4 Matching Results

Search Results

Advanced search parameters have been applied.

Impacts of Biofilm Formation on Cellulose Fermentation

Description: This project addressed four major areas of investigation: i) characterization of formation of Cellulomonas uda biofilms on cellulose; ii) characterization of Clostridium phytofermentans biofilm development; colonization of cellulose and its regulation; iii) characterization of Thermobifida fusca biofilm development; colonization of cellulose and its regulation; and iii) description of the architecture of mature C. uda, C. phytofermentans, and T. fusca biofilms. This research is aimed at advancing understanding of biofilm formation and other complex processes involved in the degradation of the abundant cellulosic biomass, and the biology of the microbes involved. Information obtained from these studies is invaluable in the development of practical applications, such as the single-step bioconversion of cellulose-containing residues to fuels and other bioproducts. Our results have clearly shown that cellulose-decomposing microbes rapidly colonize cellulose and form complex structures typical of biofilms. Furthermore, our observations suggest that, as cells multiply on nutritive surfaces during biofilms formation, dramatic cell morphological changes occur. We speculated that morphological changes, which involve a transition from rod-shaped cells to more rounded forms, might be more apparent in a filamentous microbe. In order to test this hypothesis, we included in our research a study of biofilm formation by T. fusca, a thermophilic cellulolytic actinomycete commonly found in compost. The cellulase system of T. fusca has been extensively detailed through the work of David Wilson and colleagues at Cornell, and also, genome sequence of a T. fusca strain has been determine by the DOE Joint Genome Institute. Thus, T. fusca is an excellent subject for studies of biofilm development and its potential impacts on cellulose degradation. We also completed a study of the chitinase system of C. uda. This work provided essential background information for understanding how C. uda colonizes and degrades insoluble substrates. Major accomplishments of the project include: • Development of media containing ...
Date: October 31, 2009
Creator: Leschine, Susan
Partner: UNT Libraries Government Documents Department

Biochemistry and genetics of autotrophy in Methanococcus

Description: The project investigated fundamental aspects of carbon metabolism and genetics in the methane-producing archaeon Methanococcus maripaludis. The project yielded 23 peer-reviewed publications and five reviews from 1997-2007. PDFs of the peer-reviewed publications are included in the next section. Some papers of special interest are listed below. The pathway of pyruvate biosynthesis was elucidated by a combination of biochemical and physiological studies. This work characterized the very oxygen sensitive pyruvate oxidoreductase and showed that the enzyme was irreversible under physiological conditions. Evidence for the flow of electrons from the energy coupling hydrogenase b (Ehb) was presented. These results were published in the following papers. Yang, Y.L., J.N. Gluska, and W.B. Whitman (2002) Intracellular pyruvate flux in the methane-producing archaeon Methanococcus maripaludis. Arch. Microbiol. 178: 493-498. Lin, W.C., Y.L. Yang, and W.B. Whitman (2003) The anabolic pyruvate oxidoreductase from Methanococcus maripaludis. Arch. Microbiol. 179: 444-456. Lin, W., and W.B. Whitman (2004) The importance of porE and porF in the anabolic pyruvate oxidoreductase of Methanococcus maripaludis. Arch. Microbiol. 181: 68-73. Porat, I., W. Kim, E.L. Hendrickson, Q. Xia, Y. Zhang, T. Wang, F. Taub, B.C. Moore, I.J. Anderson, M. Hackett, J.A. Leigh, and W.B. Whitman (2006) Disruption of the Ehb hydrogenase operon limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis. J. Bacteriol. 188: 1373-1380. The presence of a novel pathway of aromatic amino acid biosynthesis was discovered and elucidated as part of these studies. These results were published in the following papers. Tumbula, D. L., Q. Teng, M. G. Bartlett, and W. B. Whitman (1997) Ribose biosynthesis and evidence for an alternative first step in the common aromatic amino acid pathway in Methanococcus maripaludis. J. Bacteriol. 179:6010-6013. Porat, I., B.W. Waters, Q. Teng, and W.B. Whitman (2004) Two biosynthetic pathways for the aromatic amino acids in the archaeon Methanococcus maripaludis. J. Bacteriol. ...
Date: March 31, 2009
Creator: Whitman, William B.
Partner: UNT Libraries Government Documents Department

Functional Analysis of Arabidopsis Sucrose Transporters

Description: Sucrose is the main photosynthetic product that is transported in the vasculature of plants. The long-distance transport of carbohydrates is required to support the growth and development of net-importing (sink) tissues such as fruit, seeds and roots. This project is focused on understanding the transport mechanism sucrose transporters (SUTs). These are proton-coupled sucrose uptake transporters (membrane proteins) that are required for transport of sucrose in the vasculature and uptake into sink tissues. The accomplishments of this project included: 1) the first analysis of substrate specificity for any SUT. This was accomplished using electrophysiology to analyze AtSUC2, a sucrose transporter from companion cells in Arabidopsis. 2) the first analysis of the transport activity for a monocot SUT. The transport kinetics and substrate specificity of HvSUT1 from barley were studied. 3) the first analysis of a sucrose transporter from sugarcane. and 4) the first analysis of transport activity of a sugar alcohol transporter homolog from plants, AtPLT5. During this period four primary research papers, funded directly by the project, were published in refereed journals. The characterization of several sucrose transporters was essential for the current effort in the analysis of structure/function for this gene family. In particular, the demonstration of strong differences in substrate specificity between type I and II SUTs was important to identify targets for site-directed mutagenesis.
Date: March 31, 2009
Creator: Ward, John M.
Partner: UNT Libraries Government Documents Department

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Description: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.
Date: July 31, 2009
Creator: N. Price, Morgan; S. Dehal, Paramvir & P. Arkin, Adam
Partner: UNT Libraries Government Documents Department