BioData Blogs

Christie Wilcox is now passionate toward conservation biology, although she didn’t originally start off that way. While she always had an affinity to nature and animals, she didn’t realize that she wanted to be a biologist until she “stumbled” upon it in college. “When I’m at the beach and everyone is running away from jellyfish, I get excited and run up closer to check it out!”

Wilcox began at Eckerd College in St. Petersburg, Florida, as a double major in physics and marine biology. After her first semester, Christie decided that the more advanced math that physics required was not for her, so she dropped physics and continued with her major in marine biology. Once Christie became more involved in marine biology, she realized that she wanted to focus more on cells and how they function, and their inter-relationships to the whole animal.

During her sophomore year at Eckerd College, Wilcox approached her mentor, Dr. Nancy Smith, to get involved in one of her projects. Smith had previously worked with fiddler crabs and was studying its impact on mangroves in the area. Together, Wilcox and her mentor designed a research project. Shortly thereafter, Christie was out sloshing through the mangrove marshes. Their research consisted of two studies. In the first, a transect study, the mangroves were left alone and every couple of weeks their trunk diameters were measured and leaves were counted. Wilcox statistically examined the number of crab burrows and plants in the area and their affect on the mangroves. The second study consisted of a manipulation experiment and was more hands-on as mesh cages without tops were built to prevent crabs from getting into the area. Wilcox got her hands dirty as she dug up every plant around the mangroves, built the meter by meter cage 25 cm into the ground, and removed any crabs within the caged area. In the other experimental condition, the crabs were not restricted from the mangroves. Wilcox sought to determine how the crabs affected plant growth and its soil chemistry.

“Fieldwork in Florida’s heat is no picnic,” says Wilcox, who spent hours outdoors digging in the sand and the sun. It also contained some inherent dangers. During one exhausting day of digging cages, Wilcox tuned around and found herself within 10 feet of a 15-foot alligator sunning himself. “I remember crawling back to my car as slowly as possible… As far as I could tell he had no interest in eating me – he was just getting comfortable. It found a big patch of sandy, plant-free soil right where I was working. That’s field work in Florida for you!”

Wilcox became a published author in July of 2009 when her study was published in the journal Marine Biology. The study found that fiddler crabs have a marked effect on the mangroves growth rate, as well as some factors in the soil. When the crabs were present, the soil was more oxygenated and had a lower salinity, which made it easier for the mangroves to grow. Those mangroves became taller, thicker, and bushier. In short, more crabs meant healthier and happier mangroves.

Upon graduating from Eckerd in 2007 with a degree in marine science with a concentration in biology, Wilcox worked as a research assistant in Dr. Stuart Critz’s lab at the Lake Erie College of Osteopathic Medicine (LECOM). Dr. Critz’s lab studies heart cells, particularly focusing on their adenosine pathways. Wilcox was involved in experiments studying the effects of A_2B receptor stimulation on survival kinases. A_2B receptors are one of 4 types of adenosine receptors located in the heart and have not been studied as intensely as the others. Western blots were the primary methodology being utilized. They found that the A_2B receptor typically promoted survival pathways.

Wilcox has just begun her PhD program in cell and molecular biology at University of Hawaii. The program requires her to complete three lab rotations prior to selecting her project. She is studying avian genetics in Hawaii’s native bird population for her first rotation.

As a conservation biologist, Wilcox’s goal is to use cellular and molecular technique to protect endangered or threatened species. “I want to have a conservation edge to whatever I end up doing. I figure its sort of giving back to the nature that I’ve loved and has given so much to me for so long.” While she definitely wants to have research as a significant role in her career, Wilcox says she would probably enjoy teaching and would consider being the professor who also participates in research. “But,” she adds, “I also see myself working for a conservation organization and being very happy about it as well.”

• Follow Christie’s Blog: Observations of a Nerd

• Follow Christie on Twitter: @NerdyChristie

• Visit Christie’s Google Page

• Read Christie’s 2009 Publication: Marine Biology DOI: 10.1007/s00227-009-1253-7

Our weekly compilation of science news for the week of August 23, 2009.

Autonomous underwater robot reduces ship fuel consumption: The Office of Naval Research is a front runner in supporting and bringing forth innovative solutions to fuel consumption challenges.

Eyeless creature discovered in undersea tunnel: A previously unknown species of an eyeless crustacean was discovered lurking inside a lava tube beneath the seafloor.

Fly eyes help researchers ‘see’ new proteins involved in memory: Research report in the journal Genetics identifies new proteins involved in memory, and provides new insight into fragile X mental retardation.

To read the study:

Cziko, A., McCann, C., Howlett, I., Barbee, S., Duncan, R., Luedemann, R., Zarnescu, D., Zinsmaier, K., Parker, R., & Ramaswami, M. (2009). Genetic Modifiers of dFMR1 Encode RNA Granule Components in Drosophila Genetics, 182 (4), 1051-1060 DOI: 10.1534/genetics.109.103234

Mitochondrial DNA replacement successful in Rhesus monkeys: New procedure may halt some serious inherited diseases, a study suggests.

To read the study:

Tachibana, M., Sparman, M., Sritanaudomchai, H., Ma, H., Clepper, L., Woodward, J., Li, Y., Ramsey, C., Kolotushkina, O., & Mitalipov, S. (2009). Mitochondrial gene replacement in primate offspring and embryonic stem cells Nature DOI: 10.1038/nature08368

Obese people have ‘severe brain degeneration’: A new study finds obese people have 8 percent less brain tissue than normal-weight individuals. Their brains look 16 years older than the brains of lean individuals, researchers said on Tuesday.

Small peptide found to stop lung cancer tumor growth in mice: Scientists have discovered a treatment effective in mice at blocking the growth and shrinking the size of lung cancer tumors, one of the leading causes of cancer death in the world.

Study finds radiation risk for patients: At least four million Americans are exposed to high doses each year, and about 400,000 patients receive more than the maximum annual exposure allowed for nuclear power plant employees.

Upward lightning caught on camera: Duke University researchers have captured images of lightning bolts shooting upwards.

USC study finds changes in DNA patterns are linked to prenatal smoke exposure: A new study by researchers at the Keck School of Medicine of the University of Southern California has found that the life-long effects of maternal smoking during pregnancy may occur through specific changes in DNA patterns.

Vitamin D may be heart protective: A deficiency of the sunshine vitamin may worsen plaque accumulation in vessels of diabetes patients.

To read the study:

Oh, J., Weng, S., Felton, S., Bhandare, S., Riek, A., Butler, B., Proctor, B., Petty, M., Chen, Z., Schechtman, K., Bernal-Mizrachi, L., & Bernal-Mizrachi, C. (2009). 1,25(OH)2 Vitamin D Inhibits Foam Cell Formation and Suppresses Macrophage Cholesterol Uptake in Patients With Type 2 Diabetes Mellitus Circulation, 120 (8), 687-698 DOI: 10.1161/CIRCULATIONAHA.109.856070

What Britney Spears can reveal about Alzheimer’s: Researchers may have found a way to identify those most at risk of developing the neurological disorder simply by asking them whether they recognize celebrities such as Britney Spears and Johnny Carson.

World’s last great forest under threat: The world’s last remaining “pristine” forest – the boreal forest across large stretches of Russia, Canada and other northern countries – is under increasing threat, a team of international researchers has found.

Results and Analysis of BioData’s Laboratory Management Survey

In a survey commissioned by BioData, 94 researchers from 74 institutions worldwide were asked a series of questions regarding their management of research data. The survey’s purpose was to learn about and prove the need for knowledge management systems in academic research. 80% of the researchers surveyed believe their labs are not run efficiently.

William Noble, associate professor in the Department of Genome Sciences at the University of Washington recently published “A Quick Guide to Organizing Computational Biology Projects,” an article dealing with management of data related to the bioinformatics field. When one thinks about managing laboratory data, it can be overwhelming to think of all the files, graphs, images, and results that come with every experiment. Noble explains that while organizing files and documenting progress seem mundane, “These issues are important because poor organizational choices can lead to significantly slower research progress.”

Over the past two years, BioData has worked with over 30 research groups providing them with a research management service. Dr. Noble may be referring to actual management of files and folder, but we have learned that having a systematic way of organizing results and data, promotes research and makes the lab a more pleasant work place.

Data Organization

Data organization is key to saving time and frustration when you don’t have to waste time looking for where you stored everything. As one frustrated PhD student expressed, “I have got so much data on a thousand different machines… and I cannot keep track of it all. I do not remember what I save to what or where it is, whether I’ve backed it up or not. Anytime I’m getting ready for a conference, presentation, or review I spend hours and hours just trying to find everything! Everything else in my life is overly organized except the one thing that is most important—my RESEARCH! I dread having to write my thesis because I don’t think I’ll be able to find all my data…” If your data is organized and stored in one place, it is easy to keep track of and access whenever you need it.

Another reason why data organization is so important, Noble explains, is that “someone unfamiliar with your project should be able to look at your computer files and understand in detail what you did and why.” As one researcher told us, “… Each lab is left to its own devices to archive data and institutional knowledge. As per usual, experiments get repeated as grad students graduate and new ones come in…” When a new researcher joins the lab, they can easily see what you worked on, so time and money is saved by not having repeat experiments conducted. Noble cites other people who may be interested in viewing your laboratory data: “This ‘someone’ could be any of a variety of people: someone who read your published article and wants to try to reproduce your work, a collaborator who wants to understand the details of your experiments, a future student working in your lab who wants to extend your work after you have moved on to a new job, your research advisor, who may be interested in understanding your work or who may be evaluating your research skills.” The most important person, Noble points out is your data needs to be organized, for yourself because after a couple of months, your likely to forget details and “you will either have to then spend time reconstructing your previous experiments or lose whatever insights you gained from those experiments.”

Keeping all of your data in context is hard. We see researchers running three to five experiments concurrently, spending hours on collecting results – but neglect to document it properly. Documenting data may seem like a tedious, wasteful step, but each researcher must think of its long-term benefits, as it is the one of the main qualities seen in organized labs

Data also has to be accessible and stored securely. 56% of the researchers surveyed stored their data on a hard drive. There is a problem with storing data in one place, as many learned the hard way from Hurricane Katrina, when an incredible amount of data was lost. One researcher from New Orleans’ Tulane University pointed out, “Before Hurricane Katrina, there was no backup system at all. Now, they issued everyone a 80GB external drive and gave them stern warnings that there would be no rescue missions for hard drives if another levee breach occurred… Surely we can do better than this.”

Online Data Storage

Noble suggests storing data online, as hard drives cannot be accessed once you are out of the lab, and as another researcher pointed out “I think there should be online storage of research data … so when ever you have time you can analyze your data.” In fact, 80% of researchers said they would store data online in a secure server, with many expressing concerns about security, citing a need for “a rock solid privacy policy and some serious security.”

We learned from this survey that many are in need of an online knowledge management tool that is safe and secure. While the importance of data organization may have been overlooked, researchers are now becoming more aware of its role in running an efficient and productive lab.

BioData is committed to helping researchers in the scientific community optimize and manage their knowledge and data. To learn more about BioData’s online knowledge management tool visit www.biodata.com

Read “A Quick Guide to Organizing Computational Biology Projects”

Noble, W. (2009). A Quick Guide to Organizing Computational Biology Projects PLoS Computational Biology, 5 (7) DOI: 10.1371/journal.pcbi.1000424

Thanks to all who participated in our survey, “How Do You Manage Your Research Data?”

Congratulations to M.H. of California on winning the MinoHD.

Look for our upcoming blog post discussing our survey results.

Our weekly compilation of science news for the week of August 16, 2009.

Caltech researchers pinpoint neurons that control obesity in fruit flies: Research could lead to the development of a new model for the study of human obesity and its treatment.

DNA evidence can be fabricated, scientists show: With fabricated blood or saliva, “you can just engineer a crime scene,” said the lead author of a new study.

To read the study:

Frumkin, D., Wasserstrom, A., Davidson, A., & Grafit, A. (2009). Authentication of forensic DNA samples Forensic Science International: Genetics DOI: 10.1016/j.fsigen.2009.06.009

Methane seeps from Arctic sea-bed: Scientists say they have evidence that the powerful greenhouse gas methane is escaping from the Arctic sea-bed.

Neural pathway missing in tone-deaf people: Nerve fibers that link perception and motor regions of the brain are disconnected in tone-deaf people. The new finding identifies a particular brain circuit that appears to be absent in these individuals.

To read the study:

Loui, P., Alsop, D., & Schlaug, G. (2009). Tone Deafness: A New Disconnection Syndrome? Journal of Neuroscience, 29 (33), 10215-10220 DOI: 10.1523/JNEUROSCI.1701-09.2009

Researchers develop new, more-sensitive assay for detecting DNA methylation in colon cancer: A study published in this week’s online issue of Nature Biotechnology, demonstrates a unique and highly sensitive method for detecting methylation-associated cancers.

To read the study:

Li, M., Chen, W., Papadopoulos, N., Goodman, S., Bjerregaard, N., Laurberg, S., Levin, B., Juhl, H., Arber, N., Moinova, H., Durkee, K., Schmidt, K., He, Y., Diehl, F., Velculescu, V., Zhou, S., Diaz, L., Kinzler, K., Markowitz, S., & Vogelstein, B. (2009). Sensitive digital quantification of DNA methylation in clinical samples Nature Biotechnology DOI: 10.1038/nbt.1559

Snorkel rice could feed millions: A paper in the journal Nature, describes how the plant elongates rapidly in response to being submerged. One of the scientists, Motoyaki Ashikari from Nagoya University in Japan, said “the impact is huge”.

To read the study:

Hattori, Y., Nagai, K., Furukawa, S., Song, X., Kawano, R., Sakakibara, H., Wu, J., Matsumoto, T., Yoshimura, A., Kitano, H., Matsuoka, M., Mori, H., & Ashikari, M. (2009). The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water Nature, 460 (7258), 1026-1030 DOI: 10.1038/nature08258

Tasmanian devils have no star networkers: Study suggests stopping the spread of facial tumors may be harder than previously thought.

Tests begin on drugs that may slow aging : Excitement among some researchers has picked up with the apparent convergence of lines of inquiry involving genes and restricted diets.

Tobacco might produce vaccine for stomach virus: Tobacco produces protein for vaccine against the stomach bug called Norovirus.

U.S. life expectancy rises to 78 Years: U.S. life expectancy has risen to a new high, now standing at nearly 78 years, the government reported Wednesday