PMB Seminar Schedule

Spring 2018

January 16, 2018

Reproductive Isolation and Habitat Divergence: The Emergence of Parallel ‘Habitat-selection’ Traits during Replicate Instances of Edaphic Specialization in the Genus Mimulus

Dr. Jay Sobel, Department of Biological Sciences, Binghamton University (SUNY)

Host: Dr. Seema Sheth

January 23, 2018

No seminar during this date


January 30, 2018

The Long and the Short of it: Characterizing Sulfur-cycling in Microbial Communities with Long Read Sequencing Platforms

Dr. Lizzy Wilbanks

Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barabara

Host: Dr. Manuel Kleiner

Abstract: Metagenomic sequencing of both host-associated microbiomes and free-living microbes has revolutionized our understanding of microbial communities. However, the assembly of genomes and classification of genome fragments (“binning”) from short-read Illumina sequencing remains a major computational challenge. We have been experimenting with three different long read sequencing platforms, PacBio, Illumina synthetic long reads and Oxford Nanopore, to evaluate innovative solutions to the current challenges in metagenomics. Our study system, the “pink berry” consortia are macroscopic, photosynthetic microbial aggregates dominated by two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1), which in previous work, we have demonstrated catalyze a complete sulfur cycle within these aggregates.

February 6, 2018

Better Measurement of the Microbiome by Statistical Modeling of High-throughput Sequencing

Dr. Benjamin Callahan, Department of Population Health and Pathobiology, North Carolina State University

Host: Dr. Manuel Kleiner

Abstract: Long read assemblies from PacBio have produced megabase sized contigs and complete or ‘closed’ population genomes for the dominant species in community. Furthermore, we show that taxon specific patterns of DNA methylation (from restriction modification systems) can be used to bin unidentified sequence fragments to dinstinct species. Long read data facilitates discovery of horizontal gene transfers and novel population level structural variants in uncultured bacteria, including transposes, CRISPRs and prophage. These assemblies have facilitated our analysis of this sulfur cycling symbiosis: in the genome of the sulfate reducing bacterium in the consortia, we discovered a horizontally transferred genomic island containing a light sensitive sodium pumping rhodopsin – the first report of phototrophy in a sulfate reducing bacterium.

February 13, 2018



Host: TBD

February 20, 2018


Dr. Joshua Vandenbrink, Department of Biology, University of North Carolina, Greensboro

Host: Dr. Imara Perera


February 27, 2018

Evolution & Modularity of Ammonia Oxidation Pathways

Dr. Lisa Stein

Department of Biological Sciences, University of Alberta

Host: Dr. Manuel Kleiner

Abstract: With genomic and metagenomic sequence data becoming increasingly inexpensive, there is a need for computational tools for integrating such data into biologically-informative models.  I will discuss two areas where evolutionary and network models are helpful for understanding complex problems in biology.  In the first part of the talk, I will describe an evolutionary model of the resolution of the recent “alpha” genome duplication in the model plant Arabidopsis thaliana.  By comparing the Arabidopsis genome to those of several relatives, we find that the pattern of gene losses after the genome duplication reflects the origins of this duplication as the merging of two similar but not identical parental genomes (e.g., an allopolyploidy).  Even long after the polyploidy event, the identity of these two genomes can still be distinguished in their polyploid descendants, with functionally coherent sets of genes retained from each parent.  In the second part of the talk, I will use ruminant metagenomics as an example of how taking a metabolic network approach to metagenomics yields insights about ecosystem structure that are not apparent from taxonomic or gene-centric analyses.

March 6, 2018

No Seminar- Spring Break

March 13, 2018

DNA Replication Timing Programs in Maize and Arabidopsis

Dr. Bill Thompson, Plant and Microbial Biology Department, North Carolina State University

Host: Dr. Deyu Xie

Introduction: Bill Thompson holds the position of Distinguished University Research Professor at North Carolina State University and is currently two years into his third five-year plan for retirement. Over the years, his research interests have included genome organization, molecular evolution, transcriptional and post-transcriptional gene regulation, chromatin structure, gene silencing, and, most recently, DNA replication – all in vascular plant systems. He has mentored 23 PhD students and 37 postdoctoral associates, and served as PI for several large interdisciplinary training grants as well as numerous individual and collaborative research grants. Paying homage to Mendel, he started his career working on Pisum, but has also studied Osmunda, Avena, Vigna, Atriplex, Nicotiana, Arabidopsis, and Zea.

Bill grew up in New England and graduated from Princeton in 1966, where he was president of the Outing Club and nearly flunked statistics by failing to attend the 7:30 am classes. He received his PhD from the University of Washington in 1970, where he majored in Botany and minored in Plant Physiology, Mountaineering and Sailing. He then moved back to the East and did postdoctoral research at Harvard until 1972. He was saved from a position at Minnesota by a last minute action of the legislature, and instead became an Assistant Professor at the University of Massachusetts. In Amherst, he bought a house, started a family, and thought he could live happily ever after. However he was recruited to Stanford only two years later by the offer of a faculty position at the Carnegie Institution’s Department of Plant Biology. He remained at Carnegie until 1986, when he accepted his current position at North Carolina State University – where he originally intended to stay only 5 years or so, but found he could live happily ever after.

March 20, 2018



Host: TBD

March 27, 2018

Mighty Oaks from Little Acorns Grow: Phylogenomic Data Add New Branches to the Quercus Tree of Life

Dr. Paul Manos, Department of Biology, Duke University

Host: Dr. Jenny Xiang

April 3, 2018


Dr. Jim Costas, Department of Biology, Western Carolina University

Host: Dr. James Mickle

April 10, 2018


Dr. Todd De Zwaan, Automated Greenhouse Strategy Lead, Monsanto

Host: Dr. Anna Stepnova

April 17, 2018

Peroxisome Dynamics in Arabidopsis

Dr. Bonnie Bartel, Department of BioSciences, Rice University

Host: BW Wells speaker- Alexandria Szakacs

April 24, 2018



Host: TBD

May 1, 2018


PMB Seminars Archive