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. |
Linoleic Acid  This research is focused on two components. First, the metabolic disposition and biological activity of oxidized derivatives of linoleic acid is being actively investigated. The major pathway for oxygenation of linoleic acid involves production of 13-hydroperoxyoctadecadienoic acid by the action of lipoxygenases or cyclooxygenases. This is followed by reduction of the hydroperoxy fatty acid to the hydroxy derivative (13-HODE) and the subsequent dehydrogenation of 13-HODE to the 2,4-dienone 13-OXO. Research efforts are currently focused in two areas related to this metabolic pathway. One area of emphasis involves unraveling the biochemical contribution of 13-HODE dehydrogenase to cellular regulation. A second area of interest involves identification of crucial cellular targets interacting with key metabolites of oxidized linoleic acid. Both chemical and biochemical techniques are employed to address these questions and elucidate these pathways.
A second major area of interest involves attempts to elucidate the mechanism by which conjugated derivatives of linoleic acid, known as CLAs, inhibit mammary tumorigenesis. The CLAs have been shown to be non-toxic inhibitors of both initiation and post initiation events during mammary carcinogenesis. The emphasis in these investigations involves an examination of the potential modulation of the oxidative metabolism of polyunsaturated fatty acids by CLA. Again, identification of biological targets and the elucidation of metabolic pathways available to CLA are major goals of these NIH-supported investigations. |
Involvement of p59fyn in XEphA4 signaling  Eph class receptors are cell surface proteins that, when activated by their ligands, cause cell-cell repulsion, which is used to limit cellular interactions, thus aiding in a variety of processes, such as tissue formation and guidance of migrating cells. Activation of one member of this family in Xenopus laevis, XEphA4, leads to reorganization of the actin cytoskeleton via a mechanism involving inhibition of the small GTPase XRhoA. The rest of the biochemical pathway by which XEphA4 mediates its effects is largely unknown. This project will test the hypothesis that the tyrosine kinase Fyn (a member of the Src family of non-receptor tyrosine kinases) is involved in signaling by XEphA4. The hypothesis will be tested using a Xenopus laevis embryo assay system. This system allows expression and activation of XEphA4 in early frog embryos (at a time when the receptor would not normally be expressed), which results in loss of cell adhesion, change in cell shape, and loss of cell polarity by epithelial cells. Candidate molecules in the signaling pathway, such as Fyn in the current project, can be tested by expressing mutant forms of the candidate molecule alone or in conjunction with XEphA4 and assessing the effect on embryo phenotype. The hypothesis will be tested using experimental approaches that comprise four objectives, each of which tests a prediction based on the hypothesis. Objective 1 will test whether constitutively-active Fyn can recreate the XEphA4 phenotype. Objective 2 will determine whether inhibition of Fyn prevents the phenotypic effects of XEphA4. Objective 3 will test whether constitutive activity of XRhoA can prevent the effects of active Fyn. Objective 4 will assay for changes in Fyn activity levels in response to XEPhA4 activity. This project should add greatly to understanding of Eph receptor signaling, and will have broader impact through training of graduate and undergraduate students, including pre-service secondary-level biology teachers, and through outreach programs to local secondary schools. |
Rhizosphere Influence on Hydrocarbon Metabolizing Microorganisms  The goal of this project is to use cultivation and non-cultivation based methods to characterize the microbial populations associated with plant rhizospheres in hydrocarbon-impacted soils. A series of plots have been established in polynuclear aromatic hydrocarbon (PAH) impacted soils that have been planted with species native to Michigan. Preliminary results with these plots indicate that individual plant species have different effects on the extent of hydrocarbon removal. In this research project, experiments will be conducted to evaluate the different influences that unique plant species have on the microbial communities inhabiting the rhizospheres. This will be performed by analyzing soil samples collected from different plots at various time intervals. Microbial communities will be characterized by 1) sequencing a gene that will enable the identification of microorganisms present (16S rRNA genes) 2) sequencing genes involved in PAH-degradation (PAH dioxygenases), and 3) comparing carbon utilization profiles of rhizosphere samples. It is anticipated that these experiments will reveal microbiological factors that enable some plants to accelerate the removal of PAHs from contaminated soils, whereas others hinder their removal. The broader impacts include developing an ecological framework for understanding how an applied technology like phytoremediation can be optimized. Some aspects of this project will also be integrated into a semester long cooperative laboratory experience for a microbial ecology and plant physiology class taught during the same semester. Further, this support will be used to increase research opportunities for underrepresented populations through local outreach and through additional, formal NSF channels (e.g. REU and RET supplements). |
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. |
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