Mandwal, A. | bioRxiv Science

bioRxiv2023

Metabolic Interactive Nodular Network for Omics (MINNO): Refining and investigating metabolic networks based on empirical metabolomics data

Metabolomics is a powerful tool for uncovering biochemical diversity in a wide range of organisms, and metabolic network modeling is commonly used to frame results in the context of a broader homeostatic system. However, network modeling of poorly characterized, non-model organisms remains challenging due to gene homology mismatches. To address this challenge, we developed Metabolic Interactive Nodular Network for Omics (MINNO), a web-based mapping tool that takes in empirical metabolomics data to refine metabolic networks for both model and unusual organisms. MINNO allows users to create and modify interactive metabolic pathway visualizations for thousands of organisms, in both individual and multi-species contexts. Herein, we demonstrate an important application of MINNO in elucidating the metabolic networks of understudied species, such as those of the Borrelia genus, which cause Lyme disease and relapsing fever. Using a hybrid genomics-metabolomics modeling approach, we constructed species-specific metabolic networks for three Borrelia species. Using these empirically refined networks, we were able to metabolically differentiate these genetically similar species via their nucleotide and nicotinate metabolic pathways that cannot be predicted from genomic networks. These examples illustrate the use of metabolomics for the empirical refining of genetically constructed networks and show how MINNO can be used to study non-model organisms. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/548964v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@8cdee6org.highwire.dtl.DTLVardef@7de3ddorg.highwire.dtl.DTLVardef@fac57forg.highwire.dtl.DTLVardef@1bc2efe_HPS_FORMAT_FIGEXP M_FIG MINNO tool facilitates refining of metabolic networks, multi omics integration and investigation of cross-species interactions. C_FIG

bioinformatics↗

bioRxiv2019

A biochemical mechanism for time-encoding memory formation within individual synapses of Purkinje cells

Within the classical eye-blink conditioning, Purkinje cells within the cerebellum are known to suppress their tonic firing rates for a well defined time period in response to the conditional stimulus after training. The temporal profile of the drop in tonic firing rate, i.e., the onset and the duration, depend upon the time interval between the onsets of the training conditional and unconditional stimulus. Direct stimulation of parallel fibers and climbing fiber by electrodes was found to be sufficient to reproduce the same characteristic drop in the firing rate of the Purkinje cell. In addition, the specific metabotropic glutamate-based receptor type 7 (mGluR7), which resides on the Purkinje cell synapses, was found responsible for the initiation of the response, suggesting an intrinsic mechanism within the Purkinje cell for the temporal learning. In an attempt to look for a mechanism for time-encoding memory formation within individual Purkinje cells, we propose a biochemical mechanism based on recent experimental findings. The proposed model tries to answer key aspects of the \"Coding problem\" of Neuroscience by focussing on the Purkinje cells ability to encode time intervals through training. According to the proposed mechanism, the time memory is encoded within the dynamics of a set of proteins -- mGluR7, G-protein, G-protein coupled Inward Rectifier Potassium ion channel, Protein Kinase A and Protein Phosphatase 1 -- which self-organize themselves into a protein complex. The intrinsic dynamics of these protein complexes can differ and thus can encode different time durations. Based on their amount and their collective dynamics within individual synapses, the Purkinje cell is able to suppress its own tonic firing rate for a specific time interval. The time memory is encoded within the effective rate constants of the biochemical reactions and altering these rates constants means storing a different time memory. The proposed mechanism is verified by a simplified mathematical model and corresponding dynamical simulations of the involved biomolecules, yielding testable experimental predictions.\n\nAuthor summaryHebbian plasticity is a widely accepted form of learning that can encode memories in our brain. Spike-timing dependent plasticity resulting in Long-term Potentiation or Depression of synapses has become the default mechanistic explanation behind memory formation within a neuronal population. However, recent experiments of conditional eyeblink response in Purkinje cells have challenged this point of view by showing that these mechanisms alone cannot account for time memory formation in the Purkinje cell. To explain the underlying mechanism behind this novel synaptic plasticity, we introduce a biochemical mechanism based on protein interactions occurring within a single synapse. These protein interactions and the associated effective rate constants are sufficient to encode time delays by auto-induced inhibition on a single excitatory synapse, suggesting that synapses are capable of storing more information than previously thought.

neuroscience↗