B I N G H AM T O N B I O C H E M I S T R Y C L U B | F A L L 2 0 1 3 V O L I I I I S S U E 0 0 2
BINGHAMTON BIOCHEMISTRY CLUB
BIOCHEMISTRY CLUB EXECUTIVE BOARD
President Lance Kong Vice President Morgan Zhao
C O V ER Secretary Travis Lageman Treasurer Steve Kwon
JEOL Field Emission SEM Adipocytes Nikki Naim 3
Historian Stephanie Jiang Newsletter Coordinator Betty Chu Magazine Coordinator Jenny Tse
L E T T ER S FR O M T H E V I C E P R E S ID EN T M A GA ZI N E C OO R D IN A TO R
Lance Kong Jenny Tse L I T ER A T U R E R E V I EW S 4
Psychiatric Illness and Intellectual Disability in the Praderâ€“ Willi Syndrome with Different Molecular Defects - A Meta Analysis Stephanie Vogel
The Human Microbiome Project Phillip Sander
Effect of a magnetic field on Drosophila under supercooled conditions Jenny Tse
Academic Coordinator Nikki Naim Academic Peer Advisors Sophie Russ and Kurnvir Singh
IM A G E
PUBLICATIONS COMMITTEE Jenny Tse Betty Chu Gavriella Hecht Jiyeon Park Phillip Sander Stephanie Vogel
F A C U LT Y Q & A 7-9
Dr. Peter Gerhardstein Gavriella Hecht
Letter from the Magazine Coordinator
Letter from the VP Dear Fellow Students, Faculty, and Alumni, As the Biochemistry Club continues to grow and adapt to the ever-changing demands of the student body and the surrounding community, I inevitably wonder how far the club can really go, but not without reminiscing about our modest beginnings. With our sustained expansion and diversification, we hope to maintain our support and representation of students who study biochemistry, chemistry, biology, neuroscience, and other related fields. It has only been almost two years since our transition from a niche advisory board to an eclectically functional club. It has been quite a change. Now as the fall semester ends, we have to reflect on our capabilities as a club. In past semesters, we have had great success in events that we hosted such as the Student-Faculty Mixer, miniBridge, Academic Tournament, Advising Seminar, and Mentorship Program (just to list a few). However, we can still make progress. With everyoneâ€™s continued support, we will continue to organize these events and present new opportunities, such as bringing in graduate or post graduate speakers and offer more academic assistance on campus. I envision an improved Biochemistry Club in the near future, capable of making even more of a meaningful impact on our campus for the students we serve.
Dear readers, Thank you for reading this second issue of Titin of Fall 2013. The magazine would not be possible without our writers and editors from the Publications Committee, who have been a joy to work with the entire semester. Many thanks are also due to Nikki for providing the cover photo and Dr. Gerhardstein for giving the time to share his thoughts in the Q&A. Secondly, I would like to congratulate Gavriella Hecht and Jiyeon Park who will be leading the magazine next semester. Their fresh ideas will undoubtedly make a positive impact on this still young publication. If you have any comments or would like to take part in one of our future issues, do not hesitate to email me, Gavriella, or Jiyeon. Sincerely, Jenny Tse
Sincerely, Morgan Zhao
See you in the Spring semester! Our meetings will be at 7PM on Mondays in SL310. All majors are welcome!
MiniBridge on November 22nd at West Middle School. BINGHAMTON BIOCHEMISTRY CLUB
Psychiatric Illness and Intellectual Disability in the Prader–Willi Syndrome with Different Molecular Defects - A Meta Analysis Review by Stephanie Vogel
Prader-Willi Syndrome (PWS) is a genomic imprinting disorder that is estimated to occur in one out of every 15,000 births. It is a result of the deficiency of paternally expressed gene(s) in the chromosome 15q11-13 region. Parental deletion in this chromosomal region is the most prevalent cause of PWS; however, it can also be caused by maternal uniparental disomy (mUPD) of chromosome 5. Patients diagnosed with this disorder often experience feeding difficulty, respiratory problems at birth, neonatal hypotonia, hypogonadism, obesity, obsessive and compulsive behaviors, mental disabilities, and psychiatric illness during adulthood. If clinical features are present, molecular genetic testing is used to confirm the diagnosis of PWS. The lack of consensus on whether the distinctions between 15q11-q13 paternal deletion and mUPD are apparent and have clinical significance was the impetus for Guo-ding Zhan (Children’s Hospital, Fudan University, Shanghai, China) and his colleagues to research this association, especially since this information is essential for treating patients and counseling families. Zhan and his colleagues conducted their research by carefully evaluating and filtering out published studies involving these two causes of PWS. These researchers sifted through 581 records and determined that only thirteen of these studies passed the screening process. Out of these thirteen studies, 423 PWS patients experienced a 15q11-q13 paternal deletion and 318 suffered from mUPD. The researchers proceeded to perform metaanalysis on these select studies to assess the level of intellectual disability and frequency of psychiatric illness in order to observe any correlations that might occur between 15q11-q13 paternal deletion and mUPD. The results concluded that substantial differences are preva-
lent between 15q11-q13 parental deletion and mUPD, including the severity of neurocognitive impairment and the frequency of psychiatric illness. Patients with paternal deletion had lower VIQ and FSIQ scores; more specifically, their verbal IQ was more affected than their performance IQ. However, patients with mUPD were more susceptible than those with paternal deletion to psychosis and bipolar disorders. These findings provide a foundation for the development of evaluation and management guidelines for treating individuals with PWS. They illustrate that it is necessary for individuals with PWS who exhibit psychiatric illness to receive more diligent care. Overall, this analysis is meant to encourage researchers to design experiments targeted at elucidating the genetic basis of psychiatric illness. The differences between cases with paternal deletion and mUPD arise from the chromosome 15q11–q13. This chromosome dominates the regulation of genomic imprinting, an epigenetic process in which gene expression is dominated by the parent-of-origin. The deficiency of paternally expressed gene(s) in the 15q11-q13 region is the primary reason for PWS. However, the gene(s) responsible for the full spectrum of PWS phenotypes remain unclear.
Reference: Yang L, Zhan G-d, Ding J-j, Wang H-j, Ma D, et al. (2013) Psychiatric Illness and Intellectual Disability in the Prader–Willi Syndrome with Different Molecular Defects - A Meta Analysis. PLoS ONE 8(8): e72640. TITIN
The Human Microbiome Project Review by Phillip Sander The Human Microbiome project (National Institutes of Health, USA) was piloted in an effort to characterize the myriad microbial communities found inside and on the human body, and to analyze the role of these microbes in human health and disease. Collectively known as the Microbiome, these communities outnumber human somatic and germ cells ten fold, and control several metabolic functions not encoded in the human genome that are necessary for human health. These include extracting calories from indigestible foods, synthesis of essential vitamins and amino acids, and protecting the host from pathogens. Potential connections between a ‘healthy’ Microbiome and human health are already beginning to emerge. Researchers discovered that bacterial species of the vaginal Microbiome undergo a major shift in preparation for birth, where the birth canal passage provides the child with its first ‘inoculation.’ A deliberate alteration of these communities, by way of antibiotic treatment, was preliminarily observed and seen to increase the rate of allergic reactions and lead to other diseases. This may help to explain previous studies that have linked cesarean delivery to a higher risk of asthma, diabetes and obesity. Cesarean section may bypass this natural immunizing opportunity and leave newborns more vulnerable to infections, demonstrating just how important it is to better understand our relationship with the Human Microbiome. Inability to reproduce necessary growth conditions in the lab previously prevented scientists from isolating, culturing and sequencing the majority of microbial species present in the human body. Metagenomics, the study of microbial communities, has helped circumvent this issue by using advances in technology and analytical methods, such as polymerase chain reaction (PCR), which allows microbial communities to be examined directly from environmental samples. The HMP is using 16S rRNA and metagenomic sequencing to characterize the complexity of the human Microbiome at various sites on the human body. Scientists routinely use this technique to compare RNA from mixed samples in order to determine if new, novel organisms exist. The 16S rRNA gene is short, only 1,542 base pairs, so copying and sequencing is very cost effective. The first initiative of the project was to develop a reference set of microbial genome sequences and obtain a prelimiBINGHAMTON BIOCHEMISTRY CLUB
nary characterization of the human Microbiome. Several body sites were studied, including the gastrointestinal and female urogenital tracts, oral cavity, naso-pharyngeal tract, and skin. The first clinical phase completed in July 2010 provided huge sets of data about the complexity of the human Microbiome and led scientists to discover new, novel organisms. However, analyses of the microbial diversity have been challenging and certain taxa which have not had their 16S sequences included into the database may be misclassified or unidentified. Systemic differences do exist in the human biome, however their detection must be facilitated with the proper statistical measures that are sensitive to low abundance taxonomies. After a clearer picture of the ‘core human biome’ emerges, if one exists, researchers and health professionals may be able to use the data to correlate deviations from this core biome to disease susceptibility. Even though the regulatory mechanism, by way of which these bacteria face pathogens, is not entirely clear, further studies will shed light on the symbiotic relationship between humans and the plethora of bacteria we house.
References: 1. Turnbaugh P, Ley R, Hamady M, et al. The Human Microbiome Project. Nature (2007); 449: 803-809 2. Aagaard K, Riehle K, Ma J, Segata N, Mistretta T-A, et al. (2012) A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy. PLoS ONE 7(6): e36466. doi:10.1371/journal.pone.0036466 3. National Research Council (US) Committee on Metagenomics: Challenges and Functional Applications. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington (DC): National Academies Press (US); 2007. 1, Why Metagenomics? Available from: http:// www.ncbi.nlm.nih.gov/books/NBK54011/ 5
Effect of a magnetic field on Drosophila under supercooled conditions Review by Jenny Tse The viability of organs for transplantation is substantially dependent on time. The human heart, for example, can only retain its functionality if it is transplanted within four to seven hours, which under certain circumstances may not be feasible. This narrow time-frame, coupled with a limited number of organ donors, makes it necessary to find new techniques to improve preservation times and delay deterioration. The current method for organ preservation is induced hypothermia at 4°C, which minimizes reperfusion injury, or the resulting cell damage upon returning blood flow. One possibly more effective alternative recently explored by researchers in Japan is the supercooling of organs with a magnetic field.
freezer using a magnetic field of 0.5mT. Flies preserved in the freezer were essentially frozen to extinction at various temperatures and time periods: 0°C for 1 hour, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, and 96 hours; at -2°C and -4°C for 1 hour, 6 hours, 12 hours, 24 hours, and 48 hours; at -6 and -8°C for 1 hour and 6 hours; and at -10°C for 1 hour (Table 1). The Drosophila were then re-warmed to room temperature and studied for 24 hours. At 0°C to -8°C, when all of the flies had died in the control group, there were still some alive in the experimental group. For example, at -4°C for 24 hours, 15 of 45 flies survived in the experimental group, while all the Drosophila in the control exhibited no movement upon warming.
Supercooling is a phenomenon in which liquid water is cooled below 0°C, but does not solidify. Although supercooling is naturally unstable, this state can be stably maintained in a laboratory by applying pressure and voltage. Previously, in 2005, another group of Japanese scientists compared cellular damage to organ grafts supercooled to -4°C, at which the metabolism is reduced to one-seventeenth, and cooled to 4°C, at which the metabolism slows to one-tenth of its original function. To compare the viability of the organs they measured the levels of various biochemical markers, such as creatine phosphokinase and aspartate aminotransferase. These enzymes are typically present in minute concentrations in the blood so elevated levels are indicative of damage. Of the heart, liver, and kidney grafts, the most significant reductions in biomarkers in the supercooled samples compared to the induced hypothermia samples were found in the liver and kidney preservation solutions. 1
While progress has been made, research on the effects of magnetic fields has not been uniform. It has been reported that a 0.2 mT magnetic field improved the healing of bone fractures in humans, but there have not been any biomarkers identified to prove a sensitivity to magnetic fields. Although this research is preliminary, it may one day be applied to organs to maximize the viability of preserved organs.2
More recently, in 2012, researchers studied the effects of supercooling on Drosophila, or fruit flies, in a program
References: 1. Monzen K, Hosoda T, Hayashi D et al. The use of a supercooling refrigerator improves the preservation of organ grafts. Biochemical and Biophysical Research Communications. 2005; 337: 534-539. doi:10.1016/j.bbrc.2005.09.082 2. Naito M, Hirai S, Mihara M, Terayama H, Hatayama N et al. Effect of a Magnetic Field on Drosophila under Supercooled Conditions. PLoS ONE. 2012; 7(12): e51902. doi:10.1371/ journal.pone.0051902
Table 1. The survival rate of the Drosophila at 24 hours after the preservation in the supercooled condition with or without the magnetic field (in parentheses).
Q&A WITH D R . P ETER G ERHARDSTEIN Interview by Gavriella Hecht
Dr. Gerhardstein is a professor in the Psychology Department who has amassed ample life experience in the field. He has had opportunities as an undergraduate at Carlton College, both as a researcher and graduate student at the University of Minnesota, a Postdoctoral Fellow at the University of Arizona and in other positions in the world of psychology. Though he has experience dealing with different types of psychology, Dr. Peter Gerhardstein currently focuses specifically on visual perception and memory. He researches perception in children and infants, with his most recent research involving toddlers transferring between 2D and 3D activities.
How long have you been teaching at Binghamton and what classes do you teach?
16 years. I teach perception, a developmental course on infant memory, graduate level statistics, graduate seminars, perception lab, intro [psych] and a few others.
Where did you attend school for your undergraduate degree?
I went to Carlton College. Carlton is in the middle of Minnesota. It’s a very small town and it’s very different from Harpur. The total enrollment was then and is now well under 2000. I was a psychology major and a computer science minor. At that point the psychology department at Carlton was 4 people. I did a senior project that involved brain imaging.
What did you do after you graduated Carlton?
I got a job and spent a year working, and discovered it was pretty boring. I called up my advisors [from Carlton] and said I want to go to grad school. They were pretty frank in saying; “You didn’t really get enough research experience to make you very appealing. So, you should go up to the University BINGHAMTON BIOCHEMISTRY CLUB
of Minnesota and see what is going on there.” I walked into the university about a week before classes started. There was a guy there from SUNY Buffalo who had just moved and was looking for someone to help program experiments. So I became their programmer for a little while. That lab did visual perception in adults. He had what was called a vax computer with him. He literally had more computing power than the school I had been matriculating at as an undergrad. That computer changed the way people did visual perception research. Suddenly we could put an experiment together in 3 or 4 days, instead of 3 or 4 weeks.
How about after grad school?
I went to a post doc in Arizona in a lab that did research into stroke survivors. I spent a couple years there. My then fiancé, and now wife, got a job and needed to move to the East Coast. I applied for some post docs on the East Coast, and I was accepted into the lab of a woman who did developmental research on infant memory. At the time she was looking for someone to do research on slightly older kids using touch screens. She brought me into that lab at Rutgers and I spent 3 years there. Then I got hired at Binghamton in 1997 and I’ve been here since then. I have therefore, background training in adult visual perception and in the development of visual perception and memory. Many people were developing hypotheses about vision that suddenly made a little more sense. It helped the research quite a bit. 7
What were some of the theories?
In the 1920’s and 30’s there was a group called the Gestalt school, which came with the phrase “The whole is greater than the sum of the parts.” That’s actually a mistranslation from the German. The Gestalts school was a group of psychologists who thought about perception and how it might work. They came up with a bunch of organizational rules for perception. They said the visual world is complicated and in order to make sense of it the visual system has to impose some sense on it. One rule was called good continuation, now called collinearity, it said that things that were aligned together will get grouped together. Another was called proximity, which is that things that are close together will get grouped together. It was just a bunch of grouping principles. This misquoted phrase about “The whole is greater than the sum of the parts,” was a suggestion that closure, or the entity of the unit of perceived grouping that comes from that, is somehow more important that individual pieces that came to that. The saying is misquoted in that what they really meant was that this closed region, this figure, which comes out of this, is an emergent property of these rules. This has come in perceptual circles to be known as higher order processing. This is more my line of research.
Who are you showing the Gabor patches to?
In many experiments we have adult observers look at them. There is a very carefully controlled mathematical construct allowing us to control the grayness and brightness of the Gabor patches. In some circles of Gabor patches there was an S contour, which is created by taking the circle, chipping it in half, and moving half of the circle down. In the circles we manipulated angles of the contours. The subjects are shown a first stimulus, then a blank interval, then a second stimulus and asked which they saw the contour in. This tells us how detectable a closed circle is versus an S. Adults show a big advantage when the contour is closed, known as the closure superiority effect. We are now asking the question of when during development kids start to show the close superiority effect. There are levels of disability of levels of injuries toward development. There are also levels of disability during development. This is what we are after. We know adults not only see closure, but that closure conveys an advantage over their perception. We want to know is there a point at which infants or children develop this closure ability and can we relate it to brain development.
A Gabor patch with a circle contour. These and S-shaped contours were shown to subjects to test their visual perception.
What other kinds of research are you doing right now?
One line of research that I’m doing is a set of studies into what is called the video deficit effect. We are looking at how infants and little children stitch together information to be able to see the world. More generally what it is, is a project into researching how very young children preschool and below learn from videos and touch screen. A lot of parents saying their kids are great with a smartphone. However, them playing around with and actually acquiring information from that medium are two very different things. The question is why do kids have so much trouble with transferring across video contexts. One theory says that right around when kids learn language at 18-24 months, the video deficit effect should be done by 36 months but our own research shows that’s not true. We can make the video deficit effect appear much older than that. So, that’s not the right explanation. Somebody else says that the actual video is the issue. Kids know that the people on the TV are not actually speaking to them. We are actually testing that in the lab right now. We set up a closed circuit TV so that we can talk to kids over a closed circuit loop on a big TV and then they learn that way. Then a second kid sees a video of what the first kid saw. They are seeing exactly the same thing that the first kid saw, but it’s not interactive. We don’t know the outcome because we just started it but the suggestion from our data is that this is going to matter a great deal. That it’s not the video aspect; the 3D to 2D per say, it’s the live translation. Again, it looks like there is a point at which a kid will overcome that issue as well.
In what way can your data be applied?
One of the things that these data are certainly useful for is suggestions about how you construct children’s television shows. It is certainly a suggestion about how you would construct children’s interactions within a classroom using this kind of media. The American Academy of Pediatrics in the 90s, issued a recommendation that children under 2 should not watch television at all. Within the last couple years, they reissued and strengthened this recommendation. They said no kid under 2 should be exposed to television at all. They did this initially on the basis of the research by a guy named Dan Anderson at UMass Amherst, who said let’s find out what kids are really doing in front of the TV. He put cameras in these people’s houses and recorded them for weeks on end. What he found was that young kids don’t watch television actively all that much. He then scored their play with siblings and/or peers while in the presence of the television being on versus when it was off. Even though they weren’t actually attending to it, when the television was on the quality of their play degraded significantly. In other words it’s a serious distraction to them.
Q A Q A
What is your position? If I had to do it over I would get rid of all the TVs in my house. I grew up in a house without TV. It doesn’t necessarily damage people, but it turns out that it’s hard to keep kids from watching TV.
Is there any advice you have to offer others interested in researching this topic?
Don’t read the parenting magazines. Parenting magazines are fun. They are running stories about how to build a super baby. Ways to raise your child so that they will develop some kind of super cognitive ability. Then a couple of labs did carefully controlled studies and said nope it doesn’t do anything.
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