Biology subjects

Abrams, A.

Publications and source records attributed to Abrams, A..

3 recordsLinked to original sources

bioRxiv2020

Molecular topography of an entire nervous system

Nervous systems are constructed from a deep repertoire of neuron types but the underlying gene expression programs that specify individual neuron identities are poorly understood. To address this deficit, we have produced an expression profile of all 302 neurons of the C. elegans nervous system that matches the single cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses unique codes of [~]23 neuropeptide-encoding genes and [~]36 neuropeptide receptors thus pointing to an expansive "wireless" signaling network. To demonstrate the utility of this uniquely comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression across the nervous system and (2) reveal adhesion proteins with potential roles in synaptic specificity and process placement. These data are available at cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity and function throughout the C. elegans nervous system.

neuroscience↗

bioRxiv2020

Do carbonated beverages reduce bleeding from gill injuries in angled Northern Pike?

The premise of catch-and-release angling is that most fish survive fisheries interactions. Therefore, it is common for anglers, management agencies, and other organizations to share information on handling practices and other strategies that are believed to improve fish welfare and survival. Recent media coverage has sensationalized the use of carbonated beverages to treat bleeding fish, an intervention that is purported to stop bleeding but has yet to be validated scientifically. We captured Northern Pike (Esox lucius) via hook and line, experimentally injured their gills in a standardized manner, and treated them with either Mountain Dew, Coca Cola, or carbonated lake water and observed the duration and intensity of bleeding, as well as overall blood loss (using gill colour as a proxy) while the fish was held in a lake water bath. As a control, we had a group of experimentally injured fish that did not have liquid poured over their gills before the observation period. All treatments and the control were conducted at two different water temperatures (11-18 {degrees}C and 24-27 {degrees}C) to determine if the effects of pouring carbonated beverages over injured gills is temperature dependent. When compared to the control, we found that the duration and intensity of bleeding increased regardless of the type of carbonated beverages used in this study, and there was no effect of water temperature. Use of chilled versus ambient temperature beverages similarly had no influence on outcomes. As such, there is no scientific evidence to support the use of carbonated beverages for reducing or stopping blood loss for fish that have had their gills injured during recreational angling based on the context studied here. This study reinforced the need to scientifically test angler anecdotes and theories when it comes to best practices for catch-and-release fishing.

ecology↗

bioRxiv2019

Expression profiling of the mature C. elegans nervous system by single-cell RNA-Sequencing

A single neuron and its synapses define the fundamental structural motif of the brain but the underlying gene expression programs that specify individual neuron types are poorly understood. To address this question in a model organism, we have produced a gene expression profile of >90% of the individual neuron classes in the C. elegans nervous system, an ensemble of neurons for which both the anatomy and connectivity are uniquely defined at single cell resolution. We generated single cell transcriptomes for 52,412 neurons that resolve as clusters corresponding to 109 of the canonical 118 neuron classes in the mature hermaphrodite nervous system. Detailed analysis revealed molecular signatures that further subdivide identified classes into specific neuronal subtypes. Notably, neuropeptide-related genes are often differentially expressed between subtypes of the given neuron class which points to distinct functional characteristics. All of these data are publicly available at our website (http://www.cengen.org) and can be interrogated at the web application SCeNGEA (https://cengen.shinyapps.io/SCeNGEA). We expect that this gene expression catalog will spur the goal of delineating the underlying mechanisms that define the developmental lineage, detailed anatomy, synaptic connectivity and function of each type of C. elegans neuron.

neuroscience↗