Wabash Blogs Summers in Science -

July 31, 2006

Nolan '08 Spends Summer in Research in Hays Hall

I am currently conducting research in organic chemistry in the Chemistry Department at Wabash College. This is my second summer doing research with Dr. Paul LePlae. This summer, I have begun work in the exciting new field of organocatalysis.

Alex Nolan '08 - My project involves identifying molecules that accelerate particular reactions. The molecules we find interesting are chiral organic molecules because they have the potential to give pure chiral products.  In addition, these catalysts can accelerate reactions at a rate faster than has been previously reported.  Another benefit of organocatalysts is that they do not require the presence of a potentially hazardous metal.

Most of my time has been spent synthesizing organocatalysts. More recently, I have begun studying the kinetics of reactions that involve organocatalysts.  I use NMR (Nuclear Magnetic Resonance) to determine the rate of reaction and how that rate is influenced by several variables including: amount of catalysts, substrates, and cocatalysts. Future studies will investigate the integration of a cocatalyst within the present organocatalyst.

I am indebted to the Wabash Chemistry Department for supporting undergraduate research. My independent research experiences have enhanced my ability to think critically and solve problems.  This opportunity will help me achieve my educational and career goals after leaving Wabash.

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July 27, 2006

Dan Albrecht: Etching Silicon Chips in Cutting Edge Research

Dan Albrecht — This summer I am working on nanotechnology research focused on porous silicon biochips.

Silicon is one of the most technologically important materials; it’s utilized extensively in microelectronics fabrication and silicon chips are found in just about everything, from X-Boxes and personal computers to dishwashers and car engines.

However, when silicon is etched with hydrofluoric acid to create porous silicon (silicon with a surface of numerous tiny pores), new characteristics arise. Porous silicon can emit light, making it potentially useful as a biosensor inside the body and its large surface area allows the tiny pores to be coated with any variety of molecules that could be used in medical diagnostics or disease treatment.

There is one drawback in that the tiny pores degrade easily once the silicon has been etched, but recent studies have shown that the attachment of organic molecules to the chips prevent degradation while still preserving the porous characteristics. There are several different chemical reactions used to attach organic molecules to silicon chips and exploring these lie at the heart of my project.

Under the mentorship of Dr. Lon Porter in the Wabash Chemistry Department, I am etching silicon chips and functionalizing them via three different chemical reactions. Each involves a different mechanism: one uses a carbocation catalyst, another employs a Lewis Acid catalyst, and a thermal reaction that only requires heat.

After the reaction is complete, I put the chips in simulated stomach and intestinal fluid to see how the chips would degrade if ingested by a potential patient. Although all three reactions reportedly yield the same product, we see a difference in the degree of chip stability that results from these reactions. In addition, I am also experimenting with three different sets of organic functional groups: hexane (six carbons long), dodecene (twelve carbons long), and octodecene (eighteen carbons long), to see how the varying carbon chain lengths prevent oxidative degradation of the porous silicon.

This project is quite a departure from traditional labs in my science classes. Being able to research, set up, and carry out my own project gives me a feeling of significance and independence I hadn't felt before in the lab. Before the beginning of the Fall semester, the Porter Lab is adding a new microwave reactor that will allow us to react chips using a beefed-up version of the same microwave ovens used in the kitchen. I plan to extend my research with Dr. Porter into the Fall semester and hope to continue into either medical school or grad school after my senior year here at Wabash.

I feel like my background in science from Wabash allowed me to jump into the research setting with ease and gave me the capacity to pick up new laboratory techniques that will be helpful as I continue with my research in the future.This internship has been an excellent opportunity and I only wish I'd done it last summer, too.

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July 21, 2006

J.P. Manalo: Protein Identification and DNA Replication

J.P. Manalo —This summer, I am continuing an independent research project (begun in the spring semester) in the Chemistry Department at Wabash on the role of proteins in biomineralization events in plants.

Under the guidance of Dr. Aaron Wyman, I’ve been able to isolate proteins that associate with grape raphides, which are biominerals composed of calcium oxalate and produced naturally in grapes.Calcium oxalate is also a major component of human kidney stones. Thus, the prime focus of this research is to investigate potential mechanisms to alleviate the pain caused by kidney stones by identifying proteins that control the growth of calcium crystals.

Over the summer, I have been working to identify the optimal conditions for amplifying the grape genes corresponding to numerous isolated raphide associating proteins (RAPs) using PCR, in an effort to clone them.PCR stands for polymerase chain reaction, and it is a method that allows scientists to replicate small amounts of DNA accurately and in large quantities.

The resulting PCR products are then analyzed using agarose gel electrophoresis in order to determine their size and number of base pairs.From this work, we next intend to sequence these DNA fragments and continue to clone full-length copies of these genes in an effort to determine if their expressed protein products influence grape raphide size and morphology.

Working with Dr. Wyman and another summer student researcher, Ahson Ali, has been a great experience for me, as our research with biominerals is set in a pleasant and light environment.The number of laboratory techniques that I’ve learned this summer will be beneficial to me in my future endeavors when I plan to pursue a career in the medical field. The coursework and lab work at Wabash College definitely prepared me for this summer experience.

I would like to thank the Chemistry Department at Wabash College for granting me this opportunity to perform research this summer. I would especially like to thank Dr. Wyman for selecting me to do research with him and for mentoring me over the summer.

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July 20, 2006

Lincoln Smith: Biology at Cold Spring Harbor Laboratory

Lincoln Smith — I am currently doing a biology research internship at Cold Spring Harbor Laboratory on Long Island. I am thankful for this opportunity since the researchers at Cold Spring Harbor Lab show such a dedication to their work. This is evidenced by the caliber of work and scientists which have supported the institution for years like Dr. James Watson, one of the discoverers of the structure of DNA. Among the committed faculty of this institute is a Wabash College alumnus, Dr. W. Richard McCombie, in whose lab I am currently working. I have been given an independent research project in genomics under the guidance of another Ph.D. in this lab. 

A goal of many cancer researchers is to sequence multiple gene targets across multiple individuals with cancer. This is in hopes of finding a correlation between sequence differences and cancer. By traditional methods of gene isolation and sequencing, the cost of this would be astronomical. More inexpensive means are needed to pull target genes from the genome for sequencing.

My project is looking at effective means of using DNA probes to pull multiple, specific DNA targets from a genome for sequencing. 

During this internship I have been able to observe scientific practice of an extraordinary level. The best part is being able to experience and learn it first hand. I am being taught some of the details of genomics like designing and using proper primers and reaction buffers for experiments. 

More importantly, however, I am being taught some of the broader scientific skills that can be applied to genomics or any area of research. These are skills like searching scientific literature and computer databases with efficiency for needed protocols and information. Additionally, I have been learning how to cover as much ground as possible with efficient experimentation. 

Wabash prepared me for this experience in immeasurable ways. The immediate exposure to primary literature that I received at Wabash has prepared me to search complicated papers for necessary information. Dr. David Polley arranged for an alumnus to teach a bioinformatics section in our Genetics course. That has proved useful since I must attend weekly seminars in bioinformatics. 

Dr. Eric Wetzel had also given me a chance to do independent research in his lab, and many of my friends have done the same in the labs of other encouraging professors. Dr. Wetzel took much time to help me develop solid research skills and thinking. The broad biology education in the classroom has prepared me to learn the details of a project without forgetting the larger context of it in nature. 

Finally, the intensity of the work in class and lab at Wabash has allowed me to confidently approach the problems in my project this summer. Wabash has certainly given me the preparation I needed to complete this summer internship well. 

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July 17, 2006

Syud Ahmed: Nanotechnology at Wisconsin

Syud "Taz" Ahmed, Madison, Wisconsin — As an international student at Wabash, I was amazed by the science I was being introduced to in college. I was exposed to new concepts and ideas involving nanotechnology and materials chemistry, and of course was introduced to an array of analytical instruments.

As prepared as I thought I was, I was definitely nervous as I stepped in the University of Wisconsin, Madison chemistry building. I was afraid I might not meet up to the high standards of the top-notch research facility.

It was in very short time that I realized the tension and wrecking nerves were completely unnecessary. I realized that I truly knew exactly what I was doing and was very comfortable doing it. My colleagues were actually quite surprised how I had jumped right into a project as an undergraduate and were very impressed with my ability to work independently.

The people here were not only impressed by that, but were also impressed by the fact that I was always willing to learn when I did not know something. They were also impressed that I knew some things that many people do not know, such as how an interferometer works, or why there is a P and an R branch when taking IR readings.

By the end of the first week, I was like any other member of the research group, reading papers, running my own experiments, and using extremely powerful and expensive equipment. The two and half years of research experience I gained at Wabash working for Dr. Lon Porter were absolutely priceless; I believe it was those experiences that helped me the most.

Considering the fact that the research I did at Wabash is somewhat related to what I have been working on this summer, I seemed to have an advantage from the very start. Wabash had definitely prepared me well for this experience, which actually makes me appreciate our chemistry program a lot more in addition to the high thoughts I had of it previously.

This off campus experience has given me a better perspective of research conducted in graduate school and has definitely encouraged my decision to pursue higher studies (M.S. or Ph.D) in the fields of Materials Science.

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Steven Rhodes: Collaboration at the National Institutes of Health

Steven Rhodes, Washington, D.C. — This summer, I am working in the Laboratory of Membrane Biochemistry and Biophysics at the National Institutes of Health (NIH) / National Institute on Alcohol Abuse and Alcoholism (NIAAA), Bethesda, Maryland.

I am performing Nuclear Magnetic Resonance (NMR) studies of proteins and their interactions with biomembranes. This technique uses high magnetic fields to elucidate the physical, chemical, and structural properties of molecules. My goal for this summer is to study the interactions of the human peripheral cannabinoid receptor protein (CB2) within artificial biomembranes of controlled composition.

Working in a national laboratory has been very exciting for me. The atmosphere is quite different from academia, where graduate students pursue independent projects and set their own goals/objectives. Here, doctors and researchers work as cohesive units to tackle problems on all fronts. This feeling of being part of a larger team has been one of the greatest aspects of my summer experience. Living in the Washington, D.C. area is nice too!

After graduating from Wabash, I hope to enroll in medical school and begin working toward an M.D./Ph.D. dual degree, which combines my interests in research with the practice of medicine. Working at the NIH/NIAAA this summer has been a wonderful opportunity for me to participate in cutting edge research in an environment which is truly at the interface of laboratory science and clinical medicine.

I would especially like to thank Dr. Scott Feller for making this experience possible for me. I feel very lucky to have had the chance to play a small part in the greater collaborative effort here.

In photo: Rhodes next to an 800 MHz NMR Spectrometer.

Posted by amidonj at 07:38 AM | Comments (0) | TrackBack (0)

Trayton White: Plant Biolchemistry in Ithaca

Trayton White — During the fall semester of 2005, I received an offer from Dr. Ann Taylor to join her at Cornell University for the summer.

Ithaca, the home of Cornell, is located in a beautiful part of central New York with many gorges and waterfalls surrounding it. This means the area is also covered in hills, which is a huge change for someone born and raised in Indiana — especially when running.

Fortunately, the weather is just like back home, if you don't like it just wait ten minutes and it will change. My days out of the lab are filled with softball, exercise, and hikes, which allows for a relaxing summer break in a “gorges” part of New York.

My project for the summer is conducting a screen of 250 tomato genes known to code for protein kinases. The ultimate goal is to pinpoint which kinases are involved in the plant’s pathogen defense by deactivating the gene using a procedure called virus induced gene silencing.

The silencing of a gene is the result of the plant’s own defense system that attempts to stop viral infections from spreading. Utilizing its own defense system, this procedure causes the plant to stop developing the selected protein kinase. The plant is then grown for five weeks after which an assay is conducted. The assay consists of injecting the plant with bacteria known to cause the plant cells to die in the infected area. The cell death is due to the plant’s own defense to prevent further spreading of the bacteria to other live tissue.

When cell death does not occur, it is a good indication the particular gene silenced coded for a kinase involved in the plant’s defensive system. These particular plants are noted and a graduate student will conduct various DNA analyses on the leaf tissue samples I collect.

The environment outside is a great addition to the research experience I have acquired. Despite my lack of coursework in biochemistry or genetics, I have been using both of those fields in this new area of research. Though the summer started off shaky, it steadily got better as I learned more of the vocabulary and read more papers. My experience at Wabash helped prepare me for this.

I am particularly thankful to my science professors for the integration of journal papers into the curriculum. This allowed me to jump right into this branch of science because of my experience in the basics. While I doubt I will pursue a career in plant biochemistry, it was good for me to get my feet wet and see what it is about.

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