Biology subjects

Mathuru, A. S.

Publications and source records attributed to Mathuru, A. S..

4 recordsLinked to original sources

bioRxiv2024

Spatial mRNA profiling using Rapid Amplified Multiplexed-FISH (RAM-FISH)

Spatial localization of multiple mRNAs in intact tissues provides vital insights into development and function, yet routine multiplexed imaging remains constrained by complex workflows, specialized equipment costs, or sample preparation requirements. Here, we present Rapid Amplified Multiplexed FISH (RAMFISH), an accessible, modular, benchtop workflow for targeted spatial mRNA profiling in intact tissues and whole-mount specimens. RAMFISH achieves reliable multiplexing of over 30 transcripts through iterative cycles of standard hybridization either manually or via open-source automation and imaging in shared confocal systems. To streamline analysis, we introduce an integrated, open-source pipeline automating signal normalization, rigid and non-rigid alignment, Laplacian of Gaussian spot calling, and 30-channel composite merging. We validate the platform by mapping multiple transcripts in developing Bicyclus anynana butterfly wings and intact 14 days-post-fertilization Danio rerio larvae, resolving both historically inferred domains and newly characterized gene expression. Overall, RAMFISH methodology offers an end-to-end, completely open-source ecosystem for robust, semi-quantitative, spatial mRNA mapping on a variety of sample types. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/627193v4_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@14dc9a3org.highwire.dtl.DTLVardef@1f11e3dorg.highwire.dtl.DTLVardef@f85483org.highwire.dtl.DTLVardef@1746701_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2021

Contingent-behavior assay shows zebrafish preference for alcohol is biphasic

Alcohol use disorders are complex, multifactorial phenomena with a large footprint within the global burden of diseases. Here, we report the development of an accessible, two-choice self-administration zebrafish assay (SAZA) to study the neurobiology of addiction. Using this assay, we first demonstrated that, while zebrafish avoid higher concentrations of alcohol, they are attracted to low concentrations. Pre-exposure to alcohol did not change this relative preference, but acute exposure to an alcohol deterrent approved for human use decreased alcohol self-administration. A pigment mutant used in whole-brain imaging studies displayed a similar relative alcohol preference profile, however, mutants in CCSER1, a gene associated with alcohol dependence in human genetic studies, showed a reversal in relative preference. The presence of a biphasic response (hormesis) in zebrafish validated a key aspect of vertebrate responses to alcohol. SAZA adds a new dimension for discovering novel alcohol deterrents, and studying the neurogenetics of addiction using the zebrafish.

neuroscience↗

bioRxiv2019

Application of Optogenetic Amyloid-β Distinguishes Between Metabolic and Physical Damage in Neurodegeneration

The brains of Alzheimers Disease patients show a decrease in brain mass and a preponderance of extracellular Amyloid-{beta} plaques. These plaques are formed by aggregation of polypeptides that are derived from Amyloid Precursor Protein (APP). Amyloid-{beta} plaques are thought to play either a direct or an indirect role in disease progression, however the exact role of aggregation and plaque formation in the ethology of Alzheimers Disease is subject to debate, not least because the biological effects of soluble and aggregated Amyloid-{beta} peptides are difficult to separate in vivo. To investigate the consequences of formation of Amyloid-{beta} oligomers in living tissues, we developed a fluorescently tagged, optogenetic Amyloid-{beta} peptide that oligomerizes rapidly in the presence of blue light. We applied this system to the crucial question of how intracellular Amyloid-{beta} oligomers underlie the pathologies of Alzheimers Disease. We show that, although both expression and induced oligomerization of Amyloid-{beta} were detrimental to lifespan and healthspan, we were able to separate the metabolic and physical damage caused by light-induced Amyloid-{beta} oligomerization from Amyloid-{beta} expression alone. The physical damage caused by Amyloid-{beta} oligomers also recapitulated the catastrophic tissue loss that is a hallmark of late AD. We show that the lifespan deficit induced by Amyloid-{beta} oligomers was reduced with Li+ treatment. Our results present the first model to separate different aspects of disease progression.

developmental biology↗

bioRxiv2017

Familiarity with companions aids recovery from fear inzebrafish

Interaction with social partners during or after a stressful episode aids recovery in humans and other mammals. We asked if a comparable phenomenon exists in zebrafish (Danio rerio) that live in shoals in the wild. In the first experiment, we observed that most quantifiable parameters of swimming behavior were similar when zerbafish swam alone or with companions. However, after exposure to an alarm substance (Schreckstoff), individuals recovering alone continued to display behaviors associated with fear after removal of the stimulus, while those recovering with companions did not. In the next two experiments, we examined the role of familiarity of companions. Subjects spent more time in the vicinity of familiar companions in a two-choice assay. While both familiar and unfamiliar companions reduced behavioral signs of distress, familiar companions additionally modulated cortisol and endogenous isotocin in subjects. Shortly after being united with familiar companions, isotocin spiked followed by a dampening of circulating cortisol levels. These results suggest that zebrafish experience fear attenuation in the presence of others and familiar companions are more effective at buffering the stress associated with escaping predation. Changes in behavior, circulating cortisol and isotocin levels due to social partners are reminiscent of changes due to amelioration of fear in some mammalian species in the presence of companions. The two phenomena may be related.

animal behavior and cognition↗