## Welcome to FST 104L!<img src="https://hackmd.io/_uploads/S1LENWEOn.jpg" width="256" >
### Teaching team
<center>
<img src="https://hackmd.io/_uploads/SymjZCEdh.png" width="120">

Instructor: Luxin Wang, Ph.D.\
Office: 3210 Robert Mondavi Institute-South\
Email: [e-mail]\
Office phone number: 530-752-7552\
Office hours: by appointment
</center>

<center>
<img src="https://hackmd.io/_uploads/SJMUb04On.png" width="150" >

Laboratory Manager: Matthew Ford\
Email: [e-mail]
</center>

<center>
<img src="https://hackmd.io/_uploads/BJ1LXCNd2.png" width="100" > Jay
<img src="https://hackmd.io/_uploads/B1oHkyS_2.png" width="100" > Austin
<img src="https://hackmd.io/_uploads/H1ll5HcCp.jpg" width="80" > Ashlyn
<img src="https://hackmd.io/_uploads/r1AEm8cCT.png" width="150" > Melissa

Teaching assistants and TA office hours:\
Jay Liu Email: [e-mail] Fridays 10-11AM in 3143 RMI North (hybrid)\
Austin Weber Email: [e-mail] by appointment only \
Ashlyn Lightbown Email: [e-mail] Thursdays 3-4 pm in 3143 RMI North\
Melissa Chen Email: [e-mail] Mondays 1:30-2:00 pm in 3143 RMI North
</center>

## Location and time
Lectures: Mondays 9:00-9:50 AM (Olson Hall 118)\
Discussion (paper presentation): Wednesdays 9:00-9:50 AM (Olson Hall 118)\
Laboratory: **RMI North 1127**

## Course description:
This laboratory course aims to train students in the laboratory methods used in the microbiological analysis of foods. These experimental methods are used for studying microorganisms involved in food processing and food production environment, quality, and safety.

## Grading

| Entries |Points total |
| -------- | -------- |
| Lab reports (9 total) | 180 points (20 points per report) |
| Discussion attendance | 20 points |
| Paper presentation | 40 points |
| Final exam | 60 points |
| Total | 300 points |

* 5 point will be deducted for past the due day unless a note to TA is sent ahead of time. This point-deduction rule also applies to your lab reports. For the step-by-step manual, you can choose any paper among the 8 papers we will discuss in the class.
* Notification to the instructor about any absence from the lecture/discussion/lab is expected. Such notification can be sent via message in Canvas or email. It is expected that the notification will be received before the class starts. If under emergency situation, text message can be sent to 530-852-1660 or can be sent after.
* The final grades will be A+, A, A-, B+, B, B- based system.

---

## Lab reports
A lab report needs to be prepared after each lab and it is due 10 days (including weekends) after the lab is completed. Should you need additional time due to reasons, e.g. health emergency, please let Luxin and the TAs know. We are more than happy to work with you on the scheduling of the report due days. A lab report should contain the following parts and will be graded as following:
1. Title of the lab and your name (1 point).
2. Introduction and background of the experiment (5 points). At least 4-5 sentences are expected from you to talk about the background and use of the techniques or labs.
3. A summary paragraph of materials and methods (4 points).
4. Results. Please present your data in tables or figures and describe them. If you have photos, please also include that. No more than two photos. (8 points). 4-5 sentences for each table/figure.
5. Discussion. Please discuss your results. Are they what you expected? Why your results are different from what you expected or from others’ results? (2 points). There are also discussion questions after each lab for you to address. Minimum requirement: answer the discussion questions listed after each lab.

---

## Paper presentation
The entire class will be divided into 8 groups. The presentation will be a group presentation focusing on the discussion paper assigned for that week. The presentation will be 40 points. The following sections are expected to be covered in the presentation:

| Presentation component | Points total |
| -------- | -------- |
| Presentation title (paper title) | 2 points |
| Background and knowledge gap | 4 points |
| Materials and methods | 10 points |
| Results | 10 points |
| Discussion | 14 points |
| Total | 40 points |

* For **Materials and methods** (10 points): Please make step-by-step instructions based on materials and methods section of the paper and make visualization in the flowchart format(You can use source like Biorender.com).
* For **Results** :Please summarize every major findings in the results section of the paper.
* For **Discussion**: this part should consist of 1. significance of this study paper 2. discussion about the limitations of the paper 3.connections between this paper and the lab for that week.

## Proposed discussion schedule
#### 2024 Spring paper presentation order [link](https://docs.google.com/spreadsheets/d/1DsvmZwEBTXdK8hiIwqlTZsspbn3iBV85tMq4pYLZuxA/edit?usp=sharing). (Using Davis edu account to view)
| Week | Laboratery with YT video from 2021 | Discussion |Discussion topic/event |
| -------- | -------- | -------- |-------- |
| 1 | Lab 1 | April 3^rd |[Development of a Robust Method for Isolation of Shiga Toxin-Positive *Escherichia coli* (STEC) from Fecal, Plant, Soil and Water Samples from a Leafy Greens Production Region in California](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065716) |
| 2 | Lab 2 [<img src="https://hackmd.io/_uploads/Hknd2ZVd2.png" alt="Image" width="25">](https://www.youtube.com/watch?v=Ed2Pdj1dqVQ&list=PLBZKF-s2DPS1DXmEwXLvUfdk1yQm7OyT0&index=2) | April 10^th |[Indicator microorganisms in fresh vegetables from “farm to fork” in Rwanda ](https://www.sciencedirect.com/science/article/abs/pii/S0956713516307216)|
| 3 | Lab 3 [<img src="https://hackmd.io/_uploads/Hknd2ZVd2.png" alt="Image" width="25">](https://www.youtube.com/watch?v=_FpaSqJvlEg&list=PLBZKF-s2DPS1DXmEwXLvUfdk1yQm7OyT0&index=1) | April 17^th |[Evaluation of rapid screening techniques for detection of Salmonella spp. from produce samples after pre-enrichment according the FDA BAM and a short secondary enrichment](https://ami-journals.onlinelibrary.wiley.com/doi/10.1111/lam.12422) |
| 4 | Lab 4 [<img src="https://hackmd.io/_uploads/Hknd2ZVd2.png" alt="Image" width="25">](https://www.youtube.com/watch?v=jRg0zJVPCeE&list=PLBZKF-s2DPS1DXmEwXLvUfdk1yQm7OyT0&index=10) | April 24^th |[Thermal inactivation of *Escherichia coli* O157:H7, *Salmonella* and *Listeria monocytogenes* in breaded pork patties](https://ift.onlinelibrary.wiley.com/doi/abs/10.1111/j.1750-3841.2006.00264.x)|
| 5 | Lab 5 [<img src="https://hackmd.io/_uploads/Hknd2ZVd2.png" alt="Image" width="25">](https://www.youtube.com/watch?v=rIiAjJ8B3fg&list=PLBZKF-s2DPS1DXmEwXLvUfdk1yQm7OyT0&index=9) | May 1^st |[Isolation of lactic acid bacteria with probiotic potentials for kimchi, traditional Korean fermented vegetable ](https://www.sciencedirect.com/science/article/abs/pii/S0023643816301657)|
| 6 | Lab 6 [<img src="https://hackmd.io/_uploads/Hknd2ZVd2.png" alt="Image" width="25">](https://www.youtube.com/watch?v=FFtZJxmS8LQ&list=PLBZKF-s2DPS1DXmEwXLvUfdk1yQm7OyT0&index=11) | May 8^th |[Microbiological quality and incidence of *Staphylococcus aureus* and *Bacillus cereus* in vegetarian food products ](https://www.sciencedirect.com/science/article/abs/pii/S0740002098902568)|
| 7 | Lab 7 [<img src="https://hackmd.io/_uploads/Hknd2ZVd2.png" alt="Image" width="25">](https://www.youtube.com/watch?v=lv6c0lLS4Pc&list=PLBZKF-s2DPS1DXmEwXLvUfdk1yQm7OyT0&index=12) | May 15^th |[Antifungal activity of phenyllactic acid against molds isolated from bakery products](https://journals.asm.org/doi/10.1128/AEM.69.1.634-640.2003)|
| 8 | Lab 8 [<img src="https://hackmd.io/_uploads/Hknd2ZVd2.png" alt="Image" width="25">](https://www.youtube.com/watch?v=5c41OHGeX9c&list=PLBZKF-s2DPS1DXmEwXLvUfdk1yQm7OyT0&index=13) | May 22^nd |[Reduction of *Salmonella* in ground chicken using a bacteriophage ](https://www.sciencedirect.com/science/article/pii/S0032579119314841?via%3Dihub) |
9 | Lab 9 [<img src="https://hackmd.io/_uploads/Hknd2ZVd2.png" alt="Image" width="25">](https://www.youtube.com/watch?v=3JSDIbK5Spo&list=PLBZKF-s2DPS1DXmEwXLvUfdk1yQm7OyT0&index=15) | May 29^th |[Improved template preparation for PCR-based assays for detection of foodborne bacterial pathogens ](https://journals.asm.org/doi/10.1128/AEM.66.10.4539-4542.2000)|

**No lab or discussion in the week of May 29th due to Labor Day Monday**

---

## Lab schedule
📕Visualized protocol 📝Lab report guideline 📚Whiteboards

| Lab info | Materials |
| -------- | -------- |
| [Lab 1 Basic microbiology techniques](https://hackmd.io/@g4P5SSbiSriJQ-hJMcd9fg/HJoAA54_n) | [📕](https://drive.google.com/file/d/1cabH53NUgBohDMGqJmC5FQ4LBCFoHrmw/view?usp=sharing) [📝](https://drive.google.com/file/d/1W5j4uHnsbZ_U08JYu1EzIVluBNcS2IQy/view?usp=sharing[) [📚](https://drive.google.com/drive/folders/1fTtah1ODjaAgfftGLeRezkXVeCrHBOMT?usp=sharing)|
|[Lab 2 Indicator microorganisms: enumeration and characterization](https://hackmd.io/@g4P5SSbiSriJQ-hJMcd9fg/Sy8x0ynO2) | [📕](https://drive.google.com/file/d/1kwv5VQfchfw9Pgtb3Qv6cLV-Lm9DXFLn/view?usp=sharing) [📝](https://drive.google.com/file/d/1UEMgvG23E6bvhQ9S4gjs5pjpqnoHAOmD/view?usp=sharing) [📚](https://drive.google.com/drive/folders/1DK6zxwy1EAm15_kXcsRXNlkckjGMKt56?usp=sharing) |
| [Lab 3 Sampling and the detection of pathogens](https://hackmd.io/qkXeZnKWQkW8cV6x8jA8BQ?both=) | [📕](https://drive.google.com/file/d/1UY_ueldBB_O124W8p1cKIdpPeDgsNY08/view?usp=sharing) [📝](https://drive.google.com/file/d/1w_Tx0_cRATLBVRZpb0wUdC5jdBZUPO96/view?usp=sharing) [📚](https://drive.google.com/drive/folders/19JmU9_KZSttGxDWd2bbT8HTxeoFVmZ7W?usp=drive_link) |
| [Lab 4 D- and Z-values and the concept of validation](https://hackmd.io/pQ-VnO9IRlGFYEFmrVThWQ) | [📕](https://drive.google.com/file/d/11vlNuwlj07irpewUXQpwDypA1ITmJHP6/view?usp=sharing) [📝](https://drive.google.com/file/d/19B50ktTV5VpME-RXvWEqXsFFWU01rnk0/view?usp=sharing) [📚](https://drive.google.com/drive/folders/1w-BK4ZJ_hLx3mRkeDx01S-EzWrCjwG8m?usp=sharing)|
| [Lab 5 Bacterial fermentation and lactic acid bacteria](https://hackmd.io/2e63lWjGTyqXgOlB6JLJPQ) | [📕](https://drive.google.com/file/d/1-EZ7v7PwbdyucsHvhUUYnuDSeQq21hFt/view?usp=sharing) [📝](https://drive.google.com/file/d/1AhJWPYk_bU37yQR66ROd50fRncKDp2bY/view?usp=sharing) [📚](https://drive.google.com/file/d/1-09vj64rfSDhRwq85GlRldIejViV0fdG/view?usp=sharing)|
| [Lab 6 Gram + bacteria: *Staphylococcus* and *Bacillus*](https://hackmd.io/HN5cOcJ3RBSNhm_pWZiEVQ?view) | [📕](https://drive.google.com/file/d/1Ns0i6MmkRliXHGwdAtvW8r4DG5srPSto/view?usp=sharing) [📝](https://drive.google.com/file/d/1aols0GrLwKOSNrUYPjzTOB1mwiHOFvHF/view?usp=sharing) [📚](https://drive.google.com/drive/folders/1-3dvl45EL6ypyM_nPULM_x2r6Yx4eZzQ?usp=drive_link) |
| [Lab 7 Yeasts and molds](https://hackmd.io/@g4P5SSbiSriJQ-hJMcd9fg/SJ-Qg8BhT) | [📕](https://drive.google.com/file/d/1SztOiEoke-ikL6MXvhq9jSdRL4y5a7I8/view?usp=sharing) [📝](https://drive.google.com/file/d/1XkEC3cJP0Xf9mT-oYfqsoB0ggkgOJbNz/view?usp=sharing) [📚](https://drive.google.com/drive/folders/1-BUcwQnoTVFJUY8hBRehe1U5Jl0J-buU?usp=sharing)|
| [Lab 8 Bacteriophage](https://hackmd.io/@g4P5SSbiSriJQ-hJMcd9fg/rJ9bQIS36)| [📕](https://drive.google.com/file/d/1vsfRPj7rh9rv80y5D-BZ0582k97NzOzz/view?usp=sharing) [📝](https://drive.google.com/file/d/1wfet5jI7-CcTSk8INtzkWxvvRj_PESL3/view?usp=sharing) [📚](https://drive.google.com/file/d/1XOMs5CoAif7rmWLfyZcpBolKMHdBpR7i/view?usp=sharing) |
| [Lab 9 DNA extraction and polymerase chain reaction](https://drive.google.com/file/d/1vAQr6VjXe_l2JEcFBpn9LWDgK8kwDL9t/view?usp=sharing) | [📕](https://drive.google.com/file/d/1LXj8-TXem4acmWsXQHwpDHty2rFu7h9J/view?usp=sharing) [📚](https://drive.google.com/file/d/12UmENUfaF_h0vKqRpwD731eYESNSQ1Hf/view?usp=sharing) |

**Please use your UC Davis email when accessing these files**

---
## Announcements
### June 1st, 2024 annoucement
[Final review session](https://ucdavis.zoom.us/rec/share/KRVgqAzrJSRzJwoBAalIeVURl2QRIldR-vEQTwRxg6h4CfbEJE0-pSGKTheJS9CX.SaLsXjzkX_3MDqqQ?startTime=1717265037000).
### Apri 29th, 2024 annoucement
[*Salmonella* latex test video ](https://www.youtube.com/watch?v=k7g8rcEA_go)

[*Salmonella* preenrichment protocols shown in FDA BAM ](https://www.fda.gov/media/166699/download)
### Apri 13th, 2024 annoucement
**The schedule for week 3 lab**
| Date | Opening Window |
| -------- | -------- |
| Monday | 1:00pm to 3:00 pm |
| Tuesday | 10:00am to 12:00 am |
| Wednesday | 1:00pm to 3:00 pm |
| Thursday | 10:00am to 12:00 am |
| Friday | 11:00am to 1:00 pm |

### Apri 3rd, 2024 annoucement
Microscope and Gram Stain specific protocol can be found (adapted from MIC 103L)

[1. Microscope parts](https://drive.google.com/file/d/15tCPMxekoiHlgNO0d-eewjRBHdavL_NM/view?usp=sharing).
[2. Step by step protocol](https://drive.google.com/file/d/1nN7jY-UiJ3VdbBjZvz9Kixpsf_22JCn6/view?usp=sharing)
### Apri 1st, 2024 annoucement
1. **DO NOT** bring your own lab coat (like the one used in CHEM 2 series), since we will provide you disposable lab coat, but **please bring your safety goggles**.
2. First time in a microbiology lab? Afraid of being lost? Don't worry, we got you back. We introduce you **visualized protocol** (VP), which visually demonstrate the steps to complete the lab from begining to end. VP for each lab is listed in this page.
3. Room number for the lab section is RMI North 1127
4. **General requirement** can be found [here](https://drive.google.com/file/d/1FgaO0achqb3ksWQstvYEzJ_RCHlvd2Yy/view?usp=sharing)
5. Whiteboard picture can be found at 📚Austin's whiteboard.