Some of the 115 graduate students currently enrolled in our PhD Program
B.S., CHEMISTRY-BIOCHEMISTRY
FORT LEWIS COLLEGE
Single Molecule and Biochemical Investigations of Tn5 Transposase - DNA Interactions
The Tn5
transposon is a prokaryotic transposition system that uses only three
macromolecular components to complete its transposition reaction.
These modules are, 1) the transposase, 2) the 19 base pair recognition
sequences that are recognized by the transposase and, 3) target DNA.
The versatility of the system lies in the fact that any DNA sequence
can be placed between the two recognition sequences, allowing for the
delivery of any genetic material into the genome of an appropriate
organism via the Tn5 system.
In addition to being a useful biotechnological tool, Tn5
provides me with means to study protein-DNA interactions. The
transposase has specific recognition sequences, yet also has a
significant non-specific DNA binding activity. These two modes of
binding allow for a variety of experiments investigating the mechanisms
the transposase uses to interact with DNA.
My work has
focused on studying the protein - DNA interactions of the transposase
using two different experimental systems. Using biochemical and
molecular biological techniques, I have investigated an alternate mode
of binding and dimerization used by the transposase and found that it
may represent a mechanism for inhibition of the transposition
reactions. I am currently studying Tn5 transposition at the
single molecule level in collaboration with a group in Chicago. In
these experiments I use long molecules of DNA tethered to magnetic
beads to study the interactions of the transposase with both
non-specific and specific DNA. It has been exciting to work with two
groups, one in Madison using the tools of biochemistry and molecular
biology to study Tn5, and one in Chicago where I am in the
middle of the development of a new field, the study of protein - DNA
interactions at the single molecule level.
The
Biochemistry Department at the University of Wisconsin at Madison was
an excellent choice for me. The size and scientific diversity of the
department allowed me to completely explore my interests before joining
a lab. The department has a very strong support system for graduate
students so that I felt welcome and at home from the first day I walked
in the building. I have made life-long friends with many of my
classmates.
Madison is a wonderful place to live. The
city is very civic-minded, with active, thoughtful citizens and a
culture that values social awareness, health and intellectual pursuits.
There are numerous activities to be found within the city limits:
running out to Picnic Point, dining out on the Capitol Square or the
East Side, music at the Terrace, hiking in the Arboretum, cross-country
skiing on Lake Mendota, mountain biking at the Quarry... and enjoying the
sunset and beer with friends at the University's Memorial Union Terrace
are just a few of the ways I have enjoyed myself here in Madison. The
city of Madison and the Department of Biochemistry are vibrant and
exciting places to live life and do science.
B.S., MOLECULAR BIOLOGY
PURDUE UNIVERSITY
TACCt at UW-Madison
Transforming
acidic coiled coil (TACC) proteins are conserved in a wide range of
species from yeast to humans. They have been shown to be centrosomal
proteins and involved in mitotic spindle assembly. The mitotic spindle
is an elaborate macromolecular machine devised by the cell to ensure
that the chromosomes are equally segregated during mitosis. Mitotic
spindle assembly is an important step in mitosis and errors in the
spindle can lead to cell cycle arrest, mis-segregation of chromosomes,
and genomic instability, which in turn leads to serious human diseases
including developmental defects and cancer. I am interested in the
role of the Xenopus TACC homolog, maskin, in spindle assembly.
What
first attracted me to the biochemistry department at the University of
Wisconsin-Madison was its excellent reputation and exciting science.
What kept me here was the city of Madison. The city and university are
a perfect complement to each other. The environment has been ideal for
personal and professional growth. I have learned to think in a new way
and how to better approach problems. I have also had the opportunity
to try new activities I never thought I would before, such as
skydiving, caving, and mechanical bullriding. Whatever your choice may
be, I can't recommend the University of Wisconsin-Madison enough. In
addition to the excellent research opportunities the department has to
offer, it also has the bonus of being dangerously close to Babcock
Hall, famous for their ice cream. On summer afternoons, there is a
steady stream of people from the biochemistry building to Babcock for
ice cream!
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B.A., BIOCHEMISTRY
COLLEGE OF WOOSTER
The Effects of Upstream DNA on Open Complex Formation of E. coli RNA Polymerase
Transcription
initiation is a key level of regulating gene expression. Given the
importance of RNA polymerase in prokaryotic gene expression, there is
an intense focus on how RNA polymerase interacts with promoter DNA to
form an "open" DNA-polymerase complex capable of binding NTPs and how
these interactions are regulated. My research examines the contacts
DNA upstream of the -35 hexamer makes with the polymerase exterior and
how these interactions affect the events which control entry and
subsequent unwinding of the DNA start site (+1) in the jaws of
polymerase which contain the catalytic site.
I decided
to attend UW-Madison because of the exciting and challenging research
opportunities and the friendly atmosphere within the department. In
addition to the high quality of research being performed at UW, coming
to Madison has allowed me to pursue other interests such as performing
with the UW Wind Ensemble and the Edgewood Chamber Orchestra.
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B.S., BIOCHEMISTRY
WEST VIRGINIA UNIVERSITY
Substrate Channeling in Glutamine-Dependent Amidotransferases
In
enzymes with multiple active sites, where the product generated from
one site is a substrate for the next, it would seem logical to assume
that the active sites would be clustered closely together in the
protein. This, however, turns out not to always be the case. One
family of enzymes, the glutamine-dependent amidotransferases, utilizes
substrate channeling to avoid diffusion of reactive intermediates.
These enzymes, which catalyze the assimilation of reduced nitrogen into
key biological molecules like nucleotides and amino acids, connect
distant active sites with molecular tunnels through the interior of the
enzyme. The lengths of these molecular tunnels can vary from enzyme to
enzyme. The tunnel used in glutamine phosphoribosylpyrophosphate
amidotransferase is only 20 A in length whereas the tunnel used by
carbamoyl phosphate synthase is considerably longer, at roughly 100 A
in length. My research involves the cloning, over-expression, and
x-ray structural analysis of another member of the enzyme family,
asparagine synthetase B.
As for Madison itself, I love
it here. The city has so many diverse activities to choose from that
you're bound to find someone else who is interested in the same things
you are. Or, for that matter, find a few new things you're interested
in. Since I've been in Madison, I think I can honestly say I've
learned as many "important" lessons outside the classroom as I have in
it. For example, I've learned that, between my bus pass and my bike,
there's really no need for a car in this town. After one weekend when
three friends and I decided to try our skills on a mechanical bull,
I've learned that I will never have a career in the rodeo. And I've
also learned that, while it may seem like a good idea when your friend
asks you in class one morning if you'd like to go skydiving, it seems
like considerably less of a good idea when you are actually crouched in
the doorway of the airplane preparing to jump.
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B.S., BIOCHEMISTRY AND MOLECULAR AND CELLULAR BIOLOGY
THE UNIVERSITY OF ARIZONA
Characterization of the ABCA1 gene and its role in high-density lipoprotein formation and cholesterol metabolism
My
research focuses on ABCA1, a gene recently attributed to high-density
lipoprotein (HDL) deficiency in two diseases, Tangier Disease and
familial hypoalphalipoproteinemia. A patient's HDL level is a strong
indicator of risk for developing premature coronary heart disease
(CHD). CHD is a major cause of death in much of the world, so
understanding the mechanism of ABCA1 action in HDL formation has the
potential to revolutionize CHD treatment and prevention. I am currently
identifying in vitro protein partners that interact with ABCA1, which
may be involved in the proper folding, stabilization, and translocation
of ABCA1.
Choosing a grad school can be a difficult
decision, but UW-Madison Biochemistry made that choice very easy for
me. The sense of community amongst the faculty and graduate students,
along with the exciting research opportunities, creates a comfortable
and stimulating research environment. Because of this, collaborations
within the department are common, and have benefited my research
tremendously. The city of Madison is amazing in itself. I especially
enjoy running and biking along the beautiful lake shore areas. And if
you're like me, you love to eat. Madison's wide range of restaurants
will satisfy even the most daring appetites! From the friendliness of
Madison, to the countless recreational activities, how can you not
choose Madison?
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HON. B.S., CHEMISTRY
UNIVERSITY OF TORONTO
What modulates [2Fe2S] cluster properties?
[2Fe2S] ferredoxins are electron-transfer proteins mediating
one-electron redox process in various biochemical systems. Based on
the physicochemical properties of their [2Fe2S] cluster, these proteins
can be placed into one of three groups: plant-type, vertebrate-type, or
Rieske-type ferredoxins. Because the overall structure of these
proteins is very similar, it is believed that minor variations in the
cluster environment are responsible for the observed differences in
their physicochemical properties. Using a combination of NMR and EPR
spectroscopy as well as theoretical calculations, my research aims to
define these environmental variations between vertebrate- and
plant-type [2Fe2S] ferredoxins.
Having lived all my life in big cities, I was a bit afraid of moving to
a small town like Madison. While I still miss the hustle-bustle of a
large metropolis, I've come to realize that Madison too has a lot to
offer. The Biochemistry Department at UW-Madison has a great graduate
program, providing students with unlimited opportunities for learning
and carrying out research. When one gets tired of working, there are
an infinite number of things to do, my favourites being biking, skiing,
going out to one of Madison's many ethnic restaurants, shopping at the
Farmer's Market, and hanging out at the Memorial Union terrace, just
enjoying a beautiful sunny day. And if I feel like I just can't go on
anymore without walking in the overcrowded streets of an "armpit of
America", as my friend would say, Chicago is only three hours away.
Hence, Madison really does have something to offer for everyone
regardless of what they are looking for -- maybe you should come and
experience it for yourself.
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B.S., CHEMISTRY
UTAH STATE UNIVERSITY
Apoptotis, P49, and Family Life
Apoptosis
is a cell suicide pathway that is highly conserved from worms to humans
and is crucial in development, prevention of cancer, and as an
anti-viral defense. I am interested in the cellular processes involved
in apoptosis, in particular the proteolytic caspase cascade. Using
site-directed mutagenesis, recombinant viruses, in vitro
assays, and other biochemical approaches, I am studying how baculovirus
P49 blocks apoptosis. Understanding how this novel viral protein
inhibits caspases will give unique insight into caspase activation and
regulation.
The faculty and students of the
Biochemistry Department have a wide variety of research interests and
are very congenial and collaborative. I am always impressed with the
high quality of research achieved in the department as well. In
addition to the great research and academic atmosphere, UW-Madison is a
fun place to go to school. Whether playing in the intramural
basketball leagues, watching the Badger football team at Camp Randall
stadium, or enjoying some famous Babcock Dairy ice cream, I've found
plenty to do in addition to research. And if you happen to get hurt
(doing research or something else like playing basketball), the health
care is great and covers anything from knee surgery to having a baby.
Trust me, my wife and I know!
I am married (Adrian) and
have two children (Rebecca and Scott). Madison has been a great place
to raise a family. In addition to the nice people here in Madison,
there are free concerts, a great parks and recreation system, a free
zoo, beautiful lakes, and other wonderful things to see and do in the
outlying country. We love living here in Madison.
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B.S., CHEMISTRY EDUCATION
M.S., CHEMISTRY
SEOUL NATIONAL UNIVERSITY, KOREA
Structure determination of calmodulin-related proteins in Arabidopsis thaliana by x-ray crystallography
Calmodulin
is one of the representative calcium sensors in plants and animals. In
plants, there are more than ten calmodulin isoforms, putative
calmodulins and calcium dependent protein kinases with a
calmodulin-like domain. There are only a couple of calmodulins in
animals. My research project is to determine the three dimensional
structures of the proteins which contain a calmodulin-like domain by
X-ray crystallography to elucidate the diverse calcium signal
transduction mechanism in plants. Structural biology in the Department
of Biochemistry at UW-Madison is getting stronger thanks to the Center
for Eukaryotic Structural Genomics (CESG) and the National Magnetic
Resonance Facility at Madison (NMRFAM).
I started
horseback riding through the UW Hoofers Program two years ago. I never
rode a horse before I came to Madison. I go to the Hoofers Equestrian
Center once a week to enjoy this pleasant outdoor activity. Madison is
such a wonderful place for other outdoor activities, such as running,
hiking, sailing, and biking. Since my arrival in Madison in the fall of
2001, now I consider Madison as my second hometown. I feel as
comfortable as I do in my original hometown, the Chiak Mountain in
Korea.
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B.S., CHEMISTRY
UNIVERSITY OF LOUISVILLE
Equity and Enzymology, who could ask for anything more?
Understanding
the biochemical reactions, which when summed, yield a living organism
is certainly an exciting way to spend one's life. Harnessing this
personal drive to make scientific progress, through clear thinking,
sound laboratory practice and elegant experimental design, is what
graduate school should be about. The focus placed on the formation of
quality scientists in our department ranks very high among my reasons
for choosing Biochemistry at UW-Madison. We are a department as
committed to producing future colleagues as we are to contributing
ground-breaking discoveries.
Scientifically, I am
interested in the mechanism by which proteins bind DNA
non-specifically. The enzymes catalyzing recombinational DNA repair
rely on this class of interaction, as DNA damage is not restricted to
specific DNA sequences. In the Cox Lab, we study recombinational DNA
repair in both Escherichia coli and Deinococcus radiodurans.
In these bacterial organisms, repair of damaged DNA is largely
dependent upon the RecA protein to catalyze recombination events. My
project centers around the recombination mediator proteins RecFOR,
which direct the binding of RecA to single-stranded DNA under certain
conditions.
My project has been difficult, but
extremely rewarding. It draws widely upon my background knowledge in
fields as disparate as mathematical topology and biophysical chemistry.
My training is concentrated on learning to synthesize new theories from
what is already known. This is the central skill of the scientist, and
I am proud of how I've developed professionally at UW.
Madison
has been a great place to grow personally as well. While here, I've
been able to maintain many hobbies, while accruing sailing and home
improvement skills (our first home!). My wife enjoys the area very much
as well and is steadily advancing her teaching career. We've found
Madison to be a very hospitable, diverse, and safe community. The fine
arts are well-represented and the free Vilas Zoo and Olbrich Botanical
Gardens certainly provide for the cultural development of young people
like ourselves.
The UW is outstanding among
Universities; Madison is likewise notable among cities. Working,
living, and learning here have been opportunities I will always
cherish. I encourage anyone thinking of doing his or her Ph.D. to apply
to UW-Madison without reservation.
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B.S., CHEMISTRY
B.S., CROP SCIENCE
UNIVERSITY OF ILLINOIS, URBANA-CHAMPAIGN
Developing Reagents for Small Molecule Target Identification
I
work to develop methods for discovering the binding partners for
biologically active small molecules. We hope to utilize these methods
to identify the protein targets of hits from cellular high-through-put
screens of small molecule libraries made in our lab. Identifying the
molecular mechanism of action of small molecules, such as drugs, offers
a wealth of useful information for determining the biological functions
of proteins and for understanding drug side effects.
The
Biochemistry Department at Madison is terrific. The quality of
individuals here is unparalleled. The focus here is science and fun,
not pretension. The collaborative and supportive atmosphere in this
department is refreshing and invigorating. After 3 years, I'm still
pleased with my decision to come here.
I think Madison
is a great place to live. My apartment is just a short 5-10 minute
walk to work. I also maintain a garden plot in the community gardens on
picnic point near campus. Wisconsin is a beautiful state. The scenery
here is just gorgeous! Madison is surrounded by 3 lakes, which are
great for sailing and ice fishing. There are even beaches here. We
have it all! If you ever have the chance to visit, I wouldn't pass it
up!
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B.S., CHEMISTRY
B.S., BIOLOGY
BUTLER UNIVERSITY
What is the mechanism by which synaptotagmin regulates neurosecretion?
The
release of neurotransmitters from neurons and hormones from
neuroendocrine cells occurs through exocytosis of secretory vesicles.
This transmission takes place on a millisecond time scale and relies on
calcium-triggered fusion of secretory vesicles with the plasma
membrane. The mechanism for calcium-triggered fusion remains unclear.
Current findings suggest that synaptotagmin proteins are the molecular
means by which calcium regulates membrane fusion. My research focuses
on determining the functional role of synaptotagmin in exocytosis and
investigating the biochemical properties responsible for its mechanism
of regulation.
I continue to be thankful that I decided
to come to the UW-Madison Biochemistry Department for graduate school.
The high level of research conducted here is made possible by the
supportive environment fostered by other students and professors.
Besides a wonderful biochemistry department, Madison and the University
of Wisconsin have a lot to offer. I am not only able to pursue my
interests in Biochemistry, but also my interests outside of science. At
different points throughout my time here, I have been able to take
advantage of the multiple opportunities that are available. Through
such things as playing on a Biochemistry softball team, getting
involved in Intervarsity Graduate Christian Fellowship, playing
intramural soccer, assistant coaching a high school girls cross-country
and track team, attending UW home football games with other
Biochemistry students, snowboarding with friends and enjoying the
lively environment of Madison, I continue to grow here as a
well-rounded person and scientist.
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B.S,, BIOCHEMISTRY
UNIVERSITY OF ILLINOIS, URBANA-CHAMPAIGN
Regulation of germline development in the nematode Caenorhabditis elegans
Our
lab studies the regulation of animal development at the molecular
level. We are interested in controls of cell fate and patterning
within multi-cellular tissues. The model organism C. elegans
enables the identification and analysis of developmental regulators
that are used throughout the animal kingdom. My project focuses on how
germline stem cells are controlled by the GLP-1 (Notch) signaling
pathway. I have taken a multi-faceted approach to identify
genes that act downstream of GLP-1 in germline development. I use a
combination of biochemical, genetic, and molecular biological
techniques to elucidate the role and regulation of candidate genes.
Madison
is a fantastic place to be a graduate student. Madison offers the
perfect balance -- a strong academic community and multiple
opportunities to enjoy life outside of lab. The physical space of our
departmental building is open to encourage collaboration and facilitate
idea sharing. Furthermore, all of the labs on campus that use C. elegans
as a model for their studies meet bi-weekly to discuss our current work
and exchange technical advice. In addition, Madison offers many fun
things to do. The lakes provide a peaceful space to relax, and there
are many bike and hiking trails to enjoy around town. To release
stress, I play indoor and outdoor soccer. I also enjoy going to
concerts and plays at the Madison Civic Center and attending Big Ten
sporting events. So far, my four years in Madison have been great.
It's going to be hard to move on to the next challenges wherever I
continue my studies.
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B.S., CHEMISTRY
BUTLER UNIVERSITY
RXR transactivation and p160 family coactivator regulation in 1,25(OH)2D3 mediated transcription
Vitamin
D, discovered here at UW-Madison, is vital for many processes in the
body. The active hormonal form of Vitamin D, 1α,25dihydroxy vitamin D3 (1,25D3), acts via the Vitamin D Receptor (VDR). VDR, when bound with 1,25D3,
heterodimerizes with and transactivates the retinoid X receptor or
RXR. These proteins bind to DNA through specific vitamin D response
elements in promoter regions of target genes. To further facilitate
transcription initiation, coactivator proteins are recruited. These
coactivators, such as SRC/p160 family and CBP, attach VDR/RXR to the
basal transcription machinery and RNA polymerase II. Target genes of
vitamin D are very diverse and are found in many tissue and cell
types. Specifically, our lab and my research are focused on the
actions of 1,25D3 in two of the major target tissues, bone
and intestine. Through these tissues, serum calcium can be tightly
regulated by calcium channels and bone mineralization. I work to
further elucidate mechanisms by which RXR is being transactivated and
the recruitment of coactivator proteins integral to these processes.
Choosing a graduate program in Biochemistry can be difficult. My
decision was made very easy with one visit to the city of Madison and
the campus here at the University of Wisconsin. The prestige, national
merit, leading professors, and rich history are a few things that make
this department the best in the nation. Interdepartmental
collaboration with other highly ranked departments here allows for
extensive research possibilities.
In life beyond lab, the campus and city are alive with activity and
culture. The lakes allow for sailing in the summer and hockey and ice
fishing in the winter. There are great winding country roads to bike
on, trails for mountain biking and hiking, state parks for camping, and
hills for skiing or snowboarding. UW-Madison teams are all nationally
ranked and students, yes even graduate students, can easily get tickets
for any major sport. For the fine arts, Madison recently completed a
new Overture Center which will house the Madison Chamber Orchestra and
include a theatre for traveling Broadway plays. With all this and
more, it is no wonder that people never want to leave Madison, WI.
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B.S., BIOCHEMISTRY, RUTGERS UNIVERSITY
M.S., MICROBIOLOGY, SETON HALL UNIVERSITY
The biological role of the cardiovirus leader protein
I
am interested in the molecular biology of picornaviruses, specifically
how virally encoded proteins direct host machinery to efficient
synthesis of progeny viruses. My research is focused on characterizing
the function of the leader protein encoded by the cardiovirus group of
picornaviruses. Previous work has shown that this novel protein is
phosphorylated and may interact with the internal ribosomal entry site
(IRES) in the cardioviral genomic RNA. I am using molecular biology
techniques, biochemical assays, and immunological methods to elucidate
the role of this protein in cardiovirus infection.
UW-Madison
provides me with a first-class environment to pursue graduate study and
my research interests. The Biochemistry graduate curriculum has
rounded out my training in biochemistry fundamentals while allowing me
to choose specific coursework to compliment my research interests. In
addition to a dynamic Biochemistry Department, the University is home
to the Institute for Molecular Virology - a thriving, interdepartmental
community of virology students and faculty who are an asset to my
research training.
Madison is a fun city to live in.
When I'm not in the lab, I enjoy canoeing the lakes and rivers in and
around Madison or bicycling the miles of scenic bike paths. I've also
visited a few of Madison's many live music venues that cater to a wide
variety of musical tastes. Overall, I believe UW-Madison has unique
qualities that would be difficult to find in another graduate school.
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B.S., CHEMISTRY
UNIVERSITY OF MICHIGAN - ANN ARBOR
Structural investigation of U2 and U6 spliceosomal RNAs using nuclear magnetic resonance
The
spliceosome is a multi-megaDalton ribonucleoprotein machine that
catalyzes the removal of introns from nuclear precursor-messenger RNA.
My research focuses on an RNA complex that forms between U2 and U6
small nuclear RNAs in the active form of the spliceosome. The U2-U6
complex has been implicated in splicing catalysis, leading to the
hypothesis that, like the ribosome, the spliceosome is a ribozyme.
Currently, I am using NMR to solve the three-dimensional structure of
the U2-U6 complex. The Biochemistry Department at UW-Madison is an
excellent place to learn about and use NMR. Our NMR facility (NMRFAM)
houses several state-of-the-art spectrometers, and several exceptional
(and helpful) NMR experts.
In general, this department
is an excellent place to be a graduate student. The diversity of
science and collaborative atmosphere in the department and the
university allows students to expand their fields of research and
become well-rounded scientists. Furthermore, the city of Madison is a
great place to live. The isthmus is beautiful, and both the university
and the capital guarantee that something exciting is always happening.
It's a small city with the feel and culture of a big city. Living
downtown, I enjoy walking down State St. everyday, eating at the wide
variety of restaurants in the area, and hanging out at the lakes with
friends.
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B. S., BIOCHEMISTRY
UNIVERSITY OF NEBRASKA-LINCOLN
Discovery, design, and application of ribonuclease inhibitors
Intact
RNA and DNA are of central importance to biochemical research and
biotechnology. The preservation of these nucleic acids requires the
absence of nuclease activity. Ribonucleases are perhaps the most
problematic of nucleases because of their high natural abundance,
prodigious catalytic activity, notorious conformational stability and
resistance to proteolysis, and lack of requisite cofactors. In one of
many diverse research projects in the Raines laboratory, we are working
on the discovery and development of potent new ribonuclease
inhibitors. We study the biophysics and biochemistry of the
inhibitors, as well as their biotechnological applications.
Ribonuclease inhibitors may also have utility in vivo. Several
human ribonucleases are involved in disease, including angiogenin, a
ribonuclease that is involved in the growth of new blood vessels in
tumors.
The University of Wisconsin-Madison
Biochemistry Department is an excellent choice for graduate school.
The department is relatively laid back and we have a good deal of
freedom to develop new research projects. There are lots of high
quality and groundbreaking research projects here, but despite that,
the environment is not overly competitive. Whether you are interested
in teaching and/or research in academia or working in industry, there
are programs and funding to help build your career. For example, I am
doing an internship at Invitrogen as part of the Biotechnology Training
Program. I hope to start my own biotechnology company some day.
Madison
is a great city. My wife and I bought a house (something that would
not be possible on the East or West coast) and we enjoy gardening,
entertaining, and the many other joys of home ownership. There are
great college sports teams here and lots of intramural sports and
activities to get involved in during all four seasons. There are
excellent restaurants and bars near and even on campus. After work, it
is really fun to hang out with friends and drink a beer on the Memorial
Union Terrace overlooking Lake Mendota.
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Our alumni share their memories of our PhD program and Madison
Translational control and kick saves
I study a conserved family of 3'UTR RNA binding proteins that are
implicated in translational regulation during the development of
eukaryotic germlines. These proteins are found in a wide assortment of
organisms, ranging from yeast to plants to humans. I use C. elegans to
study the binding requirements, protein-protein interactions, and
biological significance of 3'UTR-mediated regulation.
I chose this department because of the collaborative environment and
quality of campus resources. The number of meetings and seminars is
impressive. I regularly attend group and subgroup meetings for two
labs, a campus wide yeast club meeting, and a campus wide "big worm"
meeting, in addition to seminars given by visiting investigators.
Madison is a nice place to live during your graduate career. There are
a wide variety of activities and events, both within and outside the
university. My athletic activity has blossomed here, and I now play
ultimate Frisbee and ice hockey (goalie, in fact!).
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Aimee Eggler
(PhD 2002, Mike Cox Lab)
POSTDOCRORAL RESEARCH ASSOCIATE
UNIVERSITY OF ILLINOIS - CHICAGO
DEPARTMENT OF MEDICINAL CHEMISTRY & PHARMACOGNOSY
PI: ANDREW MESECAR
How is a nucleoprotein filament formed in homologous recombination?
Homologous
recombination is a vital process in all organisms as it is required for
the repair of replication forks stalled at DNA lesions. It is also
responsible for the creation of genetic diversity in eukaryotes. In
homologous recombination, a single-stranded section of DNA is coated
with a recombinase protein. This nucleoprotein filament then searches
for homologous double-stranded DNA with which to pair. The single
strand within the filament is subsequently paired with its
complementary strand in the duplex, allowing DNA repair to proceed. I
am interested in how this filament forms. The recombinase, known in S. cerevisiae
as Rad51, must first displace the single-stranded DNA binding protein
RPA, which readily binds to single-stranded DNA as it is formed in the
nucleus. A mediator protein, Rad52, aids in Rad51 binding, and I am
investigating how Rad52 does this. I use mutagenic studies and in vitro
assays to monitor both the binding of proteins to DNA and the proteins'
ability to promote exchange of DNA strands.
The
UW-Madison Biochemistry Department was an excellent choice for my
graduate education. The high level of research conducted here is
facilitated by a supportive environment in which questioning and
learning are encouraged. Having arrived with a degree in chemistry,
this environment helped me to successfully learn the language of
molecular biology.
The city of Madison offers a wide range of activities. For example, I
play Ultimate frisbee on a local team and tutor Tibetan refugee
children at a weekly after school program. Both activities are within a
few minutes' biking distance from the Biochemistry building. Music is
another passion of mine, and Madison attracts many well-known musical
artists who play at the student union or on other local stages. Three
other biological scientists and I enjoy participating in the local
music scene with our band, u-pump.
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Marcia (Hebert) Haigis
(PhD 2002, Ron Raines Lab)
POSTDOCTORAL FELLOW
MIT
DEPARTMENT OF BIOLOGY
PI: LEONARD GUARENTE
Exploring and exploiting the interactions between ribonuclease A and ribonuclease inhibitor
I
am interested in understanding the biological roles of ribonuclease A
and ribonuclease inhibitor. To study this problem, we are currently
creating knockout mice, which are missing the gene for either
ribonuclease A or ribonuclease inhibitor. Once these model animals have
been created and characterized, we will be able to further explore the
relationship between the structure of these proteins with their
biological function(s).
The Biochemistry Department is
a great learning environment. The opportunity to interact with other
scientists has enhanced my research experience. Also, Madison has nice
lakes, the farmer's market, and the Terrace.
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Allison Lamanna
(PhD 2004, Laura Kiessling Lab)
POSTDOCTORAL FELLOW
LIFE SCIENCES INSTITUTE
PI: ROWENA MATTHEWS
The effects of multivalency and ligand architecture on N-formyl peptide receptor-mediated neutrophil chemotaxis
As
an undergraduate, I became interested in studying protein-protein
interactions, especially cell surface receptors, and their biological
implications. The Biochemistry Department at the University of
Wisconsin-Madison gave me the opportunity to explore many aspects of
this general topic, from specific structural projects to biological
studies with relevant medical implications. My current research focuses
on the N-formyl peptide receptor, a G-protein coupled receptor involved
in human neutrophil chemotaxis, and the ways in which multivalent
arrays of ligands can influence the responses of this pathway.
The department offers an unparalleled collaborative and congenial
research environment, between both professors and students, in which
students can get the most out of their graduate studies. The
interactions with my peers, within and outside of the lab, are a large
part of what attracted me to the department. I know this excellent
program will make me a better scientist and allow me to enjoy the
process.
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RESEARCH ASSOCIATE
BIOCHEMISTRY DEPARTMENT, UW-MADISON
PI: MIKE COX
RecA structure/function studies
The RecA protein is a DNA-dependent ATPase and is a central component
in the processes of homologous genetic recombination and
recombinational DNA repair. I am interested in the structural basis of
this protein's complex function. Currently, I am testing the
biochemical effects of mutations in particular regions of RecA.
The Biochemistry Department at UW-Madison is an excellent place to
conduct research. The collaborative effort among labs and the
incredible diversity of science here have enriched my experience. Best
of all, the city of Madison is a great place for my husband and I to
raise our three children while I pursue a graduate degree. The school
districts in the Madison area have high academic standards, caring
staffs, and superb extracurricular activities such as organized sports,
band, and drama. Additionally, Madison is also a safe and affordable
place to live. In fact, we bought a house after only one year. All in
all, our move to Madison and my experience with graduate school has
been a positive influence in my life, and in the lives of my family.
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Terry Meehan
(PhD 2003, Hector DeLuca Lab)
POST-DOCTORAL RESEARCHER
THE SCRIPPS RESEARCH INSTITUTE
DEPARTMENT OF IMMUNOLOGY
PI: WENDY HAVRAN
Suppression of EAE, a mouse model of multiple sclerosis, by the active metabolite of vitamin D
In
the late 1960's, the lab of Hector Deluca discovered the active
metabolite of vitamin D, 1a, 25 dihydroxyvitamin D3 (1,25 D3). Thirty
years later, his lab is still investigating the various roles this
important molecule has on mammalian systems. My interest lies in the
ability of 1,25 D3 to act as an immunosuppressant in the Experimental
Autoimmune Encephalomyelitis mouse model. In this disease model, the
mouse's immune system mistakenly identifies components of its central
nervous system as foreign, and initiates an inflammation attack which
leads to paralysis. A mouse given a sufficient amount of 1,25 D3
through diet will be protected from developing the disease. My research
is involved in trying to pinpoint where and when 1,25 D3 exerts its
immunosuppressive effect. Because this model is considered relevant to
what happens in the human disease Multiple Sclerosis, this research
could lead to insights on how to treat patients inflicted with this
disease.
Being from New England, I never thought I
would live in the Midwest. However, my former employer in Boston,
himself a PhD graduate from this department, convinced me to check out
Madison. On my visit here, I was very impressed with the quality of the
department, the friendliness of the people in Madison, the array of
extracurricular activities both in
and outside the city, and the fine German cuisine (i.e., beer). Two
years later, I am still pleased with my choice to come here.
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Kevin Mitchell
(PhD 2002, Brian Fox Lab)
TEACHING BIOLOGY AND MICROBIOLOGY
AT COMMUNITY COLLEGES
SAN FRANCISCO, CALIFORNIA
Uncovering structure/function relationships in the diiron enzyme toluene-4-monooxygenase
Toluene
4-monoooxyegnase (T4MO) is a multi-component enzyme complex that
catalyzes the hydroxylation of toluene with a high degree of
regioselectivity; p-cresol constitutes 97% of the product. Through
site-directed and random mutagenesis, we are identifying key residues
responsible for mediating this selectivity. Furthermore, through random
mutagenesis in conjunction with the development of a selection
strategy, we are attempting to redefine the regioselectivity of T4MO
and convert it from a ring hydroxylase to a benzylic hydroxylase. We
are using these same protein engineering principles to identify the
regions in the T4MO regulatory protein that are critical for its
interactions with the hydroxylase and confer specificity within the
diiron monooxygenase families.
The University of
Wisconsin is a fantastic place to go to graduate school. The science is
exciting and challenging, and is carried out in an open atmosphere that
invites collaborations and interactions with other researchers.
Furthermore, Madison itself is an outstanding place to live. In the
city and surrounding area, there are great recreational opportunities
year-round, such as mountain biking, rock climbing, kayaking/canoing,
and cross-country skiing. You can even see great blues shows in town or
Shakespeare in the woods.
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Sam Nadler
(PhD 2001, Alan Attie Lab)
RESIDENT IN INTERNAL MEDICINE
UNIVERSITY OF WASHINGTON-SEATTLE
The molecular determinants of obesity and type 2 diabetes mellitus
My
research interests have focused on the molecular determinants of
insulin resistance and type 2 diabetes mellitus. Using oligonucleotide
microarray technology, I have been involved in discovering the changes
in gene expression in adipose tissue from mice at various stages of
this disease. These experiments have indicated that there is a shift in
the burden of energy metabolism away from adipocytes in obesity and
diabetes. This research project has provided the opportunity to work
with a model of human disease at the molecular, cellular, and whole
animal level.
Madison is a wonderful place for
graduate school. The faculty in the biochemistry department are very
supportive, and the diversity and quality of research programs within
the department is extraordinary. The new biochemistry building is a
great place to do research. At the end of the day, there is a lot to do
around town. I have learned to kayak with the UW Hoofers club, play
softball with the championship biochemistry team, and participate in a
recreational soccer league in town.
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Michelle (Soltero) Higgin
(PhD 2004, Laura Kiessling Lab)
IRTA FELLOW
NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES
RESEARCH TRIANGLE PARK, NC
PI: PERRY BLACKSHEAR
Characterization and mechanistic analysis of UDP-Galactopyranose mutase from Klebsiella pneumoniae
I
have long been interested in understanding, at a chemical level, how
enzymes can perform such a diverse set of reactions. The UW-Madison
Biochemistry Department has certainly provided me with ample
opportunities to explore my particular interest. The focus of my
research is to understand how the enzyme, UDP-galactopyranose mutase,
performs a novel sugar ring expansion/contraction utilizing the redox
cofactor, flavin adenine dinucleotide (FAD).
UW-Madison is an ideal environment to pursue graduate studies.
Collaborations with any of the other excellent departments are abundant
and easy to acquire. Facilities such as the Biotech Center and
Biophysics Instrument Facility (BIF) allow you to use multiple
techniques to strengthen your research.
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