaviour.

animal behavior and cognition↗

bioRxiv2024

Highly synchronized inhibition from Purkinje cells entrains cerebellar output in zebrafish

Cerebellar function, known to be important for motor learning and motor coordination, is mediated by efferent neurons that project to diverse motor areas. To understand cerebellar function, it is imperative to study how these efferent neurons integrate inputs from the principal neurons of the cerebellar cortex, the inhibitory Purkinje neurons (PNs). In zebrafish, PNs are bistable and we show here that bistability influences spike synchrony among PNs. Bistability also alters spike correlation with motor bouts. We asked how PN population synchrony influences Eurydendroid cells (ECs), which are postsynaptic targets of PNs and are the cerebellar efferent cells in zebrafish. Using optogenetics, we artificially modulated population synchrony of PNs over millisecond time scales and showed that under conditions of high synchrony, EC firing is briefly suppressed and entrained by PN spiking. However, the magnitude of such modulation is relatively small and indicates a strong combined influence of other synaptic inputs on EC spiking. Key PointsO_LICerebellar Purkinje neurons (PN) in larval zebrafish alter simple spike correlations with each other based on cellular state. C_LIO_LIThey also alter simple spike correlations with motor bouts as a function of state. C_LIO_LIWe altered PN population synchrony in a graded manner using optogenetics. C_LIO_LIPN targets are cerebellar efferent neurons, which in teleosts are called eurydendroid cells. C_LIO_LIWhen PN population is firing with high synchrony, eurydendroid cells are entrained better than when the PN input is asynchronous. C_LIO_LIThis can explain how PNs use bistability to modulate their influence on cerebellar output and ultimately, motor behavior. C_LI

neuroscience↗

bioRxiv2022

A machine-learning tool to identify bistable states from calcium imaging data

Mapping neuronal activation using calcium imaging in vivo during behavioral tasks has advanced our understanding of nervous system function. In almost all of these studies, calcium imaging is used to infer spike probabilities since action potentials activate voltage-gated calcium channels and increase intracellular calcium levels. However, neurons not only fire action potentials, but also convey information via intrinsic dynamics such as by generating bistable membrane potential states. While a number of tools for spike inference have been developed and are currently being used, no tool exists for converting calcium imaging signals to maps of cellular state in bistable neurons. Purkinje neurons (PNs) in the larval zebrafish cerebellum exhibit membrane potential bistability, firing either tonically or in bursts. Several studies have implicated the role of a population code in cerebellar function, with bistability adding an extra layer of complexity to this code. In this manuscript we develop a tool, CaMLSort which uses convolutional recurrent neural networks to classify calcium imaging traces as arising from either tonic or bursting cells. We validate this classifier using a number of different methods and find that it performs well on simulated event rasters as well as real biological data that it had not previously seen. Moreover, we find that CaMLsort generalizes to other bistable neurons, such as dopaminergic neurons in the ventral tegmental area of mice. Thus, this tool offers a new way of analyzing calcium imaging data from bistable neurons to understand how they participate in network computation and natural behaviors. Key Points SummaryCalcium imaging - the gold standard of inferring neuronal activity - does not report cellular state in neurons that are bistable, such as Purkinje neurons in the cerebellum of larval zebrafish. We model the relationship between Purkinje neuron electrical activity and its corresponding calcium signal to compile a dataset of state-labelled simulated calcium signals. We apply machine-learning methods to this dataset to develop a tool that can classify the state of a Purkinje neuron using only its calcium signal, which works well on real data even though it was trained only on simulated data. CaMLsort also generalizes well to bistable neurons in a different brain region (ventral tegmental area) in a different model organism (mouse). This tool offers a new way of analyzing calcium imaging data from populations of bistable neurons, thereby facilitating our understanding of how these neurons carry out their functions in a circuit.

neuroscience↗

bioRxiv2021

Adaptable internal representations drive cerebellum-mediated predictive control of an innate behavior

The cerebellum is known to optimize behavioral responses via error minimization, yet how past sensory experience shapes cerebellar output is still poorly understood. We imaged cerebellar Purkinje cells (PCs) in larval zebrafish during a behavioral assay in which they learnt to expect the direction of optic flow stimulus. PCs encoded signals of expectation and a graded error signal when a deviant stimulus was encountered. The amplitude of the error signal scaled based on stimulus history over minute-timescales. Granule cells (GC) did not encode error, however, some GC types encoded putative expectation signals. When PC population-wide readouts of expectation and error signals were strong, swim latency was low and vice versa, indicating participation of these signals in motor planning. Consistent with this, lesioning the cerebellum abolished expectation-dependent modulation of swim latency. Based on these results we propose that PCs use expectation and error signals to acquire and update internal models of the world. HighlightsO_LILarval zebrafish learn to expect repeatedly encountered optic flow stimuli C_LIO_LIStimulus history over minutes contributes to an internal model of the sensory world C_LIO_LIPurkinje neuron activity encodes deviations from expected direction of optic flow C_LIO_LIThe cerebellum uses learnt expectations to generate lower latency swim responses C_LI

neuroscience↗

bioRxiv2021

Bioprinting transgenic plant cells for production of a recombinant biodefense agent

Transgenic rice cells (Oryza sativa) producing recombinant butyrylcholinesterase (BChE) as a prophylactic/therapeutic against organophosphate nerve agent poisoning, cocaine toxicity, and neurodegenerative diseases like Alzheimers were immobilized in a polyethylene glycol-based hydrogel. The cells were sustained for 14 days in the semi-solid matrix, undergoing a growth phase from days 0-6, a BChE production phase in sugar-free medium from days 6-12, and a growth/recovery phase from days 12-14. Throughout this period, the cells maintained similar viability to those in suspension cultures and displayed analogous sugar consumption trends. The rice cells in the bioprintable hydrogel also produced a significant amount of active BChE, comparable to the levels produced in liquid cultures. A considerable fraction of this BChE was secreted into the media, allowing for easier product separation. Overall, we demonstrate a simple, efficient, robust, modular, and potentially field-deployable bioreactor system for the manufacture of biologics.

plant biology↗

bioRxiv2020

Creating Clear and Informative Image-based Figures for Scientific Publications

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in three fields; plant sciences, cell biology and physiology (n=580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.

bioinformatics↗