Recombinant Danio rerio Interferon-induced GTP-binding protein MxB (mxb), partial

What is Recombinant Danio rerio Interferon-induced GTP-binding protein MxB (mxb) and what is its biological significance?

Recombinant Danio rerio Interferon-induced GTP-binding protein MxB (mxb) is a protein produced through recombinant DNA technology that replicates the structure and function of the naturally occurring MxB protein in zebrafish. The MxB protein belongs to the Mx family of proteins, which are critical downstream effectors of Type I interferons (IFNs) and represent a crucial component of the innate immune response to viral infections in vertebrates. Mx proteins are characterized by a distinct tripartite GTP-binding domain, dynamin family signature, and leucine zipper motif, all of which contribute to their antiviral functions .

The biological significance of MxB in zebrafish lies in its role in antiviral immunity. It is activated solely through the interferon pathway, making it an important molecular marker for interferon activity and viral resistance. Understanding this protein's function and regulation provides valuable insights into the evolutionary conservation of innate immune mechanisms across vertebrate species, from fish to humans .

How does zebrafish MxB protein structure compare to Mx proteins in other vertebrates?

The zebrafish MxB protein shares significant structural homology with Mx proteins from other vertebrates while maintaining species-specific characteristics. Sequence analysis reveals that zebrafish Mx contains the conserved tripartite GTP-binding domain, dynamin family signature, and leucine zipper motif that are hallmarks of Mx proteins across species. Comparative analysis shows that zebrafish Mx shares approximately 50% amino acid identity with human MxA and 69% identity with both rainbow trout and Atlantic salmon Mx proteins .

What are the recommended methods for expressing and purifying recombinant zebrafish MxB protein?

To express and purify recombinant zebrafish MxB protein, researchers should follow this methodological approach:

• Expression System Selection: For functional studies, a eukaryotic expression system is preferable as it provides proper protein folding and post-translational modifications. Common options include baculovirus-infected insect cells or mammalian expression systems.

• Vector Design: Construct an expression vector containing:

  • The zebrafish MxB coding sequence optimized for the host system

  • An appropriate promoter (CMV for mammalian cells)

  • A purification tag (His-tag or GST-tag)

  • A cleavage site for tag removal if necessary for functional studies

• Protein Expression: Transfect host cells and verify expression via Western blot using anti-Mx antibodies or tag-specific antibodies.

• Purification Protocol:

  • Lyse cells in buffer containing protease inhibitors

  • Perform affinity chromatography using the appropriate resin (Ni-NTA for His-tagged proteins)

  • Apply a second purification step (ion exchange or size exclusion chromatography)

  • Verify purity via SDS-PAGE

• Functional Verification: Confirm GTPase activity using a GTP hydrolysis assay to ensure the recombinant protein maintains its enzymatic function .

This approach will yield pure, functional recombinant zebrafish MxB protein suitable for downstream applications including structural studies, interaction analyses, and antiviral assays.

What methods can be used to induce and measure MxB expression in zebrafish models?

Several validated methods can be employed to induce and measure MxB expression in zebrafish experimental models:

Induction Methods:

• Poly(I:C) Treatment: The most established method involves exposing zebrafish or zebrafish liver cells to polyinosinic-polycytidylic acid (Poly[I:C]), a synthetic double-stranded RNA that mimics viral infection. Typically, 10-50 μg/mL Poly(I:C) can be added to cell culture medium or injected into adult zebrafish (10 μg/g body weight) .

• Purified Zebrafish IFN: Direct treatment with purified recombinant zebrafish IFN can specifically activate the interferon pathway. This provides a more controlled induction compared to Poly(I:C), which activates multiple pattern recognition receptors .

• Viral Challenge: Live or attenuated viruses can be used to induce physiological Mx expression, though this approach introduces variables related to viral replication kinetics.

Measurement Methods:

• Quantitative RT-PCR: For precise quantification of Mx mRNA levels using primers specific to zebrafish MxB. Normalize to appropriate reference genes such as ef1α or β-actin.

• Western Blotting: To measure protein expression levels using anti-Mx antibodies (note: confirm cross-reactivity with zebrafish MxB).

• Luciferase Reporter Assay: Construct containing the zebrafish Mx promoter with its two interferon-stimulated response elements (ISREs) driving luciferase expression can be used to monitor activation of the Mx promoter in response to treatments .

• In situ Hybridization: To visualize tissue-specific expression patterns of Mx transcripts in whole zebrafish embryos.

When analyzing results, researchers should account for the temporal dynamics of Mx induction, typically showing peak expression 12-24 hours post-induction, with gradual decline thereafter.

How can CRISPR/Cas9 technology be effectively used to study MxB gene function in zebrafish?

CRISPR/Cas9 technology offers powerful approaches for investigating MxB gene function in zebrafish through various gene editing strategies:

Knockout Approaches:

• Single gRNA Method: Design a gRNA targeting an early exon of the MxB gene, preferably within the GTP-binding domain. Co-inject Cas9 mRNA (300 pg) and gRNA (50-100 pg) into one-cell stage embryos. This approach typically achieves 24-59% mutation frequency at the target site .

• Multiple gRNA Strategy: To increase knockout efficiency and avoid genetic compensation responses, inject a set of four CRISPR/Cas9 ribonucleoprotein (RNP) complexes that redundantly target different regions of the MxB gene. This approach can produce null phenotypes in >90% of G0 embryos, providing more consistent results than single gRNA approaches .

• Large Fragment Deletion: Design two gRNAs flanking a critical region (e.g., the GTP-binding domain) to delete functional portions of the gene. This approach can delete fragments up to 78 kb in size .

Analysis of MxB Mutants:

• Genotyping Protocol: Extract genomic DNA from embryo fin clips and perform PCR with primers flanking the target site, followed by T7 endonuclease assay or direct sequencing.

• Phenotypic Analysis: Challenge mutant zebrafish with viral pathogens to assess changes in susceptibility.

• Compensation Analysis: To address potential genetic compensation responses that may mask phenotypes, consider:

  • Generating mutants with complete gene deletion rather than point mutations

  • Creating in-frame deletions in critical domains

  • Using an upf3a-/- background to suppress nonsense-mediated mRNA decay

Experimental Controls:

• Include a non-targeting gRNA control group

• Generate heterozygous carriers and compare with homozygous mutants

• Perform rescue experiments by co-injecting wild-type MxB mRNA

This comprehensive CRISPR approach enables researchers to elucidate the function of MxB in zebrafish antiviral immunity with high specificity and efficiency.

What are the key considerations for designing antiviral assays using zebrafish MxB protein?

Designing robust antiviral assays using zebrafish MxB protein requires careful consideration of several methodological factors:

Assay Types and Considerations:

• Cell-Based Viral Inhibition Assays:

  • Cell Selection: Zebrafish liver cells (ZFL) or embryonic fibroblast cells (ZF4) are recommended as they reflect natural MxB expression patterns

  • MxB Expression: Establish stable cell lines expressing zebrafish MxB or use transient transfection (efficiency >60% recommended)

  • Viral Challenge: Select viruses known to be inhibited by Mx proteins (e.g., rhabdoviruses, orthomyxoviruses)

  • Readout Options: Plaque reduction assays, viral titer measurements, or reporter virus systems

  • Controls: Include MxB mutants lacking GTPase activity to confirm specificity

• In Vivo Zebrafish Models:

  • Developmental Stage: For embryo studies, use 48-72 hpf embryos when innate immunity is functional

  • Delivery Method: Microinjection of virus into circulation or immersion for waterborne pathogens

  • Sample Size: Minimum 30 embryos per condition with 3 biological replicates

  • Survival Analysis: Monitor for 7-10 days post-infection with appropriate statistical methods (Kaplan-Meier)

• Biochemical GTPase Assays:

  • Protein Purity: Use protein preparations with >95% purity

  • GTP Hydrolysis: Measure using colorimetric phosphate release assays or HPLC

  • Condition Optimization: Test different pH values (7.0-8.0) and divalent cation concentrations

Data Analysis and Validation:

• Dose-Response Relationships: Test multiple viral doses and MxB expression levels

• Time-Course Analysis: Measure viral inhibition at different time points post-infection

• Statistical Analysis: Apply appropriate statistical tests (ANOVA with post-hoc tests) and report p-values

• Validation Approaches: Confirm specificity using MxB knockdown/knockout controls

When reporting results, present complete datasets including negative results to provide a comprehensive understanding of zebrafish MxB antiviral specificity.

How do zebrafish MxA and MxB proteins differ in their expression patterns and antiviral properties?

While the search results do not explicitly differentiate between zebrafish MxA and MxB proteins, we can discuss the methodological approach to investigating such differences based on known patterns in other vertebrates and general principles:

Methodological Approach to Characterize Differential Expression:

• Transcriptomic Analysis: Perform RNA-seq on different zebrafish tissues under basal and stimulated (Poly[I:C] or IFN) conditions to identify tissue-specific expression patterns of both MxA and MxB genes.

• Promoter Analysis: Compare the ISRE elements in MxA versus MxB promoters to identify differences in transcription factor binding sites that may contribute to differential regulation. The zebrafish Mx promoter contains two ISREs that are homologous to those found in many IFN-inducible genes .

• Temporal Expression Profiling: Conduct time-course experiments following stimulation to determine if MxA and MxB exhibit different kinetics of induction and persistence.

Functional Comparison Protocol:

• Protein Domain Analysis: Compare the GTP-binding domains, dynamin family signatures, and leucine zipper motifs between MxA and MxB to identify structural differences that might confer distinct antiviral specificities.

• Virus Specificity Testing: Express each protein separately in cell culture systems and challenge with a panel of viruses (RNA and DNA viruses) to determine virus-specific inhibition patterns.

• Subcellular Localization Studies: Perform immunofluorescence or fractionation studies to determine if MxA and MxB localize to different cellular compartments, which would suggest distinct antiviral mechanisms.

• Protein Interaction Profiling: Conduct co-immunoprecipitation followed by mass spectrometry to identify unique binding partners for each protein.

When interpreting results, researchers should consider that different Mx proteins often show complementary antiviral specificities, potentially providing broader protection against diverse viral pathogens than either protein alone.

What approaches can be used to investigate the role of zebrafish MxB in non-viral host defense mechanisms?

While Mx proteins are primarily known for antiviral functions, emerging research suggests potential roles in broader immune responses. The following approaches can be used to investigate non-viral defense functions of zebrafish MxB:

Experimental Strategies:

• Bacterial Challenge Models:

  • Generate MxB-overexpressing and knockout zebrafish lines

  • Challenge with common fish pathogens (e.g., Aeromonas, Mycobacterium, Vibrio species)

  • Measure bacterial burden, survival rates, and inflammatory responses

  • Compare responses between wildtype and MxB-modified fish

• Transcriptomic and Proteomic Analyses:

  • Perform RNA-seq and proteomics on tissues from MxB-overexpressing, knockout, and control zebrafish

  • Identify differentially expressed genes/proteins in pathways unrelated to viral defense

  • Apply pathway enrichment analysis to detect non-viral immune pathways affected by MxB

  • Validate key findings with qRT-PCR and Western blotting

• Interaction Network Identification:

  • Use yeast two-hybrid or co-immunoprecipitation coupled with mass spectrometry

  • Map MxB protein interactions with components of non-viral defense pathways

  • Confirm interactions using bimolecular fluorescence complementation (BiFC)

• GTPase Activity in Non-viral Contexts:

  • Develop assays to measure MxB GTPase activity in response to bacterial PAMPs or DAMPs

  • Investigate if GTPase activity correlates with non-viral immune functions

  • Test GTPase-deficient mutants in bacterial challenge models

Data Analysis Framework:

• Create comprehensive databases combining transcriptomic, proteomic, and phenotypic data

• Apply machine learning approaches to identify patterns associated with non-viral functions

• Develop network models visualizing potential MxB involvement in various immune pathways

This systematic approach will help determine whether zebrafish MxB has evolved unique functions beyond viral defense, potentially revealing new paradigms in innate immunity that may be applicable across vertebrate species.

How can structural biology approaches be applied to understand the mechanism of zebrafish MxB antiviral activity?

Structural biology provides critical insights into the mechanisms underlying zebrafish MxB antiviral activity. The following comprehensive approach combines multiple techniques to elucidate structure-function relationships:

Structural Determination Methods:

• X-ray Crystallography Protocol:

  • Express recombinant zebrafish MxB with a cleavable affinity tag

  • Purify to >95% homogeneity using affinity chromatography followed by size exclusion

  • Screen crystallization conditions (typically 500-1000 different conditions)

  • Optimize promising conditions to grow diffraction-quality crystals

  • Collect diffraction data at synchrotron radiation facilities

  • Solve phase problem using molecular replacement with human MxA (50% identity) as template

  • Refine structure to resolution better than 3.0 Å

• Cryo-Electron Microscopy (Cryo-EM):

  • Particularly useful for visualizing MxB oligomeric structures

  • Prepare MxB protein in various nucleotide-bound states (apo, GTP, GDP)

  • Flash-freeze samples on EM grids in liquid ethane

  • Collect micrographs using a high-end electron microscope

  • Process data using single particle analysis software

• Solution NMR for Dynamic Regions:

  • Express isotopically labeled (15N, 13C) domains of MxB

  • Collect multi-dimensional NMR spectra

  • Assign resonances and determine solution structure

  • Particularly valuable for flexible regions not resolved in crystal structures

Structure-Function Analysis:

• Computational Approaches:

  • Perform molecular dynamics simulations to model GTP hydrolysis

  • Use in silico docking to predict viral protein interactions

  • Identify conserved surface patches across vertebrate Mx proteins

• Mutational Analysis:

  • Design mutations based on structural data, focusing on:

    • GTP-binding pocket

    • Oligomerization interface

    • Putative viral target binding sites

  • Express mutant proteins and test their antiviral activity in zebrafish cells

  • Create a structure-function map correlating specific structural features with antiviral functions

• Oligomerization Studies:

  • Analyze oligomeric states using analytical ultracentrifugation

  • Determine the effect of GTP binding on oligomerization

  • Compare oligomerization properties with human MxA

Integration with Viral Interaction Studies:

• Create structural models of MxB-viral protein complexes

• Validate interactions using mutational analyses

• Develop structure-based drug design approaches targeting the GTP-binding pocket

This multi-technique structural biology approach will provide unprecedented insights into the molecular mechanism of zebrafish MxB antiviral activity, potentially revealing conserved and divergent features compared to mammalian Mx proteins.

How can zebrafish MxB research inform our understanding of human MxA/MxB protein function?

Zebrafish MxB research provides a valuable comparative model for understanding human Mx protein function through several methodological approaches:

Comparative Analysis Framework:

• Evolutionary Conservation Mapping:

  • Conduct comprehensive phylogenetic analysis of Mx proteins across vertebrates

  • Identify conserved domains between zebrafish MxB and human MxA/MxB

  • Map conservation onto 3D structural models to identify functionally critical regions

  • The 50% amino acid identity between zebrafish Mx and human MxA provides sufficient conservation for meaningful comparisons while allowing identification of species-specific adaptations

• Functional Complementation Studies:

  • Express zebrafish MxB in human cell lines lacking endogenous Mx

  • Challenge with viruses known to be restricted by human Mx proteins

  • Determine if zebrafish MxB can functionally substitute for human Mx

  • Test chimeric proteins combining domains from human and zebrafish Mx to identify determinants of antiviral specificity

• Comparative Promoter Analysis:

  • Compare the ISREs in zebrafish and human Mx promoters

  • Test responsiveness to various interferon subtypes from both species

  • The zebrafish Mx promoter contains two ISREs homologous to those in human Mx genes, suggesting conserved regulatory mechanisms

Translational Relevance:

• Drug Development Applications:

  • Use zebrafish as a high-throughput screening platform for compounds enhancing Mx expression

  • Test compounds identified in zebrafish models in human cell systems

  • Develop combination approaches targeting conserved pathways in both species

• Methodology for Cross-Species Validation:

  • When a function is discovered for zebrafish MxB, systematically test for conservation in human MxA/MxB

  • Use CRISPR/Cas9 technology to introduce equivalent mutations in human cells

  • Develop standardized assays applicable to both zebrafish and human systems

By implementing this comparative approach, researchers can leverage the experimental advantages of the zebrafish model (transparent embryos, high fecundity, ex vivo fertilization) while generating findings with direct relevance to human antiviral immunity .

What strategies can address genetic compensation responses when creating Mx gene knockouts in zebrafish?

Genetic compensation responses (GCR) present a significant challenge in zebrafish knockout studies, potentially masking mutant phenotypes. Based on recent advances in zebrafish gene editing, the following strategies can effectively address GCR when studying Mx genes:

Comprehensive GCR Mitigation Strategies:

• Optimized Mutation Design:

  • Full Locus Deletion: Rather than introducing small indels, delete the entire Mx gene locus to prevent transcription of any mRNA that could trigger compensation

  • Promoter Deletion: Target the promoter region containing the ISREs to prevent any transcriptional activation

  • Critical Domain Targeting: Create in-frame deletions specifically within the GTP-binding domain to produce a non-functional protein without triggering nonsense-mediated decay

  • Last Exon Targeting: Generate PTC mutations in the last exon containing critical functional domains, as these are less likely to trigger nonsense-mediated decay

• Genetic Background Modification:

  • upf3a Knockout Background: Cross Mx mutants with upf3a-/- fish to suppress nonsense-mediated decay machinery that contributes to GCR

  • Compound Mutant Approach: Identify and simultaneously knockout potential compensating genes (e.g., other Mx family members)

• Alternative Gene Silencing Approaches:

  • Morpholino Knockdown: For acute silencing that may avoid triggering long-term compensation mechanisms

  • CRISPRi: Use deactivated Cas9 fused to repressor domains to inhibit transcription without DNA mutation

  • Tissue-Specific CRISPR: Employ tissue-specific promoters to drive Cas9 expression, limiting compensation to specific tissues

Experimental Validation Framework:

• Compensation Detection:

  • Perform RNA-seq on wild-type and mutant tissues to identify upregulated genes

  • Use qRT-PCR to validate specific compensating genes

  • Develop a panel of antibodies against related proteins to detect upregulation at protein level

• Phenotypic Comparison:

  • Compare phenotypes between different mutation strategies (indel vs. deletion)

  • Assess viral susceptibility across different mutant lines

  • Document temporal aspects of potential compensation

This comprehensive approach addresses the observation that approximately 80% of engineered zebrafish mutants do not display discernible phenotypes due to GCR , ensuring more reliable functional assessment of Mx genes in antiviral immunity.

What experimental design is optimal for studying the evolution of Mx protein function across different fish species?

Studying Mx protein evolution across fish species requires a carefully structured experimental design that combines comparative genomics, functional analysis, and evolutionary biology approaches:

Comprehensive Experimental Design:

• Phylogenomic Analysis Framework:

  • Species Selection: Include diverse fish taxa spanning major evolutionary radiations (e.g., zebrafish, salmonids, cichlids, pufferfish)

  • Sequence Acquisition: Obtain Mx coding sequences through genome mining or targeted sequencing

  • Alignment Strategy: Use MUSCLE or MAFFT algorithms with codon-aware parameters

  • Phylogenetic Reconstruction: Employ maximum likelihood and Bayesian methods with appropriate substitution models

  • Selection Analysis: Calculate dN/dS ratios to identify positively selected codons using PAML and HyPhy packages

• Functional Characterization Protocol:

  • Cloning Strategy: Generate expression constructs for Mx genes from diverse fish species

  • Expression System: Use consistent cellular background (e.g., fish cell lines lacking endogenous Mx)

  • Standardized Assays: Challenge with panel of viruses representing different families

  • Quantification Methods: Measure viral replication using plaque assays, qPCR, or reporter viruses

  • Comparison Table:

  Species	Viral Target A	Viral Target B	Viral Target C	GTPase Activity
  Zebrafish	++++	++	+++	High
  Species 2	++	++++	+	Medium
  Species 3	+++	+	++++	High

• Structure-Function Correlation:

  • Model 3D structures of Mx proteins from different species

  • Identify structural variations in key domains

  • Create chimeric proteins exchanging domains between species

  • Test chimeras to map specific functional determinants

• Environmental Correlation Analysis:

  • Compile data on natural viral pathogens for each species

  • Correlate Mx functional properties with ecological niches

  • Test whether selective pressures correlate with environmental factors

Data Integration and Analysis:

• Use comparative genomics to identify conserved regulatory elements across species, particularly the ISREs in Mx promoters that are known to be present in zebrafish

• Apply ancestral sequence reconstruction to infer the evolutionary trajectory of Mx function

• Correlate sequence/structural changes with functional shifts using statistical phylogenetic methods

• Create an integrated database of Mx proteins across fish species with associated functional properties and evolutionary metrics

This experimental design provides a comprehensive framework for understanding how Mx protein function has evolved across fish species, potentially revealing adaptation to species-specific viral challenges and providing insights into the evolution of vertebrate innate immunity.

What are the current limitations in zebrafish MxB research and how might they be addressed in future studies?

Current zebrafish MxB research faces several methodological and conceptual limitations that require strategic approaches to advance the field:

Current Limitations and Solutions:

• Incomplete Functional Characterization:

  • Limitation: The full spectrum of viral targets for zebrafish MxB remains poorly defined.

  • Solution: Implement systematic screening against a diverse panel of fish and human viruses; develop zebrafish-specific viral challenge models; and utilize proteomics to identify viral and host factors interacting with MxB.

• Genetic Compensation Challenges:

  • Limitation: As observed in approximately 80% of zebrafish engineered mutants, genetic compensation responses may mask MxB knockout phenotypes .

  • Solution: Apply multiple gene editing strategies simultaneously (full locus deletion, critical domain targeting); utilize upf3a-/- backgrounds to suppress compensation mechanisms; and employ acute protein degradation systems as alternatives to genetic knockouts .

• Limited Structural Information:

  • Limitation: Unlike human MxA, no high-resolution structures exist for zebrafish MxB.

  • Solution: Prioritize structural biology approaches including X-ray crystallography and cryo-EM; leverage the 50% sequence identity with human MxA for molecular modeling; and focus on zebrafish-specific structural features .

• Translation to Human Applications:

  • Limitation: Connecting zebrafish findings to human health applications remains challenging.

  • Solution: Develop parallel experimental systems in zebrafish and human cells; create humanized zebrafish models expressing human Mx proteins; and establish standardized assays applicable across species.

• Technical Challenges in Working with Recombinant Protein:

  • Limitation: Obtaining correctly folded, functional recombinant MxB protein can be difficult.

  • Solution: Optimize expression conditions using insect cell systems; implement quality control measures for GTPase activity; and develop zebrafish-specific antibodies for detection and purification.

Future Research Directions:

• Investigate potential non-viral functions of zebrafish MxB, including possible roles in bacterial defense or cellular homeostasis

• Explore the interaction between MxB and other innate immune pathways in zebrafish

• Utilize the zebrafish model for high-throughput screening of compounds that modulate Mx expression or activity

• Develop computational models integrating structural, functional, and evolutionary data on Mx proteins across vertebrates

By addressing these limitations through innovative methodological approaches, researchers can advance understanding of zebrafish MxB function and leverage this knowledge for broader insights into vertebrate antiviral immunity and potential therapeutic applications.

How can integrative multi-omics approaches enhance our understanding of zebrafish MxB function?

Integrative multi-omics approaches offer powerful strategies to comprehensively characterize zebrafish MxB function within the broader context of antiviral immunity:

Multi-omics Integration Framework:

• Genomics and Epigenomics:

  • ATAC-seq Application: Map chromatin accessibility changes in interferon-stimulated zebrafish cells to identify regulatory elements beyond the known ISREs in the Mx promoter

  • ChIP-seq Implementation: Profile transcription factor binding at Mx promoters following viral infection

  • Whole Genome Sequencing: Analyze Mx gene locus variation across wild zebrafish populations to identify natural polymorphisms

  • Data Integration: Correlate genetic variants with expression levels and antiviral phenotypes

• Transcriptomics Approaches:

  • RNA-seq Strategy: Profile gene expression in wild-type and MxB-deficient zebrafish during viral challenge

  • Single-cell RNA-seq: Characterize cell-type specific responses and identify cells with highest MxB expression

  • Long-read Sequencing: Identify alternative splicing events in MxB transcripts

  • Analysis Pipeline: Apply network analysis to position MxB within broader antiviral response networks

• Proteomics and Interactomics:

  • IP-MS Protocol: Identify MxB-interacting proteins under basal and stimulated conditions

  • Proximity Labeling: Apply BioID or APEX techniques to map spatial protein networks

  • Phosphoproteomics: Characterize post-translational modifications of MxB

  • Quantitative Analysis: Use SILAC or TMT labeling for accurate quantification of protein dynamics

• Metabolomics Integration:

  • Targeted Metabolite Analysis: Focus on GTP/GDP ratios in MxB-expressing vs. control cells

  • Global Profiling: Identify metabolic signatures associated with MxB activity

  • Flux Analysis: Trace metabolic changes during MxB activation using isotope labeling

Data Integration and Visualization:

• Multi-dimensional Data Analysis:

  • Implement machine learning algorithms to identify patterns across omics layers

  • Apply Bayesian networks to model causal relationships

  • Develop interactive visualization tools for multi-omics data exploration

• Temporal Resolution:

  • Design time-course experiments capturing the dynamics of all omics layers

  • Construct temporal models of MxB function from activation to resolution

• Spatial Context:

  • Combine tissue-specific omics data with in situ visualization techniques

  • Map MxB function across different tissues and developmental stages

Expected Outcomes Table: