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Unveiling Hidden Neural Codes: SIMPL – A Scalable and Fast Approach for Optimizing Latent Variables and Tuning Curves in Neural Population Data

Dr. Rishabh Pathak
This research paper presents SIMPL (Scalable Iterative Maximization of Population-coded Latents), a novel, computationally efficient algorithm designed to refine the estimation of latent variables and tuning curves from neural population activity. Latent variables in neural data represent essential low-dimensional quantities encoding behavioral or cognitive states, which neuroscientists seek to identify to understand brain computations better. Background and Motivation Traditional approaches commonly assume the observed behavioral variable as the latent neural code. However, this assumption can lead to inaccuracies because neural activity sometimes encodes internal cognitive states differing subtly from observable behavior (e.g., anticipation, mental simulation). Existing latent variable models face challenges such as high computational cost, poor scalability to large datasets, limited expressiveness of tuning models, or difficulties interpreting complex neural network-based functio...
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The Cytoplasmic Function of Atm in Neurons: Beyond DNA Breaks

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Dr. Rishabh Pathak

The Ataxia-telangiectasia mutated protein kinase (ATM) is traditionally known for its role in DNA damage response, particularly in sensing and repairing DNA double-strand breaks. However, recent research has uncovered novel cytoplasmic functions of ATM in neurons that extend beyond its canonical role in DNA repair. Here are some key points regarding the cytoplasmic function of ATM in neurons:


1.      Regulation of Nucleolar Transcription:

o  ATM Activation: In neurons, ATM has been identified as a regulator of RNA-Polymerase-1 (Pol-1)-mediated transcription of nucleolar rRNA genes (rDNA). Activation of ATM, even at low concentrations of DNA double-strand break inducers, stimulates rDNA transcription in cortical neurons.

o    Transcriptional Regulation: ATM positively regulates nucleolar transcription by modulating the activity of Pol-1, which is essential for ribosomal RNA synthesis and ribosome biogenesis. Dysregulation of nucleolar transcription due to ATM deficiency may contribute to neurodegenerative processes.

2.     Nucleolar Localization:

o ATM Localization: Interestingly, ATM has been found to be robustly present in neuronal nucleoli, the subnuclear compartments responsible for ribosome biogenesis. This localization suggests a direct role for ATM in regulating nucleolar functions and ribosomal biogenesis in neurons.

o    Phosphorylation Targets: Critical regulators of Pol-1, the enzyme responsible for rRNA synthesis, display potential ATM phosphorylation sites. This indicates that ATM may directly modulate the activity of nucleolar transcription factors to regulate ribosomal biogenesis.

3.     Neurodegenerative Implications:

o Defective Ribosomal Biogenesis: Dysregulation of nucleolar transcription and ribosome biogenesis, as observed in ATM-deficient neurons, may contribute to neurodegenerative processes. Impaired ribosomal biogenesis can lead to disruptions in protein synthesis, cellular homeostasis, and neuronal function, potentially exacerbating neurodegenerative conditions.

o ATM-Related Disorders: Mutations in the ATM gene are associated with Ataxia-telangiectasia (A-T), a neurodegenerative disorder characterized by progressive cerebellar degeneration and increased cancer susceptibility. The cytoplasmic functions of ATM in nucleolar transcription provide insights into the pathophysiology of A-T and related neurodegenerative conditions.

4.    Therapeutic Implications:

o Targeting Nucleolar Transcription: Modulating nucleolar transcription and ribosome biogenesis pathways regulated by ATM could offer novel therapeutic strategies for neurodegenerative disorders associated with ATM dysfunction. Targeting ribosomal biogenesis processes may help restore neuronal homeostasis and function in these conditions.

o    Precision Medicine Approaches: Understanding the cytoplasmic functions of ATM in neurons opens up avenues for precision medicine approaches that target nucleolar transcription pathways specifically in neurodegenerative disorders linked to ATM abnormalities. Tailored interventions aimed at restoring nucleolar function could hold promise for disease management.

In conclusion, the cytoplasmic function of ATM in neurons, particularly its role in regulating nucleolar transcription and ribosomal biogenesis, represents a novel aspect of ATM biology beyond its canonical DNA damage response functions. Dysregulation of ATM-mediated nucleolar processes may contribute to neurodegenerative conditions, highlighting the therapeutic potential of targeting these pathways in neuronal disorders.

 

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