Duke Bryology Laboratory, Facilities


Facilities for Bryological Research

We have access to all the necessary equipment and facilities to conduct a broad range of bryological research at Duke. These include complete laboratory facilities for molecular work, growth facilities including controlled environment chambers, greenhouses, and experimental gardens, scanning and transmission electron microscopes, and of course the bryophyte herbarium and library. Some of the major facilities are briefly described below.

Duke Herbarium
The herbarium holdings at Duke include about 400,000 vascular plant specimens, including pteridophytes, and about 230,000 bryophytes. Herbarium assistance as well as bench and cabinet space are available for working on and managing loans from other herbaria. J. Shaw is the Curator of Bryophyte collection. The herbarium has an extensive collection of bryological books and a journal and reprint collection. For additional information, see Duke Bryophyte Collection.

Shaw Lab microscopes:
Equipment include an Olympus BX41 light microscope and SZ dissecting microscope. An Olympus DP25 digital camera is easily moved between the two microscopes, and the whole system is connected to a PC equipped with Microsuite 5 software for capturing and editing images, and for making morphological measurements.

Molecular Laboratories
All equipment necessary to perform molecular work aimed at systematic and evolutionary studies is available in the Shaw laboratory. This equipment includes: multiple thermal cyclers, microcentrifuges, -70C freezers, -20C freezers, and -4C refrigerators.

The IGSP DNA Sequencing Facility
Housed in the Biological Sciences Building is a state-of-the-art laboratory for collecting genetic data. The lab has two ABI 3730-XL capillary sequencers capable of generating 1600 sequences out to 1130 basepairs in 24 hours, or 3200 genotypes. Recently, large-fragment analysis has been developed for the lab, allowing reads out to 1000 basepairs for microsatellite markers. An Applied Biosystems 7000 Real-Time PCR instrument is maintained by the Facility for public use. In 2007 the Facility acquired a Biotage Pyromark MD pyrosequencing instrument. Allele quantification, methylation studies, and SNP detection can be done on 96 samples in 10 minutes using the Pyromark. AFLP's and microsat's are also analyzed on the 3730's out to 500 basepairs. Samples are prepared for the ABI 3730-XL’s on a Beckman Biomek FX liquid-handling robot with a multi-channel head. The FX robot transfers 96 samples at once in many housekeeping tasks, including PCR cleanup, plasmid minipreps, PCR and sequencing setup, microsatellite pooling and dilutions, and dye-terminator removal. In 2008, two ultra-high throughput instruments were installed in the facility: a Roche GS-FLX (aka “the 454”) System and an Illumina Genome Analyzer (GA). Samples are prepared for the ABI 3730-XL's on a Beckman Biomek FX liquid-handing robot with a multi-channel head. Community equipment housed and maintained in the GA Lab includes a plate centrifuge, a heated plate sealer, a dual-head gradient thermocycler, and vacuum manifolds for PCR cleanup.

Duke Biology Plant Growth Facility (BPGF)
This facility supports the educational and research needs for Duke University faculty, affiliated researchers, and students. The facility spans 8,400 square feet that is equally divided between research and teaching. Several types of controlled growth (temperature, light and humidity) chambers are provided at a modest cost.

Computing Facilities
The Shaw Lab has access to all of the software and hardware necessary for rigorous statistical analysis. Hardware includes numerous dual-processor Dell workstations and dedicated AMD Athlon Unix Servers, laser and inkjet printers, and a flatbed scanner. Software includes GeneMarker for scoring of microsatellite genotypes, population genetics software STRUCTURE, IMa, and MIGRATE, and the statistical packages JMP, SAS, and R. Software for DNA sequence and phylogenetic analysis includes: PAUP*, MacClade, MrBayes, PHYLIP, Sequencher, and MolPhy. Software for hypothesis testing and comparative methods includes: STATVIEW, DNArates, r8s, ModelTest, Discrete, Mesquite , Multi-state, Continuous, BEAST, and HYPHY.

Duke Shared Cluster Resource (DSCR):
Duke University supports a high performance Linux cluster of 680 machines and over 2700 processors connected using the Sun Grid Engine batch scheduling system. The DSCR is based on a sharing system where interested researches may purchase machines and add them to the existing cluster. Custom scripts and simulations written in Python or R can be run quickly and easily on the computer cluster.

Transmission electron microscope
We also have free access to the Biology Dept. Zeiss 10A transmission electron microscope, with attached camera that utilizes Zeiss 70mm roll film. Access to two AO/Reichert Ultracut E43 microtomes is also readily available.

Scanning electron microscope
We have free access to the Biology Dept. Philips 501 scanning electron microscope, a Ladd critical point drier and a sputter coater (Hummer V). The SEM has an attached camera body that utilizes 4 x 5 Polaroid 55 P/N film and a digital frame grabber. The Biology Dept., with generous NSF support, recently acquired a Philips ESEM with a cryo stage.

Morphometrics Lab
The Duke University Morphometrics Lab was setup during 1990/1991 from an NSF instrument grant awarded to H. Fred Nijhout. This laboratory is equipped with cameras (CCD color video camera, gray scale video camera, photometric tube security style video camera), 2-D Digitizers (6 SummaSketch pads), 3-D Digitizers (Polhemus 3Space digitizer, Reflex microscope), Image Analysis Software (Image-1, SigmaScan Pro, NIH image, ImagePro Plus), several light microscopes (2 Wild M5A steromicroscopes with camera lucida attachments, 1 Wild M420 Macroscope with C mount video camera attachment, 1 Zeiss Axioscop compound microscope with C mount video camero attachment), Sony TV Monitors, morphometrics related software (statistical software: NTSYSpc, SAS, and SYSTAT; morphometric software: Thin plate spline, Elliptic Fourier analysis, Procrustes, etc.), and Hewlett-Packard flatbed scanner.

Culture facilities
We have multiple laminar flow hoods available for the culture work needed for this project, as well as a growth room and lighted (and unlighted) racks for growing bryophytes.

Duke Library

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 Shaw Laboratory
 139 Biological Sciences Bldg.
 Box 90338
 Department of Biology
 Duke University
 North Carolina 27708

 Phone: (+1) 919 660-7345
 Fax: (+1) 919 660-7293