Collection Database Management

Thank you all for visiting the blog after my brief absence during the Thanksgiving holiday.  I hope that you and your family had an enjoyable visit and that you all are eagerly anticipating the winter holiday season.  Now that I have returned to State College, PA and the Pennsylvania State University, I can continue organizing of electronic database.  I had initially entered data into a FileMaker Pro 10 database using the default templates.  This made data entry easy, but was very cumbersome when retrieving data of interest.  I therefore designed a template that used tabs to organize like metadata.  To the right are screen captures of the tab pages as they appear in the database.

Canadian Rockies Vacation 2009 Slideshow

Click on the post title to view the entire slide show of our recent adventures in Canada.

Hartley Wood Restoration Effort

It has been my pleasure to work with many individuals performing research within the Hartley Wood and to engage with others who are trying to manage this woodlot.  One such individual is Chip Clark, who serves as the Volunteer Coordinator for the Arboretum Woodland Restoration Corp. (AWRC). He stated that, " The mission of this group is to remove invasive non-native plants from the Hartley Wood and eventually replant with native species, as part of the overall area improvements coming with the Arboretum at Penn State".  Chip has accompanied me on several trips to my research site and has always provided me with fresh insights concerning the restoration of the woodlot.  He is currently attempting to determine the  usage of trails by mountain bikers so a management plan that would help protect those trails from erosion could be drawn.  In the images to the right, Chip and a mountain biker are discussing the recent addition of water bars on a steep portion of a popular trail entering the Hartley Wood.  These bars are put into place with the understanding that they will reduce the amount of erosion caused by the "ruts" produced by bike tires.  About Aaron D. Brown, Chip stated that he had, "the most complex and detailed research project ongoing in the Hartley Wood, and it is always a great learning experience for me when I accompany him on his visits in the Wood".  I always look forward to the next time I get to visit with Chip, whether it be during a hike or over a hot cup of coffee.  To access information about the AWRC click on the title of this post and drop Chip a line to let him know you appreciate his work.   

Visualizing Extracted DNA

I have spent the better part a week extracting DNA from dried tissue samples acquired during my research in the Hartley Wood.  There is over 600 specimens in the collection, of which 420 have had their DNA extracted.  Now begins the task of confirming the presence of DNA using gel electrophoresis.  This is not to say that if DNA is absent using this visual assay that it is physically absent, only that I could not observe the bands created during the electrophoresis process.  I have not standardized the concentration of extracted DNA before running the gels and therefore some bands are easy to see and others are quite faint.  Again, this assay is only being performed as a troubleshooting tool if my PCR products are not visible when run out on a gel.  Some of these terms might be foreign to some of you and I apologize, still the main point I am trying to express is the tedious nature of describing my collection through molecular techniques.  In today's field of mycology, these molecular characteristics (DNA sequences) are valuable sources of information used to identify and describe relationships between groups or species of fungi.  To the right is the image of a gel that has been stained with Ethidium bromide and photographed under UV illumination.  The "L" in the far left lanes are the 1Kb ladder used as a reference of size and the numbers above the remaining lanes indicate the extraction codes for the specimens.

Lake Louise, Banff AB Canada

It seems as if it were just yesterday when my wife, daughter, and in-laws made the 10 day journey from Vancouver to Calgary.  During this wonderful vacation through the Canadian Rockies, we encountered many sites to numerous to discuss in a single post.  So I have decided to give you a sample of just one  destination.  We took an entire day to visit Lake Louise in Banff, AB.  This day included a hike around the beautiful lakefront, a quick mycoblitz into the adjacent forest, and a fine dinner at the luxurious Fairmont Hotel.  Although it was mid-September, there were many individuals enjoying the scenery and some even partaking in water activities such as canoeing.  My daughter Kaia and I made our way through the evergreens via a well maintained dirt trail.  Along the way she would point out mushrooms and birds for me to identify.  Our "quick" hike ended up being nearly 30 minutes in length as we found ourselves getting drawn further and further into the forest landscape.  When we had emerged and located the other members of our party, it was off for a 45 minute hike around the perimeter of Lake Louise.  It was obvious to us how exhausting the day had been on our little girl as she soon fell asleep in the backpack carrier.  In fact, she slept through the group hike AND through the entirety of our lengthy, but enjoyable meal.  It was one of the first times my wife and I had eaten a meal together without any interruptions from our extremely active daughter.  The whole family was quite pleased with the vacation and were so happy to have had the opportunity to share it with each other.  Once the 1,500 images taken during the trip have been organized, a slide show will be provided within the blog for your viewing pleasure.                                      

Overuse of Pesticides: A Disney Cartoon

Although my research deals more specifically with the description of fungal communities with a wooded habitat, I am trained in the field of plant pathology.  This field investigates many of the pests that are destructive to valued crops, such as wheat, corn, and soybeans.  Often times the use of fungicides and/or pesticides are required to reduce diseases caused by these pests.  It is therefore extremely important to design an appropriate disease management plan with regards to the use of applied products.  In a short cartoon that was recently posted on my current research adviser's Face Book page,  Mickey Mouse experiences the drawbacks of overusing such chemical controls.  For all of you dedicated mycologists, there are several scenes in which giant mushrooms are visible!  Click on the title of this blog post to find out what happens to this iconic character.

Plot Disturbance From Recent Storms

While visiting my twenty-five plots this past week, I observed that nearly twenty-five percent of them had been effected by recent wind and snow storms.  Here in University Park, PA we received a record snowfall this October 15th.  It was the earliest recorded snowfall with standing accumulation and it caused lots of damage to trees.  In the Hartley Wood there were many large trees and branches downed from the weight of the snow.  Some of this woody debris fell onto my sampling plots and made it impossible for me to thoroughly investigate those areas.  I will not be including collections from this past month in any statistical analysis of the plots.  This should  eliminate any skewing effect caused by the reduction in sampling for these effected plots.  The image to the top left shows a sampling plot in the early part of October.  The image to the bottom left is the same plot post storm with debris covering the entire area of the plot.

Permanent Sampling Plot Layout

I had an opportunity to visit my research plots this past week and make my final collections for the year.  During that time in the woodlot I reflected on the amount of time it had taken me to arrive at the appropriate number and size of my permanent sampling plots.  I also thought about the layout of the plots and recalled how difficult it was to do so when the vegetation was at its most dense.  This encouraged me to create a short five minute tutorial on how to layout a circular sampling plot while the vegetation density has decreased.  If you are interested in learning how I created these permanent sampling plots, please click on the title of this blog post or click on "Sampling Plot Layout" under the Video Links section of this blog.  Let me know if you found the video informative and if you would like to see more video footage of my research.

Visit to the Mushroom Planet

Dr. Kathie Hodge, associate professor of mycology at Cornell University, lectures about the world of fungi.  Kathie is the director of the Cornell Plant Pathology Herbarium (CUP) and teaches multiple mycology courses at the university.  Her research includes the description of fungal diversity within insect pathogens.  She states that her lab uses "both modern molecular and classic morphological approaches to understand fungal relationships and make inferences about how they have evolved".  Please click on the title of this post to view her lecture and visit her Cornell Mushroom blog.

Coffee Grounds as Cultivation Substrate

Two Cal Berkley graduate students have developed a method of cultivating gourmet mushrooms on spent coffee grounds.  The process is similar to that used by mushroom companies cultivating fungi from substrate filled bags.  The difference is the ability for the mushrooms to be grown using materials that would normally be sent into a landfill.  This team of young men have entered into the BBC World Challenge 09 and are the only accepted entry from the United States of America.  Please check out this fascinating story by clicking on the title of this blog post and vote for these environmental innovators.