Provide a concise, self-contained summary of your project. (minimum 150 words)
Your abstract should briefly address the following elements:
•Significance: What problem or question does the project address, and why is it important?
•Broad Objective: What is the overall goal of the project?
•Hypothesis: What prediction or principle is the project testing or demonstrating?
•Specific Aims: What key steps or milestones will be completed to achieve the objective?
•Methods: What experimental or technical approaches will be used?
Define three aims for your final project. (minimum one sentence per aim)
Aim 1: Experimental Aim: (this project)
i. This aim should describe the core experimental objective you will attempt during this class. List or link any relevant methods or resources you plan to use (e.g., experimental protocols, automation workflows, DNA or protein design, protein design tools, or Twist orders).
ii. You will provide a detailed step-by-step experimental plan for Aim 1 in the Experimental Design section of this assignment.
Aim 2: Development Aim
Describe the next step that would follow a successful Aim 1, extending the work beyond the scope of this course. This aim should represent a realistic progression of the project, such as executing additional experiments, solving a technical limitation, or developing the system or technology further.
Aim 3: Visionary Aim
a. Describe the long-term vision for the project. Explain how the broader concept could have an impact if fully realized.
b. Examples include:
i. Challenging an existing paradigm or clinical practice.
ii. Addressing a major barrier in a field.
iii. Enabling a new experimental capability or research approach.
Background and Literature Context
Provide background research that explains the current state of knowledge and identifies the gap in knowledge or capability that your project addresses.
1. Briefly summarize two peer-reviewed research citations relevant to your research. (minimum four sentences)
2. Explain how your project is novel or innovative. (minimum 3 sentences)
i. New applications or uses of existing biological tools or concepts.
ii. Development of new approaches, methodologies, or techniques.
iii. Ways the project challenges existing paradigms or assumptions.
iv. How the work expands the boundaries of synthetic biology.
3. Explain why your project matters and what impact it could have. (minimum of 5 sentences)
i. The problem addressed: What pressing real-world problem does your project attempt to solve?
ii. Importance of the problem: Why is this problem significant, or what critical barrier to progress in the field does it represent?
iii. Broader societal contribution: How could the outcomes of your project benefit society beyond the immediate research context?
iv. Advancement of knowledge or capability: How might the project improve scientific understanding, technical capability, or clinical practice within one or more fields?
v. Field-level change: If your aims are achieved, how could the concepts, methods, technologies, treatments, services, or preventive approaches used in this field of research change?
4. Describe the ethical implications associated with your project and identify relevant ethical principles (e.g., non-maleficence, beneficence, justice, or responsibility). (minimum 2 paragraphs)
a. First paragraph: Include what ethical implications are involved in your project. Try to suggest ethical principle(s) you may apply (e.g., non-maleficence, justice).
b. Second paragraph: Describe the measures that should be taken to ensure that your project is ethical (both in how the research is conducted and in its broader implications for society). You may wish to answer the following questions:
i. What action(s) do you propose?
ii. What are the potential unintended consequences of your proposed actions?
iii. What could you have been wrong about (e.g., incorrect assumptions and uncertainties)?
iv. What are alternatives to your proposed actions?
v. Note: In an NIH proposal, an ethics statement is used to describe the relevance of this research to public health.
Use Claude AI skills to refine your HTGAA final project experimental design.
1. Create a detailed experimental plan for your final project. Include a timeline for each part of your experimental plan (i.e., how long you would expect each step in your final project to take). (min. 15 lines/sentences—a numbered list is acceptable)
a. Include specific methods/tools/technologies/biological concepts for each part of the final project and analysis.
b. This section will be used to determine whether the experiments are well designed, feasible, and likely to succeed in testing your hypothesis.
c. Often this section is broken into discrete tasks/sub-aims.
d. For each experiment and/or analysis, include a description of your expected results.
e. If possible, include figure(s) that visually show a broad workflow of your project or a specific aspect of your experiment plan.
f. Reminder: All HTGAA projects must include some DNA design! Make sure Google form is submitted.
2. We discussed and practiced various techniques related to synthetic biology throughout the semester. Place a check next to the techniques relevant to your project.
Pipetting Lab Safety Bioethical Considerations (must check this box)
DNA Gel Art, DNA Sequencing, DNA Editing, DNA Construct Design, Restriction Enzyme Digestion, Gel Electrophoresis, DNA Purification From Gel, Databases (e.g., GenBank, NCBI, Ensembl, and UCSC Genome Browser)
Lab Automation, Creating Code for Laboratory Automation, Using Liquid Handling Robots (e.g., Opentrons), Designing a Twist Order, Creating a plan to use the Autonomous lab at Ginkgo Bioworks
Protein Design, Use of Boltz or PepMLM, Use of Asimov Kernel, Use of Benchling, Models and Notebooks, Databases
Bioproduction, Chassis Selection (e.g., DH5alpha), Registry of Standard Biological Parts, Plasmid Preparation, Bacterial Culturing, Quality Control/Analysis, Bacterial Processing (e.g., Centrifugation, Lysis, DNA Purification)
Cell Free Systems, Cell Free Reactions, Freeze-Dried Cell Free Systems, miniPCR Tools, Protein Purification
Gibson Assembly, Primer Design or Selection, PCR Reactions, Gibson Assembly, Other Cloning Methods (e.g., Restriction Enzyme Digestion or Gateway Cloning)
CRISPR, CRISPR/Cas9, Designing Prime Editing gRNA,
1. Expand upon two techniques you checked in the previous question by describing how you would utilize those techniques in your final project. (min. 4 sentences)
2. Identify any How To Grow (Almost) Anything Industrial Council companies that are associated with your final project (optional)
Asimov (Kernel)
ATCC
Basecamp Research
BioFabricate
Biome Consortia
Bolt
Boltz.bio
Cultivarium
DeepCure
Epibone
Ginkgo Bioworks
Helix Nano
Millipore Sigma
Mycoworks
New England Biolabs
Nuclera
Opentrons
SecureDNA
Takeda Pharmaceuticals
Thermo Fisher Scientific
Transfyr.ai
Twist Biosciences
Upside Foods
Waters Corporation
1. You are required to validate at least one aspect of your final project aims.
This is to ensure that you are able to successfully apply a relevant synthetic biology technique to your project. Include figures if you have them -accuracy is critical in figures, tables, and graphs.
Here is a non-exhaustive list of acceptable validations:
•Designing DNA relevant to your final project.
•Performing a PCR reaction using primers relevant to your final project.
•Performing a Gibson assembly relevant to your project.
•Creating and performing a cell-free assay related to your final project.
•Creating and running code to validate an aspect of your final project.
•Developing a model or completing a computational analysis relevant to your project.
•Designing DNA construct(s) that can express at least one gene of interest, ordering it (via Twist), and testing the expression of the construct(s) (potentially using an Opentrons robot).
1. What aspect of your final project did you choose to validate? (min. 2 sentences)
2. Write down a detailed protocol of how you validated this aspect of your final project. (numbered list or paragraph is fine)
3. What synthetic biology techniques did you utilize in validating this aspect of your final project? You can refer to the list of techniques in question 8. (min 4 sentences)
4. You must present data as part of your final project and include some analysis of that data. The data may be collected experimentally in the lab or generated as simulated data (e.g., using Asimov Kernel or another simulation method). (min 2 sentences)
2. Did you encounter any unexpected challenge(s) when performing your validation? If so, describe the challenge(s) and strategies to overcome it. If not, discuss potential problems, difficulties, limitations, and/or alternative strategies to overcome challenges in your final project. (min 4 sentences)
1. List all references cited in this assignment. (bullet-point list)
2. Create a supply list and budget for your project. (bullet-point list)
- What supplies, equipment, and budget is needed for your project to work?