faculty list of projects - UMass Amherst · Molecular genetics/mycology of plant pathogenic fungi...
Transcript of faculty list of projects - UMass Amherst · Molecular genetics/mycology of plant pathogenic fungi...
PROJECT 1
Faculty name
Li‐Jun Ma
Faculty lab website (if available)
http://www.umass.edu/comparativegenomics/index.html
Name of person to directly oversee apprentice
Li‐Jun Ma
Position of person overseeing apprentice
Faculty
Title of project
Understanding genome variation using next‐gen sequencing
Description of project
Members of the F. oxysporum species complex exhibit extraordinary genetic plasticity
and cause some of the most destructive and intractable diseases across a diverse
spectrum of hosts, including many economically important crops such as banana, cotton,
canola, melons, and tomato. This USDA funded research project employs the next
generation sequencing technology to study the sequence variations among a group of
selected genomes.
Qualifications of student
Highly motivated students with some computational background
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
Honors thesis project
independent study credit
Could this project be extended into an honors thesis?
yes
PROJECT 2
Faculty name
Geunhwa Jung
Faculty lab website (if available)
http://www.umass.edu/turfpathology/
Name of person to directly oversee apprentice
Geunhwa Jung
Position of person overseeing apprentice
Faculty
Title of project
Molecular genetics/mycology of plant pathogenic fungi
Description of project
The turf pathology lab is looking for a motivated independent research student interested
in mycology and plant pathology to work on projects involving microbiology, molecular
genetics, and bioinformatics of the plant pathogen Sclerotinia homoeocarpa. The student
would be required to perform the following duties: DNA extraction, PCR, sequencing, gel
electrophoresis, culturing and propagation of fungi, and other lab duties. Prior relevant
lab experience is preferred, however, coursework in biotechnology and/or microbiology
may suffice.
Qualifications of student
Molecular technique experiences are preferable but not required.
Number of work hours per week
10‐15 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
Could this project be extended into an honors thesis?
yes
PROJECT 3
Faculty name
Joe Elkinton
Faculty lab website (if available)
Name of person to directly oversee apprentice
Gina Davis
Position of person overseeing apprentice
Postdoc
Title of project
Population dynamics and chemical ecology of hemlock woolly adelgid
Description of project
The hemlock woolly adelgid is an invasive insect from Japan that is killing hemlock trees
throughout the eastern United States, including trees here in Amherst. We have been
studying the fluctuations in density of this insect and its interaction with its hemlock host
in order to understand why it kills some trees but not others. Part of this effort involves
quantifying the terpenes and other volatile compounds that hemlocks produce to defend
themselves against attack. Another part of the project involves releasing a beetle
predator from the Pacific Northwest that preys on the adelgid and may reduce its density,
so that it no longer kills trees.
The student would learn how we estimate the density of different life stages of the
adelgid in the field and may also learn how to identify and quantify terpenes and other
volatiles in hemlock foliage via gas chromatography.
Qualifications of student
interest in ecology or conservation biology
some training in biochemistry
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
Could this project be extended into an honors thesis?
yes
PROJECT 4
Faculty name
John Stoffolano
Faculty lab website (if available)
Name of person to directly oversee apprentice
Dr. John Stoffolano
Position of person overseeing apprentice
Faculty
Title of project
Effect of adipokinetic hormone on crop muscle contractions in flies
Description of project
The crop or storage organ of fies has recently been shown to be involved in the regulation of
blood sugar levels. It is very similar to that of humans. Adipokinetic hormone in insects is similar to
glucagon in mammals and is involved in putting carbohydrates back into the blood from glycogen
stored in the fat body. Adipokinetic hormone has been shown using various molecular techniques
to be produced in intrinsic cells in the corpora cardiaca of flies and these cells send neurons down
to the crop pump 4 where they terminate and apparently stimulate that part of the crop, which
then pumps sugars stored into the crop up into the midgut where it enters the hemolymph or
blood, thus restoring low levels of blood sugar. This project is something that a student can
complete with few complications and it would make a great honor's thesis. I have had significant
success with honor students and all of them have gone onto good graduate schools and there
research has resulted in a publication.
The student would be trained at doing microdissection and the use of a neurohormone to study
a physiological event. The student would also learn how to search and read the literature,
communicate with researchers throughout the world concerning their research, and learn how to
write a scientific paper. The student will also learn how to raise their own research animals and
how to schedule and feed them for their part of the research.
Qualifications of student
First of all, the student must be highly motivated and independent. Secondly they must
be dedicated to this project. They must get along with other students in the lab. Currently
I have 4 undergraduates working in the lab. One doing an excellent honor's thesis and 3
others working on independent projects. Finally, the student must be inquisitive and
imaginative when it comes to designing and completing their research. If the student likes
working in my lab. and working on this type of project I can provide the student with a
summer position working in the lab. Students doing honor's theses can benefit because
they can get most of the research done during the summer giving more time to class work
during their senior year.
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
3rd or 4th year student
independent study credit
Could this project be extended into an honors thesis?
yes
PROJECT 5
Faculty name
Sheila Patek
Faculty lab website (if available)
http://www.bio.umass.edu/biology/pateklab/home
Name of person to directly oversee apprentice
Patrick Green
Position of person overseeing apprentice
Graduate student
Title of project
Aggressive Signaling in Mantis Shrimp
Description of project
Patrick is a first‐year graduate student who will be initiating a research project on
aggressive signaling in mantis shrimp. This research follows from the observation that
mantis shrimp can inflict fatal injury to competitors and will compete aggressively over
limited protective cavities. Patrick is testing the hypothesis that one area of the mantis
shrimp appendage (the meral spot) is a signal of mantis shrimp strike force, and that
mantis shrimp respond to this signal in a reliable way. Eventually, this research may lead
to an investigation of how signaling changes under conditions of human‐induced ocean
acidification, which is known to weaken crustacean exoskeletons.
This project will involve behavioral observations, force transducer measurements,
identifying and handling mantis shrimp, and possibly analyzing CT scans of mantis shrimp
appendages. The apprentice will likely care for mantis shrimp, including feeding and
water quality care. Since the project is relatively new, the apprentice may also be an
intricate part of developing methods of the study.
Qualifications of student
Previous research experience, especially in behavior and/or marine animals, is preferred
(but not necessary). An ability to work collaboratively while also closely following
instruction will help the research progress efficiently. Behavioral research necessitates
strong organizational skills and a patient, cooperative demeanor. Finally, a desire to work
closely with other lab members, including attending (possibly presenting at) lab meetings
and reading substantive background literature.
Number of work hours per week
1‐5 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
unpaid
Could this project be extended into an honors thesis?
possibly
PROJECT 6
Faculty name
Elizabeth Dumont
Faculty lab website (if available)
http://bcrc.bio.umass.edu/ummnh/
Name of person to directly oversee apprentice
Katherine Doyle
Position of person overseeing apprentice
Other
Title of project
Vertebrate skeleton preparation
Description of project
The Natural History Collections contain more than 300,000 specimens of mammals, birds,
invertebrates, plants, fishes, reptiles and amphibians. These specimens represent a large
sample of the world's biodiversity with an especially strong representation of local flora
and fauna. The Collections are heavily used in numerous organismal laboratory courses,
serve as the raw material for hundreds of graduate and undergraduate research studies,
and draw attention from local and national organizations and governmental agencies.
We currently have a back log of skeletons that need to be cleaned, cataloged, and
installed into the collections. While the work can be tedious at times, students will learn
about vertebrate diversity, basic anatomy, and the skeletal differences between major
vertebrate groups. Students will also learn standard curatorial procedures employed by
collections and museums world‐wide.
Qualifications of student
Interested students must be able to work independently and be detail‐oriented. Most
specimens are in the early stages of preparation so students must be able to deal with
strong odors and be willing to get their hands dirty.
Number of work hours per week
1‐5 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
Could this project be extended into an honors thesis?
no
PROJECT 7
Faculty name
Benjamin Normark
Faculty lab website (if available)
http://people.umass.edu/bnormark/lab/Home.html
Name of person to directly oversee apprentice
Benjamin Normark
Position of person overseeing apprentice
Faculty
Title of project
Armored scale insect molecular systematics and evolution
Description of project
Several projects are available using DNA sequences and/or morphological characters to
investigate the evolution and ecology of armored scale insects (Hemiptera: Diaspididae).
Problems include inferring phylogeny, species boundaries, and population sizes. Armored
scale insects have bizarre biology ‐‐ extreme sex dimorphism, unusual genetic systems
like paternal genome elimination and parthenogenesis, dependence on maternally
transmitted endosymbiotic bacteria ‐‐ and are also enormously important as invasive
economic pests. We are constantly discovering new species. Students start by preparing
DNA and microscope slides, and move on to a PCR‐ and sequencing‐based independent
project if they wish to.
Qualifications of student
Minimum qualification: Bio 100 and 101 (taken or currently enrolled). Desirable
qualifications: enrollment in PlSoilIn 397T (Molecular Systematics Lab); very fine motor
skills (useful especially for slide‐mounting tiny insects); a strong interest in evolution,
systematics, insects, biodiversity discovery, invasive species, and/or horticultural pests.
Number of work hours per week
10‐15 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
paid
Could this project be extended into an honors thesis?
yes
PROJECT 8
Faculty name
Elizabeth Dumont
Faculty lab website (if available)
Name of person to directly oversee apprentice
Dan Pulaski
Position of person overseeing apprentice
Lab technician
Title of project
3D modeling and engineering analysis of mammal skulls
Description of project
Evolutionary biologists often look to differences among isolated populations of the same
species for evidence of divergence that may represent adaptations. The goal of this
project is to assess the mechanical function the skulls of shrews from populations that
have been isolated on islands off the coast of France for several hundred to several
thousand years. This is just a small part of a large collaborative project headed by
investigators at the Muséum Histoire naturelle in Paris. Our contribution will be to build
three‐dimensional (3D) models of the shrew skulls from CT scans, and then analyze and
compare the structural strength of those models using engineering software. (Just to be
clear, we will be doing some really neat analyses using computers, but we won't be going
to France).
Students learn how to create 3D models from CT Scans and analyze them using
engineering software. The process of building the models will require students to learn
the detailed anatomy of the skull. They will not necessarily learn all the anatomical names
(unless they want to), but they will become very familiar with the details of skull shape.
On the technical side, students will receive training in Mimics, an image segmentation
package, Geomagic Studio, a 3D model editor, and an engineering analysis program called
Strand7.
Qualifications of student
Students must have a strong interest in anatomy, biomechanics and evolution, and have
successfully completed the Intro Bio series. Good performance in Evolution and prior lab
experience would be a plus.
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
2nd year student
independent study credit
Could this project be extended into an honors thesis?
yes
PROJECT 9
Faculty name
Bethany Bradley
Faculty lab website (if available)
Name of person to directly oversee apprentice
Bethany Bradley
Position of person overseeing apprentice
Faculty
Title of project
Identifying sources of U.S. invasive plants
Description of project
There are thousands of non‐native plant species introduced to the U.S., and several
hundred have become problematic invasive species. My lab seeks to forecast invasion
risk at landscape and regional scales using tools from spatial ecology and biogeography.
This project will explore online herbaria and other published records to catalog the
estimated introduction date and source of introduction for problematic invasive species.
Improving our understanding of how invasive species arrived and spread in the past will
help us to predict risk associated with future introductions.
This project will rely on the student's skills with data searching and discovery, and may
include some trips to regional botanical gardens and herbaria to search through records
as needed. The student will also be taught some basics of working with geographic
information systems (GIS) and background in invasion ecology.
Qualifications of student
Intellectual curiosity and tenacity. Computer literacy and interest in biogeography.
Willingness to call/email contacts for further information unavailable online.
Number of work hours per week
1‐5 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
Could this project be extended into an honors thesis?
yes
PROJECT 10
Faculty name
Bethany Bradley
Faculty lab website (if available)
Name of person to directly oversee apprentice
Bethany Bradley
Position of person overseeing apprentice
Faculty
Title of project
Mapping plant invasions in Western Massachusetts
Description of project
Satellite remote sensing is a tool often used to map vegetation characteristics across
landscapes. My lab seeks to forecast invasion risk at landscape and regional scales using
tools from spatial ecology and biogeography. This project will collect preliminary field
data on the timing of spring green‐up for several invasive plants in western
Massachusetts, with a goal using those data to train remotely sensed imagery. We
hypothesize that earlier onset of plant growth in invasive species will make them possible
to map using remote sensing.
The student will learn to use GPS for field surveys, and how to convert collected field
records into a geographic information system (GIS). The project may also entail some
introduction to remote sensing data processing and analysis, as well as background in
invasion ecology.
Qualifications of student
Interest in learning about biogeography. Familiarity with GPS units and comfort with
computers a plus. Plant identification skills also a plus.
Number of work hours per week
1‐5 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
Could this project be extended into an honors thesis?
yes
PROJECT 11
Faculty name
John Stoffolano
Faculty lab website (if available)
Name of person to directly oversee apprentice
John Stoffolano
Position of person overseeing apprentice
Faculty
Title of project
Impact of the salivary gland hypertrophy virus on house fly adults
Description of project
The salivary gland hypertrophy virus is a new virus of house fly adults and causes
hypertrophy of the salivary glands and cessation of egg development. Only a handful of
research papers have been done on this virus. Our lab. is currently working on the virus.
We have the virus and the fly colony to do the research. One of the important questions
is further document how the virus affects various tissues. At the same time we need to
know how the virus impacts normal salivation, thus the spreading of the virus to infect
other flies. The house fly is the major vector of several human food pathogens, especially
E coli, thus any effort to control its reproduction and/or feeding is important and
circumvents the use of insecticides that are environmentally disastrous.
The student will learn how to handle the virus (not pathogenic to humans), inject the
virus into non‐infected flies, and dissect out infected salivary glands and retrieve the virus
for storage and later use. The student will learn how to access the literature, contact
other researchers in the field, plan an experiment, and write up a scientific paper on their
research.
Qualifications of student
The student preferably is a junior in search of an honor's thesis. All of my previous
honor's students have gone on to major universities for graduate studies and all have
become authors on the paper of their research. The student should be highly motivated,
self‐directed, independent worker, persistent, and really committed to doing a successful
research project. I am looking for someone that also wants to stay in the Amherst are for
the summer and I can pay them to continue to work on their thesis during the summer.
This way they have a major start on their thesis with less pressure during their senior
year.
Number of work hours per week
10‐15 hours per week
Are you looking for a particular type of student?
Honors thesis project
independent study credit
Could this project be extended into an honors thesis?
yes
PROJECT 12
Faculty name
Lynn Adler
Faculty lab website (if available)
http://people.umass.edu/lsadler/
Name of person to directly oversee apprentice
Lynn Adler and Jared Kelly
Position of person overseeing apprentice
Lab technician
Title of project
Extracting alkaloids: Effects of urbanization on natural selection
Description of project
This position would be an opportunity to gain hands‐on research experience, and would
be best for a practicum or workstudy student. Such positions in the lab often lead to
subsequent independent projects for motivated students.
I conducted a 3‐year field study asking how urbanization changes natural selection on
plant traits through changes in plant‐insect interactions, including herbivory and
pollination. In the field, we tracked perennial plants (Gelsemium sempervirens) for 3
years, measuring floral damage, pollination, floral size/shape, chemical defenses, and
plant reproduction each year in several sites that are either near housing developments,
or in large tracts of forest.
One of the traits that we are very interested in is the production of defensive chemicals
that could deter floral damage but also reduce pollination. In the field we collected leaves
for chemical analysis, and I am looking for 2‐3 students who would be trained in
extracting these compounds. This is a repetitive but critically important process since we
only have one sample from each plant (for which we have collected so much other data).
I am looking for students with an interest in this research area who are mature and
responsible, and who are highly attentive to detail.
I can offer paid positions to students with workstudy funds, or practicum credits.
Qualifications of student
I can accept students at any point in their college career. Preference will be given to those
with an interest in pursuing ecology research.
Number of work hours per week
10‐15 hours per week
Are you looking for a particular type of student?
Anyone!
paid or unpaid
Could this project be extended into an honors thesis?
no
PROJECT 13
Faculty name
Lynn Adler
Faculty lab website (if available)
http://people.umass.edu/lsadler/
Name of person to directly oversee apprentice
Annie Leonard
Position of person overseeing apprentice
Postdoc
Title of project
Effect of floral compounds on bee health
Description of project
Studies of plant‐herbivore and plant‐pollinator interactions have been of central importance in
understanding the factors that shape plant and animal performance and patterns of natural
selection and coevolution. Although plant‐herbivore and plant‐pollinator interactions have often
been studied separately, they are linked by a common theme, consumption of plants. For
example, we generally think of bees as mutualists that benefit – and benefit from – their
interactions with plants, but bees can also be broadly considered herbivores that consume plant
nectar and pollen. Nectar and pollen are the primary food items of the majority of bees, but in
addition to sugars and protein, these food sources also frequently contain plant secondary
compounds. Secondary compounds can directly reduce herbivore performance while providing
indirect benefits by reducing predation or parasitism; however, the impacts of secondary
compounds on bee pollinators are almost entirely unknown. Bees, like herbivores, are also part of
a food web that includes both host plants and natural enemies. Parasites are strongly implicated
in the decline of both managed and wild bees, but the impacts of secondary compounds in
mediating plant‐bee‐parasite interactions remains an almost unexplored frontier.
Students will join an ongoing project asking how common floral defense compounds affect
pathogen loads of infected bumble bees. Students will be trained in basic bee handling protocols
including rearing, preparing pathogen inocula, dissecting bees and counting pathogen cells from
gut samples.
Depending on the interests and background of the student, this project could be appropriate for
independent study, practicum, or a paid workstudy position.
Qualifications of studentStudents can be at any academic level, but should be highly motivated, independent, reliable and
detail‐oriented. Preference will be given to applicants interested in careers in ecology, animal
behavior, chemical ecology, or related fields.
Although no one in the lab has been stung (yet), students who are highly allergic to bee stings (or
seriously afraid of handling bees) should not apply.Number of work hours per week
10‐15 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
paid or unpaid
Could this project be extended into an honors thesis?
possibly
PROJECT 14
Faculty name
Jeff Podos
Faculty lab website (if available)
http://www.bio.umass.edu/biology/podos/
Name of person to directly oversee apprentice
Dana Moseley
Position of person overseeing apprentice
Graduate student
Title of project
Song Learning and Preferences by Sparrows
Description of project
This position is part of a project to study how young birds learn their songs or preferences
for songs. The undergraduate will work with two‐year‐old birds that have been trained
with song models and are maintained in the lab. The position requires that the student
be comfortable working with and caring for live animals. Tasks include feeding the birds
and maintaining clean housing spaces for the animals. I especially need someone to help
for an hour or two on either Saturday or Sunday*. In addition to bird care, there are
opportunities to work with data collected in spring 2010 and summer 2011 from these
birds. The student would track how birds learn and practice their songs over time and
compare learned songs to the training models. Students would use Microsoft excel and
two sound analysis programs (Audacity and Signal) to measure song learning.
The work is volunteer (unpaid) and would require 2‐5 hours a week depending on the
motivation of the student. This position is great for students who want to get started in a
lab and get hands‐on experience with animals and data. Students early in their college
career would be considered and encouraged to apply. More senior students would be
able to focus more heavily on the data analysis portion if so inclined.
Qualifications of student
Qualifications of student
Familiarity with Excel and basic computer use,
Safe lab protocols,
Ability to work independently but ask questions when needed,
Ability to learn new protocols quickly ,
Interest in the project.
Number of work hours per week
1‐5 hours per week
Are you looking for a particular type of student?
Anyone!
unpaid
Could this project be extended into an honors thesis?
no
PROJECT 15
Faculty name
Tobias Baskin
Faculty lab website (if available)
http://www.bio.umass.edu/biology/baskin/
Name of person to directly oversee apprentice
Heidi Rutschow
Position of person overseeing apprentice
Postdoc
Title of project
Misregulation of a key cell cycle protein
Description of project
The student will help us study the accumulation of a protein called cyclin B1;1, which is a
key regulator of the cell division cycle. My laboratory studies how plants produce organs
with specific shapes. One approach we use is developmental genetics, isolating plants
with misshapen (i.e., fat) roots. Previously we found that the cell division zone (meristem)
of one of these mutants, called radially swollen 4, accumulates huge amounts of
cyclinB1;1. This might happen because of cell cycle arrest but many other lines of
evidence show that the cell cycle continues. It appears that the in the mutant the
regulation of the protein somehow goes wrong, and we want to track this down.
For the above work, we scored the abundance of the cyclinB1;1 by using a reporter
construct that we crossed into the mutant background. We have recently obtained an
antibody against this cyclin. The student will isolate protein, run it on a gel, and use the
antibody to determine the relative abundance of the cyclin B1;1 (by doing a so‐called
western blot). This can be done not only for the mutant mentioned above but for others
as well. In this way, we can learn to what extent this cell cycle regulatory protein might
also influence mechanisms that control plant shape.
Qualifications of student
Prior lab experience is not required but desirable. Enthusiasm and reliability are
essential. Free time in your schedule for the after 10:30 am is important, preferably in a
couple of large blocks.
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
paid
Could this project be extended into an honors thesis?
yes
PROJECT 16
Faculty name
Paige Warren
Faculty lab website (if available)
Name of person to directly oversee apprentice
Paige Warren
Position of person overseeing apprentice
Faculty
Title of project
What makes an urban bird?
Description of project
The rapid urbanization of the world has profound effects on global biodiversity and
urbanization has been counted among the processes contributing to the homogenization
of the world’s biota. A comparative approach of urban biota is needed to produce
comparable methodologies to understand, preserve, and monitor biodiversity in cities.
Our project asks the question: “What makes an urban bird ‘urban’?” and with that, “Are
the same kinds of birds found across the world’s cities?” We have compiled a list of
species occurring in 10 cities in Canada, the United States, and Mexico. We need to
collect information on the life history characteristics of these species. We will use this to
compare the kinds of birds species found in the 10 cities.
The undergraduate researcher would use a variety of literature sources to compile a
database of the traits or characteristics for bird species in our list. We will use Excel for
the database, and both paper and online sources. The student should be comfortable
using excel and possess a basic knowledge of bird biology (ideally a course in Ornithology
or Behavior). We will provide training in using the online sources. A motivated student
could participate in the analysis and develop a senior thesis from the work.
Qualifications of student
Experience working with Excel or similar spreadsheets
Coursework in ornithology or animal behavior
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
3rd or 4th year student
independent study credit
paid
Could this project be extended into an honors thesis?
possibly
PROJECT 17
Faculty name
Paige Warren
Faculty lab website (if available)
http://www.umass.edu/urbaneco/
Name of person to directly oversee apprentice
Michael Strohbach
Position of person overseeing apprentice
Postdoc
Title of project
Planting more trees, but where? Assessing the potential for new street trees in Boston.
Description of project
We are looking for a lab assistant to help with a project about urban greening in Boston
(http://www.umass.edu/urbaneco/). As part of the project we are studying the potential
for an increase of the tree canopy in the city and the resulting ecological benefits.
Duties for the potential assistant would include a GIS analysis of the street tree inventory
of Boston and the development of a rule sett for the placement of new trees. This is a
great opportunity to extend your GIS skills.
Qualifications of student
‐ basic skills of ArcGIS, Excel and/or R
‐ interest in data processing
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
paid
Could this project be extended into an honors thesis?
PROJECT 18
Faculty name
Sam Hazen
Faculty lab website (if available)
http://www.bio.umass.edu/biology/hazen/
Name of person to directly oversee apprentice
Scott Lee
Position of person overseeing apprentice
Graduate student
Title of project
Plant biofuel genetics
Description of project
A recently discovered microbe, Clostridium phytofermentans, can directly convert a
broad range of biomass sources directly to ethanol without expensive thermochemical
pretreatment. The Hazen lab has developed a high throughput ethanologen bioassay
using C. phytofermentans to measure ethanol production from various plant species.
We seek an undergraduate to assist with various tasks in the laboratory relating to this
project.
Plant cultivation: soil preparation, harvesting.
Processing plant samples: grinding, weighing, dispensing and packaging.
Microbiology: anaerobic culturing of Clostridium with plant biomass.
Analytical chemistry: sample preparation and analysis using high performance liquid
chromatography.
Level of instruction and responsibility will depend on the student's interest and activity
with project.
Qualifications of student
Enthusiastic, cordial, honest, diligent, competent, reliable and punctual.
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
2nd year student
unpaid
Could this project be extended into an honors thesis?
possibly
PROJECT 19
Faculty name
Sam Hazen
Faculty lab website (if available)
http://www.bio.umass.edu/biology/hazen/
Name of person to directly oversee apprentice
Gina Trabucco
Position of person overseeing apprentice
Graduate student
Title of project
Plant biofuel genetics ‐ 2
Description of project
We modified a family of plants to down regulate a lignin biosynthesis gene to improve
biofuel‐processing quality. The plants require genotypic characterization as well as
observations of growth patterns and other mutant phenotypes.
We seek an undergraduate to assist with various tasks in the laboratory relating to this
project.
Plant cultivation: soil preparation, watering, harvesting.
Molecular biology: DNA extraction, PCR, gel electrophoresis.
Monitoring patterns in transgenic plants: recording stem height, stem/leaf phenotypes
Level of instruction and responsibility will depend on the student's interest and activity
with project.
Unpaid position can be independent study for credit.
Qualifications of student
Enthusiastic, cordial, honest, diligent, competent, reliable and punctual.
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
2nd year student
unpaid
Could this project be extended into an honors thesis?
possibly
PROJECT 20
Faculty name
Sam Hazen
Faculty lab website (if available)
http://www.bio.umass.edu/biology/hazen/
Name of person to directly oversee apprentice
Dominick Matos
Position of person overseeing apprentice
Graduate student
Title of project
Developmental and Growth Dynamics of Plants
Description of project
We seek to understand the fundamental mechanisms of vascular development and
rhythmic growth in grasses. We are utilizing a number of imaging based assays to conduct
these investigations.
We seek an undergraduate to assist with various tasks in the laboratory relating to this
project.
Plant cultivation: soil preparation, harvesting, sowing, transplanting, and watering.
Phenotyping: plant dissection, staining, image acquisition by microscopy.
Level of instruction and responsibility will depend on the student's interest and activity
with project.
Unpaid position can be independent study for credit.
Qualifications of student
Enthusiastic, cordial, honest, diligent, competent, reliable and punctual.
Number of work hours per week
1‐5 hours per week
Are you looking for a particular type of student?
2nd year student
unpaid
Could this project be extended into an honors thesis?
possibly
PROJECT 21
Faculty name
Kevin Griffith
Faculty lab website (if available)
http://www.bio.umass.edu/micro/faculty/griffith.html
Name of person to directly oversee apprentice
Kevin Griffith
Position of person overseeing apprentice
Faculty
Title of project
Engineering soil bacteria to produce biofuels
Description of project
Society relies on the use of fossil fuels to meet its ever increasing energy demands and efforts are
underway to develop alternative forms of energy including biofuels. Genetic engineering and
synthetic biology allow researchers to engineer microbes to produce a variety of biofuels including
ethanol, butanol, isobutanol, and fatty alcohols. Recent studies have shown that the soil
bacterium Bacillus subtilis is capable of fermenting sugars to produce ethanol and the pre‐cursor
to isobutanol, 2,3‐butanediol. B. subtilis is an attractive system for biofuel production because it
is a genetically tractable, several of the biosynthetic pathways leading to biofuel production are
known, and large‐scale industrial fermentation protocols have been developed.
The goal of this project is to engineer strains of B. subtilis and optimize growth conditions to
facilitate the over‐production of a variety of biofuels. Key regulatory pathways will be disrupted in
order to re‐direct the flow of carbon through biofuel biosynthetic pathways. Important enzymes
that are absent in B. subtilis will be taken from other organisms and engineered for use in B.
subtilis to produce strains that are able to produce specific biofuels like isobutanol. Since biofuels
are often toxic to microbes, it will be necessary to evolve strains of B. subtilis that have increased
resistance to these by‐products. Students working on this project will have the opportunity to
conduct independent research and learn a variety of techniques in microbiology, molecular
biology, and biochemistry.
Qualifications of student
Undergraduate research is an important component of my research program. Students
typically join my research program after their freshman or sophomore year and continue
to conduct research in my laboratory until graduation. No prior research experience is
required; however, students should have the dedication, desire, and available time to
devote to the research project.
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
Could this project be extended into an honors thesis?
yes
PROJECT 22
Faculty name
Bruce Byers
Faculty lab website (if available)
Name of person to directly oversee apprentice
Bruce Byers
Position of person overseeing apprentice
Faculty
Title of project
Female mate choice and Prairie Warbler songs
Description of project
We plan to compare singing by male Prairie Warblers to the singers' nesting success, in
order to identify features of male singing that females might use when choosing a mate.
The current phase of the project involves making measurements of recorded songs.
When that is complete, we will build a statistical model to determine the song features
that best predict nesting date.
Qualifications of student
1. Interest in animal behavior and communication.
2. Willingness to commit 10 hours per week to the project.
3. Meticulousness.
Number of work hours per week
10‐15 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
Could this project be extended into an honors thesis?
yes
PROJECT 23
Faculty name
Sheila Patek
Faculty lab website (if available)
http://www.bio.umass.edu/biology/pateklab/
Name of person to directly oversee apprentice
Sheila Patek
Position of person overseeing apprentice
Faculty
Title of project
Laboratory assistant in biomechanics/bioacoustics laboratory
Description of project
This paid position is more of an assistantship than a focused research experience. Patek
is looking for someone to help with running the lab and providing assistance with ongoing
research projects (e.g., literature searches, database entry, making figures, data
collection). The other tasks include running errands, helping with animal care (aquarium
cleaning, feeding animals), photocopying, etc.
The student would learn about how a university research lab is run and would receive
training in aquarium animal husbandry, literature searches, database management,
digital image analyses, and other data analysis/presentation skills.
Qualifications of student
‐ Experience in at least ONE of the following areas: engineering, physics, biomechanics,
evolutionary/functional morphology, general biology or marine animal care
‐ Organized, detail‐oriented, dependable and willing to learn new skills
‐ Computer prof
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
Anyone!
paid
Could this project be extended into an honors thesis?
no
PROJECT 24
Faculty name
Rolf Karlstrom
Faculty lab website (if available)
www.bio.umass.edu/biology/karlstrom/KarlstromLab.html
Name of person to directly oversee apprentice
Maggie Shen
Position of person overseeing apprentice
Lab technician
Title of project
Zebrafish Transgenics
Description of project
The lab is making a number of transgenic zebrafish lines that express fluorescent proteins
(GFP and RFP) in specific cell types. These lines serve as important tools as we study the
molecular and cellular mechanisms that guide neural and pituitary development. This
project is to use PCR‐based genotyping to identify adult zebrafish that carry the
transgenes of interest and then to set up genetic crosses to establish F1 and F2
generations. The student will also characterize these transgenic lines by documenting
fluorescence at different stages of the life cycle (embryo, larva, and adult) using a
confocal microscope.
Qualifications of student
Responsible, conscientious person. Some lab experience preferred, but we will train you
in the necessary techniques.
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
unpaid
Could this project be extended into an honors thesis?
yes
PROJECT 25
Faculty name
Rolf Karlstrom
Faculty lab website (if available)
www.bio.umass.edu/biology/karlstrom/KarlstromLab.html
Name of person to directly oversee apprentice
Mary Catanese
Position of person overseeing apprentice
Graduate student
Title of project
Mechanisms of Pituitary Growth in Zebrafish
Description of project
In the Karlstrom lab we are interested in Sonic Hedgehog(Shh) signaling and use zebrafish
as a model system. This particular project examines the role of Shh in the developing
zebrafish pituitary gland. Our focus is on endocrine cell addition and growth in the
pituitary gland along with a potential role for Shh in cell proliferation. The student will
work with a Ph.D. student on her dissertation research. The techniques involved in the
project include immunohistochemistry using antibody labeling and in situ hybridization.
The project additionally relies upon confocal imaging and cell counting in order to
quantify the effects of Shh.
Qualifications of student
We are looking for a responsible conscientious person who can learn to work somewhat
independently. We will train the student in the needed techniques, but some lab
experiences is desired.
Number of work hours per week
10‐15 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
unpaid
Could this project be extended into an honors thesis?
yes
PROJECT 26
Faculty name
Rolf Karlstrom
Faculty lab website (if available)
www.bio.umass.edu/biology/karlstrom/FishFacility.html
Name of person to directly oversee apprentice
Judy Bennett
Position of person overseeing apprentice
Lab technician
Title of project
Zebrafish Aquaculture
Description of project
An assistant is needed to help the UMass fish facility manager in a project to investigate
parameters of zebrafish health and disease. This project is to investigate whether and
how a bacterial pathogen can be dealt with in a recirculating system. The student will
help disinfect and move a small recirculating zebrafish system. The major tasks will
involve moving fish, tank cleaning and scrubbing, and reassembly of system in another
facility. The student may help develop PCR‐ or culture‐based assays for detecting the
bacterium in the system so that effectiveness of the process can be monitored. Position
can remain open with additional tank and cleaning duties on a separate system.
Qualifications of student
Responsible conscientious person who can take on some independence. We will train in
specific techniques but some lab experience is desired.
Number of work hours per week
5‐10 hours per week
Are you looking for a particular type of student?
Anyone!
unpaid
Could this project be extended into an honors thesis?
no
PROJECT 27
Faculty name
Lynn Adler
Faculty lab website (if available)
http://people.umass.edu/lsadler/
Name of person to directly oversee apprentice
Nicole Soper Gorden
Position of person overseeing apprentice
Graduate student
Title of project
The ecology of chemical defenses in flowers
Description of projectFlowers are in a constant battle to attract organisms that help them (such as pollinators) while deterring organisms that
damage them (such as florivores, which eat flowers). Flowers have several traits that serve for attraction (color, size, nectar
production, etc), and can also have traits that serve as a deterrent (e.g. flower chemical defenses). Although researchers
have spent hundreds of years studying leaf herbivores and leaf defenses, very little research has been done on florivores
and flower defenses.
This project will look at how flower attractiveness traits and flower chemical defenses affect insects that interact with
flowers, and whether damage by florivores induces chemical defenses in flowers. This summer, we manipulated
pollinators, florivores, and nectar robbers (which steal nectar without pollinating) and measured how insects interacted
with the plants. We also collected many samples that need to be processed to measure chemical defenses in flowers and
leaves, determine pollen production, and estimate plant reproduction.
This position is for a lab technician assistant whose job is to help process samples collected over the summer. Duties
include:
•�Basic chemical extractions of chemical defenses from flowers and leaves (procedures will be taught and are relatively
simple)
•�Counting and weighing seeds
•�Counting pollen from pollen samples
•�Estimating flower color (using a computer program)
•�Entering data into Excel and proofing data that has already been entered
•�Possibly helping with greenhouse work
The successful candidate(s) should be comfortable using Excel and other basic computer programs, be able to complete
frequently‐repetitive tasks, be familiar with the use of basic lab equipment, be comfortable working with chemistry, and be
able to work independently and meticulously. In return, you will learn data management skills, lab safety protocols, how to
use ImageJ to estimate color, methods of determining plant fitness, two methods of chemical extractions, and methods for
counting pollen, as well as becoming familiar with the process of research and experimental design.
This position is offered for credit (no pay) for ~ 2 students to work 10‐15 hours each a week (depending on the number of
credits taken). There is also the possibility of an independent project for a particularly interested student who has been
doing a satisfactory job with the basic work. This independent project would either be a greenhouse study growing plants
to determine the heritability of flower color in Impatiens capensis or a greenhouse study determining if damage to flowers
by scissors is equivalent to damage to flowers by insect florivores.
PLEASE NOTE: I like to interview students before hiring them. There is only one week between when applications are due
and when I have to hire someone, so make sure you include your availability for a short meeting (usually 30 min or less)
between January 30 and February 6 in your application. It would also be helpful if you could email me with your availability
Qualifications of student
Interest in the project and/or in plants, insects, ecology, or evolution
Familiarity with Excel and basic computer use
Safe lab protocols
Ability to use basic lab equipment including microscopes, pipettes, scales, etc.
Interest in doing basic chemical extractions, and comfort using mild to moderately
dangerous chemicals
Ability to work independently but ask questions when needed
Ability to do meticulous and sometimes repetitive work
Ability to learn new protocols quickly
Number of work hours per week
10‐15 hours per week
Are you looking for a particular type of student?
Anyone!
independent study credit
unpaid
Could this project be extended into an honors thesis?
possibly