ChemSemBlog

This week was our first time in Chemistry Seminar for 2010, and everyone appeared to be a tiny bit groggy and perhaps not totally ready to jump in and ask 6 questions. Whether your burden is Chemistry Seminar or a frightful bone injury requiring polyaryletherketone implants, life does go on–sometimes without you!

And with that painfully transparent intro, I segway into the talk given by our guest speaker in ChemSem this week, Ryan K. Roeder. Roeder has been conducting research into different ways in which to increase the strength of implants used in bone. In contrast to the types of implants used orally for artificial teeth, bone implants are not made from stainless steel or any kind of mixed transition metal alloy. In addition, this method does not employ the traditional procedure of removing bone from elsewhere in the patient to use in place of lost or decaying bone, a procedure known as autografting.

Rather, Roeder’s work takes him into the field of composite implants which utilize materials capable of expanding and contracting in a very similar fashion to that of real bone. Roeder’s work has led him to use an aromatic class of polymers known as polyaryletherketones. Traditionally, these were used as simple “pins” in bone. However, Roeder mixed this older method with a newer one which involves the diagonal implantation of these composite rods. The mere physics of the procedure validates its usefulness. Multiple randomly-oriented diagonal rods will increase the resistance of the implant to longitudinal tension, thus strengthening the connection while still using the same composite. This technology could improve a proven science for orthopedic patients everywhere.

I felt that the presenter did a decent job of presenting the material. He had the attention of the students much of the time because of the simplicity of the chemistry and the abundance of healthcare-bound members of the audience. I felt that this presentation was slightly less rooted in chemistry than some of the others, but it was still applicable to those present.

To the layperson, this seminar was about new ways to use materials in bone surgery to make them work better.

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This week we in Chemistry Seminar were privileged to hear from Mary L. Kraft, Ph.D. It’s always exciting to have a fellow biochemist as our guest speaker, and Dr. Kraft did not disappoint. Her talk was on the distribution of sphingolipids in the plasma membrane of intact cells, and her research showed that, as opposed to the Fluid Mosaic Model of the plasma membrane, research postulated that sphingolipid distribution is neither normal nor random, but rather clumped.

The plasma membrane is composed of a cacophony of various lipids, steroids, proteins and other organic materials. A long-time-standing suggestion used to be that the plasma membrane consisted of a bilayer of phospolipids and other membrane elements which can, in their respective layer, move about freely. Viewed superficially, this fluid-like membrane appeared to be a mosaic of organic compounds, hence the Fluid Mosaic Model.

The presence of sphingolipid clumping, however, as observed in Dr. Kraft’s research, showed that the dispersion of membrane elements is not exactly random. Utilizing N-15 as a marker, Kraft’s group reconstructed the membrane of a fibroblast cell. N-15, which primarily marked for sphingolipids, was shown as glowing yellow spots on the surface of the cell membrane. In order to ensure these colors were not simply the result of noise from non-cell contaminants in the sample Kraft did additional testing of cells containing a large amount of C-13, which was expected to appear in normal distribution throughout the cell membrane in the fatty acid tails of membrane lipids. This hypothesis wasn’t overturned by experimental evidence.

I later spoke with Dr. Kraft, commenting on the proximity of N-14 clumps to the cell nucleus. Dr. Kraft affirmed me by stating that she, too, had seen this pattern. I thought that perhaps this could suggest the correlation of sphingolipids with protein secretion from cells or with the release of various steroids associated with the smooth ER. These certainly were possibilities.

I felt Dr. Kraft was a very personable presenter. She was very apt at answering any questions we had for her, and she was willing to take extra time following the presentation to answer some additional questions I had for her. This research seems to be very promising and can hopefully lead to important details of membrane transport and cellular communication.

To the layperson, this seminar was about the body’s cells and whether their coating materials are arranged at random or in specific sections.

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This week in Chemistry Seminar we enjoyed a presentation from a new faculty of the University of Notre Dame, Amanda B. Hummon, Ph.D. It was a very interesting talk on the process of gene selection and experimentation for detecting and describing colorectal cancer, a term we all learned to avoid due to its inaccuracy.

The first part of Dr. Hummon’s presentation focused solely on cancer as a disease in general. Some basic underlying truths are present in all types of cancer, such as increased growth rate, desensitization of cells to outside stimuli, avoidance of apoptosis, high vascularization, etc. Dr. Hummon enlightened us on chemical and biochemical methods I hadn’t heard of before, such as Spectral Karyotyping and Comparative Genomic Hybridization for DNA and qRT-PCR, Microarrays and RNAi for RNA.

In addition, Dr. Hummon introduced the notion of using Mass Spectrometry to sequence amino acids within proteins, a procedure I had never heard of before. We learned of the methods scientists use to select only specific genes for study, a glorified process of elimination which includes a lot of deductive reasoning with just a pinch of guesswork. Dr. Hummon’s study produced a list of almost 50 genes on chromosome 13 that were the most likely candidates for the emergence of colon and rectal cancers. She then proceeded to give the ways in which one could differentiate between cancer cells and normal cells using Microarrays, RNAi and other techniques. We learned that Microarrays will always require confirmation via some other test, and in this case Dr. Hummon prescribed RNAi as the best method.

I greatly enjoyed this seminar because of my interests in biochemistry, human physiology and oncology. I felt Dr. Hummon, however nervous or anxious she was prior to the meat of her lecture, did a splendid job and is sure to have a multitude of pupils helping her complete very important tests in our continued battle against ignorance of cancer. I found she was very helpful during Q & A and she was very knowledgeable yet personal.

To the layperson, this seminar was all about figuring out how genetics plays a role in colon and rectal cancers.

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This week in Chemistry Seminar we enjoyed a presentation from Dr. Basar Bilgicer on the aggregation of antibodies and their “antigens” with each other. First of all, a quick recap on antibodies, what they are, what they are used for, and why they are so critical. Antibodies are proteins produced by cells of the immune system and, when bound to their specific antigen (toxin, carcinogen, etc.) will elicit an immune response to increase the number of antibodies in the blood. Antibodies, therefore, are nothing more than a traveling active site for toxins and unwanted stimuli. Instead of bringing about the harm they would typically cause, the antibody-antigen complex is recognized by cells of the immune system and pump out additional antibodies to quell the invasion of toxins. These now harmless macromolecules are then disposed of.

Dr. Bilgicer’s research was in the field of antibody aggregation using substrates acting as two different substrates. During the course of his research, he used size-exclusion chromatography to separate aggregates based on the size of the aggregate. He found that many of the aggregates identified were trimers consisting of three antibodies and three substrates bound partly to one antibody and partly to its adjacent partner. Dr. Bilgicer’s research supports this as the major product of antibody aggregation.

Dr. Bilgicer took some time warming up to the class, but he was competent and knowledgeable in his field. He’s done additional work with more natural substrates for antibodies as well. Although the substrates used in his current experiment are unnatural, the aggregation pattern should not be altered. I found this seminar to helpful in that it provided good explanations of antibody function, including the disabling of the myth that toxins are bound to the crux of the antibody instead of the end of its two prominent limbs. I thought Dr. Bilgicer could have gone into more detail, however, into the main differences between natural and unnatural substrates or into the effects of a natural solution on antibody aggregation.

To the layperson, this seminar was about one way in which the body voids itself of poisons, and how those poisons are organized after they are “caught.”

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Unbelievably, this is the last non-student seminar presentation of the semester. There have been many great speakers thus far, some who have stirred us to think deeper about chemistry and some who have stirred up other feelings. This week we had a lot of fun hearing about and smelling chemistry. Dr. Jeffrey A. Turk is a chemist working as a faculty at Alma College in Alma, MI. His specialty is making odorous chemicals to be used in perfumes and colognes.

Dr. Turk introduced us primarily to the sandalwood odor, a natural fragrance acquired from the oils of a certain species of sandalwood tree. It would obviously be ludicrous to utilize nothing but the natural oils for making perfumes, as there would be a huge deficiency (extinction) of sandalwood trees in India. This is where chemistry comes in. Dr. Turk showed a big list of all the various types of volatile alcohols present in sandalwood oils that contribute to the characteristic odor of the sandalwood tree. One of his primary concerns is to maintain a high level of atom efficiency, much like Dr. Yamamoto. He claims that the most economic method to achieve synthesis of multiple complex molecules is by the familiar method of Claisen Rearrangement. This way, there are no atoms lost in the transformation of one chemical species into another.

Although Dr. Turk is familiar with the best way to go about concocting a fragrance that will be appealing, there is still a mighty amount of guesswork involved. Although all the sandalwood derivatives smell very similar to each other, mixing and creating new species will always have uncertainty. Dr. Turk did an outstanding job of engaging the students and of making the material interesting and fun. I enjoyed the presentation as did all others. Dr. Turk gets a 9.5/10 for chemistry content, 9.5/10 for professionalism and 10/10 for student engagement. Very good!

To the layperson, this seminar was all about the chemistry behind common perfumes.

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This week in seminar we were privileged to hear from a writer at Chemical & Engineering News, Dr. Jyllian Kemsley. Although she was just an “accidental” chemistry major, she greatly enjoyed the field and went on to receive a doctoral degree. As a employee of C&EN, Kemsley has the privilege of working indirectly for the American Chemical Society, the largest science organization in the world. For those interested in science writing as a profession, Kemsley noted that one does not necessarily need to be a scientist or have a science major to work as a journalist at C&EN, which opens up the doors to a world of outside opportunity.

The presentation was done via webcam, a new kind of technology to the Dept. of Chemistry and Biochemistry at Andrews University. The use of this technology went by better than I had expected. There seemed to be other men there that were helping out with the whole presentation as well. Though there were some troubles getting both streams on the screen simultaneously, seminar proceeded unencumbered for the majority of time spent there. During the Q & A portion, Kemsley entertained the students many questions concerning science writing, including non-writing aspects of work at C&EN like science illustrators.

I’ve always been impressed with the writing in C&EN and similar magazines like Nature. The articles are usually very interesting and can be understood by a somewhat wide group of readers. This reputation has been confirmed through the presentation of Dr. Kemsley here today. I give this presentation a 9/10 for professionalism, a 9/10 for chemistry/information content and a 9/10 for student engagement.

To the layperson, this seminar talked about the sort of jobs that are available in science writing and the kind of duties associated.

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We were privileged and delighted this week to receive words from the renowned organic chemist Dr. Hisashi Yamamoto. From the start, it was evident that this was to be a stirring lecture and very engaging. Dr. Yamamoto’s love for organic chemistry came at an early age, even in high school. His journey led him to the University of Chicago where he continues his research today.

Dr. Yamamoto spoke to us on the topic of Cascade reactions and specifically in the realm of the biologically-significant polyketides. Employing the use of strong, bulky, homemade acids, Yamamoto’s team has been able to clump what used to be a 3 to 5 part series of reactions into one reaction which retains complete “atom economy,” meaning that there are no byproducts of the reaction apart from the desired product. Not only has this method been successful in yields and general economy, it has also proven to show stereospecificity in the upper 90%’s. Attributing to the economy of this process is the fact that several of the acid species were able to be recycled and reused.

Dr. Yamamoto is clearly passionate about his material, and became increasingly excited about the material as the talk progressed. All those present were engaged and enjoyed his very easy-going upfront persona. Dr. Yamamoto proved very proficient during the Q & A time, showing that he was very aware of most of the ins and outs of his research. Dr. Yamamoto achieves perfect tens in all my areas of “judgment,” which include professionalism, chemistry content and student engagement.

To the layperson, this seminar discussed how to economically make important “life” molecules in the areas of saving time and money.

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This week in seminar we were all given a very special treat: variety. Barring dentistry, mineral chemistry and geochemistry are virtually nonexistent in general, organic and biochemistry. Dr. Michael Velbel, a geochemist from Michigan State University, talked to us about different patterns of mineral erosion and other physical and molecular characteristics of minerals.

Dr. Velbel was given the challenge to connect with students who, for the most part, have not had an environmental chemistry or a geochemistry class. Some had probably never even had a lecture on the subject. I half-expected people to raise their hands and ask if this applied to Grignard reagents. Obviously, they wouldn’t do that. Dr. Velbel had a very intellectual yet friendly and approachable demeanor about him, so he easily bridged the gap of familiarity with the students. He spoke of his treks up into the hills and mountains to fetch additional data supporting the cycling of minerals in surface and ground water.

As part of his presentation, Dr. Velbel showed TEM slides demonstrating a pattern of “holes” in the solid mineral structure, indicating the location that Feldspar used to be located. He mentioned that his research included no cleaning of the samples and that they were essentially examining mud. Perhaps what Dr. Velbel will be most remembered for, however, is the slide he showed of actual atoms. Not cells, not organelles, not masses of collagenous protein, but atoms. I found this to be the most exciting part of the lecture for me. I can see why he is so fond of his beloved TEM.

Dr. Velbel stands out to me as one of the best lecturers we’ve had so far. He seemed very excited about his material and very saddened when time was up and he had to let everybody go. My judgment is as follows: 10/10 for professionalism, 10/10 for chemistry content and 8.5/10 for student engagement. The odds were out of his favor to get real stimulation in a group devoid of geochemical foundations.

To the lay person, this seminar was all about how rocks, in their small form, are affected by water in their natural environment.

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This week’s seminar we were privileged to hear from Sean Reed on the topic of allylic C-H Amination. Mr. Reed, a graduate student, came to us from the University of Illinois, Urbana-Champaign.

The main purpose of this seminar was to show the reactivity of the C-H bond in oxygenations and aminations. Typically, one doesn’t really think of alkanes as having any kind of functional group. In fact, alkanes will generally only react after being substituted with a halogen and then substituting the halogen for something else. However, Reed showed us that one could use a type of palladium compound to use as a activating group for the adjacent C-H bond.

Though this has been our first non-Ph.D. seminar presenter, I was impressed with his knowledge of organic synthesis. I was also very interested in the content of the lecture. I would be very interested to find out more of what further research reveals in this area.   I felt as though Mr. Reed had good experience working in a group setting based on his level of comfort upfront. For this seminar, I give it 9/10 for chemistry content, 10/10 for professionalism and 8/10 for student engagement.

To the layperson, I would say that this seminar was all about a specific method for making a difficult kind of chemical reaction work better.

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This week we enjoyed a presentation from Dr. Carolynn E. Anderson from Calvin College in Grand Rapids, MI. Once again, we listened to the results of research in the field of synthetic organic chemistry. The specific topic was on the synthesis of N-Alkyl Pyridones. Her research was mainly focused on finding a way to specifically bind alkyl groups to the nitrogen of a pyridone as opposed to the oxygen, since both nucleophilic sites were adding in relatively equal proportions. She shared data from NMR spectroscopy and from a crystal structure. The long-term plans for this research was for these N-Alkyl Pyridones to be used as substrates to bind in the place of sterols and some amino acids. Just like in much of organic chemistry, this is a pharmaceutical project.

Dr. Anderson did a fine job up front, and despite appearing to be slightly nervous in the beginning, she began to speak more comfortably as she delved into her material. Being very knowledgeable about the subject matter of her presentation, Dr. Anderson very hastily answered each question she was bombarded with. Since I am not a avid pursuer of organic chemistry, much of this presentation was a learning experience for me. I found it especially interesting when she spoke of the mechanisms proposed and the process by which she and her team eliminated the proposals one by one. My knowledge of NMR data is truly sub-par, but I also learned of how upfield protons can be moved downfield by certain steric interactions. I found the material of this presentation to be slightly less intense than that of Dr. Cook the week before when he talked about a “3D” Diels-Alder reaction, but I was very impressed that all this research had been done by undergraduate students. I give this presentation 9.5/10 for professionalism, 9.5/10 for chemistry content and 8/10 for student engagement.

For the layperson, this seminar talk focused on ways to make chemicals that are of interest in the pharmaceutical world, including some of the techniques to combat troubleshooting in the field of chemistry.

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Dr. Silas Cook was different from any presenter we’ve had at chem seminar thus far. In his presentation of the total synthesis of 11-O-Debenzoyltashironin he not only demonstrated his clearly proficient knowledge of organic chemistry, but he also kept students engaged who were somewhat lost the whole time. He had a very personable and “real” quality about him, unlike other characters who live in the lab.

Organic Synthesis. I can’t lie, when I saw the title of the presentation I gulped a little. When it comes to presentations on synthesis, it’s up to the presenter to make it engaging. Synthesis presentations can include a hundred slides of reactions that are interesting at first but ultimately leave people snoring in their seats. I found it very fitting, however, that he took the time to differentiate between the two types of synthesis groups, and then to cunningly segway into his subject matter and his developed synthesis.

This seminar taught me the value of a good orgo background when it comes to marketable skills in a chemical field. Knowing the reactions was only the first step in developing a synthesis that worked. One has to be ready to be creative when it comes to developing effective and low-cost syntheses for commercial use. I also learned, oddly enough, about the benefit of being persistent. Only after five years of “heartbreak” was the goal accomplished.

In a field like this, knowing how to analyze products is just as important as running the reactions themselves. IR spectroscopy and NMR are instruments I know how to operate, but the data wouldn’t be much good in my hands. If I was to pursue this kind of career, I would need to take a serious class just in reading IR’s, NMR’s, Mass Spec’s and a whole lot more. This was an area of his presentation where I feel I could have been more critical if I had been better with spectroscopic data than I am.

Overall, I was very impressed with this presentation. I give it 11/10 for chemistry content (that’s not a misprint), 9.5/10 for professionalism and 9.5/10 for student engagement.

For the layperson, this seminar brought up the process of making a naturally-occurring molecule in the lab, including the difficulties faced by chemists when reactions don’t work.

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So how about that presentation? Before I even mention the chemistry content I want to say that Dr. Allen had a fantastic presentation style that was so easy to follow and to understand. I was very impressed by his use of visuals to explain s, p, d, and f orbitals. Many students including chemistry majors can squeeze through four years of chemistry classes and have no conceptual understanding of atomic orbitals. I think Dr. Allen did a great job of clearing up a hiccup in a lot of minds.

In Chemistry Seminar last year, there was a presenter that talked about silver nanoparticles consisting of a silver ion connected to dendrimers much like the ideas presented by Dr. Allen. However, instead of the nanoparticles “trapping” a molecule within its excessively-branched infrastructure, one could use a kind of lanthanide-centered chelate attached to a host of dendrimers; and the center of the whole thing (instead of a silver ion which doesn’t take part in the reaction) would be this fluorescent Gd chelate. The idea was for a membrane cellular receptor to trigger the dendrimeric chelate covering to catabolize into smaller, non-harmful units so that the chelate could be displayed at the correct locus in the body.

In theory, this is a fun idea, but I’m concerned about a couple things. First, nitrogenous breakdown products. The body excretes nitrogen in the form of urea and uses it in amino acids, DNA, RNA and other things. If any ammonia-like substance was subjected to body tissues, toxicity could be a huge factor. Secondly, mechanism of protein-induced dendrimer breakdown without the aid of catalysts or biochemical enzymes. So a protein touches the dendrimer and the whole thing (minus the chelate) just falls apart like a glass cup sitting on the edge of a table waiting for a three-year-old to come along? I mean, even exothermic reactions (glycolysis, TCA, parts of calvin-benson, oxidative phosphorylation, etc.) require catalysts. However, I haven’t done the research or worked out the theory.

I feel that the presenter has a terrific start on what appears to be dynamite research. Confident up front and engaging in delivery, Dr. Allen has presented a convincing argument. Troy’s rating for this seminar is 9/10 for chemistry content, 9/10 for professionalism and 8/10 for student engagement.

To the layperson, this seminar was all about using different chemicals to create clearer pictures for MRI’s.

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What to say ………… I suppose I just need to start this by saying I’d never heard a single crude word said in chem seminar until today. I guess I had to get caught up. That said, let’s move on…
When Dr. Griffith first put his info on the screen, I was excited–not so much about mass spec, but about hemoglobin. Being a biochemist, I enjoy learning about atomic collisions in the human body.
In this seminar, I learned that mass spec is a legitimate and viable technique for determining protein size and shape, including all the activated structures. Additionally, I found it very interesting that alpha and beta subunits are encoded on different chromosomes. I found it very interesting that scientists use that observation to affirm evolution. I’d like to look into it more.
Professionalism being but a null factor, Dr. Griffith had things going for him. Firstly, he was very confident and knowledgeable in his subject material and was certainly very excited about mass spec. The very nature of his presentation mandated the use of many overheads, graphs, statistics, graphs, structures, graphs and still more graphs. In all seriousness, though, I was impressed by his abundant use of personal research data. I was also impressed by his proficiency in the field of human biochemistry and specifically with the secrets of HbA assembly. I was not, however, excited about the length of his presentation or his personal style. I found the use of words/phrases like “damn”, “what the hell”, “bastard” and “taking a dump” to be very inappropriate. I was also not impressed by his derogatory reference to “the German” on several occasions. I did find it ironic, though, that he was one of the only seminar speakers that professed some form of Christianity. Troy’s rating for this presentation was 9.9/10 for chemistry content, 2/10 for professionalism and 6/10 for student engagement.

To wrap up this seminar for the lay person, I would put it like this:

This seminar taught us all about the protein that carries oxygen from our lungs to the rest of our body. It also taught us how to use chemical instruments to help “see” what the protein looks like and how it’s made.

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