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 12, 2018

Dr. Jim Leebens-Mack

Department of Plant Biology, University of Georgia.

The Garden Asparagus Genome Sequence Sheds Light on the Origin and Early Evolution of Sex Chromosomes

Time: 1:30 PM

Host: Professor Jenny Xiang

February 20, 2018

Growing Plants in Space: the Effects of Microgravity on Plant Tropistic Responses

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: The physiological and organismal diversity of microbial ammonia-oxidation has experienced numerous paradigm shifts in recent times, including the discovery of anammox in 1995, ammonia-oxidizing Thaumarchaeota (AOA) in 2005, and comammox in 2016. In 2008, Dr. Martin Klotz and I proposed that the earliest N-cycle relied on anammox bacteria and their invention of enzymology to metabolize the toxic intermediates, hydroxylamine and hydrazine, to recycle nitrite-N and ammonium-N back to N2 (FEMS Microbiol. Lett. 278:146) The ability to extract electrons from hydroxylamine and/or hydrazine and conduct them to the quinone pool allowed the coupling of ammonia oxidation with energy conservation. We have named this the “Hydroxylamine/Hydrazine-Ubiquinone Redox Module” or HURM, which is unique to ammonia-oxidizing chemolithotrophy. The proteobacterial ammonia-oxidizers emerged following the great oxidation event with the invention of the copper-based ammonia monooxygenase, which aligned with HURM for energy conservation. The entirely copper-based enzymology of AOA likely evolved in conjunction with increased atmospheric O2 and bioavailability of copper; AOA rely on a yet-to-be-identified copper-based HURM.  The commonalities among all ammonia-oxidizers is their production and metabolism of toxic intermediates including NO, NH2OH, and NO2 and connecting NH2OH oxidation with the flow of electrons to the quinone pool. More recently, the central role of NO oxidation in conjunction with, or immediately following, the oxidation of NH2OH has been described for both ammonia-oxidizing bacteria and AOA, challenging us to identify and characterize new classes of NO-oxidase enzymes.

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

Studies in Similarity: Comparative Metabolomics for Botanical Phytochemical Analysis

Dr. Josh Kellogg, University of North Carolina, Greensboro

Host: Dr. Jillian De Gezelle

Abstract: The number of Americans utilizing dietary supplements has risen to well over 50% of the population, with sales nearly tripling during the 20 years since passage of the Dietary Supplement Health and Education Act.  In many cases, these dietary supplements are prepared from botanical sources in the form of extracts, teas, capsules, or tinctures.  Investigators involved in studies of natural products, botanicals, food products or neutraceuticals face a unique set of challenges with these complex mixtures, in which the identities and quantities of components present may not be fully known, and the chemical composition can vary greatly depending on the method of preparation or source material used. Our work has focused on the development of mass spectrometry-based metabolomic approaches for analysis of complex mixtures, and advanced statistical methods for facilitating comparisons between samples and identifying bioactive principles. These methods have been applied to studies of three botanical dietary supplements: Camellia sinensis (green tea), Hydrastis canadensis (goldenseal), and Mitragyna speciosa (kratom), to discover bioactive metabolites, examine and choose samples for clinical evaluation, and uncover potential adulteration.

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

Charles Darwin: Botanist

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

Host: Dr. James Mickle

April 10, 2018

Research and Product Development in the Digital Era of Agriculture

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

Host: Dr. Anna Stepanova

April 17, 2018

Peroxisome Dynamics in Arabidopsis

Dr. Bonnie Bartel, Department of BioSciences, Rice University

Host: BW Wells speaker- PMB Graduates

April 24, 2018

Dr. Francisco Gomez

Department of Plant and Microbial Biology, NCSU

QTL Mapping of Stem Biochemical Traits and Precision Phenotypping in Bioenergy Sorghum (Sorghum bicolor)

Host: Professor Candace Haigler

Abstract: Understanding the genetic architecture of important mechanical traits is critically important to application in plant breeding. Mechanical characterization is an important and now frequently used tool for phenotyping plants for crop improvement, e.g. lodging resistance. Mechanics of materials and structures in response to various external stimuli as well as information of basic building blocks that constitute the plants can be applied to study the mechanical behavior of plant stems. Here we report for the first time on the mapping of QTL for mechanical traits in sorghum in three RIL mapping populations from crosses between grain and sweet sorghum parents. The genetic architecture of biomechanical traits in the three RIL populations appear to be quantitative and pleiotropic. Six QTL affecting mechanical and morphological traits were detected; two of these QTL were consistently found in all populations and co-localized with previously cloned dwarfing genes Dw1 and Dw3. These results suggest that dwarfing genes affect the mechanical properties of sorghum and ultimately their lodging resistance while also having a profound impact on the stem’s morphology and geometry. We also demonstrate a new high-throughput pipeline to measure morpho-anatomical traits using an x-ray computed tomography (CT) in an applied sorghum breeding program.  CT estimates were highly predictive of morphological traits and moderately predictive of anatomical traits. Our approach demonstrates that CT can be a powerful tool to quantify important internal and external phenotypic information of plant stems.

May 1, 2018


PMB Seminars Archive