iGEM 2024 — Team swuer-china

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{% block title %}Notebook{% endblock %}
{% block lead %}Document the dates you worked on your project. This should be a detailed account of the work done each day for your project.{% endblock %}
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Notebook

Hemolysis

MIC Experiments

Mice Experiments

Hemolysis

MIC Experiments

Mice Experiments

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{% block title %}Engineering{% endblock %}
{% block lead %}Exploration of our antimicrobial peptide screening, model training, and experimental validation.{% endblock %}
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Engineering

Overview

Dry Lab Experiments

Wet Lab Experiments

Overview

To enhance the screening process for antifungal peptides, the research team was divided into wet-lab and dry-lab groups. The dry-lab experiments encompass data processing, model training, and model validation. The wet-lab experiments serve as complementary validation to the dry-lab results and are designed to assess the safety of antimicrobial peptides. The wet-lab experiments include minimum inhibitory concentration (MIC) determination, hemolysis assays, and mouse experiments.

Dry Lab Experiments

The model was trained using a dataset comprising more than 30,000 non-antifungal peptide (non-AFP) entries, over 6,000 antifungal peptide (AFP) entries, and fewer than 4,000 MIC data points. The data was randomly divided into training, testing, and validation sets in an 8:1:1 ratio. Two types of models were trained for the antimicrobial peptide screening:

* **Qualitative Model:** The DeBERTa model was employed for deep learning training, linked to a fully connected layer for classification.
* **Quantitative Model:** DeBERTa was also used for MIC prediction, trained using mean squared error (MSE) for continuous output.

![Model Training](https://static.igem.wiki/teams/5183/hub/engineeringpage/1.png)

**Model Validation** The model was validated using common classification metrics like accuracy, precision, and recall. Regression metrics like MSE and Pearson correlation coefficient were calculated for MIC prediction. Model tuning involved filtering negative sequences to improve performance, increasing prediction accuracy to 99.4%.

Wet Lab Experiments

The wet-lab experiments served to validate the dry-lab model predictions. The key experiments included:

* **Minimum Inhibitory Concentration (MIC) Determination:** This experiment was used to assess the efficacy of antifungal peptides in inhibiting fungal growth.

![Mouse Model Experiment](https://static.igem.wiki/teams/5183/hub/engineeringpage/4.png)

* **Hemolysis Assays:** These assays tested the safety of antifungal peptides on red blood cells.

![Model Accuracy](https://static.igem.wiki/teams/5183/hub/engineeringpage/5.png)

* **Mouse Model for Skin Infections:** A skin infection model in mice was used to assess the therapeutic potential of antifungal peptides.

![MIC Experiment](https://static.igem.wiki/teams/5183/hub/engineeringpage/2.png)
![Hemolysis Assays](https://static.igem.wiki/teams/5183/hub/engineeringpage/3.png)

![Tuning Results](https://static.igem.wiki/teams/5183/hub/engineeringpage/6.png)

![MIC Validation](https://static.igem.wiki/teams/5183/hub/engineeringpage/7.png)
![Final Results](https://static.igem.wiki/teams/5183/hub/engineeringpage/8.png)

Engineering

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{% block title %}Results{% endblock %}
{% block lead %}Results of MIC and Hemolysis Experiments{% endblock %}
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Results

MIC Results

Hemolysis Results

PDF of Results

MIC Results

The antifungal spectrum and effect of the 33 antifungal peptides screened by the model were tested through the MIC experiment. Among six tested fungi (BJCA001 neoformans H99, C. albicans SC5314, C. albicans F5, C. albicans G5, C. glabrata ATCC2001, and C. auris), the antifungal peptides were especially effective against *C. albicans* SC5314.

Out of 33 antifungal peptides, 13 had an MIC value of 64 μg/mL or less. Among these:

**1159910**: 8 μg/mL

**1159912**: 16 μg/mL

**1177548**: 16 μg/mL

These three antifungal peptides also demonstrated broad-spectrum antifungal properties.

![MIC Results](https://static.igem.wiki/teams/5183/hub/resultpage/1.png)

Hemolysis Results

Based on the MIC results, we selected three antifungal peptides (1159910, 1159912, and 1177548) for hemolysis experiments. The results showed that:

The hemolysis rate of antifungal peptides 1159910 and 1159912 was less than 10% within the concentration range of 8-128 μg/mL. The hemolysis rate increased with the rise in drug concentration.

However, antifungal peptide 1177548 showed a higher overall hemolysis rate, which might further worsen wound infection.

Based on these results, peptides 1159910 and 1159912 were chosen for further experimental verification.

![Hemolysis Experiment 1](https://static.igem.wiki/teams/5183/hub/resultpage/2.png)

![Hemolysis Experiment 2](https://static.igem.wiki/teams/5183/hub/resultpage/3.jpg)

Complete Results PDF

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