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Mary Casillas, Undergraduate WFSC Student

During the summer and fall of 2017, I interned at the Biodiversity Research and Teaching Collections (BRTC) at Texas A&M University (TAMU). The BRTC is a natural history collection, housing specimen data from a variety of organisms from all over the world. I have helped organize data and materials for the collections so that this information can be made available to the scientific and public communities. This material can be organized in files that are sent to a large collective database, VertNet. VertNet is an online database that disseminates biodiversity data from bio collections all around the world.  The database provides tools for collaborating, sharing and publishing biodiversity data. Through VertNet, anyone (including other collections and institutions) can access the data from TAMU BRTC for their own use. VertNet also trains users to practice quality biodiversity data curation and publication such that these important data can be easily used across a variety of platforms.

The process of databasing BRTC data:

My internship at the BRTC involved organizing and documenting ancillary data from specimens so that these data could be added to the BRTC databases and VertNet. Ancillary data are things taken from individual specimens, such as parasites or tissues and DNA for molecular work. I began my work in one of the -20 work freezers. These freezers house tissues, DNAs and parasites that have not been organized or entered into the collection databases and are called work freezers for this reason (the samples need to be worked on before being stored permanently in the collection). Tissues are generally samples taken from specimen’s liver, kidney, heart, ear or feces and DNA samples are usually derived from tissues samples through an extraction process in the laboratory. Parasites normally consist of ectoparasites such as ticks, fleas, or lice- that were taken from the specimen’s body.

Each type of ancillary data is located in a small tube, with the collector initials and numbers written on the outside of the tube. Tissues, DNAs and parasites are grouped in together in separate boxes for easier organization and access. To organize each type of ancillary data, tubes are organized sequentially by collector initials and number in freezer boxes with the small 9X9 grids that keep the tubes in order. Once a collector has filled a box sequentially with samples, the box is labeled with collector initials and a number and moved from a work freezer to a -80 freezer for permanent storage and the data (type of sample and box number) are transferred to the collection databases. Racks are utilized to organize freezer boxes within the -80 freezers and there are maps posted on the outside of each freezer detailing the exact locations of each freezer box. The large -80 freezers provide quality preservation of the samples, and should be opened as little as possible to prevent humidity from entering the freezers, which could cause long-term inefficiency and damage the samples and shelving.  All data from the specimens, obtained from collector catalogs, are formatted for the BRTC databases and then fed to  VertNet for screening. Once the data formats are acceptable by VertNet, the submission of biodiversity data will be added to the free domain for anyone to access.

How can the scientific and nonscientific communities use the BRTC data?

Once the data are accessible in multiple databases, both scientific and non-scientific communities can freely access the information. These communities could use the search engine to look up a specific species of interest, and find data that the BRTC (or any other biocollection) has collected for specimens representing that species. Advanced search options are available for users to search for a specimen by catalog, institution and much more. A collector can also search for specimens that have tissue data, georeferencing information, or media available. This sharing of information ensures that every bit of data collected is being applied to its full potential.

Texas A&M’s Biodiversity Research and Teaching Collections will play an integral role in the new oVert Thematic Collections Network (TCN). The project is supported by a $2.5 million National Science Foundation grant and will utilize specimens from the BRTC and other collections to make data-rich 3-D images available on-line. Texas A&M University is one of 16 institutions to be involved in this groundbreaking project, which will scan and make available museums specimens in a unique way – capturing not only external, but internal morphology. In total, 20,000 specimens representing more than 80 percent of existing vertebrate genera will be scanned utilizing non-invasive CT scanning technology. Texas A&M University will serve as a scanning hub for larger specimens, utilizing resources at the Texas Institute for Pre-clinical Studies and the A&M Libraries.

This project will begin later this fall, more details can be found within the Science article here: http://www.sciencemag.org/news/2017/08/new-3d-scanning-campaign-will-reveal-20000-animals-stunning-detail

 

Department of Wildlife and Fisheries Sciences Fall Newsletter – check it out here: WFSC Fall Newsletter!

My name is Hudson Berkhouse and I am a senior at Texas A&M University.  For the past two years I have been a Wildlife and Fisheries Sciences major (WFSC; or as I like to say, a Wi-Fi-Sci-Guy), with an emphasis on management.  Prior to becoming a WFSC major, I majored in Biomedical Sciences. I changed my major as a sophomore because I wanted hands-on field and lab experience, both of which are heavily emphasized in Wildlife and Fisheries Sciences.  Accordingly, my internship entailed working as a field technician for Dr. Light (http://people.tamu.edu/~jlight2; Associate Professor of Mammalogy at Texas A&M) during the summer between my junior and senior year.  For this internship, I spent the majority of my time collecting biodiversity data at several ranches in South Texas owned by The East Foundation (http://www.eastfoundation.net/).

This work involved trapping small mammals and collecting data from them.  While most of the animals we trapped were ultimately freed, some were retained and prepared as scientific specimens to be installed at the Texas A&M University Natural History Museum, the Biodiversity Research and Teaching Collections (BRTC; https://brtc.tamu.edu/home-2/).  The BRTC is a large warehouse east of campus where over one million animal specimens are housed.  These specimens include birds, mammals, amphibians and reptiles, fishes, parasites, and marine invertebrates from around the world.  BRTC specimens are invaluable and are used internationally for research as well as to teach life history and taxonomy classes at Texas A&M.

The specimens that we chose to retain from the field, to be installed in the BRTC as scientific specimens, had to be prepared in a way that ensures their preservation.  Specimens kept for preparation were carefully and humanely euthanized and immediately stored at freezing temperatures to preserve them until they could be processed.  After they could be transported back to the BRTC, the careful work of specimen preparation could begin.  The specimens were removed from the freezer and allowed to thaw.  When I prepared my specimens, I would first brush them for ectoparasites, which, if any where present, I would collect in a small vial for use by other researchers.  The animal would then be weighed, sexed, and measured.  I would then take a small, round biopsy sample from the ear of each individual as well.  This ear sample would ultimately be used to determine what types of pathogens, if any, the animal was carrying thus enabling researchers to develop a pathogenic profile of the area from which the animal had been collected.

Once the tasks dealing with the external part of the specimen had been accomplished, I could then begin to remove the animal’s pelt and stuff it with cotton and wire.  This had to be done very carefully, following specific protocols, so that the pelt could be retained as close as possible to its original condition.  See previous posts by Noel Lyon (https://brtc.tamu.edu/2015/06/10/small-mammal-preparation-at-the-brtc/) and Stefan Hill (https://brtc.tamu.edu/2015/07/06/mammal-preparation-at-the-brtc-stephan-hill/) detailing the preparation process. Because the collections at the BRTC are used to teach university classes as well as for research, it is important to make sure that all specimens are in good condition.  The animals we collected from the East Properties, for instance, are ultimately going to form a collection specifically intended to present a biodiversity profile of the South Texas region.

 

Another important part of the preparation process is the removal of the individual’s organs and the retention of their inner tissues.  Any tissues which are kept are potential data sources for future projects.  Keeping track of these tissues ensures that the maximum amount of data is retrieved from each specimen, making the most of these valuable resources. I usually retained heart, kidney, and liver tissues from my specimens and I placed these tissues in clearly labelled vials stored at freezing temperatures.  The finished product was a stuffed and sewn pelt, an intact skeleton (which had to be left in a cleaning tank for tissue removal; see previous posts by Stefan Hill (https://brtc.tamu.edu/2015/06/03/stefan-hill-dermestid-care-level-expert/)), and several vials containing various tissues for future research.

Specimen preparation is an interesting job, but one that needs to be undertaken carefully and methodically. The two other undergraduates I worked with, Joshua Brown and Hunter Folmar, were extremely helpful and always willing to give me advice, as they both had more experience in specimen preparation than I did.  I would also say that learning how to humanely cull these animals and carefully prepare them as intact specimens was the most important skill I learned during my valuable experience as a field technician.  This is because the preparation process not only taught me how to properly clean an animal but also gave me a much better understanding of mammal anatomy.

My name is Hudson Berkhouse and I am a senior Wildlife and Fisheries Sciences major at Texas A&M University.  One of the reasons I was originally drawn to this major was that it combines a thorough scientific education in many wildlife-related scientific fields with hands-on training and experience.  Accordingly, students seeking a degree in Wildlife and Fisheries Sciences must, at some point in their undergraduate years, fulfill an internship that is in some way related to their studies.  For my internship, I was able to work as a field technician and on several other tasks for Dr. Light, a professor of Mammalogy, at Texas A&M during the summer of 2015.

The field-based project I worked on was a biodiversity research project in South Texas based at several ranches owned by the East Foundation (http://www.eastfoundation.net/).  During my internship, I traveled with other field technicians to the ranches to collect data concerning the presence and abundance of small mammals.  Because most of the land in Texas is privately owned and therefore difficult to access for research purposes, this project is able to provide important data towards a better understanding of the distributions of wildlife spread across Northern Mexico and Southern Texas.

As I mentioned earlier, my team was concerned primarily with data collection on small mammals, or “smammals” as we affectionately referred to them.  Towards this end, our daily routine consisted of setting Sherman traps in the early evening when it had begun cooling off, retrieving those traps early the next morning before it got too hot, and collecting both data and specimens from the animals we had trapped.

Although every aspect of this process was interesting to me, I specifically want to describe the data and specimen collection process.  When we went out into the field to retrieve our traps in the mornings, we made sure to bring all equipment necessary for gathering data with us.  Collecting the data as soon as possible was important because it reduced stress on the animals, ensured that whatever specimens we chose to retain would be in good shape, and protected the accuracy of our data by reducing opportunities for human error.

 

Some of transects where we trapped were intended to yield data only, whereas others were set with the goal of specimen retention.  Animals found in traps that fell into the former category were weighed, sexed, measured, and freed. During this process we took note of any obvious deformities or ectoparasites that could be found on the animal.  The most important data from these transects involved which species could be found at different locations throughout the ranch. The goal of the latter type of transect (where specimens were retained) was to collect a few specimens of each species, destined for preparation and preservation.  Accordingly, those animals belonging to species that had already been collected were freed, whereas members of the different target species were culled and preserved.  Throughout all of these steps it was impressed upon me that minimizing the stress each animal must undergo, whether they are to be freed or culled, is of the utmost importance.

Part of what made this internship such a valuable experience was the insight into field work it gave me, as well as a much better understanding of what it is to do scientific research in my field of study.  I also greatly enjoyed getting to know my coworkers in an arena outside the classroom.  As a result of my job that summer, I know and respect my fellow students more, and have a much better understanding of the professional aspects of my major.

One of my main projects during my internship at Texas A&M University’s Biodiversity Research and Teaching Collections (BRTC) was sorting through and organizing a collection of tissue samples from past research by Dr. Ira Greenbaum. These tissue samples were primarily harvested from a variety of Peromyscus species over decades of research. Totaling over 7,000 combined liver, heart, kidney, and testicle samples, the collection had been stored inside freezers in Dr. Greenbaum’s lab for some time, until those freezers started to fail.  Luckily the BRTC was able to take in these tissue samples and continue to preserve them by placing them within the Genetic Resources collection.   Notably, the skins and skulls from which these tissue samples were taken are already included within the Mammal Collection. Therefore, obtaining these tissue samples greatly benefits the collections overall as now we have all samples associated with each specimen. As one can imagine, sorting through all these frozen tissues is a huge and somewhat numbing (literally) task. Fortunately for the staff at the BRTC, there is an army of undergraduate interns such as myself that will work on such projects.  The task may have been simplistic in itself, but it gave me some insight to the efforts that are required at times during real scientific research.

Organizing the Greenbaum tissue collection involved taking the tissue samples out of the original cardboard storage boxes, placing them into new plastic vial storage containers, and recording their information into an excel tissue spreadsheet where they could be easily located. These new containers were organized into a 9 x 9 grid system capable of holding up to 81 individual vials; columns were labeled A through I and rows labeled 1 through 9. Each new container was numbered and entered into the tissue excel file on an individual spreadsheet that had the empty cell slots organized A1-I9 ready for vial placement.   Written on the side of every vial contained the initials of the researcher, followed by that collector’s collector number and a letter designating its tissue type.  This information would be recorded into the spreadsheet alongside the cell number giving each tissues’ specific location.    After organizing all the tissues from the storage into new containers, the next step was to cross reference the organized vials’ collection ID with another excel spreadsheet from the Mammal Database that contained the specific information about each individual specimen from which the tissue came from.  The purpose of this cross-listing was to record that a specimen cataloged in the Mammal Collection did indeed have a tissue and note the tissue location (box and cell slot). Although time consuming, the overall process was fairly straightforward and once I got into the rhythm of creating new excel sheets for each tissue box, reading the tissue information, and entering it into the excel file, I was able to fly through the process. My knowledge of the Excel program definitely increased as I discovered faster keyboard shortcuts to enter the data at a much more efficient rate. It wasn’t exciting work but by listening to music, TED Talks lectures, and audiobooks, I was able to stay focused and relaxed enough that time went by much faster. The biggest challenges and frustrations involved with this project was merely trying to decipher some of the written information on the vials. A combination of illegible hand writing and non-permanent ink made reading a fair number of tubes almost impossible.  I would either have to look for patterns in the numbering system of how they were originally sorted to deduce what was written or simply record UNREADABLE in the Excel file.

After accumulating several dozen hours doing this project, I often wondered what the overall purpose of this project was. Then about halfway through the semester, I happened to stumble upon a magazine article highlighting the importance of biodiversity collection museums. The author pointed out that they play an important role by tying together a number of scientific fields including genetics, population studies, migration patterns, evolutionary history, and taxonomy that can be used to further benefit the goal of conservation. These tissue samples that I had been sorting were a contribution to that direct effort.  They can be used by future researchers for generations to come for a variety of studies to further advance the field of biodiversity.

My name is Stefan Hill and during my final semester as an undergraduate at Texas A&M University, I had the fortunate pleasure of interning at Texas A&M University’s Biodiversity Research and Teaching Collections (BRTC).   It was the busiest semester I have had to date in my entire college career, but the experience I gained as an intern in these short few months have been one of the highlights of my academic study.  I learned the ins and outs of how the specimens in the collection are selected, prepared, and managed for long term storage to promote the process of biodiversity conservation.  One of these processes that I was directly involved with included the care of the dermestid beetle colonies used to clean animal skeletons.  These beetles will eat the flesh off a skeleton and after a few days of chowing down, will leave a perfectly intact skeleton.  It was pretty fascinating to observe this process first hand.  I was able to witness all kinds of animals being placed into these colonies and, after only a matter of days, coming out looking completely unrecognizable.  From watching deer, bear, and alligator heads to whole shark and squirrel bodies being consumed was a pretty cool experience overall.

The procedure of specimen preparation that I was involved in went in this sequence: Specimens would be skinned and tagged and placed in a freezer until there was room for them in the beetle colony.   A metal tag with an ID number was then matched with the specimen number as a secondary means to keep track of each individual specimen.  This is especially important because the beetles tend to move everything around and the skeleton becomes dismantled while the bugs are feeding. Once removed from the bugs, the skeletons are soaked in a 3:1 ratio of water to ammonia hydroxide to further clean the bones of oils and organic matter for 12 hours.   If left to soak any longer, the chemical can actually do damage to the bones so it is crucial to remove them within this time frame.  From the beginning I was warned that ammonia hydroxide is a very strong irritant and is incredibly volatile.   Therefore, when using ammonia lots of ventilation as well as eye protection is needed, otherwise your throat, nose, and eyes will become horribly agitated by the fumes.  Once removed from the chemical solution, the skeletons are air dried for 24-48 hours, boxed up, and placed into the freezer for another 7-10 days for a final fumigation step.  After freezing, the specimen is assigned an identification number and installed into the collection for final storage.

The only real downside working with the beetles was the smell.  The colonies were located in a separate shed several hundred feet behind the BRTC building for good reason.  These things stank like no one’s business.   The decaying carcasses combined with the beetle excrement and substrate creates a very strong, pungent, unique smell.   It’s not necessarily a smell that makes you gag or get sick, but it’s still not all that pleasant to work with for long periods of time – mainly because it sticks to your clothes and is very noticeable to anyone else afterwards.   I learned that lesson pretty early on after working with the beetles one afternoon and then biked back to campus on a particularly hot day for my next class.   Sitting through a 50 minute lecture radiating a funky, mutated B.O. while my classmates conspicuously wrinkled their noses was enough ostracism for me to start bringing a change of clothes any time I worked with the beetles.

Excellent article from NY Times about collections!

Libraries of Life – NYTimes.com.

New publication from Curator’s Voelker and Light of the BRTC!

River barriers and cryptic biodiversity in an evolutionary museum – Voelker – 2013 – Ecology and Evolution – Wiley Online Library.

Come paint with us December 4th from 6:30 till 9:30 at Downtown Uncorked! We will be generating funds to support our biodiversity research, student training, and conservation.  Your registration includes 3 hours of instruction from the Purple Turtle Art Studio and all supplies. Downtown Uncorked serves wine, beer, appetizers and pizzas so plan to enjoy a snack and glass of wine while you paint. You will leave with your very own masterpiece on a gallery wrapped 16 x 20 inch canvas.

Registration is $50 and is due at the event. Funds from this special night will be made immediately available at the Texas A&M Foundation to support research activities by the Biodiversity Research and Teaching Collections at Texas A&M University.  Please make checks payable to the Texas A&M Foundation, account # 05-57639. Contributions are not tax-deductible. To reserve your space for the evening, please e-mail us at brtc@tamu.edu

We guarantee a great time!