Virally Induced Gene Silencing

I am searching for a M.S. (or very talented undergraduate) to carry out a project using virally induced gene silencing (VICS) in the plant family Zingiberaceae. VICS is a form of RNA interference (RNAi). We will be working with Dr. Chelsea Specht's lab at UC Berkeley to study the effects of gene silencing of MADS box genes in flower development in the the tropical gingers. Part of the work will be done in Dr. Specht's lab, and part at UNCG. This would make a good M.S. project for an entering student.

Springer quotes my review on their website

My review of the new book"Pollen Terminology: An Illustrated Handbook" appeared in the latest Plant Science Bulletin (55: 2, p. 77), and has been quoted on the Springer website.

Botany 2009 talks - click on a tltle to see the abstract

36	Image Quiz: Teaching plant ID on the computer and with games	Conference Wide	Kirchoff, Bruce K..
44	DNA-Align, A New Cross-Platform Multiple Sequence Alignment Tool	Conference Wide	Kirchoff, Bruce K.; Remington, David L.; Healey, Christopher.
67	Paedomorphic Secondary Xylem and Secondary Woodiness in Xanthorhiza simplicissima, Coreopsis gigantea, and Mahonia bealei	Developmental and Structural Section	Dulin, Max; Kirchoff, Bruce K..
68	A New Type of Visual Key Based on Bayesian Principles	Systematics Section	Kirchoff, Bruce K.; Pawar, Snehal; Kale, Pinaz; Remington, David L.; Sadri, Fereidoon.
364	Teaching plant identification through effective homework	Teaching Section	Kirchoff, Bruce K..

Graduate Assistantships available for 2009/2010

UNCG still has graduate teaching assistantships and both in-state and out-of-state tuition waivers available for 2009/2010. We offer an M.S. degree in Biology. You can find out more about the department on our web page (http://www.uncg.edu/bio/). Information specifically about the Biology M.S. program can be found here. To apply for Graduate School at UNCG please visit the Graduate School website for prospective students.

I am actively recruiting students in plant structure and development, and biological pedagogy. An M.S. in plant structure is a great stepping stone to a Ph.D. Working with me you will learn to understand plant structure in a way that is relevant to understanding gene action. At the end of your M.S. degree you will have a firm foundation for future molecular work.

Read our paper on Plant Structure Ontology and gene annotation to get a sense of the types of issues we are working with in my lab.

New paper in press, and new presentations

Now in press

Wang, H.-F., Kirchoff, B. K., Qin, H.-N., Zhu, Z.-X. in press. Reproductive morphology of Sargentodoxa cuneata (Lardizabalaceae) and its systematic implications. Plant Systematics and Evolution

Papers presented at the 2009 Association of Southeastern Biologists in Birmingham,AL, April 1 - 4, 2009

Kirchoff, B. K. and Baskauf, S. 2009. Woody Plants of the Southeastern United States: A Field Botany Course on CD. Association of Southeastern Biologists, Birmingham, AL. April 1 – 4, 2009.

Kirchoff, B. K., Pawar, S., Kale, P., Remington, D. and Sadri, F. 2009. A New Type of Visual Key Based on Bayesian Principles. Association of Southeastern Biologists, Birmingham, AL. April 1 – 4, 2009.

Dulin, M., and Kirchoff, B. K. 2009. Paedomorphic Secondary Xylem and Secondary Woodiness in Xanthorhiza simplicissima, Coreopsis gigantea, and Mahonia bealei. Association of Southeastern Biologists, Birmingham, AL. April 1 – 4, 2009.

Dokuzoglu, N., Healey, C. G., Hsiao, J., Kirchoff, B. K., and Remington, D. 2009. A new, cross-platform DNA alignment tool. Association of Southeastern Biologists, Birmingham, AL. April 1 – 4, 2009. (You can download a Beta version of the alignment tool here.)

Sustainabilty Fair

I will be participating in the UNCG Sustainability Scholarship Fair on April 21, 5:00 - 7:00 PM in the Gatewood Studio Arts Building.

I have been elected a Faculty Fellow in the Lloyd International Honor's College

Morphbank on imaging standards

My paper with Steven Baskauf on digital image standards has been cited by Morphbank as an important contribution toward establishing imaging standards. Morphbank is an NSF funded repository of scientific images. You can find our paper linked from my publications page (or click here). The Morphbank new item is here: Morphbank :: Toward Standards for Photographing Living Plants.

Work cited in new book

My 2004 paper with Drs. Richter, Remtington and Wisniewski (Complex Data Produce Better Characters. Systematic Biology 53: 1-17) has been cited in Dr. Tod Stussey's new book "Plant Taxonomy: The Systematic Evaluation of Comparative Data." The paper deals with the question of morphological characters and character states. Dr. Stussey cites my work as showing that subjectivity can enter into the process of creating character states, although he admits that when we used more complex data there was less "subjectivity." Unfortunately, he did not cite our 2007 follow-up study (Kirchoff, B. K., S. J. Richter, and D. L. Remington. 2007. Characters as Groups: A New Approach to Morphological Characters in Phylogenetic Analysis. Taxon 56: 479-492) that proposed a method to deal with the problem we identified in 2004. The problem of creating reliable and valid morphological characters remains a real one; one that will only be solved when we begin to understand how entangled we are with our data.

You can read Dr. Stussey's comments on my work here (go to p. 79).

Pre-print of Heliconia latispatha manuscript

Our paper on flower development in Heliconia latispatha is now out on-line. The link below will take you to an pre-print.

Kirchoff, B. K., L.P. Lagomarsino, W. H. Newman, M. E. Bartlett and C. D. Specht. 2009. Early floral development of Heliconia latispatha Benth., a key taxon for understanding the evolution of flower development in the Zingiberales. American Journal of Botany 96 (3) pre-print (updated to a reprint once the paper is out)

Abstract: We present new comparative data on early fl oral development of Heliconia latispatha , an ecologically and horticulturally important tropical plant within the order Zingiberales. Modifi cation of the six members of two androecial whorls is characteristic of Zingiberales, with a reduction in number of fertile stamen from five or six in the banana families (Musaceae, Strelitziaceae, Lowiaceae, and Heliconiaceae) to one in Costaceae and Zingiberaceae and one-half in Marantaceae and Cannaceae. The remaining five infertile stamens in these later four families (the ginger families) are petaloid, and in Costaceae and Zingiberaceae fuse together to form a novel structure, the labellum. Within this developmental sequence, Heliconiaceae share with the ginger families the possession of an antisepalous staminode, a synapomorphy that has been used to place Heliconiaceae as sister to the ginger family clade. Here, we use epi-illumination light microscopy and reconstruction of serial sections to investigate the ontogeny of the Heliconia flower with emphasis on the ontogeny of the staminode. We compare fl oral development in Heliconia with that previously described for other species of Zingiberales. A comparison of fl oral structure and development across Zingiberales is presented to better understand the evolution of the fl ower in this charismatic group of tropical plants.

Snehal Pawar joins lab

Snehal Pawar received her M.S. in Computer Science at UNCG in December 2008. Her thesis project involved the development of a new type of visual Bayesian key. She is continuing work on this project in my lab as she begins her job search. We will present a paper on the key at the Association of Southeaster Biologists meeting in April, and at the Botanical Society in America meetings this July.

Plant Ontology paper is out

Kirchoff, B. K., E. Pfeifer, and R. Rutishauser. 2008. Plant Structure Ontology: How should we label plant structures with doubtful or mixed identities? Zootaxa 950: 103–122

Here is a link to my first post on this topic.

Abstract: This paper discusses problems with labelling plant structures in the context of attempts to create a unified Plant Structure Ontology. Special attention is given to structures with mixed, or doubtful identities that are difficult or even impossible to label with a single term. In various vascular plants (and some groups of animals) the structural categories for the description of forms are less distinct than is often supposed. Thus, there are morphological misfits that do not fit exactly into one or the other category and to which it is difficult, or even impossible, to apply a categorical name. After presenting three case studies of intermediate organs and organs whose identity is in doubt, we review five approaches to categorizing plant organs, and evaluate the potential of each to serve as a general reference system for gene annotations. The five approaches are (1) standardized vocabularies, (2) labels based on developmental genetics, (3) continuum morphology, (4) process morphology, (5) character cladograms. While all of these approaches have important domains of applicability, we conclude that process morphology is the one most suited to gene annotation.

Review of my Woody Plants software

The first review of the program Woody Plants of the Southeastern United States: A Field Botany Course on CD has appeared in the Plant Science Bulletin. The full text of the review is below. I will post a link to the online version as soon the Botanical Society of America's website is repaired.

Woody Plants of the Southeastern U.S.: A Field
Botany Course on CD. Kirchoff, Bruce. 2008. ISBN
13:978-1-930723-62-7. (CD US$27.00) Missouri
Botanical Garden Press, P.O. Box 299, St. Louis,
Missouri 63166-0299

Woody Plants of the Southeastern United States: A
Field Botany Course on CD provides a wonderful
tool for teaching and learning taxonomy in general
as well as the specific flora mentioned in the title.
Formatted for Windows machines, the program is
quite simple. After registering, the user selects one
of four options: building a list from the available
families, genera, or species; studying the items on
the list; taking a quiz; and taking a test. Study can be
with or without prompts and can be either advanced
slide-by-slide by the user or automatically advanced
by the program. The quizzes are shorter than the
tests and have the display of text prompts as an
option, while tests do not.

While the CD is aimed at the Southeastern US, the
families represented include many of broader
distribution which might make this CD-ROM of
interest to a wider audience in the US, Canada, and
possibly elsewhere in the Northern Hemisphere.
There are 55 families represented, many with
multiple genera, and each species shown has at
least four high quality photographs available, most
species with more. Some even have over a dozen
photographs of various taxonomically-useful
features.

It would be nice if this CD-ROM also came in Mac
and Linux formats, but given the capacities of the
newer Intel-based Macs and of various Linux tricks,
that may not be an insurmountable impediment to
users of those operating systems. Buy a copy today
for your introductory class to use in practicing
taxonomic features and the quick identification of
common woody plants.

-Douglas Darnowski, Department of Biology, Indiana
University Southeast

Max Dulin is graduating!

My M.S. student, Max Dulin, will defend his Thesis on December 1 at 2:00 PM in room 314 Eberhart. The title is "An Investigation of Xylem Structure in Mahonia bealei using Data from Xanthorhiza simplicissima and Coreopsis gigantea." The abstract is reproduced below. We hope to publish this research in the near future.

The stem and secondary xylem anatomy of Xanthorhiza simplicissima, Coreopsis gigantea, and Mahonia bealei are described and characterized in the study. One focus of the study was to determine the degree of paedomorphosis in the secondary xylem of the three plants. Another goal was to assess their woodiness in a phylogenetic context to determine how their woodiness was derived (whether from woody or nonwoody ancestors). Quantitative measurements and observations from slides and macerations were done using light microscopy and confocal microscopy. The secondary xylem of all three species has a degree of paedomorphosis. Coreopsis gigantea has the greatest degree. It possesses vessel elements whose length either decreases or remains the same across the xylem, vessels with pseudoscalariform lateral wall pitting and simple perforation plates, raylessness, libriform fibers, and abundant xylary parenchyma. Xanthorhiza simplicissima has an intermediate degree, possessing decreasing vessel element lengths, libriform fibers, and upright ray cells. Mahonia bealei has only the paedomorphic characteristics of stable vessel element lengths and libriform fibers. Phylogenetic analysis indicates the species are secondarily woody. A major conclusion is that the degree of paedomorphosis reflects the species release from mechanical requirements.

Paper on flower development in press

The Heliconiaceae occupies a pivotal position in the phylogeny of the Zingiberales (see arrow on image - click here for image source). The family occurs between the ginger families (to the left of the arrow), and the three basal families related to the bananas (to the right of the arrow). The main morphological character that places them here is the possession of a staminode opposite one of the sepals in the Heliconiaceae. The ginger families all have a staminode in this position, the banana-related families do not.

The paper is a comprehensive description of flower development in one species of the Heliconiacae, Heliconia indica. In addition to discussing the placement of the family, we clarify the placement of the flowers in the inflorescence, and the evolution of the nectary in the order.

Kirchoff, B. K., L.P. Lagomarsino, W. H. Newman, M. E. Bartlett and C. D. Specht. in press. Early floral development of Heliconia latispatha Benth., a key taxon for understanding the evolution of flower development in the Zingiberales. American Journal of Botany

Seminar inviation, Arizona-Sonora Desert Museum

I have been invited to give a talk on my teaching innovations at Arizona-Sonora Desert Museum on December 18, 2008. Woody Plants of the Southeastern United States: A Field Botany Course on CD is an award winning program for teaching plant identification on the computer.

Paper on Plant Ontology in press

Kirchoff, B. K., E. Pfeifer, and R. Rutishauser. in press. Plant Structure Ontology: How should we label plant structures with doubtful or mixed identities? Zootaxa (as part of special issue on Updating the Linnean Heritage. Names as Tools for Thinking About Animals and Plants)

The paper is a critique of the Plant Ontology, a controlled vocabulary (an ontology) that is intended to describe plant structure, growth, and developmental stages. The Ontology is being developed to prove a framework for gene annotation. It is intended to allow cross-species queries in databases of DNA sequences. Although it has enjoyed some success, the ontology has only been developed for a few species. Our concern is that as the ontology is expanded terms will need to be found for plant organs that are either intermediate in structure, or whose morphological identity is questionable. These plant parts cannot easily be labeled with a single term. The paper reviews five alternative approaches to gene annotation and concludes that, though the plant ontology can be improved, the best method of annotating plant structure and developmental genes is most likely process morphology. Process morphology was developed by Rolf Sattler in the early 1990s and uses sets of developmental processes instead of structural categories to describe plant structures. The method has been made quantitative by a number of authors including Bernard Jeune, Denis Barabé, and Christian Lacroix.

David Lee visit

Dr. David Lee, Florida International University and The Kampong (National Tropical Botanical Garden) will visit my lab on October 20. He is an expert is plant colors. Please stop by and meet him.

I join an iPlant Grand Challange Team

I have been invited to join one of the first iPlant Grand Challenge teams. The iPlant Collaborative is a $50,000,000 NSF funded project to develop a cyberinfrastructure around community supported Grand Challenges in the plant sciences. I have been invited to participate in the Computational Morphodynamic team led by Eric Mjolsness and Elliot Meyerowitz (among others). The team will work to create a new computational approach to studying plant development. The approach will seek to bridge the gaps between biochemical, cellular, and organismal levels of understanding. Central to the approach is the hope that much of the necessary information can be computationally extracted from images and used to help create computational models of development. The first workshop will be held December 15-18, in Tucson.

Update on Image Standards

As a follow-up to our work on photographic image standards for plants, Steve Baskauf has created a series of web pages that illustrate the standards more thoroughly than we could do in our paper. My original post on this subject is linked here. Steve's new pages can be found by clicking on this link.