# Summer 2021 Task List

7 June 2021 - Colby [EcoEvoDevo Lab](https://hackmd.io/@EcoEvoDevoLab/AngeliniLab) Group

## The next few days: June 9 - 14

For the next few days Dave and Devin will be dividing their attentions among several different commitment. Both will remain accessible by email and/or text. Dave will also be in his office most of the time.

You should focus on the list of near-term goals and tasks below. Not everything here needs to be completed. We'll resume closer work together on Tuesday.

### Tasks for everyone to complete
- [x] Complete the Moodle lab safety training module
- [x] Attend the lab safety training session **Wednesday 1pm**
- [x] Get a HackMD user account and try editting some docs. For example, remove your name from this list:

- [x] Check out [Charis's tutorial on Markdown and HackMD](https://hackmd.io/@6LjCUxqnQs2slmz-UhLmkA/HackMD_tutorial_Charis)
- Learn how to convert an unchecked box into one that's checked!
- [x] Complete the self-directed [R tutorial](https://hackmd.io/@aphanotus/Rtutorial), and the exercises at the end.
- [x] Let Dave and Devin know dates when you will be away during the summer.
- [x] Pilar: Please show Charis and Dylan how to use the microscope-mounted Motic cameras and software. You should all try this on both set-ups (in the beetle area, and in the insectary) -- Have Charis and Dylan help with beetle imaging!
- [x] **Friday, 10:00am**: The European EvoDevo Society is presenting a free online seminar that may be interest. Matthew Harris of Boston Children’s Hospital will give a talk entitled, *These fins were made for walking: exposing developmental potential for limb development latent within fins*. Just go to https://www.evodevo2020.eu/webinars/

### Tasks to work on as time becomes available
- [ ] Keep the bugs and beetle in good health! Please go through the bugs and be sure they have clean cages. Move *Jadera* eggs into hatchling dishes as necessary.
- [ ] Practice *Oncopeltus* egg injections. This is described in the [SOP on microinjection](https://hackmd.io/@EcoEvoDevoLab/microinjection#Injecting-eggs-of-Oncopeltus-or-Jadera). [Set-up](https://hackmd.io/@EcoEvoDevoLab/microinjection#Setting-up-staged-embryo-collections) some *Oncopeltus* cages to produce fresh eggs. Find healthy adults and place them in a new cage *without* cotton. [Prep the egg arena](https://hackmd.io/@EcoEvoDevoLab/microinjection#Preparing-the-arena). The next day, add cotton early in the morning. As soon as you see newly laid eggs, [collect them](https://hackmd.io/@EcoEvoDevoLab/microinjection#Loading-the-arena) for injection, following the protocol.
- [ ] Convert old lab SOPs to HackMD [lab website](https://hackmd.io/@EcoEvoDevoLab/AngeliniLab). Start with the protocols on insect care.
- [ ] Check out [*Bugs in our Bacykard*](http://www.bugsinourbackyard.org/), and think about writing contributions to the [blog](https://bugsinourbackyard.org/blog/).
- [ ] Read from the background [Reading List](https://hackmd.io/@EcoEvoDevoLab/EcoEvoDevoLabReadingList)
- Start with [Fawcett et al. 2018](https://www.nature.com/articles/s41467-018-04102-1)

- [ ] Check out the [tutorial on the Linux command line interface (CLI)](https://hackmd.io/@EcoEvoDevoLab/linuxbasics)

## Skill/Knowledge Building

### Workshops
- [ ] [Intro to the Linux command line](https://hackmd.io/@EcoEvoDevoLab/linuxbasics)
- [ ] Linux for RADseq analysis
- [ ] [Qiime2](https://qiime2.org/) microbiome analysis
- [ ] Making graphs with R ([Intro to R](https://hackmd.io/@aphanotus/Rtutorial))
- [ ] [Statistics in R](https://hackmd.io/@aphanotus/StatsInR)
- [ ] Photography, in general
- [ ] Photomicrography
- [ ] Bee [Macrophotography](https://hackmd.io/s/r1FcQYF-m)
- [ ] Using Adobe Suite / ImageJ / Outreach
### Background Information
- [ ] Regulation of organ growth
- [ ] [Insect appendage patterning](https://pubmed.ncbi.nlm.nih.gov/16112665/)
- [ ] Animal weapons
- [ ] Insect diversity

## Summer Projects

### Beetles

Sexually selected weapons are among the most extreme and diverse morphologies in the animal world. They are often massive in size and grow drastically out of proportion with the body. It is therefore unsurprising that weapons have captured the attention of biologists for centuries. Yet, despite this interest, fundamental questions of their evolution and development remain. My lab group is currently conducting a large-scale artificial selection experiment on the developmental mechanisms regulating weapon growth in the broad-horned flour beetle, *Gnathocerus cornutus*. During the summer of 2021, we plan to conduct and analyze high-throughput genome mapping (RAD-seq) of divergent selection lines, preform follow-up measurements of gene expression, and test the function of specific genes using methods such as RNA interference and CRISPR/Cas9 gene editing.

- Image beetles
- Morphmetric measurements
- Analyze those data
- DNA extraction for RADseq (~500 beetles)
- RADseq data analysis
- Functional genetic tests
- RNAi
- CRISPR (?)
- target pathways
- growth: warts, fat, hpo
- patterning: dac
- sex determination: dsx

### Bugs

While current technology makes genome sequencing and editing accessible, many aspects of genome structure remain poorly understood. The soapberry bug, *Jadera haematoloma*, has 7 haploid chromosomes, of which one, the “m-chromosome” does not undergo recombination. This summer we will work to develop CRISPR/Cas9 gene editing for use in this species, with the goal of testing the expression and recombination of transgenic constructs from the *Jadera* m-chromosome, the X chromosome, and other autosomes. These results will provide in-sights into chromosome-level regulation of gene expression.

- Routine bug care.
- Especially work in increase the numbers of *Jadera*.
- Set-up FR food regimes for Michael: use Jane Swart’s high and low conditions
- CRISPR: *Oncopeltus*
- knockout *vermillion* (*v*)
- CRISPR: *Jadera*
- knockout *vermillion* (*v*)
- insert an mNeonRed reporter
- Identify a potential endogenous promoter?
- Get a construct from a lab that's had success? Marce Lorenzen?
- Submit Jhae genome to NCBI
- Create a BioProject
- Submit genome reads to SRA
- Submit txome reads to SRA
- Submit transcriotome to TSA
- Request RefSeq annotation
- RNAi targeting EGF pathway components

### Bees

Bumblebees are charismatic animals that play a special role in the ecology of Maine. However, several species are currently experiencing population declines due to pesticide exposure, the spread of bee-specific diseases and habitat destruction. Previous work by my lab group has found that Maine islands harbor unique assemblages of bumblebee species, and detected the presence of known pathogens. From previous summers, we have collected geospatial data on bumblebee distributions, species IDs, and gut microbiome composition. During the summer of 2021, we will work to advance this project in several ways: (1) continue collections of bumblebees from key field sites, such as Colby’s campus and Allen Island; (2) analyze geospatial and microbiome data to examine patterns of diversity; (3) build on our present [outreach website](https://hobbes.colby.edu/bee.map/), which provides community reporting of project data.

- Field work
- Sample from campus (outside Eustis) weekly (collection limits: 3 individuals per species and caste). But photograph all bees.
- Sample Allen Island at least once per month (plan dates)
- other location? islands?
- Sample *Bombus* gynes in Fall 2021 and Spring 2022 from specific sites (Colby, Allen Island): How does microbiota change through overwintering?
- Update [outreach website](https://hobbes.colby.edu/bee.map/)
- Pull data continuously from [GBIF](https://www.gbif.org/)
- Add a tab that explains the background on bees and the research project. Explain what the layers are. Avoid “GIS” and “raster” jargon?
- Add the microbome data. How? What does Mark's analysis tell us? Perhaps have a tab with a seperate map that distills him findings.
- Link the Bee Map to [BioB](https://bugsinourbackyard.org/)

### Outreach

- Finish the *Bugs in our Backyard* coloring book
- Blogging at https://bugsinourbackyard.org/blog
- Butterfly Garden at Hungry Caterpillar Daycare
- ID guides
- teaching resources for young kids
- Waterville Creates
- Coastal Maine Botanic Gardens