[bioundgrd] Fwd: Summer projects for Sophomore and Juniors

[MacKenzie Outlund]

Dear Student,

I hope your spring courses are progressing well.

This summer I have several on-campus biotechnology research projects, which
are in need of student assistance. If you are interested in a field like
pharmaceutical production, biofuels, or greening our parks, check out the
project descriptions at the end of this email. All the projects can be
long-term UROP, and have the potential to lead to presentation at a
conference
and publication.

If you are interested in any of the proposed projects, please send me a copy
of your resume, along with an email explaining your specific interest.
Summer
projects are usually for pay, but the "for credits" option is possible if
that
is what you want to pursue.

Yours,

J.-F. Hamel
jhamel at mit.edu

Summer 2010 Projects:

1. Evaluation of a novel enzyme-based membrane for measuring glycerol

Glycerol is a popular carbon substrate to grow recombinant *E. coli*, for
making therapeutics. The YSI Company (www.ysi.com) is developing a novel
assay for their analyzer. The student involved with the project would
compare (using statistical analysis) the results obtained with the YSI
technology with those obtained by HPLC. The project would also involve
conducting actual recombinant * E. coli* fermentations and measuring
glycerol consumption.

The student involved with the project would receive training on the analyzer
from a YSI company expert.

2. Using the smart shake flask and microreactor for study the growth of E.
coli
and gene expression

Novel technologies are now available to monitor pH and dissolved oxygen in
real-time, in the shake flask and microreactor, which enable the study of
cell
growth and gene expression at high cell concentrations. The student involved
in
this project will use such technologies to develop recipes for growing E.
coli
at high-cell densities (OD>30) and for producing the Green Fluorescent
Protein.
The project will involve medium design and metabolic studies. The
small-scale
process will be scaled up in a 20-L scalable bioreactor. The project is
sponsored by the Merck company.

3. Study of monoclonal antibodies (MAb) from eukaryotic cells (e.g.,
mammalian cells) in a novel single-use (plastic) stirred-tank bioreactor
The research and development side of the Millipore Company, based in
Bedford, MA, has developed a novel bioreactor, for which few data are
available regarding cell growth kinetics, oxygen mass transport, and MAb
production.

The on-campus student(s) working on this project would work closely with an
MIT intern, based at Millipore this summer. There would also be frequent
interactions with senior researchers at Millipore.

4. Evaluation of novel hollow-fiber filters for processing mammalian cell
culture, and purification of MAb
The AsahiKASEI Bioprocess Company (www.ak-bio.com), the US subsidiary of a
large Japanese Company, needs data on a novel hollow-fiber filter designed
for cell separation and recovery of the secreted product (e.g., MAb).

The student(s) would work closely with US and Japanese researchers from the
company, and would first carry out cell culture experiments in the
bioreactor to produce sufficient cell culture for the filtration studies.

5. Production of biofuels (i.e., ethanol) from sugarcane bagasse, sorghum
and
seaweed
*Project A:* In this project, the student will study the influence of
temperature, the percentage of solids, and residence time, using sugarcane
bagasse. This substrate will be ground to certain specifications and treated
with an acid or a base to produce a hydrolyzate. Pretreatment products
(sugars) and byproducts (inhibitory degradation compounds) will be measured
using chemical/biochemical assays and FTIR. The effectiveness of the
sugar-containing hydrolyzate will be evaluated by yeast fermentation, for
ethanol production.

*Project B:* In this project, the student will optimize the use of two
enzymes in an integrated process for the liquefaction and saccharification
of Milo sorghum. Sorghum has drawn new interest as a fuel substrate given
its drought resistant nature and its good production with limited water. The
enzymes, alpha-amylase and glucoamylase, are traditionally used sequentially
in a two-step bioprocess. Each enzyme has specific requirements when
employed alone (for alpha-amylase: 85°C, pH 5.7, 2 hours;  for glucoamylase:
65°C, pH 5.0, 12 hours). When designing the novel integrated bioprocess,
intermediate temperatures and pHs (at which both perform well) will be
identified. The extent of enzyme hydrolysis will be measured from the
released sugars, using chemical/biochemical assays. The effectiveness of the
sugar-containing hydrolyzate will be evaluated by yeast fermentation, for
ethanol production.

*Project C: In this project, the student will design a process for
extracting
polysaccharides from seaweed, to then extract fermentable sugars from them
and to assess their relative value for making biofuels.

6. Enhancing the biodegradation of bags used to collect animal waste
The proposed project is part of the Park Spark project -
http://parksparkproject.com/home.html
This is a project will introduce digesters into public parks in urban areas
and use dog waste as the raw materials to make methane. There are on-going
discussions with the city of Cambridge's parks and recreation as well as
Cambridge Art Council aiming to implement the project in Cambridge, this
summer.

One challenge is that the "biodegradable" bag used to collect the waste
needs to meet specific criteria, and degrade in an acceptable period. The
MIT project would look into low-cost and safe solutions for enhancing the
degradation kinetics of the bag.

The UROP would be set up as part of MIT's Public Service Center.
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