2021 Virtual Meeting Series
Friday July 9, 2021 (10:30AM – 12:00PM Pacific Time)
Techniques for Isolating DNA from Tough Samples
|Jackie Goordial, University of Guelph
Squeezing DNA from a rock: DNA extractions from low biomass settings
In this tutorial I will draw on experience in mineral permafrost and ocean crust samples to discuss methods to obtain genomic material from low biomass samples. I will discuss how (and when) to tweak common commercial DNA kits for low biomass samples (including lysis considerations and elution alterations), the use of flow cytometry to concentrate cells, and finally – options for amplifying DNA for downstream analysis when you get very small amounts.
Friday June 4, 2021 (10:30AM – 12:00PM Pacific Time)
How to Build Capacity for a Thriving Research Lab at a PUI (Primarily Undergraduate Institution)
|Rika Anderson, Carleton College
Conducting research with undergraduates at a small liberal arts college [10MB PDF]
We will discuss how to build up a successful research program at a primarily undergraduate institution (PUI). We will cover topics like teaching and research expectations at small liberal arts colleges (SLACs) and other PUIs, how to strike a balance between research and teaching at PUIs, how to design projects that fit the undergraduate student timeline, how to recruit and retain students in a diverse and equitable lab environment, avenues of research funding, and publishing with undergraduate co-authors.
|Terry McGlynn, California State University Dominguez Hills
How to develop an undergraduate research lab with long-term sustainability [1MB PDF]
I will describe the great variety of PUIs, including the ranges of expectations and resources in small liberal arts colleges and regional public universities. I will discuss what what it’s like to operate an undergraduate-centered research program, and describe a variety of strategic approaches to maintaining an active undergraduate research laboratory over the duration of your career.
|Additional resources identified by meeting participants:
Friday May 7, 2021 (10:30AM – 12:00PM Pacific Time)
New Microbial Physiology Techniques
|Roland Hatzenpichler, Montana State University
Next-generation physiology: Why and how to measure microbial phenotypes under (close to) in situ conditions
We will discuss cutting-edge approaches to measure microbial phenotypes and metabolic activities under as close to in situ conditions as experimentally possible. We will focus on non-destructive techniques capable of observing individual bacterial and archaeal cells that can be followed up by additional methods to further characterize cells of interest. Specifically, we will discuss how substrate analog probing and stable isotope labeling techniques, in combination with fluorescence- or Raman microscopy-based observation of intact cells, can test hypotheses generated via metagenomics and lead us towards a deeper understanding of microbial ecophysiology. Maybe more excitingly, we will discuss how these techniques can be employed to turn traditional workflows upside down and design experiments in which the phenotype of a cell is examined first and the genotype second.
Monday April 5, 2021 (10:30AM – 12:00PM Pacific Time)
New Tools in Bioinformatics
|Jake Weissman, University of Southern California
Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns
Maximal growth rate is a basic parameter of microbial lifestyle that varies over several orders of magnitude, with doubling times ranging from a matter of minutes to multiple days. Growth rates are typically measured using laboratory culture experiments. Yet, we lack sufficient understanding of the physiology of most microbes to design appropriate culture conditions for them, severely limiting our ability to assess the global diversity of microbial growth rates. Genomic estimators of maximal growth rate provide a practical solution to survey the distribution of microbial growth potential, regardless of cultivation status. We developed an improved maximal growth rate estimator (gRodon) and predicted maximal growth rates from over 200,000 genomes, metagenome-assembled genomes, and single-cell amplified genomes to survey growth potential across the range of prokaryotic diversity (the EGGO database); extensions allow estimates from 16S sequences alone as well as weighted community estimates from metagenomes.
|Ben Tully, University of Southern California
EukMetaSanity: A customizable workflow for the gene prediction and annotation of Eukaryotic genomes
The prediction of protein-coding regions in eukaryotic genomes requires multiple computationally and time intensive processes to accurately determine gene structure. Generally, eukaryotic gene prediction relies on a combination of transcript evidence, protein homology, and/or sequence signatures. EukMetaSanity incorporates the steps, repeat prediction, ab initio gene prediction, and evidence-based gene prediction into a single pipeline that can determine high-quality intron/exon boundaries for novel eukaryotic genomes. Along with an implementation that takes advantage of the distributed structure of high-performance computing clusters, EukMetaSanity has the ability to annotate 100-1,000s of eukaryotic genomes/MAGs/SAGs in short time-scales relative to current implementations and approaches. And while the need for this level of parallelization is not commonplace, recent marine eukaryotic MAG datasets suggest that practical solutions at scale will be necessary soon.
Learn more about the C-DEBI Virtual Meeting Series