Center for High Performance Scientific Computing (CHIPS-Comp)  A Beowulf-type cluster of 20 dual Alpha EV6 833, 750 and 667 MHz workstations with a Scalable Coherent Interface (SCI) network accelerates the progression of parallel programming tasks and exchange of information across the processors. This architecture allows for an extremely powerful supercomputing capability that may be used by researchers in diverse fields to process data at rates not achievable with conventional computing systems. The center can support research in materials science, nuclear physics, parallel computing, and can offer know-how as well as consulting services in material science and nuclear physics and access to computational methods development expertise. |
PiezoBiosensor for Detecting Complex Environmental and Chemical Agents  This technology is an apparatus with multiple piezoelectric mass sensors for use in immunochemical detection of diagnostically relevant analytes. The detection is in real time, and each piezoelectric mass sensor comprises a piezoelectric crystal with a receptor surface containing recombinant antibodies that are specific for a particular antigen. The technology measures the binding of antigens to the recombinant antibodies by tracking a change in mass on the receptor surface which is detected as a change in resonant frequency. This technology emerged from a research program oriented toward developing piezobiosensors and electrochemical sensors for detection in complex environmental and clinical samples. The research program is focused on combining the excellent sensitivity of electrochemical and mass sensing with the superb selectivity of biological recognition processes (e.g., protein-protein interactions, DNA-protein interactions, carbohydrate-protein interactions). |
Center for Biomedical Research This center supports state-of-the-art research facilities for biomedical research, promotes and publicizes biomedical research, and aggressively encourages and supports initiatives for support of biomedical research. The center sponsors research presentations and colloquia, provides funds to support pilot research projects, and identifies novel funding. In addition, the center assists with the development and submission of proposals for external funding of major multi-investigator equipment, (b) provides and maintains readily accessible multi-user equipment facilities, and (c) facilitates access to specialized facilities and services. In addition to supporting and promoting collaborations among its members, the center facilitates interactions between members and other institutions, including pharmaceutical and biotechnology companies, and promotes access to biomedical research equipment within the center. |
PCAP- Parallel Contig Assembly Program (formerly CAP3 - Method for solving repeating problems with constraints)  The PCAP whole-genome assembly program, developed at Michigan Tech, can process tens of millions of reads into long sequences. The PCAP package is a set of programs for generating a genome assembly from a set of reads and a set of forward-reverse read pairs. PCAP can handle a genome of 30 Mb on a computer with one processor, a genome of 300 Mb on a shared-memory computer with 10 processors, and a genome of 3 Gb on a distributed computer cluster of 100 processors. The program has several features to address issues in whole-genome assembly increasing efficiency and accuracy. Test results completed on a mouse whole-genome data set of 30 million reads, show that the assembly computation was efficient enough to handle a whole-genome data set. Accuracy tests performed on a human chromosome 20 data set of 1.7 million reads indicated acceptable accuracy rates.
PCAP contains a few major programs for generating an assembly and a few minor programs for formatting an assembly and collecting statistics on an assembly. In addition, PCAP contains several Perl Scripts for automatically running the major and minor programs in the proper order. PCAP produces a contiguous assembly with a low global misassembly rate and is efficient in computer memory. An assembly in .ace file format produced by PCAP can be viewed and edited in Consed. |
Analysis and Annotation Tool (AAT) Most small engines still use traditional carburetor technology which produces decreased reliability and increased emissions when compared to fuel injection. Current electronic fuel injection technology is not cost effective for application in small engines. This technology allows for the manufacture of a low-cost mechanical fuel injector that can be utilized in place of a traditional carburetor. Development work to-date suggests that the mechanical injector can be designed to simply replace existing carburetors on production small engines without any significant redesign other than a means to connect the injector to the engine’s camshaft. |
MAP: A Multiple Alignment Program The MAP program computes a multiple global alignment of sequences using iterative pairwise method. The underlying algorithm for aligning two sequences computes a best overlapping alignment between two sequences without penalizing terminal gaps. In addition, long internal gaps in short sequences are not heavily penalized. So MAP is good at producing an alignment where there are long terminal or internal gaps in some sequences. The MAP program is designed in a space-efficient manner so long sequences can be aligned. Note that sequences must be all DNA/cDNA sequences or all protein sequences. |
Biological Processes that Involve Nucleic Acids The primary focus of the research is the investigation of nucleic acid damage processes utilizing the independent generation of reactive intermediates in nucleosides and nucleotides. Investigations center around the generation of a variety of C-3'-nucleoside radicals and the elucidation of the fate of these species. To facilitate the independent generation of radical intermediates in these biological systems a variety of modified nucleic acids are required which have the ability to function as radical precursors. These modified derivatives can be synthesized using modern synthetic organic techniques and incorporated into DNA and RNA either chemically or enzymatically. By elucidating the mechanisms and consequently the fate of these species several questions can be addressed concerning the role of nucleic acid damaging agents in the development of disease and the aging process. |
Analyzing the Euglenoid Plastid Genome Dr. Eric W. Linton is analyzing the plastid genome of euglenoid protozoans. The chloroplast of land plants, site of photosynthesis and oxygen production in plants, was inherited from green algal ancestors. Euglenoid protozoans have chloroplasts that derive from green algae as well, but through an engulfment process whereby a host cell took in a green alga and retained it as part of the cell. Chloroplasts were probably gained and lost several times during evolution of modern euglenoids. By sequencing the complete chloroplast genomes of several euglenoid species that have chloroplasts and several that lack them, the researchers will gain insight into how many times chloroplasts were acquired and lost, and how the host genomes interacted with the chloroplast genomes during this process. Undergraduate and graduate students, as well as high school teachers, will be involved in hands-on research in genomics. An integrative software program for aligning DNA sequences will be further developed and distributed to the scientific community. Euglenoid chloroplasts contain genes found in disease-causing protozoans, and complete genome sequences should provide insight into the origins of these genes. |
Biogeochemical Exploration of Acidic and Neutral Hypersaline Environments of Australia This is a collaborative project of Drs. Melanie R. Mormile, Francisca E. Oboh-Ikuenobe (University of Missouri-Rolla), and Kathleen C. Benison (Central Michigan University) to determine if evaporites truly trap a representative population of microorganisms from hypersaline environments. If this is found to be true, these findings can possibly be extrapolated to microorganisms entrapped in ancient or possibly extraterrestrial evaporites and used to describe previous microbial communities and therefore, make interpretations about past water chemistries and past climates. Microorganisms represent the basic life forms existing in most environmental settings. They are sensitive to climatic parameters, and can influence water chemistry, biological activity, and mineralization. Evaporite minerals are a wealth of paleoenvironmental data due to their sensitivity to climate, water chemistry, and hydrology. In addition, evaporites can form in extreme environmental conditions, such as extremely acid saline lakes in Western Australia. These lakes might serve as good analogs to Mars. Traditionally, studies of evaporite settings and their deposits have overlooked microorganisms largely because they are generally poorly preserved in the rock record. However, through this research, answers to the following questions will be found: What microorganisms are present in the lake waters, groundwaters, and sediments of acid and neutral saline lake environments? Are the microorganisms found living in the waters represented in the fluid inclusions of the evaporite minerals? Are the microorganisms specific acidophiles? What role did the microorganisms play in the evolution of the water chemistry? To answer these questions, a sampling trip will be made to Australia to collect a comprehensive set of lake water, groundwater, evaporite, and siliciclastic sediment samples. The following objectives will be achieved: 1. Identify and compare the biological remains in halite and gypsum with those in their parent waters and sediments. Both traditional culture methods and molecular biology techniques will be used to compare the microbial populations in the environments listed above. 2. Grow evaporite crystals under laboratory conditions to study selected environmental influences on crystal formation and the microorganisms that become entrapped. 3. Identify any differences in microorganisms (ranging from prokaryotes to freshwater dinoflagellates and algae) between neutral and moderately acidic saline lakes and groundwaters in Victoria and Western Australia, between neutral and extremely acidic saline lakes within a small region of Western Australia, as well as among extremely acidic saline lakes and groundwaters in Western Australia. The 16S rDNA from the bacteria isolated from these environments will be sequenced and compared. 4. Constrain depositional, environmental, and climatic conditions using basic sedimentology, petrography, fluid inclusion studies, and palynology. Sedimentary structures and grain characteristics will be used to trace depositional history.
We anticipate that novel microorganisms will be found. These organisms can possibly be used for the bioremediation of contaminated sites that are impacted by extremes in saline and acidic conditions. In addition, our findings will have implications for future Mars research and the possibility that life can occur on planetary bodies besides Earth. Of all the planetary bodies explored, Mars most closely resemble Earth. In particular, terrestrial acid sedimentary systems are similar in general mineralogy, geochemistry, and geomorphology to the Martian surface. Furthermore, this project will be responsible for the training of students ranging from undergraduate level to Post-Doctoral students. There is also a significant outreach component that includes a partnership with the St. Louis Science Center as well as a course on the geology and microbiology of extreme environments targeted towards K-12 educators. |
Environmental Microbiology Research An ABI 310 automated DNA sequencer and a Biolog microbial identification system improves the capacity for environmental microbiology research in Central Michigan. While the primary use of this equipment will be for environmental microbiology research at CMA and Alma College, a secondary but equally important use of this equipment will be for research and teaching by additional CMU Biology faculty. The equipment will meet the needs of a growing number of researchers utilizing molecular techniques. Further, the instruments will be integrated into a number of courses that will reach students at a wide range of levels in their academic preparation. Through additional programs, including the Ronald E. McNair Post Baccalaureate Achievement Program, students underrepresented in the sciences will continue to be encouraged to participate in research projects utilizing the requested instrumentation. |
Using Maize as a Model System to Study a Novel Family of Helitron Related Transposable Elements Transposable elements have played an integral role in evolution and they constitute the most abundant entities in the eukaryotic genome. Helitrons are a recently-discovered family of transposable elements that apparently transpose through replication and strand replacement. Despite their abundance, there is no direct genetic evidence or proof for the existence of an autonomous Helitron. The investigators recently described two maize mutants that were caused by Helitron insertion and provided the first evidence that an active Helitron may reside in the present-day maize genome. This Small Grant for Exploratory Research will establish the direct genetic evidence of an active Helitron. This is high-risk project because the assertion that these maize mutants are caused by relatively recent insertion of Helitrons is based on the assumption that these were isolated in the 1900s. However, there remains a remote possibility that these mutants may represent remnants of ancient alleles that were not discovered earlier. The approach is potentially high pay-off because understanding the mode of transposition of this novel family of transposable elements may yield tools for crop improvement and provide novel insights into genome structure and organization. The objective of the project is to genetically identify the autonomous Helitron by monitoring various maize lines for somatic and heritable reversion events. This is essential in order to definitely identify an autonomous element and establish maize as a system to study the transposition of Helitrons. Broader Impact: The proposed research will provide interdisciplinary training opportunities for both undergraduate and graduate students in Genetics, Molecular Biology and Bioinformatics and reach out to high school students involved in the field experiments. A new course has been developed specifically to integrate Bioinformatics into the mainstream undergraduate and graduate curricula at Oakland University. The students will gain hands-on experience in gene discovery and annotation of sequence data generated by the proposed research. |
C-3'-Nucleic Acid Radicals: Generation and Mechanistic Investigations Oxidative processes are at the heart of numerous chemical and biochemical processes, including the damage of nucleic acids by ionizing radiation or specific drug interactions. This project involves the synthesis of modified nucleosides and nucleotides that will permit the elucidation of the mechanism of degradation of C-3' nucleotide radicals in DNA and RNA. Modifed nucleosides containing photoactive functional groups will be synthesized and incorporated into small DNAs and RNAs designed for the investigation of damage events. The nature and fate of nucleoside radicals derived from these site-specifically functionalized nucleic acid systems will be explored by a variety of chemical, analytical, and biophysical methods. A curriculum for a Master of Science degree will be developed, targeting specific groups in an effort to increase the pool of underrepresented minorities in the chemical workforce. This program specifically targets students who are ill prepared for graduate studies or who have not been successful in previous attempts to receive a graduate degree due to a lack of proper preparation.
Professor Amanda Bryant-Friedrich, of the Department of Chemistry at Oakland University, is developing an understanding of the chemical processes which result in the damage of DNA and RNA. Radiation, drug interactions, and other oxidative processes can lead to the formation of nucleic acid radicals. Through the synthesis and manipulation of modified nucleic acid subunits, Professor Bryant-Friedrich is elucidating the mechanisms by which these radicals lead to nucleic acid degradation. Professor Bryant-Friedrich is also working toward increasing the representation of women and minorities in the chemical workforce. Through development of a Master of Science program at Oakland University, Professor Bryant-Friedrich will provide a program targeting students who are academically ill-prepared for graduate study, placing them on track for employment or for placement in competitive doctoral programs. |
home | about us | contact us
Powered by IEI © 2006 - 2010 | All rights reserved.