REU 2006 Projects
2006 REU Participants: Phil Torres, Amanda Foskett, Patrick Videau, Fern Langham, Chris Daniels, Emily VanDam and Robert Henry (left to right).
- Carbon Cycling in Tidal Marsh & Wetlands
- Development of a New Species Database Application
- Practical Applications of Curatorial Herbarium Skills
- Difficult DNA Extraction: Mollusk Shells
- Botanical Treasures of the Ewell Sale Stewart Library
- Population Genetics of Culex restuans
- A Review of the Haliplidae (Coleoptera) of Mongolia
Productivity and Respiration in Tidal Freshwater and Saltwater Marshes of the Delaware River Estuary.
Amanda Foskett
Duke University
Mentors: Drs. Vile and Velinsky
Tidal marshes and wetlands, at the transition between the land and aquatic environment, are highly productive ecosystems that perform important ecological functions such as providing habitats for a variety of wildlife species, buffering watershed-derived pollution, and influencing global carbon cycling. Predicted sea-level rise due to global climate change may put tidal marshes at risk, especially tidal freshwater marshes that undergo salinity intrusion as the seawater moves farther upstream. We measured carbon dioxide (CO2) fluxes at three tidal marsh sites along a salinity gradient in the Delaware River estuary to determine soil and plant respiration and gross primary production (GPP) rates. Both GPP and respiration rates were significantly highest at the brackish site (8-10 ppt; p < 0.05), and lowest at the freshwater site (p < 0.05). Ongoing laboratory experiments further indicate that salinity intrusion may increase the rate of soil respiration. Sea-level rise accompanied by salinity intrusion is therefore likely to result in drastic changes to the carbon cycling of freshwater marshes.
Development of the New Species Database Application
Chris Daniels
Rochester Instute of Technology
Mentors: Dr. Don Charles and Daniel Mellott
Keeping track of newly described species can be a laborious and meticulous process—one that’s perfect for a computer! The New Species File is a component of the ANSP Diatom Collection which houses recently described species and related reference information. With the New Species Database application, Phycology staff can add, remove, update and retrieve new species information quickly and easily by using their computer. Once this information is validated, cards can then be printed out and added to the New Species File based on stored electronic data maintained by the New Species File SQL Database, New Species File Application and other Phycology computer applications.
By focusing research on design and usability, custom user interference components were created to provide users with a range of options to increase their productivity. Similarly, automation of database tasks allows developers maintaining the system to easily extend new functionality to the system. Along with automation, other design considerations have allowed for the application to be scalable and flexible to future changes through the use of design patterns, object orientated design/programming and “functors.” Through these efforts, the beginning steps have also been taken to release this data online via the World Wide Web with the intention of using ASP 2.0, Atlas and the Google Maps API.
Practical Application of Curatorial Herbarium Skills: Field Collection at Ker-Feal in Chester County and Web Site Design for the Forster Collection from the 1770s.
Emily VanDam
Muhlenberg College
Mentors: Drs. Lucinda McDade and James Macklin
My summer project began with an immersion in training so that I quickly acquired the skills necessary to be employed as a Herbarium Curatorial Assistant. These skills included mounting and linen stripping of specimens, plant identification, freezing specimens, filing, refoldering, data basing and imaging. I was then able to apply these skills to two projects: specimen collection at Ker-Feal in Chester County and the creation of a website for the Forster collection of the Academy. The long-term project goal of Ker-Feal is to collect and identify all plant specimens located within the 150 acre property boundary. Two hundred specimens have been collected thus far. Each specimen has been collected in duplicate, so that one can be mounted and stored for the Barnes Foundation and the other for the Academy.
When not collecting and processing specimens, I used data basing and imaging techniques to create a website to showcase the Forster collection. This website will serve as an important reference for students, teachers, and researchers. The Academy has 26 specimens from Captain James Cook’s second expedition to the Pacific of 1772-1775 and one specimen from his first voyage during 1768-1771. These specimens were collected by Johann Reingold Forster and his son, Georg Forster. Using the Schneider Kreuznach Digital Imaging Camera, I took images of each specimen and attached them to the Herbarium Database using Microsoft Access. The images were then manipulated with Adobe Photoshop CS2 and compiled into a webpage that displays each specimen and lists its current and original determination as well as its family and type information. The site also provides links to other sources of information on the Forster collections and Cook expeditions.
Experiments in Difficult DNA Extraction: The Creation of a Protocol to Extract DNA from Mollusk Shells
Patrick Videau
Goucher College
Scientist Mentor: Anthony Geneva
Following the development of PCR (polymerase chain reaction), DNA extraction has become a pivotal tool in innumerable fields ranging from cladistics to forensic science and medicine. DNA sequencing has made possible many exciting advancements such as sequencing the full genomes of numerous species. DNA extraction and sequencing has added many useful tools to species-based classification systems using differences that can only be elucidated through DNA analysis. Specifically, highly conserved regions of both nuclear and mitochondrial DNA can be compared among species to determine their common ancestry and provide an approximate age of species divergence. In these experiments, attempts were made to extract DNA from a 150-year-old catfish, an 80-year-old formalin-fixed salmonid, and mollusk shells and tissue ranging from one to twenty one years old. Extractions were performed on both fish specimens yet sequencing, followed by a BLAST search, resulted in solely human DNA. Fish DNA may have been extracted as well but not in sufficient quantities for sequencing since fish-specific primers were not used. All molluscan shell and tissue extractions yielded sequencable DNA by utilizing a novel cetyltrimethylammoniumbromide (CTAB)-based protocol. To determine if a valid protocol was created, extraction products were amplified with mollusk-specific primers that bind to domain 2 of 28S mitochondrial DNA and then sequenced. Phylogenetic analyses of the sequences generated in this study support the viability of this novel extraction method. This technique was also used to generate sequences for previously unanalyzed samples and these results are congruent with morphological analyses, providing strong evidence that the newly developed protocol was effective. Further research is necessary to understand the true scope of this protocol by experimenting widely across molluscan taxa and correcting for specific complications.
Digital Imaging Project: Botanical Treasures of the Ewell Sale Stewart Library
Fern Langham
Syracuse University
Mentor: Eileen Mathias
The Academy of Natural Sciences, founded in 1812, is home to the world's finest natural history libraries, unparalleled in literature on the world’s biodiversity between 1650 and 1950. The objective of this project is to make accessible, to the global community, the wealth of information contained in the Academy's rare book collections in The Ewell Sale Stewart Library. Specifically, this REU intern aims to showcase the Library’s botanical treasures from the 16th through 19th centuries.
Research scientists have accessed the library and specimen collections through interlibrary loans through the mail or on-site visits. This intern aims to provide immediate access to rare archived material through digital images and information provided on the Internet and CD-ROM. To produce these goals, the intern will use the Albert M. Greenfield Digital Imaging Center for Collections to digitize images using state-of-the-art equipment. Works will be digitized from selected original plates from over a dozen rare botanical books by the most renowned illustrators including Mark Catesby, William Curtis, Leonhart Fuchs, Maria Sibilla Merian, Pierre Joseph Redouté, Christoph Jakob Trew et al. The images will be scanned using a PowerPhase FX digital image acquisition workstation including a TTI Reflex 45ei camera, Phase One PowerPhase FX camera scanning back, and an Apple PowerMac G4 with 60GB, 867MHz, 512MB Ram.
Furthermore, this intern will design and make accessible, to a global audience, a comprehensive web site featuring the scanned plates. The web site will be designed with an interactive, user-friendly interface compatible with all web browsers, using xHTML, Javascript, and CSS. Ultimately, this digital exhibit will be featured on the Library’s website and will offer virtually unlimited access to a selection of rare botanical art collections for scientists, education and the general public.
Population Genetics of a Local Disease Vector, Culex restuans, Reveals Large Populations Sizes and Flaws in an Established Species Identification Test.
Robert Henry
University of Maryland Eastern Shore
Mentor:
Dr. Dina M. Fonseca
Culex restuans is an endemic New World mosquito that occurs from Canada to Uruguay. Although commonly found infected with West Nile virus and considered a principal vector of this and other deadly infectious diseases in the US, very little is known about this mosquito. Because Culex species have very low morphological variability we separated Cx. restuans from Cx. pipiens, an introduced species, using a DNA based rapid assay. To examine the genetic structure of Cx. restuans we optimized three multiplexes of a panel of 17 microsatellite loci, previously developed for this species. We surveyed six populations from New York State and Georgia (257 specimens, average sample size of 42.8). We also examined populations over time by comparing samples from 2003 and 2005 collected both in Albany and in Staten Island, NY. We found evidence that the rapid assay commonly used to differentiate important Culex species in the US is flawed. This is based on the microsatellite evidence and sequences of ND4, a mitochondrial locus. In addition, we found that populations of Cx. restuans are very homogeneous across the eastern United States and across time, indicating large effective population sizes and negligible effects of local vector control.
A Review of the Haliplidae (Coleoptera) of Mongolia
Phil Torres
Cornell University
Mentor: Dr. Jon Gelhaus
The Mongolian species of Haliplidae (Coleoptera:Adephaga) are reviewed. Haliplidae are commonly called "Crawling Water Beetles" and are an exclusively aquatic family with around 200 species. All material used in this was generated from a 4 year survey of aquatic insects in the Selenge River Basin and the Darkhad region in north-central Mongolia.
Eight Haliplus species in two subgenera are recorded from this country: Haliplus (Liaphlus) basinotatus, H. (L.) fulvus, and a third possibly undescribed H. (L.) species are newly recorded for the country while additional range and locality records are provided for H. (Haliplus) steppensis and H. (H.) sibiricus. No new records were found for the remaining previously recorded species: H. (H.) lineolatus, H. (H.) apicalis, and H. (L.) flavicollis.