Individual Final Project

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Sarcoptes scabiei Suspected Here!

FinalSlide

HTGAA 2026 Final Project: Sarcoptes exploit host geometry – developing assay to measure redox landscape in stratum corneum of goat

By Charley Naney

SECTION 1: ABSTRACT

  1. Provide an abstract/summary for your project. (minimum 150 words) • Should be a self-contained description of the project • Should contain brief outline of:
  • Significance: The ectoparasitic mite Sarcoptes scabiei exploits the stratum corneum of mammalian skin, including hosts within the Bovidae family (subfamily Caprinae), notably the genera Capra (goats) and Ovis (sheep). While S. scabiei infects a broad range of mammals, this project focuses on caprine hosts (Capra), which provide a tractable and agriculturally relevant system. Goats and sheep share a common ancestor within Caprinae but diverged approximately 4–5 million years ago, adapting to distinct ecological geometries. Goats evolved in heterogeneous, vertical, and discontinuous mountain environments, whereas sheep adapted to more homogeneous, open, and flock-oriented landscapes. These divergent ecological pressures have shaped not only behavior and morphology but potentially the spatial structure of skin physiology, including barrier properties, microenvironmental heterogeneity, and host–parasite interactions. Sarcoptes scabiei is a globally distributed, highly contagious parasite of major veterinary and public health concern. Cross-host transmission is frequently observed in practice: infestations in sheep may spread to goats, dogs, and humans in shared environments, reflecting the long cohabitation of these species under both natural and artificial selection over the past 8,000–10,000 years. This deep ecological and evolutionary entanglement suggests that Sarcoptes scabiei operates within host-derived microenvironments that are conserved enough to permit transmission, yet variable enough to shape infection dynamics. This project introduces a spatially resolved diagnostic concept: rather than sampling lesions indiscriminately, it targets the peri-lesional boundary, hypothesized to represent a localized maximum in reactive oxygen species (ROS) generated by host immune activity. By developing a small-scale assay—potentially leveraging fluorescent ROS probes—to detect this spatial oxidative signature, I aim to create a rapid, geometry-informed approach to identifying mite-associated lesions. While species-level discrimination of Sarcoptes lineages may not be feasible within the project timeline, this approach can be strengthened through triangulation, integrating spatial ROS signals with observational and survey-based metadata (host species, lesion morphology, transmission context). Together, these elements may yield a more robust and field-deployable diagnostic framework. Beyond immediate application, this work addresses a broader evolutionary and biophysical question: how parasites exploit host tissue geometry to create stable microenvironments, and how those environments can be detected through their spatial redox signatures. In this sense, Sarcoptes scabiei infection becomes not only a veterinary problem, but a model system for understanding how geometry, evolution, and immune dynamics converge in living tissue.
  • Broad objectives: I will develop spaitially resolved diagnostic assay for detecting Sarcoptes scabiei infection, or evidence of burrows in epidermal layers of skin, using fluorescent ROS probes capable of detecting oxidative stress signature in caprine skin. This approach will include farmer education and a survey for targeting host and environmental metadata, and skin targeting of peri-lesional microenvironments. Testing data can later be combined with transcriptomic sequencing, as other researchers are starting to do to develop putative genes that can be analyzed to develop more exact assay-based biomarkers for diagnosis, prognosis, and more targeted therapy with effective surveillance, as only a recovering Epidemiologist, goat and sheep farmer, returned to Evolutionary Microbiology can dream up.
  • Hypotheses: Sarcoptes scabiei infection or infestation, need to decide on best state variable terminology here, is a pathogenic process involving reorganization of the geometry of the stratum corneum. The mites burrow to feed, make shelter, and lay eggs which results in a diffusion-constrained microenvironment ideal for assaying host immune responses surrounding, including what I hypothesize to be a localized region with maximum concentration of ROS distributed within a peri-lesional boundary.
  • Specific aims
  • Null Hypothesis: In probable Sarcoptes scabiel infested goats, ROS levels will be uniformly distributed across lesion core, peri-lesional boundary tissue, with no spaitial enrichment at lesion boundary.

Alternative Hypothesis: In probable Sarcoptes scabiel infested goats, a localized maximum of ROS at the peri-lesional boundary in caprine skin will be present.

  • Methods to be employed • Use lay language (i.e., understandable by the general public) as much as possible SECTION 2: PROJECT AIMS
  1. Outline three aims of your final project (min. 3 sentences, at least one for each aim) Aim 1: Baseline Fluorescence Mapping of Herd The subject (i.e., goat, sheep, other mammal frequently in-contact with herd) is visually inspected using system for suspected lesions indicative of possible infestation. A low toxicity fluorescent dye or marker may be applied to skin surface to survey skin surface to establish baseline imaging conditions. A portable light source (i.e., UV or visible excitation light) will be coupled with imaging device (i.e., smartphone camera with accessory macro lens) will be used capture images of skin regions where first coat of fluorescent die label is applied. This region can include suspected lesion or control region. These images are then analyzed to establish baseline fluorescence patterns and instructions to improve collection of baseline images. Aim 2: Reactive Oxygen Species Detection in Herd Low toxicity in-field application of fluorescent probe capable of interacting with reactive oxygen species is applied to the skin surface, including the lesion and surrounding peri-lesional region. The sample will not be fixed with formaldehyde, a known carcinogen, but instead will be air dried with optional portable fan to accelerate non-chemical fixation process. Excitation will then be reached with appropriate light source, at which point scan and capture of ROS signals will be completed. Spatial variation in fluorescence intensity will then be analyzed to identify biologically active regions, including potential peri-lesional infestation boundaries. Aim 3: Image Analysis and Risk Stratification in Herd Captured images from Aim 1 and Aim 2 are analyzed using computational methods, including intracellular artificial neural network circuit for analogue machine learning modeler to identify patterns of fluorescence intensity associated with peri-lesion activity. The system will classify individual animals in herd based on risk levels to identify individuals requiring further testing as well as guiding further testing and treatment. In some embodiments, the system may be deployed to integrate data across multiple animals to support herd-level decision-making.

  • State or link any methods/experimental protocols/OpenTrons protocols/DNA or protein designs/protein design tools or models/Twist orders you will use

  • Quality Control and Validation This is a scientific embodiment, so before system is packaged for any farmer with a smart phone and a goat, an appropriate confirmatory analysis using cutting edge laboratory methods will be performed. Analysis will be conducted using automation and high-throughput systems. The validation protocol will be developed with guidance from MIT HTGAA 2026. Validation steps may be used to correlate field-detected fluorescence signals with molecular or biological markers of infestation.

  • You will provide a detailed, step-by-step outline of how you will achieve your goal for the first aim in the experimental design portion of this assignment (i.e., in question 7)

  • Feel free to run your goal by a TA • The second aim should be a medium-term aim that is a follow-up to your first aim and focused on goals beyond this class, building toward your third, visionary aim

  • For example, your second aim may be to successfully execute a set of experimental protocols, solve a specific problem, or develop a specific technology building upon the goals of your first aim. • The third aim should be a visionary, long-term aim

  • Reveal how the larger goal of the project can be impactful

  • Examples: challenging an existing paradigm or clinical practice, addressing a critical barrier to progress in the field, describing how you envision a new technology to change how a certain type of research is conducted SECTION 3: BACKGROUND

  1. Provide background research for your final project. This should describe the current state of knowledge related to your project and be a critical evaluation of the literature that identifies the gap in knowledge that this project will fill. Cite at least 2 peer-reviewed research papers. (min. 4 sentences)
  2. Describe how your project is innovative (min. 3 sentences) • Examples of topics to discuss
  • Novel applications, usage, or development of theoretical concepts, approaches, methodologies, instrumentation, and/or interventions
  • How it challenges current theories, paradigms, or ways in which technology/biological tools are used
  • How your project pushes the boundaries of synthetic biology
  1. Briefly expand upon the significance of your final project. (min. 5 sentences) • Examples of topics to discuss
  • There are several ways my project solves a pressing problem in the world. First and foremost, it provides any farmer with a smart phone and my kit, which I hope they can buy at Walmart or Tractor Supply, or they can pick one up for free where such conveniences are not available. The kit will include low-toxicity fluorescence, snap on macro lens, uv flashlight, QR code with registration for an App. They can then snap photo of their cat, and prompt will say not goat. They find goat, prompt correct animal, take photo here but part hair first, ect. This tool will empower them to test their intuition about an animal in the herd that they think may be infested with Sarcoptes scabiei without spending hundreds or thousands of dollars to expose every animal in the herd to toxic treatments for prevention or to consult a vet before they know if they have a problem. For example, “sulfur lime,” which is one of the treatments I am referring to, coats the entire animal in reactive oxygen species. In contrast, S. scabiei is highly localized and as an obligate parasite with a very long evolutionary tail will move from one susceptible animal to the next at a leisurely pace. Granted when enough animals are infested it can be a hard chain of transmission to break, but early detection and localized remediation is effective. Early detection is critical in this regard. Another challenge is the random way it enters herd, often because neighboring farmers are in the same boat. Then there are all the intermediate hosts between herds. The only viable alternative to my solution is marrying a vet or having a kid go to vet school, but my kit is a lot cheaper.
  • Importance of the problem it solves or the critical barrier(s) to progress in the field that the proposed project addresses
  • The ways in which it contributes to the larger society
  • How the proposed project will improve scientific knowledge, technical capability, and/or clinical practice in one or more broad fields
  • How the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field will be changed if the proposed aims are achieved
  1. Describe the bioethical considerations involved in your project. (min. 2 paragraphs) • First paragraph: Include what ethical implications are involved in your project. Try to suggest ethical the principle(s) you may apply (e.g. non-maleficence, justice)? • 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:
  • What action(s) do you propose?
  • What are potential unintended consequences of your proposed actions?
  • What could you have wrong (e.g., incorrect assumptions and uncertainties)?
  • What are alternatives to your proposed actions? • Note: in an NIH proposal, an ethics statement is used to describe the relevance of this research to public health SECTION 4: 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) • Include specific methods/tools/technologies/biological concepts for each part of the final project and analysis • This section will be used to determine whether the experiments are well designed, feasible, and likely to succeed in testing your hypothesis • Often this section is broken into discrete tasks/sub-aims • For each experiment and/or analysis, include a description of your expected results • If possible, include figure(s) that visually shows a broad workflow of your project or a specific aspect of your experimental plan SECTION 5: TECHNIQUES, TOOLS, AND TECHNOLOGY
  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 Pipetting Lab Safety Bioethical Considerations (must check this box) DNA Gel Art DNA Sequencing DNA Editing (e.g., CRISPR) DNA Construct Design Restriction Enzyme Digestion Gel Electrophoresis DNA Purification From Gel Databases (e.g., GenBank, NCBI, Ensembl, and UCSC Genome Browser) Opentrons Creating Code for Laboratory Automation PyLabRobot Using Liquid Handling Robots (e.g., Opentrons) Protein Design Protein Design Models and Notebooks Databases Tools BioProduction BioProduction Chassis Selection (e.g., Dh5alpha) Registry of Standard Biological Parts FreeGenes Plasmid Preparation Bacterial Culturing Quality Control/Analysis Bacterial Processing (e.g., Centrifugation, Lysis, DNA Purification) Cell Free Cell Free Reactions Freeze-Dried Cell Free Systems miniPCR Tools Week 7: Gibson Assembly Primer Design or Selection PCR Reactions Gibson Assembly Other Cloning Methods (e.g., Restriction Enzyme Digestion or Gateway Cloning) Week 8-9: CRISPR CRISPR/Cas9 Designing Prime Editing gRNA Creating Twist Order
  3. 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) SECTION 6: PROJECT VALIDATION
  4. 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: • Performing a PCR reaction using primers relevant to your final project • Performing a Gibson assembly relevant to your final project • Designing DNA relevant to your final 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 of the expression of the construct(s) (potentially using an OpenTrons robot) 10a. What aspect of your final project did you choose to validate? (min. 2 sentences) 10b. Write down a detailed protocol of how you validated this aspect of your final project. (Numbered list or paragraph is fine) 10c. 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)
  5. 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) SECTION 7: ADDITIONAL INFORMATION
  6. List all references cited in this assignment (bullet-point list)
  7. Create a supply list and budget for your project (bullet-point list)
  • What supplies, equipment, and budget is needed for your project to work?