New (old) course: Botanical Diversity BIOL 110 Fall, 2014

What: “Bot Div” will provide an introduction to the plants and macroalgae of New England, including systematics and natural history. The course will focus on the Hadwen Arboretum, which is just a few blocks from the Clark main campus. The Arboretum was donated to Clark by Obadiah Hadwen (1824-1907) and presents a mix of native and exotic plants, including invasive species. Bot Div students will create a series of “plant portraits” that will contribute to a web-based virtual flora of the Hadwen Arboretum. The class will also include joint workshops with Prof. Elli Crocker and students in ARTS 128 “Drawing: Sense of Place”. For Biology students, the workshops will develop observational and rendering skills; for Art students the workshops will raise awareness about plant structure and botanical illustration. Products of the workshops will be included in the web-based virtual flora and a student gallery exhibition.

When: Mon/Thurs 1:25-2:40 and Thurs 2:50-5:50; with additional weekend field trips.

Prerequisites: Introductory Biology 101/103 and 102.

Here are some of the plants that can be found in the Hadwen Arborteum:

Magnolia acuminata, the "cucumber tree"

Magnolia acuminata, the “cucumber tree”

Sciadopitys verticillata, the Japanese "umbrella pine"

Sciadopitys verticillata, the Japanese “umbrella pine”

Fallopia japonica, "Japanese knotweed", an aggressive invasive plant

Fallopia japonica, “Japanese knotweed”, an aggressive invasive plant

Maianthemum racemosum, false Solomon's seal (native)

Maianthemum racemosum, false Solomon’s seal (native)

 

Summer Undergraduate Research opportunity in fungal molecular phylogenetics

The Hibbett laboratory at Clark University seeks a talented undergraduate with interests in phylogenetic methods for a NSF-supported research experience associated with the Open Tree of Life Project (described below). Candidates should have experience in analytical methods for molecular systematics (sequence database searches, alignment, and phylogenetic analysis). Interest in fungi would be helpful, but is not essential.

OpToL“The Open Tree of Life Project seeks to develop tools to enable synthesis of phylogenetic trees and taxonomy into a comprehensive phylogeny of all life that can be updated by members of the systematics community. A key requirement of this project is that the source trees be available in electronic form. However, in a recent survey of fungal (and other) phylogenies, we found that only about 17% of published fungal phylogenetic studies have available trees. To address this situation, and to provide training in phylogenetic methods, we propose to have students supported with REU funds generate phylogenetic trees that correspond to important published studies in fungal systematics for which there are no treefiles available (i.e., following the Materials and Methods sections of published works, students will obtain and analyze data in an effort to regenerate published phylogenetic trees). These analyses will then be published in PLOS Currents Tree of Life, deposited in TreeBASE and Dryad, and integrated into the Open Tree phylogeny database using tools that the project has developed (currently, Phylografter is our tool for tree editing, taxon mapping, and integration, but it may be replaced by summer 2014). This work is important and necessary, because the vast majority of published phylogenies do not have trees available in electronic form, and many researchers who have been contacted have been unable to provide the trees. This work will provide the students with extensive experience in phylogenetic methods, and it will also demonstrate the importance of data archiving to achieve reproducibility in phylogenetic studies.”

Support is available for ten to twelve weeks, beginning as early as June 1, 2014. To apply, please send a single PDF file containing a cover letter (describing relevant experience, and stating dates of availability), resume, and contact information for two references to dhibbett@clarku.edu. This position is available for current undergraduates who are U.S. citizens, U.S. nationals, or permanent residents of the United States. Applications will be collected until March 26 (or until the position is filled).

 

Undergraduate researchers, Spring 2014

This semester we are fortunate to have three new undergraduate researchers in the lab, Sara Waldman, Dorothy Tang and Christie Joyce. Sam Kovaka is also continuing to work with us.

Sam Kovaka

Sam Kovaka

Sam is continuing his bioinformatics work with us. Presently, he is retrieving photoreceptor genes from the genomes of Lentinus tigrinus and many other fungi. This work will complement experimental studies on light-dependent pileus induction in L. tigrinus that will be performed by Christie and Alicia.

Sara Waldman

Sara Waldman. The little Petri dishes on the counter contain Fraxinus embryos.

Sara is working with Mitchell Nuhn on the Boletinellus merulioides/Fraxinus americanus symbiosis. She is trying to establish co-cultures of the fungus with the plant and compare survivorship of the plant with and without its fungal partner. The challenge is that the plant embryos have to be dissected out of the seed and germinated on agar to obtain seedlings. Tricky.

 

Dorothy and Christie are working on our emerging Lentinus tigrinus development projects, along with Alexis Carlson, Alicia Knudson and Laszlo Nagy. Dorothy is helping to obtain and genotype single spore isolates (haploids) that we hope to use in a bulk segregant analysis aimed at understanding the genetic basis of the secotioid phenotype. Christie will be helping develop a system for fruiting L. tigrinus under different wavelengths of light, in an effort to understand the mechanism of pileus induction. Pictures of L. tigrinus in all its forms are posted here.

Dorothy Tang culturing L. tigrinus.

Dorothy Tang 

Christie Joyce scoring clamp connections.
Christie Joyce

Otto departs

Today our friend Otto Miettinen and his family, Annina and Kelo, returned to Finland. It seems like only yesterday that they arrived.photo 2

Otto will complete his Marie Curie Fellowship, and then transition into a new position as curator of fungi in the Botanical Institute in Helsinki. It is always a little sad when people leave the lab, but it is great that Otto will take up this new post, and I trust that we will have opportunities to collaborate and visit in the future. We had a nice going-away party in Otto’s furniture-free apartment. Otto impressed us in so many ways, not least of all for his modern adaptation of the standing writing desk.

Otto's office

scimitar

kuva

A very large fungal phylogenomic tree

Sam Kovaka’s Directed Study (BIOL 299) project last semester involved creation of a large phylogenomic tree using fungal genomes housed at the JGI MycoCosm portal. Sam implemented a pipeline that uses a set of gene clusters from 186 fungal genomes available on MycoCosm in mid-2013. The genes are aligned and concatenated, poorly aligned regions are removed with Gblocks, and the phylogeny is estimated with RAxML. The tree is then parsed into its component clades using least common ancestor statements. The strategy for parsing the tree is similar to that employed in the “mor” project that was developed in my lab way back in 2005, although that used only one gene, nuc-lsu rRNA. To read more about Sam’s project, visit the web site he created, or go straight to the tree below and then click on the terminals to open up the subclades (e.g., Agaricomycotina). I believe that this is the most complete genome-based fungal phylogeny currently available. Thanks to Igor Grigoriev, Bobby Otillar and Robert Riley at JGI for helping Sam (who is a second-year undergraduate in our lab) with this project.

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Science Cafe Woo

Kelly_Ana picI am just back from a presentation at the Science Café Woo, hosted by the Nu Café in Worcester, and organized by Ana Maldonado-Contreras and Kelly Hallstrom from UMass Medical School (Kelly was a student researcher in my lab at Clark while she was an undergraduate, and worked with my former PhD student, Jason Slot). Tonight, I talked about the work that I did with Dimitris Floudas and many others on the evolution of white rot, and its possible correlation with the decline in coal deposition at the end of the Permo-Carboniferous (and how this result was overblown in the blogosphere). This was one of the most fun, energizing events that I have done in a long time. I have always been invigorated by my interactions with non-professional biologists, whether through the Boston Mycological Club or other organizations, and this was no exception. I certainly enjoy teaching undergraduates at Clark University, but non-professional/non-student audiences really bring something special, namely pure interest and curiosity, unburdened by concerns about grades and career advancement. Tonight’s crowd was engaged and relaxed, and they asked great questions! This experience reminded me why I got into biology in the first place, and it highlights the importance of citizen-science.

This was the eighth Science Cafe this year. The last one was given by my colleague John Baker. Kelly and Ana just received an Outreach Seed Grant from the American Society for Biochemistry and Molecular Biology, so there will be more of these events coming in Worcester in 2014.

Update 12/31/13: Karl Hakkarainen has a piece about the Science Cafe event on Worcester Connects. Karl’s article led me to  new examples of how the study with Dimitris et al. has been skewed in the on-line press, including one piece that asks “What caused the great coal crash of 300 million years ago?

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Polyporales genomes in Mycologia

At last, the polypore genomics issue of Mycologia (vol. 105, no. 6) has appeared. This issue contains eleven articles based on three new genomes of Polyporales, Bjerkandera adusta, Ganoderma lucidum and Phlebia brevispora. These are the first (but surely not the last) genomes published in Mycologia. This project represents the intersection of the NSF-funded PolyPEET project and the Saprotrophic Agaricomycotina project, supported by the JGI Fungal Genomics Program. Titles and links to abstracts from the Mycologia website are copied below the cover (the illustration is by Javier Ruiz-Dueñas). Many thanks to everyone who worked on these projects.

Mycologia 105(6) cover

Special Section: Genomics of Polyporales

Toward genome-enabled mycology. David S. Hibbett, Jason E. Stajich, and Joseph W. Spatafora.

Phylogenetic and phylogenomic overview of the Polyporales. Manfred Binder, Alfredo Justo, Robert Riley, Asaf Salamov, Francesc Lopez-Giraldez, Elisabet Sjökvist, Alex Copeland, Brian Foster, Hui Sun, Ellen Larsson, Karl-Henrik Larsson, Jeffrey Townsend, Igor V. Grigoriev, and David S. Hibbett.

Polyporales genomes reveal the genetic architecture underlying tetrapolar and bipolar mating systems. Timothy Y. James, Sheng Sun, Wenjun Li, Joseph Heitman, Hsiao-Che Kuo, Yong-Hwan Lee, Frederick O. Asiegbu, and Åke Olson.

A phylogenetic overview of the antrodia clade (Basidiomycota, Polyporales). Beatriz Ortiz-Santana, Daniel L. Lindner, Otto Miettinen, Alfredo Justo, and David S. Hibbett.

Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay. Chiaki Hori, Jill Gaskell, Kiyohiko Igarashi, Masahiro Samejima, David Hibbett, Bernard Henrissat, and Dan Cullen.

Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes. Francisco J. Ruiz-Dueñas, Taina Lundell, Dimitrios Floudas, Laszlo G. Nagy, José M. Barrasa, David S. Hibbett, and Angel T. Martínez.

Genomewide annotation and comparative genomics of cytochrome P450 monooxygenases (P450s) in the polypore species Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora. Khajamohiddin Syed, David R. Nelson, Robert Riley, and Jagjit S. Yadav.

Diversity and evolution of ABC proteins in basidiomycetes. Andriy Kovalchuk, Yong-Hwan Lee, and Fred O. Asiegbu.

Comparative genomics and evolutionary analysis of hydrophobins from three species of wood-degrading fungi. Anthony C. Mgbeahuruike, Andriy Kovalchuk, and Fred O. Asiegbu.

Distribution and bioinformatic analysis of the cerato-platanin protein family in Dikarya. Hongxin Chen, Andriy Kovalchuk, Susanna Keriö, and Fred O. Asiegbu.

Evolution of RNA interference proteins dicer and argonaute in Basidiomycota. Yang Hu, Jan Stenlid, Malin Elfstrand, and Åke Olson.

Undergraduate research opportunities for Spring 2014 (and beyond)

Our lab will have two research opportunities for undergraduates in spring 2014 (with potential to extend into the summer and beyond), both involving cultural studies of fungi. Please read below for details of the positions, and how to get involved.

Project 1: Mycorrhizal synthesis studies in Boletinellus merulioides (the “ash bolete”) and Fraxinus americana (white ash). Background: Boletinellus merulioides is a mushroom-forming fungus that occurs almost exclusively in association with ash trees. The nutritional mode of B. merulioides is controversial, with some authors suggesting that it forms mycorrhizal associations with ash (in which the fungus receives sugars from the tree, which then benefits by enhanced uptake of mineral nutrients). In a pilot study, PhD student Mitchell Nuhn has developed methods to germinate F. americana seeds in culture (on agar) and then co-inoculate F. americana and B. merulioides onto peat-vermiculite. Preliminary results suggested that survivorship of F. americana seedlings is enhanced in the presence of B. merulioides, implying that there is indeed a symbiotic association between the two species, but the sample size was insufficient to achieve a statistically significant result. Scope of the project: You will receive training in methods for germinating F. americana seedlings (an admittedly tedious process that requires that the plant embryos be dissected out of the seeds) and establishing the co-culture with B. merulioides. You will establish a large number of seedlings with and without the fungus partner, record survivorship data at several time points after inoculation, and assist in statistical analyses of the data. This project will be conducted under the direction of Mitchell Nuhn and David Hibbett.

Boletinellus merulioides. Photo by Mitchell Nuhn.

Boletinellus merulioides. Photo by Mitchell Nuhn.

Project 2: Genetics of fruiting body development in Lentinus tigrinus. Background: Lentinus tigrinus is a mushroom-forming fungus that occurs in two forms in nature, one “agaricoid” and the other “secotioid”. Both forms are “pileate-stipitate”, meaning that they have a cap and a stalk. The agaricoid form has exposed gills that release spores to the air, whereas the secotioid form has a layer of tissue that encloses the spore-bearing structures. Thus, spores are not released into the air by the secotioid form. Previous work has suggested that the secotioid form is conferred by a recessive allele at a single locus, and recently whole genome sequences have been produced for two monokaryons (haploids), one with the secotioid allele and the other with the agaricoid allele. Master’s student Alexis Carlson has developed methods to perform controlled crosses of L. tigrinus and produce mushrooms in culture. Scope of the project: You will receive training in methods for growing L. tigrinus in culture, including isolation of monokaryotic single-spore isolates and fruiting of mushrooms in culture. You will perform back-crosses to tester strains to genotype the isolates with respect to the fruiting body locus (and in the process confirm that this is a unifactorial trait). You will then extract DNA from the genotyped SSIs, which may be used later in bulk segregant analysis to identify the secotioid locus. This project will be conducted under the direction of Alexis Carlson and David Hibbett.

The "secotioid" form of L. tigrinus. The "agaricoid" form woudl have gills visilble below the cap. Photo by Alexis Carlson/Laszlo Nagy.

The “secotioid” form of L. tigrinus fruited in culture. The “agaricoid” form would have gills visible below the cap. Photo by Alexis Carlson/Laszlo Nagy.

Both projects will provide training in microbiological techniques and have potential to be expanded into long-term projects (including Master’s projects). Project 1 may be of particular interest to students with interests in environmental biology, plant biology, and fungal ecology, while Project 2 may be more appropriate for students with interests in genetics, developmental biology and genomics. Both projects require attention to detail, excellent organizational skills, and manual dexterity. As a member of our lab group, you would be expected to attend weekly (or semi-weekly) lab meetings, and you would be invited to come along on field trips and mushroom forays. Our lab includes a friendly group of students and post-docs at various career stages, with very diverse interests. We are always looking for students who are curious about the natural world and enjoy working in groups. Academic credit may be arranged through a Directed Study course (BIOL/ES/BCMB 299).

To apply, please send an e-mail to David Hibbett. Indicate if you have a preference for either project, and include a list of the Biology courses that you have taken, and the name of one Clark-based reference (ideally, someone who has worked with you in a lab setting, such as a Teaching Assistant). Please also feel free to get in touch with questions.