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VIRTUAL JOURNAL CLUB

Virtual Journal Club COVID-19 has shown us that some things, like journal clubs, can be effectively done on-line. This opens up the possibility to include participants from different universities or even companies, as we are constrained only by time-zone differences. Both trainees and PIs are encouraged to join, but the goal is to make this a trainee-based discussion with minimal PI input except to clarify and steer the discussions.   This virtual journal club will take place in the spring semester, 2021. If there is enough interest, we can continue it the following fall. We will meet for 1 hour each Wednesday at 3 pm (eastern time), beginning on January 27 and ending May 5.   Format: In order to accommodate as many presenters as possible, we will have two 30 min presentations each week (15 min presentation/15 min discussion). These can be independent or coordinated (e.g., a technique paper followed by an application paper using that technique). Preference will be given to trainees (students, postdocs), but anyone is welcome to present if slots are available. We will provide a signup sheet with the complete schedule shortly after the New Year. The schedule will show papers that have already been chosen.   Scope and choice of paper: All areas of metabolomics analytical technology (MS, NMR, other), bioinformatics/chemoinformatics/biostatistics, and applications are welcome. While the most recent literature (within ~2 years) is encouraged, highly impactful older papers are also appropriate. The overall goals are to get introduced to interesting papers in metabolomics and to learn something new from them. People should not present work from their own lab, but it is fine to present work from another group that participates in the journal club. We want to use this to build community, so we encourage presenters to reach out to authors of papers to ask questions in preparation and to invite them to join. Papers will be posted in advance for participants to read in preparation for the presentations.   Many papers will be too long to fit into these short timeslots. Therefore, presenters should not feel compelled to cover everything. In fact, just focusing on a key take-away, such as a method, analysis or result and explaining it in detail with a few figures or tables is better than trying to cover the whole paper.   If you are interested in participating in this virtual journal club, send an email with your name and position (student, postdoc, staff, faculty, other) to Karen Howard. She will add you to the list and will send you a schedule, signup list, and zoom link after January 4. This Virtual Journal Club is facilitated by the Metabolomics Association of North America

VIP

VIP Vertically Integrated Project: Undergraduate Research Team   Systems Biology of Chemical Defense and Innate Immunity   Overall Goal: To provide a rich undergraduate research experience conducting a systems biology study of the model organism, Caenorhabditis elegans. This small nematode is one of the best studied animals in science and has been the foundation for numerous discoveries in basic biology and human biomedicine. However, less is known about C. elegans in its environment and interactions with other organisms. C. elegans lives in complex ecological niches with numerous microbes, some of which are food and others pathogenic. One such microbe is Pseudomonas aeruginosa, which is pathogenic to both humans and C. elegans and which produces small molecules that can kill worms, including 1-hydroxyphenazine (1-HP), which will be used in our undergraduate research efforts. Previous research from the Edison lab has shown that C. elegans can glycosylate 1-HP, redering it non-toxic to other worms. Our team will conduct ecological, laboratory, and computational studies to better understand the mechanism that C. elegans uses to defend itself against P. aeruginosa.   Overall Structure of the Team: In order to more safely conduct research during the COVID-19 pandemic, the team will be organized into 4 groups. We meet for an hour each week as an entire team through Zoom. The groups meet on a regular basis through Zoom to discuss specific questions related to that group and to get help from Prof. Edison and graduate students in his lab.   Field collections: This group looks for new isolates of C. elegans in nature. This information is extremely valuable, because it will allow a population genetics analysis of C. elegans throughout Georgia and beyond. Students will be working with an established database and repository called the C. elegans natural diversity resource (CeNDR), which has instructions and a smartphone app for collecting C. elegans in the wild. Students will learn how to collect and culture nematodes and identify new strains through PCR reactions and DNA sequencing. The ideal students for this group will be outdoor/hiking enthusiasts who are interested in ecology and genetics. This group is open to students at UGA as well as partnering institutions from Fort Valley State University and Savannah State University in the Peach State LSAMP network.   Laboratory research: This group will work in the Edison lab in the CCRC at UGA. They will conduct quantitative measurements of the toxicity of 1-HP on various strains of C. elegans, including those collected in the field. They will determine the mechanism of toxin inactivation by using analytical techniques such as HPLC and in some cases could also conduct gene expression studies using RNAseq on a subset of strains. This group will also support the field collection group by conducting molecular characterizations of specimens collected. During COVID-19, this group will be limited to 3 UGA students, but once we can expand face-to-face operations, additional students in the Peach State LSAMP network can get lab experience as well, especially during summer.   Computation and bioinformatics: This group will develop new bioinformatics tools to find gene families in C. elegans that might be responsible for chemical defense and innate immunity. We will utilize the CeNDR database, which includes genomic sequences of hundreds of natural isolates from around the world. The UGT (UDP-glucuronosyltransferase) gene family is responsible for attaching a carbohydrate molecule to a toxin, which inactivates the toxin. The challenge is that there are over 70 UGT genes in C. elegans. Students will learn computer programming and genome analysis skills. This group is open to students at UGA as well as partnering institutions from Fort Valley State University and Savannah State University in the Peach State LSAMP network.   NMR: The NMR group will learn to analyze 1D and 2D NMR data of metabolites. The Edison lab and CCRC NMR Facility collect NMR reference data for the BMRB database, and VIP students will get experience in analyzing and assigning these reference datasets. When COVID-19 allows, VIP students in this group will get training in NMR data acquisition.   For more information, contact Prof. Art Edison.

BINF 4550/6550

Introduction to Bioinformatics This class is offered every fall semester, and taught with Jim Leebens-Mack and Jonathan Arnold. It is for advanced undergraduates or graduate students. The overall class focuses on systems biology, with introductions to omics (metabolomics, genomics, and RNAseq), an overview and introduction to trees for analysis of phylogentic and omics data, and an introduction to programming in MATLAB. The 3 instructors attend and participate in most of the classes, so it is not a traditional team-taught class.

NMR BASICS

Lecture notes in NMR I have compiled a set of 9 lectures that provide an overview of NMR. I hope to update these soon.