Biology and Biochemistry
2016-2017 Research Projects
The Bio
Bunch
Basta Lab Research
Projects
Combatting antibiotic resistance
• Problem: Antibiotic resistance is an emerging global public health
concern. Deaths attributable to AMR are expected to surpass other major
causes of death by 2050.
12
Deaths, in millions
10
8
6
4
2
Major causes of death
worldwide
2050
2015
Identify
essential
protein
Learn as
much as
you can
about
what it
does
Develop
drug to
inhibit
protein
Kill
bacterium
0
Virtually all bacteria possess a
peptidoglycan layer that is essential for
their growth and viability.
Basta Lab Research
Projects
Combatting antibiotic resistance
Project 1: Investigating new drug targets in mycobacterium species.
L,D-transpeptidases
PG biosynthesis
amino acid racemases
NCDAA incorporation
Identify
essential
protein
Learn as much
as you can
about what it
does
L,D-transpeptidases
there are five E. coli
L,D-transpeptidases
Develop drug
to inhibit
protein
Kill bacterium
Project 2: Understanding why some bacteria, like E. coli, modify their peptidoglycan.
e risk of biological warfare on the rise, strategies are needed to combat emerging biologic
The development of new antimicrobials can contribute to warfighter protection.
Basta Lab Research
Projects
Combatting biological weapons
of mass destruction
• Problem: Biological agents like conotoxins have the potential to be used
as weapons, and measures to counter exposure to aerosolized toxins
need to be investigated.
• Hypothesis: We can use synthetic biology to engineer bacteria to
counter aerosolized toxins.
determine
response of
microbiome to
conotoxins
engineer
respiratory
microbiome to
counter toxins
enhance
warfighter
protection
without
cumbersome PPE
These studies will be conducted in collaboration with Dr. Sarah Glaven at NRL. We are
working to 1) establish an iGEM team at USNA, and 2) prepare midshipmen for a summer
internship at NRL.
HIV Research in the O’Carroll lab
- HIV continues to affect millions of people
worldwide.
- There is no vaccine and emerging resistance
to current treatments necessitates the search
for novel therapeutics.
Integrated virus
- HIV is a retrovirus – it has an
RNA genome that is reverse
transcribed to DNA, which is then
integrated in the chromosome of
the infected cell.
RT
RT
Human chromosome
HIV needs to escape unspliced from the nucleus
Integrated viral genome
Human chromosome HIV replicates in the nucleus, but it
needs to export its unspliced RNA
genome to the cytoplasm to be
packaged into new virus particles.
✔
Spliced mRNA
Unspliced mRNA
HIV has evolved to produce the
protein Rev, which specifically
recognizes the Rev-response element
(RRE) and mediates the export of the
unspliced HIV genome.
RRE
*
Rev
✔
Packaging
Translation
The RRE is a perfect drug target
because it is essential for HIV
replication.
We will be performing structurefunction studies to learn the
mechanistic details of Rev-RRE
interactions.
How can YOU help?
- We will employ various biochemical,
biological, and biophysical approaches.
- We work with non-infectious forms of the
virus to understand its biochemistry.
Students will:
- Learn to purify RNA and proteins
- Study RNA-protein interactions using
fluorescently labeled RNA.
- Prepare RNA-protein complexes for
structural studies.
- Use molecular biology techniques to
construct plasmids that carry various
mutations.
- Use cell culture to assess function
- Learn to analyze and interpret data and
prepare presentations.
Sweet Lab: Isolation and study of extremophiles
image credit: Charles Sweet
http://usnapsp.blogspot.com/2012/04/bromex-2012-wrap-up.html
Nghiem, S.V., et al., Proc. Bionature 2013
Sweet, et al., Mar. Drugs 2015, 13 (8), 4701-4720
Sweet Lab: Bioprospecting for algal biofuel feedstocks
Estuarine algae isolated
from the Severn in winter
(cold-tolerant algae may
have beneficial fuel oils)
Image credit: Charles Sweet
Sam Brad,
Bowman Scholar ‘16
Brynn Umbach,
Trident Scholar ‘14
Next-gen processing
and distillation (Bio-SPK)
of drop-in biodistillate
for boats and jets
Image credit: Solix Biosystems
Image credit: USNA PAO
(U.S. Navy photo by Mass
Communication Specialist 2nd Class
Josue L. Escobosa/Released).
Gypsy moths, their virus, and red
oak leaves
Research in the Rehill Lab AY 2017
Gypsy Moth-Red Oak Projects
1. Isolation and Identification of Red Oak Tannins (in
conjunction w/ Dr. Dillner) {liquid chromatography, mass
spectroscopy and NMR spectroscopy}
Previously: Jacob Cole (Research Award Winner 2012),
Josh Kotler, Ian Eisenhauer, Awad Mohamed
2. Feeding Studies: How do gypsy moth caterpillars respond
to various tannins in their diets?
{raising and handling caterpillars, statistical analysis of
growth and development, dissection of caterpillars}
Previously: Amanda Lau, Andrew Almonte
Also…
• Feeding Studies: How do leaf defenses vary within
the canopy of forest trees as well as among trees at
different stages of development (seedling, sapling,
canopy size tree) {raising and handling caterpillars,
diet preparation, statistical analysis of growth and
development , leaf collection?}
• Previously: Harold Hickey (Research Award Winner
2013), Jenn Underhill
Schlessman lab research projects
.
Research Focus: Protein structure-function studies, primarily
using x-ray crystallography
Primary project: Structural studies of Staphylococcal nuclease
(SNase) variants
Determine protein X-ray crystal structures to identify molecular
determinants of protein electrostatics behavior and support protein
engineering projects
Techniques: grow protein crystals, collect X-ray diffraction data, & use
computer software to determine & analyze protein structures
Collaborative project with The Johns Hopkins University
Department of Biophysics
crystal
diffraction image
electron density map
Harms, Schlessman, Sue, and García-Moreno, PNAS(USA), 2011.
crystallographic
model
Why should we care about protein electrostatics?
Classical view of proteins:
nonpolar inside, polar/ionizable groups outside
Fundamental biochemical processes require electrostatic charge formation, movement or removal: catalysis,
H+ transport, e- transfer, ligand binding, & more
Current algorithms fail to reproduce pKa values for
internal ionizable groups based on atomic coordinates
SNase structural and spectroscopic studies have
identified numerous response modes to internal
ionizable groups (K, E, D, R, H, S, T, Y):
o local unfolding
o water penetration
o internal ion-pair formation
o domain-swapping
T62R
V66R
Schlessman et al., in preparation
Long-term goals: a more accurate dielectric constant for protein
interiors, more robust algorithms for proteins electrostatics
simulations, & ability to engineer & control useful artificial proteins
Applications of Protein Electrostatics Studies
Protein engineering studies include:
K36
o design & creation of internal ion-pairs and
water-binding sites to distinguish between
high-strength hydrogen bonds & Coulomb
interactions in the protein interior & as
model to build an enzyme active site
o creation & removal protein cavities to
probe the effects on protein stability
o "switches" that trigger protein unfolding
(useful in drug delivery) or dimerization
(potential model for neurodegenerative
disease initiation)
What could you engineer?
CAVEAT: Is SNase unique?
E23
E23 / K36
Robinson, Castaňeda, Schlessman
& GarcÍa-Moreno, PNAS 2014
Recent students: Logan Oliver ‘15, Nick Olson ‘15, Aaron Yallowitz ’15;
with Asst. Prof. Isaac: Andrew Marthy ’12, Colin Kelly ‘12, Joe Gehrz,’11, Joe
Georgeson ’10; with Assoc. Prof. Shirley Lin: Pat Wiedorn ’11
Associate Professor Daniel Morse
Biological roles and regulation of A to I RNA editing
Adenosine Deaminases that Act on
RNA (ADARs) catalyze hydrolytic
deamination of adenosines within
double-stranded RNA
Adenosine (A)
Inosine (I)
A to I conversion changes
the sequence and the
structure of RNA.
Codon Changes Increase
Protein Diversity
Regulation of Translation,
Localization, and Stability
Regulation of
Translation
Regulation of
Splicing
The biological consequences
depend on the type of RNA
and where editing occurs
within the RNA.
Figure shows possible
consequences of mRNA editing.
In vitro selection of structure-switching RNA aptamers that can
be used as very sensitive and specific molecular probes
complex
structure
fluorophore
No ligand, fluorescence
is quenched
fluorophore
Fluorophore moves away
from quencher,
fluorescence increases
The figure shows how a structure-switching aptamer works.
Current efforts are focused on selecting aptamers that can detect inosine.
This will provide a tool for studying ADAR function and regulation.
Smith Lab Research Projects
How do small molecules and nanoparticles interact with
biological membranes?
We use a range of methods to
answer this question, including
fluorescence spectroscopy,
electron paramagnetic resonance
(EPR) spectroscopy,
microbiological growth studies,
mutagenesis assays, and
differential scanning calorimetry.
Josh Sohn making
liposomes.
Liposomes derived
from specific tissues or
prepared from purified
lipids are used to model
lipid bilayers of cells.
Students currently working on this :
Brandon Foster, Mitch Larios, Ashley Paek
How does the structure of a bifunctional metalloprotein
change as switches between roles?
high
Cytoplasmic aconitase
Iron-responsive element
binding protein-1
High intracellular [Fe2+ ]
Low intracellular [Fe2+ ]
We use spectroscopic and biochemical techniques to analyze
the structural changes that occur as the protein transitions
between its two functional states.
On Smith and Frank Byrd are currently working on this project.
What are the biochemical changes that occur in a
deciduous leaf over the course of a season?
Gingko biloba
– a “living fossil”
There are changes to :
- anti-oxidant levels
- pigments, including
chlorophyll, carotenoids
- metal ions (Mg2+, Fe2+
Mo2+ , Cu2+ )
- total nitrogen
- presence of photosynthetic
proteins
- total RNA (inc. mRNA)
levels
- and more
Abbie Sigman (‘12)
developed an anti-oxidant
assay based on the
oscillating reaction from
Integrated Lab 3.
We use a variety of spectroscopic, chemical, and biochemical
techniques to analyze the leaf samples.
There are no students currently working on this project.
The Biochemistry Concentration
• Requirements:
– Complete all requirements for the chemistry
major
– Take SC336
– Take two semesters of biology (SB251 and
higher)
– And perform either
• One year of biochemically-related
independent research (SC495/496)
• OR
• One semester of research or Capstone and
one biochemically-themed elective
What will qualify as biochemically-related research?
– Uses biochemical methods or materials
(e.g. materials science studies of silk,
cellulose)
– Has application to a biological or biochemical
problem
(e.g. environmental chemistry, medicinal
chemistry, natural products chemistry)
– Uses chemical or computational methods to
study a biomolecule
(e.g. X-ray crystallography, computational
studies of fluorinated peptides, biofuels)
– Others? – come talk to us!