Biology subjects

Kantor, B.

Publications and source records attributed to Kantor, B..

3 recordsLinked to original sources

bioRxiv2023

Brainways: An Open-Source AI-based Software For Registration and Analysis of Fluorescent Markers on Coronal Brain Slices

A central current trend in neuroscience involves the identification of brain-wide neural circuits associated with complex behavior. A major challenge for this approach involves the laborious process for registration and quantification of fluorescence on histological brain slices, as well as the difficulty of deriving functional insight from the complex resulting datasets. As a solution, we developed Brainways, a simple-to-use AI-based open-source software for the identification of neural networks involved in a specific behavior, from digital images to network analysis. Brainways offers automatic registration of coronal slices to any 3D brain atlas, and provides quantification of fluorescent markers (e.g. activity marker, tracer) per region, as well as statistical comparisons with visual mapping of contrasts between conditions. A built-in partial least squares task analysis provides the neural patterns associated with a specific contrast, as well as network graph analysis representing functional connectivity. Trained on atlases for rats and mice, Brainways currently provides above 80% atlas registration accuracy and allows the user to easily adjust the outputs for better fit. Below, a case study validation of Brainways is demonstrated on a previously published data set describing the neural correlates of empathic helping behavior in rats. The original results were successfully replicated and expanded upon, due to the exponentially larger sample size that covered over a 100 times more brain tissue compared to the original manual sampling. Brainways thus provides a fast, accurate solution for quantification of large-scale projects and facilitates novel neurobiological insights about the structural and functional neural networks involved in complex behavior. Brainways has a highly accessible GUI and is functionality exposed through a Python-based API, which can be enhanced for different applications.

neuroscience↗

bioRxiv2023

All-in-one AAV-delivered epigenome-editing platform: proof-of-concept and therapeutic implications for neurodegenerative disorders

Safely and efficiently controlling gene expression is a long-standing goal of biomedical research, and the recently discovered bacterial CRISPR/Cas system can be harnessed to create powerful tools for epigenetic editing. Current state-of-the-art systems consist of a deactivated-Cas9 nuclease (dCas9) fused to one of several epigenetic effector motifs/domains, along with a guide RNA (gRNA) which defines the genomic target. Such systems have been used to safely and effectively silence or activate a specific gene target under a variety of circumstances. Adeno-associated vectors (AAVs) are the therapeutic platform of choice for the delivery of genetic cargo; however, their small packaging capacity is not suitable for delivery of large constructs, which includes most CRISPR/dCas9-effector systems. To circumvent this, many AAV-based CRISPR/Cas tools are delivered in two pieces, from two separate viral cassettes. However, this approach requires higher viral payloads and usually is less efficient. Here we develop a compact dCas9-based repressor system packaged within a single, optimized AAV vector. The system uses a smaller dCas9 variant derived from Staphylococcus aureus (Sa). A novel repressor was engineered by fusing the small transcription repression domain (TRD) from MeCP2 with the KRAB repression domain. The final dSaCas9-KRAB-MeCP2(TRD) construct can be efficiently packaged, along with its associated gRNA, into AAV particles. Using reporter assays, we demonstrate that the platform is capable of robustly and sustainably repressing the expression of multiple genes-of-interest, both in vitro and in vivo. Moreover, we successfully reduced the expression of ApoE, the stronger genetic risk factor for late onset Alzheimers disease (LOAD). This new platform will broaden the CRISPR/dCas9 toolset available for transcriptional manipulation of gene expression in research and therapeutic settings.

bioengineering↗

bioRxiv2021

Adolescent rats extend help to outgroup members, highlighting a neural network for group identity categorization.

Prosocial behavior, in particular helping others in need, occurs preferentially in response to the perceived distress of ones own group members, or ingroup. The development of neural mechanisms underlying social selectivity towards ingroup members are not well established. Here, we used a rat helping behavior test to explore the development and neural basis of ingroup bias for prosocial behavior in adolescent rats. We previously found that adult rats selectively help others from their own social group, and that this selectivity is associated with activation in reward and motivation circuits. Surprisingly, we found that adolescent rats helped both ingroup and outgroup members, evidence suggesting that ingroup bias emerges in adulthood. Analysis of brain-wide neural activity, indexed by expression of the early-immediate gene c-Fos, revealed increased activity for ingroup members across a broad set of regions, which was congruent for adults and adolescents. However, adolescents showed reduced hippocampal and insular activity, and increased orbitofrontal cortex activity compared to adults. Adolescent rats who did not help trapped others also demonstrated increased amygdala connectivity. Together, these findings demonstrate that biases for group-dependent prosocial behavior develop with age in rats and suggest that specific brain regions contribute to this prosocial selectivity, overall pointing to possible targets for the functional modulation of ingroup bias. One Sentence SummaryProsocial selectivity increases with age in parallel with hippocampal and insular activation, providing insight into the neural classification of group membership.

neuroscience↗