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.

Post This To My

Hide Sites

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.

Post This To My

Hide Sites

This week’s seminar was entitled Visualizing Lipids in Plasma Membranes.  The speaker was Dr. Mary L. Kraft, a biochemist and an assistant professor at the University of Illinois. She received her bachelor’s degree from the University of Illinois in Chicago and her PhD from the University of Illinois at Urbana-Champaign.  She then did her postdoctoral studies at Stanford University.  The speaker was really interesting.  She gave a background that made the presentation easy to follow.  The topic was also really interesting.

One of the new things I learned from this seminar was that virus envelopes contain more cholesterol and sphingolipids than the host cells.  Another thing I learned was that how well proteins work depends on the surrounding lipids.  I also learned about secondary Ion Mass Spectroscopy (SIMS).

The other students seemed to be attentive during the seminar.  There were also a good number of questions at the end, and the speaker answered all of them well.

This seminar did encourage me to look into learning a little more about the topic.  However I don’t think I would be very interested in doing any research on it, nor would I be interested in attending the speaker’s school for graduate studies.

The reason I think that this seminar was so interesting is because the speaker was excited about the topic and because of the biochemistry content.

If I were to describe this seminar in one sentence it would be “determining how the lipids in the membrane of fibroblast behave.”

Post This To My

Hide Sites

The speaker for seminar this past Thursday Feb 18th was Dr. Mary L. Kraft from the University of Illinois. She spoke about her research regarding recent attempts to better understand sphingolipids and prove or disprove the ‘lipid raft’ model for virus propagation.

Dr. Kraft began her presentation by telling the audience that a cell membrane is a selectively permeable membrane of a cell that is made up of phospholipids, along with cholesterol, glycons, and transmembrane proteins. Dr. Kraft decided to look at membrane organization for determining cell function, instead of proteins because that area has rarely been studied. More specifically, she looked at how depleting concentration of cholesterol and sphingolipids that are found grouped up in certain areas of the membrane, cause a change in cell function. The primary instrument used was the high resolution mass spectrometer. By feeding certain atoms to label specific cholesterol/lipids, they are able to detect them on the mass spectrometer.

One of the things that I learned from this lecture is that carbon-13 enrichment in the cells show in the images if the plasma membranes are intact or not. Another thing that was interesting to learn about was the method by which carbon-13 is incorporated into the fatty acids. First carbon-13 is fed to different organisms and those organisms then produce different by-products, some of which are fatty acids infused with the carbon-13. This is then used for tagging the cells. One thing that I was slightly curious about was what all the scientists working on these projects use for “labels” other than carbon-13 infused fatty acids.

Overall, I could see that many of my fellow students enjoyed the presentation and had many questions to ask at the seminar’s completion.  These questions were answered well, and clarified many points in the presentation. The presentation did encourage me to learn more about the subject and it seemed like a very intriguing process. This presentation gave a direct visualization of heterogeneous sphingolipid distribution.  I won’t mind hearing more from Dr.Kraft at a future seminar session.

Post This To My

Hide Sites

This week’s presentation was done by Dr. Mary L. Kraft. The title of her presentation was “Direct visualization of heterogeneous sphingolipid distribution in the plasma membranes of intact cells.” Dr. Kraft is currently an assistant professor of chemical and biomolecular engineering at the University of Illinois – Urban Champaign. Her research on plasma membranes had many biomedical applications such as facilitating the treatment of viral infection. Her presentation was easy to follow and understandable.

From her presentation, I learned that plasma membranes contain a region which is rich in sphingolipids and cholesterol, although they are often described as “uniformly distributed.”  In her research, she used mass spec to collect the readings of entire surface of the plasma membrane that is being studied. However, since its resolution was low, she used secondary ion mass spec to obtain higher resolution of the “picture.” In order to observe the distribution of real cells, C12 and N15 ions were used in place of original elements in sphingolipids. Her finding was that there is a sphingolipid-rich micro domains, and this region was found in all the other plasma membranes that were tested, although the location is not exact. All cells showed similar looking domains.

My questions during her presentation included 1) You used C13 and N15 in your research, is it possible to use other isotopes such as deuterium? 2) Can there be any problems with using isotopes instead of original element? 3) what led you to study plasma membranes? and 4) what are some of the practical applications of this research other than treating viral infection?

Post This To My

Hide Sites

This week’s seminar was “Visualizing Lipid in Plasma Membranes” by Mary L. Kraft. She is an assistant professor at the University of Illinois at Urban-Champaign. She received a B.S. in Biochemistry from the University of Illinois at Chicago, and a Ph.D from the Department of Chemistry at the University of Ilinois at Urbana-Champaign. Following that she finished postdaoctoral studies at Stanford University . Currently, she focuses on the development of high-resolution compositional imaging techniques that are used to investigaet the causes and consequences of heterogeneous lipad and cholestrol distribution within the plasma memebranes of mammalian cells.

First, she started the presentation by explaining the basic information with a picture of cellular plasma membrane. The proper membrane organization is required for fuction, however, there are no direct methods to look detail of membrane. Furthermore, Dr.Kraft discussed about direct approach to probe cell membrane organization. Since the light resolution is poor , it did not give a good chance to get structure well. However, she found out the process of high resolution secondary ion mass spectrometry which gave very clear image without killing the cell. With this process, she continued to analyze and detremine the concetration.

Overall, the presentation was pretty interesting and infomative. I learned about the high resolution secondary ion mass spectrometry and how it helped to investigate heterogeneous lipid . The questions that I had for this seminar was what made to study or be interested studying cholestrol and sphingolipd. Lastly, we had pretty good questioning and anwsering time.

Post This To My

Hide Sites

On February 18, 2010, there was a presentation which was about properties of cellular membrane of the life.  The guest speaker was Mary L. Kraft. The title of the presentation was Visualizing Lipids in Plasma Membrane. She is an assistant professor of the University of Illinois, in Urbana-Champaign. Her presentation was very calm and tranquil. Even though it was not easy for me to understand her presentation thoroughly, it was a good chance to know deeper knowledge of the properties and composition of cellular plasma membrane than I learned in other chemistry and biology classes.

Dr. Mary L. Kraft started her presentation introducing us the basic information of cellular plasma membrane. It is composed of two lipid layers and there are various kinds of lipid in the membrane such as cholesterol, glycans, and transmembrane protein. The selective permeability of the membrane plays an important role as a barrier of the cell.

For direct approach to prove cell membrane organization, Dr. Mary L. Kraft used a high resolution secondary ion mass spectrometry (SIMS) which is new for me. It is used to reveal a map of elemental and isotopic composition. She told us that there are only seven SIMS in U.S.A. Throughout the presentation, I wonder when the instrument was developed and became commercially used and how she was able to conduct the experiments with it.

I would tell my friends that the presentation was about finding out the organization of cell membranes that is mainly composed of various kinds of lipids.

Post This To My

Hide Sites

The speaker for ChemSem this week was Dr. Mary L. Kraft from the University of Illinois. She spoke on her research regarding recent attempts to better understand sphingolipids and prove or disprove the ‘lipid raft’ model for virus propagation. Though much of the lecture was enigmatic, there were several interesting points which she mentioned.

First of all, it is fairly difficult to do this research for a number of reasons. Mostly, cellular research with spectrometry tends to be done on dead cells, which has a potential for ruining experiments. If the goal is to understand how these cells and lipids function in a living cell, a living cell needs to be photographed. Until last summer this was very difficult in terms of high resolution pictures, but Dr. Kraft discussed the process of high resolution secondary ion mass spectrometry as a way of seeing the surface of a cell very clearly without necessarily killing the cell. In so doing she was able to gain clear images of the surface of the top of a cell which allowed her to analyze it and determine the concentrations of spingolipids present in a given area.

I will admit much of the biology escaped me in this portion of the presentation. The aggregate seemed to suggest that the experiment had used heavy isotopes of nitrogen and carbon to tag various parts of the lipids. These portions, and their concentrations, were then detectable in the instrument at analytical values. I was curious to find out what the amount of heavy isotope was in a given lipid and whether or not this was likely to affect the outcome of the experiment. Furthermore, it was unclear why the specific fibroblast cell was chosen for sphingolipid analysis rather than another type or multiple types of cell. Did fibroblasts offer conditions that were more suitable for experimentation? Finally, though the overall science was interesting, I was curious what the other applications of high resolution secondary ion mass spectrometry were and if Dr. Craft had investigated any of those projects as well as the spingolipid analysis work she is currently involved in.

Overall Dr. Kraft appeared to be a very well versed and capable scientist, though some of her material was lost in translation when speaking to a Chemistry based rather than Biology based audience. The research itself clearly holds pharmaceutical applications in terms of understanding disease better, and in that the lecture was interesting.

Post This To My

Hide Sites

We’ve been having a queue of Illinois researchers this semester and Mary L. Kraft both graduated from the University of Illinois and works there as an assistant professor in the Department of Chemical and Biomolecular Engineering. Her presentation skills were not particularly remarkable, however the topic was one that the biochemistry class was studying at the time and we had just read the article by Kai Simons about his Lipid Raft theory.

Mary L. Kraft introduced us to her research on lipids in plasma membrane with basic information on the plasma membrane, mentioning the Mosaic Model, and the Lipid Raft theory. One of the primary reasons the research began is the large amount of sphingolipids found in the stolen coat of host cellular membrane in viral budding (“wolf in sheep’s clothing evolutionary method”). She then explained what equipment the research was using to better characterize the lipids and cholesterols in the cellular membrane. Secondary ion mass spectroscopy (SIMS) is much like regular mass spectroscopy but produces an image from the analysis, as if it was finding pixels. However the resolution of SIMS is too low to properly analyze the small cellular membranes. So, the research team turned to high resolution SIMS, normally used in astrological studies, analyzing hard materials from outer space. It is much more destructive than MS as it analyzes pieces of atoms and diatomic species that fly off, instead of molecular pieces. Also, it can only determine the intensity of the concentration of the species, but also it can recognize very fine details. Important to the research team, HRes SIMS can recognize the mass difference between 12C15N (26.9996 amu) and 13C14N (27.0059), which would be used to label the celluluar membrane.

First they metabolically labeled carbon and nitrogen to be incorporated into the sphingolipids of the membrane. In the image obtained from HRes SIMS, they found that only 2% of the labeled nitrogen was metabolized into other species aside from the sphingolipid, a negligible amount. Comparing the distribution of the labeled carbon against the labeled nitrogen image showed that enrichment was not an artifact of topography – that is, it showed that the membrane was not puckered in places to make it appear as if there was a higher concentration of sphingolipid. It was clear that sphingolipids are heterogeneous and compartmentalized, supporting the Lipid Raft theory.

Their next goals are to determine the distribution of cholesterols in the membrane. An even broader question they want to answer is why they are distributed in such a manner. Finally, they hope to understand more about influenza budding, possibly by tagging antibodies with fluorescent ions. In the Q-and-A session, I asked if they would be using the same methods used for the sphingolipids to analyze the cholesterol distribution. She responded that if the method works the same then it would do, but the big question was “How do we get good labeling?” Also, I wondered if the research could be considered conclusive as they had only done three imagings. In the answer to a different question, Kraft said that to make sure that the membrane had completely incorporated the fluorescent nitrogen, they waited at least 7 days, which explains why they have such few results. She also mentioned that they would need at least a dozen analyses.

Laymen’s Summary of Chemistry Seminar: There’s a controversial theory about the composition of the cellular membranes – that is that the arrangement of the lipids and cholesterols that make it up is actually somewhat organized, not completely random. So one of the evidences for this crazy Lipid Raft theory is viral budding, when at the end of its life cycle, a virus uses the host cell’s membrane to escape and make more viral babies. When they saw that the membrane that the virus stole was chock full of sphingolipids, they thought, cool! We should look into this. And so they did, with technology usually used for studying space rocks and feeding fluorescent nitrogen and carbon to cells, they produced images highlighting the sphingolipid distribution. What they found supported the crazy Lipid Raft theory, so now they are going to look at the cholesterols too. Understanding how and why this all works can lead to great medical advances.

Post This To My

Hide Sites

The presentation this week (2-18-10) was titled “Visualizing Lipids in Plasma Membranes.”  The presentation as given by Dr. Mary L. Kraft, who is an assistant professor in the Chemical and Bio molecular engineering department, at the University of Illinois. Her research is directed to establishing the driving forces that result in the stable cell membrane organization, and finding the correlation between membrane organization and disease.

Dr. Kraft began her presentation by telling the audience that a cell membrane is a selectively permeable membrane of a cell that is made up of phospholipids, along with cholesterol, glycons, and transmembrane proteins. Dr. Kraft decided to look at membrane organization for determining cell function, instead of proteins because that area has rarely been studied. More specifically, she looked at how depleting concentration of cholesterol and sphingolipids that are found grouped up in certain areas of the membrane, cause a change in cell function. The primary instrument used was the high resolution mass spectrometer. By feeding certain atoms to label specific cholesterol/lipids, they are able to detect them on the mass spectrometer.

Dr. Kraft spoke clearly with no accent, so she was easily understood. However, I did have trouble following along sometimes because of my lack of knowledge in this area. She ended on time, and many questions followed in the Q/A session.

Overall, I think that Dr. Kraft’s research has a lot of potential, and it will be interesting on the results from her research. This area seems interesting, however I do not know enough about it to determine whether or not I would be interested in this field of research.

Post This To My

Hide Sites

The seminar this week was a mildly interesting talk on both the organization of plasma membrane structures in cells and the development of imaging technology that is used to identify the different components of plasma membranes.

I say mildly interesting because I found the parts involving the imaging technology to be both interesting and informative, mostly because of the technical aspects of the lecture. The sections that involved biochemistry were not all that interesting to me, largely due to the biological aspects of the talk and my lack of interest in biochemistry.

One of the things that I learned from this lecture is that carbon-13 enrichment in the cells show in the images if the plasma membranes are intact or not. Another thing that was interesting to learn about was the method by which carbon-13 is incorporated into the fatty acids. First carbon-13 is fed to different organisms and those organisms then produce different by-products, some of which are fatty acids infused with the carbon-13. This is then used for tagging the cells. One thing that I was slightly curious about was what all the scientists working on these projects use for “labels” other than carbon-13 infused fatty acids.

If I were describing the content matter of this week’s lecture to one of my non-science friends, I would tell them that it was about marking cells so that we can see certain ones through imaging processes, and also how scientists are working to make the imaging technology better, so to see the cells more clearly.

Post This To My

Hide Sites

Dr. Mary Kraft came from Illinois to give a presentation on “Direct visualization of heterogeneous sphingolipid distribution in the plasma membranes of intact cells”. Proper membrane organization is required for function, and it has been thought in the past that plasma membranes are homogeneous in their distribution of contents.

The research that Dr. Kraft is involved in has to do with lipid rafts within the plasma membrane and finding what they are involved in. Just recently it was found that these lipid rafts exist across a plasma membrane, giving it a heterogeneous distribution of contents. They have found that viral envelopes that have come off from a cell have higher amounts of cholesterol and sphingolipids than the rest of the cell membrane. Within experimental conditions, if cholesterol and sphingolipids were decreased, viruses that detached from those cells were incomplete and inactive.

Dr. Kraft has taken this knowledge and is trying to find how much of the cell surface is covered with these domains with higher concentrations of sphingolipids and later she will look at the domains with cholesterol. The machine that they have been using to look at plasma membranes is the high-resolution secondary ion mass spectrometer. This gives a better resolution than a regular mass spec, but it is also more destructive and Dr. Kraft made a couple comments that once an area of the cell surface has been looked at with this, it is to degraded to get any other images.

Dr. Kraft had a very interesting presentation with many images to illustrate her findings. I would describe this talk to a non-science friend as a new way of looking at cell surfaces to see the composition of them.

Post This To My

Hide Sites

It is always nice when the chemistry seminar involves something that you are currently studying. Obviously, the farther my education goes the more I can understand current research.  The chemistry seminar today applied to the Biochemistry class I am currently taking. Dr. Mary Kraft gave a presentation entitled “Visualizing Lipids in Plasma Membranes.”  Dr. Kraft is an assistant professor at the University of Illinois. The work she is involved in is attempting to test the lipid raft theory by mapping the location of sphingolipids in the plasma membrane.

Kraft uses high resolution secondary ion mass spectrometry to map the sphingolipids. To do this they use a machine called a cameca NanoSIMS 50 that maps the elemental and isotopic composition.  It determines the intensity of the ions at each location and molecules are fragmented into atomic and diatomic secondary ions. This technique improves the resolution of simply secondary ion mass spectrometry by twelve times, allowing resolution around hundred nanometers to be seen. To make the sample a stable isotope, in this case carbon-13 and nitrogen-15 are incorporated into the lipid membrane.   The cells are labeled metabolically which means that the cells are fed the labeled isotopes. The Nitrogen-15 allows us to see the concentration of sphingolipids and the carbon-13 allows us to see the lipid membrane at the same time. Using this technology Kraft is able to conclude that sphingolipids are heterogeneously distributed which supports the raft hypotheses. In the future Kraft hopes to find if sphingolipids co-localize with cholesterol.

The presentation was well explained and informative. I had two questions pertaining to the material. Why do lipids other than the sphingolipids not become labeled by nitrogen-15? Also, I was curious if this same image processing could be used for proteins in tumors. If I were describing this seminar to a family member I would say it was looking at a specific type of lipid or fat in cell membranes.

Post This To My

Hide Sites

This week’s speaker was Mary L. Kraft, who received a Ph.D. from the Department of Chemistry at the University of Illinois at the Urbana- Campaign. She presented on her current research which focuses on the development of high resolution compositional imaging techniques used to investigate the causes and consequences of lipid and cholesterol distribution within the plasma membrane. Specifically the distribution of nitrogen-15(N-15) and carbon-13(C-13). During this presentation Kraft made much eye contact, had an adequate voice level, and enjoyed the topic. I found this topic of applied research very interesting since it also tied in with subjects I’m studying now. Some new things I learned dealt with the incorporation of N-15 and C-13 in sphingolipids and other cellular lipids. It was amazing that this Study took seven days in which the different cells were fed N-15 and after two days any trace of N-14 had disappeared.

Lipid domains are enriched by cholesterol (CHO) and sphingolipids in the plasma membrane are hypothesized to influence membrane-mediated processes. During their research they developed a raft hypothesis which talks about the plasma membrane of cells that are made up of a combination of glycosphingolipids and protein receptors organized in glycolipoprotein microdomains termed lipid rafts. These specialized membrane microdomains compartmentalize cellular processes by serving as organizing centers for the assembly of signaling molecules, influencing membrane fluidity and membrane protein trafficking, and regulating neurotransmission and receptor trafficking. Raft membranes are enriched for cholesterol and sphingolipids and contain clustering proteins trans membrane proteins. They found virus envelopes to contain more CHO and sphingolipids than the host cell. There were also virus buds from domains enriched by CHO and sphingolipids.

This research group also wanted to determine whether the depletion of CHO or sphingolipids had adverse affects to the budding and signal transduction adhesion and other cellular processes. There were different rates of diffusion due to different environments, but they were still unsure whether CHO depletion really affected anything. Direct approaches to probe cell membrane organizations were used involving Secondary Ion Mass Spectrometry (SIMS). Some problems that arose were poor lateral resolutions and the image was 12X larger than needed. They then tried using a high- resolution SIMS which gave a good map of the elemental and isotopic composition of the N-15 and C-13 in the sphingolipids and other cellular lipids. This machine was more specific and it’s fascinating that there are only seven in the country.

In another part of Kraft’s study a distinct stable isotope of the elements mentioned were incorporated into each membrane component. Component-specific secondary ions revealed the distribution in each lipid. N-15 was then found to incorporate into 100% of cellular sphingomyelin, while C-13 with its various lengths were incorporated into all cellular lipids or fatty acids. Using Nano-SIMS gave Kraft the ability to see enriched N-15 and C-13 region and whether or not the cell became damaged. This helped them in gathering accurate results and allowed them to see what was truly happening. In conclusion, they were able to find that the sphingolipids were heterogeneously distributed, which supported their raft hypothesis. They have future plans to work with influenza and virus budding.

Many students seemed to enjoy the presentation and many questions were asked during the end. These questions were answered well clarified many points in the presentation. The presentation did encourage me to learn more about the subject and it seemed like a very intriguing process. The presenter didn’t speak much about her school of graduate studies so I wasn’t necessarily encouraged to go there, but I’m sure she would have been open to questions. This presentation gave a direct visualization of heterogeneous sphingolipid distribution.

Post This To My

Hide Sites

This week’s speaker was Mary Kraft from the University of Illinois.  Her topic was visualizing the sphingolipid distribution in the plasma membranes of cells.  Plasma membranes are what separate the cell interiors from the cell exteriors.  They consist of phospholipids that have polar head groups and nonpolar tails.  Proper membrane organization is needed for correct functioning.  It is hypothesized that lipid domains enriched with cholesterol (CHO) and sphingolipids could influence membrane-mediated processes.  It is a controversial hypothesis that is difficult to test.  However, there is some evidence for this.  Viruses contain more CHO and sphingolipids than their host cells.  It is also confirmed that depletion of CHO and sphingolipids adversely affect viruses and cells.  But, the hypothesis is difficult to prove conclusively because in biology, changing one factor affects ten other factors.

Secondary ion mass spectrometry (SIMS) is used to probe cell membrane organization.  This procedure was originally intended for materials analysis, so it had to be modified for cells.  Lateral resolution is very poor, and water has to be removed from the samples.  In SIMS, beam molecules are fragmented into atomic and diatomic secondary ions, and detectors pick up specific mass to charge ratios.  Component specific secondary ions are used to reveal lipid distribution across the plasma membrane.  The isotopes 13C and 15N are used to monitor the lipids.  15N is able to be incorporated into 100% of cellular sphingomyelin but only 2% of phosphatidylethanolamine.  To incorporate 13C into lipids, labeled fatty acids of varying lengths and degrees of saturation are put into the cell.  NanoSIMS is used to visualize the plasma membrane.  The sphingolipids are pinpointed by 15N, and 13C shows the plasma membrane.  More work is needed to establish statistics, with regard to population variation.

This was a well done presentation.  It was easy to follow and to understand.  I was interested to learn about SIMS, as it is a technique I have never seen before.  Kraft’s group wishes to investigate the influenza virus using the labeling techniques.  I would like to know if other viruses such as HIV can also be investigated using this procedure.  I would also like to know what kind of lateral resolution is considered good, and what angle of ion ejection gives the best yield during SIMS.  In summary, this presentation was about finding out the lipid distribution of cellular membranes using labeling isotopes and mass spectrometry techniques.

Post This To My

Hide Sites

This week’s installment of ChemSem was presented by Mu-Hyun Baik an Associate Professor at the University of Indiana. His topic concerned better methods of catalyzing water decomposition to gain the electrons that would be necessary in creating long chain synthetic organic fossil fuel imitations.

In understanding the energy shortage, several issues need to be taken into account. The right fuel of the future must have high energy density, ease of creation, transportability, and low pollution output. This eliminates ethanol, hydrogen, and solar power because of their various shortfalls. It seems the best solution to the overall problem is the one that has been functioning in nature for a few millenia. Taking water and carbon dioxide, the results of combustion, and adding energy (solar most likely) to synthesize carbon chains is fundamentally the process that would lead to almost limitless renewable energy. Granted, for this version of synthetic photosynthesis, the products would be alkanes rather than sugars, but the root mechanisms are the same. This is the process Dr. Baik discussed.

In his research he used a Ruthenium catalyst to aid in the catalytic splitting of water. It did lower the energy penalty of splitting water, but also had several shortfalls including decomposition. After a long process in which he finally came to a conclusion on the reaction mechanism at play in the removal of the electrons from the molecule, Dr. Baik discussed the future of his project which included his desire to develop methods of using an Iron catalyst instead of the less common Ruthenium.

The lecture was very involved and Dr. Baik was a very engaging and interesting speaker to listen to. He mentioned that the most successful catalyst they had developed thus far was Cobalt based, but he did not delve into the reasons for that or why an element one step up from Iron worked better. Furthermore, he only briefly discussed the other side of the synthetic photosynthesis equation involving the conversion of CO2. I was curious about whether Rhodium functioned in a clear manner and if this was the reason behind the switch to Cobalt as a catalyst, or if any Rhodium testing had been done at all. I realize that Ruthenium was a slower reaction helping to understand the mechanism and possibilities for Iron, in the same way was Rhodium used for analysis of Cobalt?

Regardless, Dr. Baik did an impressive job of both explaining his project and its possibilities for the future as well as tying all of his material into the present day applications and value it presents to the marketplace.

Post This To My

Hide Sites

The chemistry seminar that was held on January 28, 2010 was titled “Peptide Design Using Unnatural Amino Acids & Multivalent Antibody Aggregation,” and the speaker was Basar Bilgicer. However, he only presented about multivalent antibody aggregation. Basar Bilgicer was born in Istanbul and received a bachelor’s degree in chemistry at Bogazici University, Turkey. Following that, he received a Ph.D. at Tuff University.

He has studied the thermodynamics and kinetics of multivalent interactions. To be more specific, he studied the association of bivalent antibodies.  He began the presentation by showing the shape of IgG. The Y shape of IgG allows it to easily bind to other molecules. The two arms of this IgG can bind to an antigen since two arms are really flexible.  He used chromatography to separate aggregates based on the size. And then he found out that trimers were the most popular aggregates.

Moreover, although there are a lot of different types of binding, there are two binding types that work best. They are monovalent and bivalent binding; monovalent is binding with one arm and bivalent is binding with two arms. He compared the energy loss between monovalent and bivalent. Since bivalent binds with two arms, we would assume that it would lose twice the amount of monovalent, but surprisingly, it was not. the loss that would be assumed is twice as much as monovalent, however, it was not.

Overall, his presentation was interesting because immunology is the one subject that we can always find in our life. When we get hurt and sick, the body’s reaction can be studied by understanding immunology. Also, he was such a good speaker that we had really good time asking and answering questions.

Post This To My

Hide Sites

The presentation held on Feb 4, 2010 was “Functional Interrogation of Gene Driving Colorectal cancer.” The speaker was Amanda B. Hummon who is currently Assistant Professor at Notre Dame. She received A.B. in chemistry at Cornell University, following she received Ph.D. at University of Illinois. She studied gene regulations in colorectal cancer with RNA interference as her graduate work. Actually, she and her group are working on combining proteomic and functional genomics approaches to develop novel methodologies to explore alterations in signal transduction pathways in cancer at Notre Dame.

Professor Hummon starts the presentation with showing the cancer cell an explaining general information for cancer. It was interesting to know basic understanding of cancer cell such as it has all same gene and genome is like other cells but, the equilibrium is different and chemical differences makes phenotypically behave different.  There are six things that can give better understanding on cancer cell, such as studying DNA , RNA, Protein, Network, Pathway, and function.  Additionally, there are some techniques that can specifically explore DNA, RNA, and function. The spectral karyotyping(SKY) and comparative genomic hybridization were used to explore DNA. The technique, qRT-PCR and microarray were used to study RNA. According to her presentation, microarray is a good technique to see a broad map for gene but not details. After she researched, she found out that the chromosome 13 and 20 were highly affected.

Overall, her presentation was really interesting to see because I was curious about cancer. It was good opportunity to learn about cancer cell as well as gene expression, and benefits of microarrays.

Post This To My

Hide Sites

I thoroughly enjoyed Dr. Biak’s visit this past Thursday, not only can he hold an audience’s attention, but he can feed them too! I believe it is safe to say that food to a college student is as good as gold, so with some full stomachs in the audience he was off to a great start. Dr. Mu-Hyun “Mookie” Baik came to us from the Chemistry Department of Indiana University-Bloomington where he is currently the Associate Professor of Chemistry & Associate Professor of Informatics.  Biak received his Ph.D. in Theoretical Inorganic Chemistry at the University of North Carolina Chapel Hill (Go Tarheels!).  It was easy to see from the get go that Biak was excited about what he does for a living in fact, he even admitted that he would do it for free! I am sure that all the other presenters enjoyed what they were doing too, but Biak really seemed excited about chemistry, and made graduate school very appealing.  Aside from his jokes (which were really funny) Biak’s presentation style was great, probably the best I’ve seen thus far.

In a nut shell the Biak group is focused on developing artificial photosynthesis, particularly water oxidation. Water is an ideal molecule because it is a natural source for electrons, and we have tons of it. Biak has devised a method that would use solar energy to free electrons from water by electrolysis and would then direct these freed electrons to another reaction that would fix them along with carbon from carbon dioxide into fossil fuels.

This seminar was very practical, although it would be a while before it could become mainstream, the future implications for energy and the way we use it could solve our energy crisis. Some new things I learned from seminar were 1. A field of chemistry based almost entirely on informatics, 2. How much more efficient fossil fuels could be, and 3. No matter how advanced our technology gets it is still very hard to mimic the way nature oxidizes water.

Question I have are 1. How long do you think it would take to make this a part of our everyday living? 2. What obstacles do you see in the way of achieving your goal? 3. are there other research groups that have come close to oxidizing water and harvesting its energy too?

Post This To My

Hide Sites

The chemistry seminar that was held on Feb. 11, 2010 was “Solving the Energy Crisis by Splitting Water.” The guest speaker, Mu-Hyun Baik is currently associate professor at Indiana University. Before he came to Indiana University, he received his B.S. in chemistry in Germany, and his Ph.D. in theoretical graduate research.

Indeed, Dr. Baik’s research group is interested in transition metal chemistry with heavy emphasis on catalysis. Currently he is working with computer stimulations in studying water oxidation. The interesting thing in his research is he used computer stimulations for the experiments. He mentioned that computer stimulators can offer great insight but it also can cause problems such as number crunching. Also the predictions are difficult. The data should be real, relevant, and useful.

Moreover, his research is also based on mechanisms of how transitional metal system can activate small molecules. When he especially tried to mimic the concept of photosynthesis with lots of water, they found out that the electrons are produced by splitting water. Following that he studied on Ru0based water oxidation catalyst. As a result, all electrons are appeared as paired and three possible states of Ru were also found.  Currently, he is planning to work on a Fe-based water oxidation catalyst.

Overall, his presentation was really good because he was really enthusiastic and passionate on his research. His voice was loud enough to get all the attention from audience and even he used a lot of jokes to engage the audience.

Post This To My

Hide Sites