224 Matching Results

Search Results

Advanced search parameters have been applied.

[Stone path]

Description: Photograph of a stone pathway in Kyoto, Japan. The pathway is visible in the foreground. The path is lined with a row of bushes and a wooden fence on each side. A house is partially visible in the background at the end of the path.
Date: 1978
Creator: Gough, Ray
Partner: UNT College of Visual Arts + Design

Pathways, Networks, and Systems: Theory and Experiments

Description: The international conference provided a unique opportunity for theoreticians and experimenters to exchange ideas, strategies, problems, challenges, language and opportunities in both formal and informal settings. This dialog is an important step towards developing a deep and effective integration of theory and experiments in studies of systems biology in humans and model organisms.
Date: October 30, 2004
Creator: Nadeau, Joseph H. & Lambris, John D.
Partner: UNT Libraries Government Documents Department

Supplementary materials: Improving saccharification efficiency of alfalfa stems through modification of the terminal stages of monolignol biosynthesis

Description: Supplementary materials accompanying an article on improving saccharification efficiency of alfalfa stems through modification of the terminal stages of monolignol biosynthesis.
Date: September 27, 2008
Creator: Jackson, Lisa A.; Shadle, Gail L.; Zhou, Rui; Nakashima, Jin; Chen, Fang & Dixon, R. A.
Partner: UNT College of Arts and Sciences

MicrobesOnline: an integrated portal for comparative and functional genomics

Description: Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.
Date: September 17, 2009
Creator: Dehal, Paramvir S.; Joachimiak, Marcin P.; Price, Morgan N.; Bates, John T.; Baumohl, Jason K.; Chivian, Dylan et al.
Partner: UNT Libraries Government Documents Department

Independent Assessment of Technology Characterizations to Support the Biomass Program Annual State-of-Technology Assessments

Description: This report discusses an investigation that addressed two thermochemical conversion pathways for the production of liquid fuels and addressed the steps to the process, the technology providers, a method for determining the state of technology and a tool to continuously assess the state of technology. This report summarizes the findings of the investigation as well as recommendations for improvements for future studies.
Date: March 1, 2011
Creator: Yeh, B.
Partner: UNT Libraries Government Documents Department

Importance of systems biology in engineering microbes for biofuel production

Description: Microorganisms have been rich sources for natural products, some of which have found use as fuels, commodity chemicals, specialty chemicals, polymers, and drugs, to name a few. The recent interest in production of transportation fuels from renewable resources has catalyzed numerous research endeavors that focus on developing microbial systems for production of such natural products. Eliminating bottlenecks in microbial metabolic pathways and alleviating the stresses due to production of these chemicals are crucial in the generation of robust and efficient production hosts. The use of systems-level studies makes it possible to comprehensively understand the impact of pathway engineering within the context of the entire host metabolism, to diagnose stresses due to product synthesis, and provides the rationale to cost-effectively engineer optimal industrial microorganisms.
Date: December 2, 2009
Creator: Mukhopadhyay, Aindrila; Redding, Alyssa M.; Rutherford, Becky J. & Keasling, Jay D.
Partner: UNT Libraries Government Documents Department

Customizable Modality Pathway Learning Design: Exploring Personalized Learning Choices through a Lens of Self-Regulated Learning

Description: Open online courses provide a unique opportunity to examine learner preferences in an environment that removes several pressures associated with traditional learning. This mixed methods study sought to examine the pathways that learners will create for themselves when given the choice between an instructor-directed modality and learner-directed modality. Study participants were first examined based on their levels of self-regulated learning. Follow-up qualitative interviews were conducted to examine the choices that participants made, the impact of the course design on those choices, and what role self-regulation played in the process. The resulting analysis revealed that participants desired an overall learning experience that was tailored to personal learning preferences, but that technical and design limitations can create barriers in the learning experience. The results from this research can help shape future instructional design efforts that wish to increase learner agency and choice in the educational process.
Date: May 2016
Creator: Crosslin, Matthew Blake
Partner: UNT Libraries

Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination

Description: Genome rearrangements often result from non-allelic homologous recombination (NAHR) between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs) induce NAHR-dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR) occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR-dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer.
Date: August 27, 2010
Creator: Hoang, Margaret L.; Tan, Frederick J.; Lai, David C.; Celniker, Sue E.; Hoskins, Roger A.; Dunham, Maitreya J. et al.
Partner: UNT Libraries Government Documents Department

Characterization of the Cobalamin and Fep Operons in Methylobium petrolphilum PM1

Description: The bacterium Methylobium petroleophilum PM1 is economically important due to its ability to degrade methyl tert-butyl ether (MTBE), a fuel additive. Because PM1 is a representative of all MTBE degraders, it is important to understand the transport pathways critical for the organism to survive in its particular environment. In this study, the cobalamin pathway and select iron transport genes will be characterized to help further understand all metabolic pathways in PM1. PM1 contains a total of four cobalamin operons. A single operon is located on the chromosome. Located on the megaplasmid are two tandem repeats of cob operons and a very close representative of the cob operon located on the chromosome. The fep operon, an iron transport mechanism, lies within the multiple copies of the cob operon. The cob operon and the fep operon appear to be unrelated except for a shared need for the T-on-B-dependent energy transduction complex to assist the operons in moving large molecules across the outer membrane of the cell. A genomic study of the cob and the fep operons with that of phylogenetically related organisms helped to confirm the identity of the cob and fep operons and to represent the pathways. More study of the pathways should be done to find the relationship that positions the two seemingly unrelated cob and fep genes together in what appears to be one operon.
Date: September 6, 2005
Creator: Ewing, J
Partner: UNT Libraries Government Documents Department

Metagenomic Analysis of Microbial Symbionts in a Gutless Worm

Description: Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulphur-oxidizing and sulphate-reducing bacteria, all of which are capable of carbon fixation, thus providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits.
Date: May 1, 2006
Creator: Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N.; Hunteman, Marcel; Richter, Michael; Gloeckner, Frank Oliver et al.
Partner: UNT Libraries Government Documents Department

BIOPAX REPORT SPRING 2007

Description: In July 2004, the Department of Energy (DOE) allocated funds in support of the development of A Data Exchange Format for Biological Pathway Databases (BioPAX). The primary objective of the BioPAX initiative is the development of a standard data exchange format for biological pathway data. This standard will significantly ease the analysis of biological pathways in the life sciences. Support from the DOE has enabled BioPAX to make significant progress towards its objective. We were able to build a very active community of pathway data and software tool providers. Work is continuing on the BioPAX standard with meetings, input and feedback provided for Level 3 of the standard and beyond.
Date: June 1, 2007
Creator: Sander, Chris
Partner: UNT Libraries Government Documents Department

Genomic islands predict functional adaptation in marine actinobacteria

Description: Linking functional traits to bacterial phylogeny remains a fundamental but elusive goal of microbial ecology 1. Without this information, it becomes impossible to resolve meaningful units of diversity and the mechanisms by which bacteria interact with each other and adapt to environmental change. Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house functionally adaptive traits 2. In the case of environmental bacteria, these traits are largely inferred from bioinformatic or gene expression analyses 2, thus leaving few examples in which the functions of island genes have been experimentally characterized. Here we report the complete genome sequences of Salinispora tropica and S. arenicola, the first cultured, obligate marine Actinobacteria 3. These two species inhabit benthic marine environments and dedicate 8-10percent of their genomes to the biosynthesis of secondary metabolites. Despite a close phylogenetic relationship, 25 of 37 secondary metabolic pathways are species-specific and located within 21 genomic islands, thus providing new evidence linking secondary metabolism to ecological adaptation. Species-specific differences are also observed in CRISPR sequences, suggesting that variations in phage immunity provide fitness advantages that contribute to the cosmopolitan distribution of S. arenicola 4. The two Salinispora genomes have evolved by complex processes that include the duplication and acquisition of secondary metabolite genes, the products of which provide immediate opportunities for molecular diversification and ecological adaptation. Evidence that secondary metabolic pathways are exchanged by Horizontal Gene Transfer (HGT) yet are fixed among globally distributed populations 5 supports a functional role for their products and suggests that pathway acquisition represents a previously unrecognized force driving bacterial diversification
Date: April 1, 2009
Creator: Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel; Gontang, Erin; McGlinchey, Ryan et al.
Partner: UNT Libraries Government Documents Department

Invariability of Central Metabolic Flux Distribution in Shewanella oneidensis MR-1 Under Environmental or Genetic Perturbations

Description: An environmentally important bacterium with versatile respiration, Shewanella oneidensis MR-1, displayed significantly different growth rates under three culture conditions: minimal medium (doubling time {approx} 3 hrs), salt stressed minimal medium (doubling time {approx} 6 hrs), and minimal medium with amino acid supplementation (doubling time {approx}1.5 hrs). {sup 13}C-based metabolic flux analysis indicated that fluxes of central metabolic reactions remained relatively constant under the three growth conditions, which is in stark contrast to the reported significant changes in the transcript and metabolite profiles under various growth conditions. Furthermore, ten transposon mutants of S. oneidensis MR-1 were randomly chosen from a transposon library and their flux distributions through central metabolic pathways were revealed to be identical, even though such mutational processes altered the secondary metabolism, for example, glycine and C1 (5,10-Me-THF) metabolism.
Date: April 21, 2009
Creator: Tang, Yinjie; Martin, Hector Garcia; Deutschbauer, Adam; Feng, Xueyang; Huang, Rick; Llora, Xavier et al.
Partner: UNT Libraries Government Documents Department

Optimal flux patterns in cellular metabolic networks

Description: The availability of whole-cell level metabolic networks of high quality has made it possible to develop a predictive understanding of bacterial metabolism. Using the optimization framework of flux balance analysis, I investigate metabolic response and activity patterns to variations in the availability of nutrient and chemical factors such as oxygen and ammonia by simulating 30,000 random cellular environments. The distribution of reaction fluxes is heavy-tailed for the bacteria H. pylori and E. coli, and the eukaryote S. cerevisiae. While the majority of flux balance investigations have relied on implementations of the simplex method, it is necessary to use interior-point optimization algorithms to adequately characterize the full range of activity patterns on metabolic networks. The interior-point activity pattern is bimodal for E. coli and S. cerevisiae, suggesting that most metabolic reaction are either in frequent use or are rarely active. The trimodal activity pattern of H. pylori indicates that a group of its metabolic reactions (20%) are active in approximately half of the simulated environments. Constructing the high-flux backbone of the network for every environment, there is a clear trend that the more frequently a reaction is active, the more likely it is a part of the backbone. Finally, I briefly discuss the predicted activity patterns of the central-carbon metabolic pathways for the sample of random environments.
Date: January 20, 2007
Creator: Almaas, E
Partner: UNT Libraries Government Documents Department

Macro-System Model Project #AN011 (Presentation)

Description: A review of the Macro-System Model for hydrogen production pathways analysis, including objectives, accomplishments, collaborations, and future work. Presented at the 2010 U.S. Department of Energy Hydrogen Program and Vehicle Technologies Program Annual Merit Review and Peer Evaluation Meeting, June 7-11, 2010, in Washington, DC.
Date: June 8, 2010
Creator: Ruth, M. F.; Diakov, V.; Sa, T. J. & Goldsby, M.
Partner: UNT Libraries Government Documents Department

Symbiosis insights through metagenomic analysis of a microbialconsortium

Description: Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here, we used a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut, and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulfur-oxidizing and sulfate-reducing bacteria, all of which are capable of carbon fixation, providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model which describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments which it inhabits.
Date: September 1, 2006
Creator: Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N.; Hunteman,Marcel; Richter, Michael; Gloeckner, Frank Oliver et al.
Partner: UNT Libraries Government Documents Department

A program to assess microbial impacts on nuclear waste containment

Description: In this paper we discuss aspects of a comprehensive program to identify and bound potential effects of microorganisms on long-term nuclear waste containment, using as examples, studies conducted within the Yucca Mountain Project. A comprehensive program has been formulated which cuts across standard disciplinary lines to address the specific concerns of microbial activity in a radioactive waste repository. Collectively, this program provides bounding parameters of microbial activities that modify the ambient geochemistry and hydrology, modify corrosion rates, and transport and transform radionuclides under conditions expected to be encountered after geological waste emplacement. This program is intended to provide microbial reaction rates and bounding conditions in a form that can be integrated into existing chemical and hydrological models. The inclusion of microbial effects will allow those models to more accurately assess long term repository integrity.
Date: February 20, 1996
Creator: Horn, J. & Meike, A.
Partner: UNT Libraries Government Documents Department

Plant biochemistry course, 1993

Description: This paper provides a brief description of a summer lecture course on metabolic pathways and regulation of flow through these pathways in plants. Descriptions of the 1992 course held at La Jolla,Ca; 1993 course held in Madison, Wis, and plans for the 1994 course projected for East Lansing, MI.
Date: December 31, 1993
Partner: UNT Libraries Government Documents Department

Quarterly report of Biological and Medical Research Division, April 1955

Description: This report is a compilation of 48 investigator prepared summaries of recent progress in individual research programs of the Biology and Medical Division of the Argonne National Laboratory for the quarterly period ending April,1955. Individual reports are about 3-6 pages in length and often contain research data.
Date: April 1, 1955
Creator: Brues, A.M.
Partner: UNT Libraries Government Documents Department