UBD Human

Ubiquitin-D Human Recombinant
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Description

Biological Functions

UBD operates through two primary mechanisms:

  1. Proteasomal Degradation: Directly targets substrates for degradation via the 26S proteasome without requiring ubiquitin conjugation .

  2. Immune Regulation: Modulates cytokine expression (e.g., IL4, IL5) and T-cell activity, acting downstream of FOXP3 in regulatory CD4+CD25hi T cells .

Functional RoleMechanismAssociated PathwayReferences
Protein DegradationCovalent substrate tagging via E1/E2 enzymes (UBA6, USE1)Proteasome-mediated proteolysis
Immune RegulationSuppression of T-cell proliferation and IL4/IL5 expressionFOXP3 signaling in T-reg cells
Kidney Disease ModulationInteraction with APOL1 risk variants (G1/G2)APOL1-associated nephropathy

UBD-APOL1 Interaction in Kidney Disease

  • Genetic Association: African ancestry-linked UBD variants correlate with reduced UBD expression and increased risk of APOL1-associated focal segmental glomerulosclerosis (FSGS) .

  • Functional Mechanism:

    • UBD overexpression reduces APOL1-G1/G2 protein levels (not G0) via proteasomal degradation, mitigating cytotoxicity .

    • Co-immunoprecipitation confirms physical interaction between UBD and APOL1 risk variants .

Immune Modulation via FOXP3

  • UBD overexpression in T-helper cells mimics FOXP3 effects, inducing IL1R2 and suppressing proliferation without FOXP3 upregulation .

  • Transcriptome analysis identifies LGALS3 as a FOXP3-specific regulatory marker absent in UBD-transduced cells .

Clinical Implications

UBD’s dual role in protein turnover and immune regulation positions it as a therapeutic target:

  • APOL1-Associated Nephropathy: Enhancing UBD expression could mitigate G1/G2 APOL1 toxicity .

  • Autoimmune Disorders: Modulating UBD activity may restore T-regulatory cell function in diseases like lupus or rheumatoid arthritis .

Research Gaps and Future Directions

  1. E3 Ligase Requirement: Whether UBD conjugation requires E3 ligases remains unresolved .

  2. Tissue-Specific Roles: UBD’s expression in non-immune tissues under inflammatory conditions warrants further study .

  3. Therapeutic Development: Small molecules enhancing UBD-APOL1 interactions could slow kidney disease progression .

Product Specs

Introduction
Ubiquitin D (UBD), a member of the ubiquitin protein family, functions as a ubiquitin-like modifier (UBL). This protein has the capability to create covalent bonds with other proteins, marking them for breakdown by the 26S proteasome. UBD is believed to be involved in regulating the cell cycle, innate immunity, and apoptosis. As a TNF-alpha inducible protein, it's likely that UBD plays a role in the immune response.
Description
Recombinant Human UBD, produced in E. coli, is a single, non-glycosylated polypeptide chain. It consists of 188 amino acids (with amino acids 1-165 being of particular interest) and has a molecular weight of 20.9kDa. The UBD sequence is fused to a 23 amino acid His-tag at its N-terminus and is purified through proprietary chromatographic techniques.
Physical Appearance
A clear, sterile solution without any color.
Formulation
The UBD protein solution is provided at a concentration of 0.25mg/ml. It is formulated in a buffer containing 20mM Tris-HCl (pH 8.0), 40% glycerol, 0.15M NaCl, and 1mM DTT.
Stability
For short-term storage (up to 2-4 weeks), the product can be stored at 4°C. For longer storage, freezing at -20°C is recommended. To ensure optimal stability during long-term storage, consider adding a carrier protein such as HSA or BSA (0.1%). It is important to minimize repeated cycles of freezing and thawing.
Purity
The purity of this product exceeds 90.0%, as assessed by SDS-PAGE analysis.
Synonyms

Ubiquitin D, Diubiquitin, Ubiquitin-like protein FAT10, UBD, FAT10, UBD-3, GABBR1.

Source
Escherichia Coli.
Amino Acid Sequence

MGSSHHHHHH SSGLVPRGSH MGSMAPNASC LCVHVRSEEW DLMTFDANPY DSVKKIKEHV RSKTKVPVQD QVLLLGSKIL KPRRSLSSYG IDKEKTIHLT LKVVKPSDEE LPLFLVESGD EAKRHLLQVR RSSSVAQVKA MIETKTGIIP ETQIVTCNGK RLEDGKMMAD YGIRKGNLLF LACYCIGG.

Q&A

What is Understanding by Design (UBD) and how does it apply to human research?

Understanding by Design is a planning framework that emphasizes backward design—beginning with desired outcomes before determining evidence and planning learning experiences. In human research contexts, UBD provides a structured approach to designing studies by first identifying enduring understandings and essential questions. For example, in human geography research, UBD frameworks help researchers identify core concepts like "Human beings create, learn, share, and adapt to culture" and "Cultures are dynamic and change over time" before developing methodologies . This approach ensures research design remains focused on substantive insights rather than merely procedural outcomes. Implementing UBD in research requires formulating essential questions that guide investigation, determining what evidence will demonstrate understanding, and then designing research methodologies that will generate the needed evidence.

How do researchers distinguish between enduring understandings and secondary concepts in UBD human studies?

Researchers distinguish enduring understandings from secondary concepts by evaluating their transferability, significance, and durability. Enduring understandings represent the "big ideas" that have lasting value beyond the classroom or specific research context. In human geography, examples include concepts like "Spatial patterns and organization of human society are arranged according to political, historical, cultural, and economic factors" . To identify these core concepts, researchers should:

  • Evaluate whether the concept offers explanatory power across multiple contexts

  • Determine if the concept connects to other major ideas in the field

  • Assess whether the concept has significance for both experts and novices

  • Consider whether the concept has demonstrated importance over time

Secondary concepts, while important, tend to be more context-specific, time-bound, or procedural in nature.

What methodologies are most effective for developing essential questions in UBD human research?

Effective essential questions in UBD human research should be open-ended, thought-provoking, and require higher-order thinking. From the examined materials, successful methodologies include:

  • Connecting to enduring understandings: Questions like "How do different political and economic systems affect civic life?" connect directly to enduring understandings about human social structures

  • Employing disciplinary lenses: Formulating questions through specific disciplinary perspectives (economics, history, political science) and multiple viewpoints

  • Targeting conceptual tensions: Questions that highlight tensions or contradictions (e.g., "How do perspectives about the past differ, and to what extent do these differences inform contemporary ideas and actions?")

  • Creating hierarchical question sets: Developing both overarching questions and supporting sub-questions that guide investigation

Researchers should evaluate potential questions based on their ability to stimulate ongoing inquiry rather than yield simple, definitive answers.

How can researchers integrate experimental design principles with UBD frameworks in human studies?

Integrating experimental design with UBD frameworks requires a sophisticated approach that combines outcome-focused planning with rigorous methodological controls. Based on research in experimental design for big data analysis, researchers should:

  • Begin with utility functions: Define clear utility functions that quantify the expected return of experimental settings, similar to how UBD emphasizes starting with desired outcomes

  • Employ decision analysis: Select optimal experimental settings that maximize expected returns, aligning with UBD's backward design principles

  • Implement sampling windows: When unable to sample at specific design points, utilize "design windows" or "sampling windows" consisting of near-optimal designs

  • Apply iterative design approaches: As shown in Algorithm 1 from the research literature, select training samples, determine maximum likelihood estimation of parameters, and iteratively improve designs

The integration is particularly valuable for large dataset analysis, where UBD principles help researchers maintain focus on meaningful outcomes while experimental design principles ensure methodological rigor.

What strategies address contradictions between qualitative and quantitative data in UBD human research frameworks?

When contradictions arise between qualitative and quantitative data in UBD human research, researchers should employ several strategies:

  • Contextual analysis: Examine the context in which each type of data was collected, recognizing that differences may reflect contextual variables rather than true contradictions

  • Multi-method validation: Implement triangulation approaches to validate findings through multiple methodological approaches

  • Parameter re-estimation: As demonstrated in experimental design literature, contradictions may require re-estimating parameters based on different correlation structures in data

  • Comparative utility assessment: Compare the information value of different datasets using concepts like observed information matrices:

Covariance Structure of XEstimated covariance of
No correlation(−0.98, 0.28, 0.08)
Positive correlation(−1.02, 0.30, 0.08)
Negative correlation(−1.00, 0.29, 0.08)

This data shows how different correlation structures affect parameter estimation, suggesting that contradictions may be systematically related to data structure rather than random error .

How do researchers balance between predetermined UBD frameworks and emergent discoveries in human studies?

Balancing predetermined UBD frameworks with emergent discoveries requires methodological flexibility and epistemological awareness. Based on research practices in UBD contexts, effective balancing strategies include:

  • Adaptive design procedures: Implement procedures that allow for modification of research approaches based on interim findings, similar to the subsetting procedures described in experimental design literature

  • Comparing random vs. designed approaches: Evaluate the utility of predetermined designs against randomly selected samples or emergent approaches (as shown in the comparison where "the randomly selected data subset size had to be roughly doubled to obtain a higher utility than for the designed approach")

  • Establishing reflexive checkpoints: Build in regular evaluation points to assess whether predetermined frameworks continue to align with emerging data

  • Maintaining epistemological flexibility: Recognize that different knowledge structures may emerge requiring adaptation of original frameworks

This balance is particularly important in human research contexts where complex social phenomena may not conform to initial frameworks despite rigorous design.

How can UBD approaches bridge disciplinary boundaries in human research?

UBD approaches effectively bridge disciplinary boundaries by focusing on transferable concepts and methodologies. Based on evidence from human geography and experimental design literature, successful interdisciplinary applications include:

  • Identifying cross-disciplinary essential questions: Questions like "How do geography, climate, and resources affect the way people live and work?" connect multiple disciplinary perspectives

  • Employing multiple analytical lenses: Examining research questions "through a variety of disciplinary lenses (e.g., economics, history, political science) and multiple perspectives"

  • Developing shared conceptual frameworks: Establishing common conceptual structures like the three big ideas identified in human geography:

    • Patterns and Spatial Organization

    • Impacts and Interactions

    • Spatial Process and Societal Change

  • Applying methodological principles across domains: Utilizing experimental design principles from one domain (e.g., information matrices in statistical design) to inform approaches in another domain (e.g., human geography research)

This bridging function is particularly valuable in complex human research that inherently spans multiple disciplines and methodological traditions.

What frameworks exist for integrating UBD principles into different stages of human research development?

Frameworks for integrating UBD principles across research development stages include:

  • Stage-specific Backward Design: Adapt UBD's three-stage backward design process (identify outcomes, determine evidence, plan experiences) to the research development process:

    • Early stage: Focus on enduring understandings and essential questions

    • Middle stage: Determine evidence needed and methodological approaches

    • Late stage: Implement research design and analysis

  • Big Ideas Matrix Framework: Organize research according to the three big ideas from human geography with corresponding methodological approaches:

    • Patterns and Spatial Organization: "Spatial patterns and organization of human society are arranged according to political, historical, cultural, and economic factors"

    • Impacts and Interactions: "Complex relationships of cause and effect exist among people, their environments, and historical and contemporary actions"

    • Spatial Process and Societal Change: "A spatial perspective allows for a focus on the ways phenomena are related to one another in particular places"

  • Inquiry Standards Integration: Incorporate standards like "construct meaningful questions," "gather and evaluate sources," and "develop claims using evidence" as structured phases in research development

  • Optimal Design Adaptation Framework: Apply principles from optimal experimental design (as described in section 4.1 of the experimental design literature) to different research phases

These frameworks provide structured approaches to ensuring UBD principles inform all stages of human research development.

How do cultural and geographic factors influence the application of UBD in human research contexts?

Cultural and geographic factors significantly influence UBD application in human research through multiple mechanisms:

  • Variation in enduring understandings: What constitutes an "enduring understanding" may vary across cultural contexts, requiring researchers to assess the cultural specificity of proposed big ideas

  • Contextual essential questions: Questions considered "essential" in one cultural context may have different relevance in another, as implied by geographic curriculum questions like "How does diversity impact society?"

  • Cultural variation in evidence standards: What constitutes valid evidence of understanding may vary across cultural contexts, requiring adaptation of research methodologies

  • Geographic influence on spatial frameworks: Research in different geographic contexts may require different applications of spatial concepts like "Population Distribution" and "Population Composition"

Researchers working across cultural contexts should conduct preliminary research to identify culturally-specific enduring understandings and adapt essential questions accordingly.

What metrics effectively evaluate the success of UBD implementation in human research projects?

Effective metrics for evaluating UBD implementation success include:

  • Alignment metrics: Measure the degree of alignment between research questions, methodologies, and findings

  • Utility function outcomes: Quantify the information gain from research designs using concepts from experimental design literature like observed information matrices

  • Transferability assessment: Evaluate whether findings contribute to enduring understandings that transfer beyond specific research contexts

  • Methodological efficiency indicators: Compare resource requirements between UBD-designed approaches and traditional approaches, similar to the comparison of designed versus random sampling approaches that found "the randomly selected data subset size had to be roughly doubled to obtain a higher utility than for the designed approach"

How can researchers address the challenges of implementing UBD in long-term human studies?

Long-term human studies present unique challenges for UBD implementation that researchers can address through:

  • Temporal adaptation frameworks: Develop structured approaches for periodically revisiting and potentially revising enduring understandings and essential questions as research progresses

  • Methodological continuity protocols: Establish protocols for maintaining methodological continuity even when specific techniques evolve

  • Phased implementation: Structure research into phases with distinct UBD frameworks that build upon each other

  • Longitudinal alignment matrices: Create matrices that map relationships between short-term and long-term research questions and methodologies

PhDs in Lifelong Learning at UBD demonstrate this long-term adaptation with flexible duration options for full-time (24-60 months) and part-time (24-84 months) studies , suggesting models for structuring long-term research with appropriate flexibility.

How are digital technologies transforming UBD approaches in human research?

Digital technologies are transforming UBD approaches through several mechanisms:

  • Big data analytics integration: As demonstrated in experimental design literature, big data approaches require adaptation of traditional experimental design principles, similarly affecting UBD application in human research

  • Enhanced visualization of spatial relationships: Digital technologies enable more sophisticated visualization of the spatial patterns central to human geography UBD frameworks

  • Computational modeling of complex relationships: Advanced computational approaches allow researchers to model complex relationships described in UBD frameworks like "impacts and interactions"

  • Automated pattern recognition: Machine learning approaches can identify patterns in human behavior and spatial organization that inform UBD frameworks

These technological developments enable more sophisticated implementation of UBD principles while also requiring adaptation of traditional UBD frameworks to accommodate new forms of evidence and analysis.

What emerging ethical considerations are reshaping UBD applications in human research?

Emerging ethical considerations are reshaping UBD applications through:

  • Rights-based frameworks: Integration of human rights considerations into research design, as suggested by curriculum content on "the role of the Universal Declaration of Human Rights (UDHR) and nongovernment organizations (NGOs such as Save the Children or the Red Cross) in how human rights have been addressed in different countries"

  • Inclusivity imperatives: Greater emphasis on ensuring research designs account for diverse human experiences and perspectives

  • Data privacy frameworks: Evolution of ethical standards regarding data collection and use, particularly relevant to big data approaches in human research

  • Community-based participatory approaches: Increasing emphasis on involving research subjects in the design and execution of research

These ethical considerations require researchers to adapt UBD frameworks to explicitly incorporate ethical dimensions throughout the research process.

Product Science Overview

Structure and Function

Ubiquitin-D is composed of 165 amino acids and has a molecular weight of approximately 18 kDa. It shares structural similarities with ubiquitin, a highly conserved protein found in all eukaryotic organisms. Ubiquitin itself is a 76 amino acid protein that is involved in tagging proteins for degradation .

The primary function of Ubiquitin-D is to covalently modify target proteins, tagging them for destruction in the proteasome. This process is vital for maintaining cellular homeostasis by removing damaged, misfolded, or excess proteins. Ubiquitin-D is involved in various biological processes, including the regulation of the immune response, cell cycle, and apoptosis .

Preparation Methods

Recombinant Ubiquitin-D is typically produced using Escherichia coli (E. coli) expression systems. The gene encoding Ubiquitin-D is cloned into an expression vector, which is then introduced into E. coli cells. These cells are cultured under specific conditions to induce the expression of the recombinant protein. After expression, the protein is purified using techniques such as affinity chromatography and size-exclusion chromatography to achieve high purity levels .

Biological Significance

Ubiquitin-D plays a significant role in the immune system by regulating the activity of various immune cells. It is involved in the positive regulation of I-kappaB kinase/NF-kappaB signaling, which is crucial for the immune response to infections and inflammation . Additionally, Ubiquitin-D is implicated in the response to tumor necrosis factor and interferon-gamma, highlighting its importance in immune regulation and inflammation .

Research and Applications

Recombinant Ubiquitin-D is widely used in research to study protein degradation pathways, immune responses, and cell cycle regulation. It serves as a valuable tool for investigating the mechanisms of protein ubiquitination and the role of ubiquitin-like modifiers in cellular processes. Researchers utilize recombinant Ubiquitin-D to explore its interactions with other proteins and its impact on various signaling pathways .

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