University of Georgia

About: University of Georgia is a education organization based out in Athens, Georgia, United States. It is known for research contribution in the topics: Population & Gene. The organization has 41934 authors who have published 93622 publications receiving 3713212 citations. The organization is also known as: UGA & Franklin College.

Biofilm Formation and Control in Food Processing Facilities

Abstract: Microorganisms on wet surfaces have the ability to aggregate, grow into microcolonies, and produce biofilm. Growth of biofilms in food processing environments leads to increased opportunity for microbial contamination of the processed product. These biofilms may contain spoilage and pathogenic microorganisms. Microorganisms within biofilms are protected from sanitizers increasing the likelihood of survival and subsequent contamination of food. This increases the risk of reduced shelf life and disease transmission. Extracellular polymeric substances associated with biofilm that are not removed by cleaning provide attachment sites for microorganisms newly arrived to the cleaned system. Biofilm formation can also cause the impairment of heat transfer and corrosion to metal surfaces. Some of the methods used to control biofilm formation include mechanical and manual cleaning, chemical cleaning and sanitation, and application of hot water.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Abstract: Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

Stream ecosystem function in urbanizing landscapes

Abstract: Ecologists have described an urban stream syndrome with attributes such as elevated nutrients and contaminants, increased hydrologic flashiness, and altered biotic assemblages. Ecosystem function probably also varies with extent of urbanization, although there are few stream networks in which this prediction has been studied. We examined functional characteristics of 6 tributaries of the Chattahoochee River near Atlanta, Georgia, USA, whose catchments differed in degree of urbanization. We conducted short-term NH4- and PO4-addition experiments to measure nutrient uptake velocity, which is the rate at which a nutrient moves through the water column toward the benthos. Both NH4 and soluble reactive P uptake velocities decreased as indicators of urbanization (i.e., % of catchment covered by high-intensity urban development) increased. The amount of fine benthic organic matter (FBOM) also decreased with increasing urbanization, and uptake velocities were directly related to FBOM. Uptake velocities wer...

The F-box protein family.

Abstract: The F-box is a protein motif of approximately 50 amino acids that functions as a site of protein-protein interaction. F-box proteins were first characterized as components of SCF ubiquitin-ligase complexes (named after their main components, Skp I, Cullin, and an F-box protein), in which they bind substrates for ubiquitin-mediated proteolysis. The F-box motif links the F-box protein to other components of the SCF complex by binding the core SCF component Skp I. F-box proteins have more recently been discovered to function in non-SCF protein complexes in a variety of cellular functions. There are 11 F-box proteins in budding yeast, 326 predicted in Caenorhabditis elegans, 22 in Drosophila, and at least 38 in humans. F-box proteins often include additional carboxy-terminal motifs capable of protein-protein interaction; the most common secondary motifs in yeast and human F-box proteins are WD repeats and leucine-rich repeats, both of which have been found to bind phosphorylated substrates to the SCF complex. The majority of F-box proteins have other associated motifs, and the functions of most of these proteins have not yet been defined.

Rapid recent growth and divergence of rice nuclear genomes

Abstract: By employing the nuclear DNA of the African rice Oryza glaberrima as a reference genome, the timing, natures, mechanisms, and specificities of recent sequence evolution in the indica and japonica subspecies of Oryza sativa were identified. The data indicate that the genome sizes of both indica and japonica have increased substantially, >2% and >6%, respectively, since their divergence from a common ancestor, mainly because of the amplification of LTR-retrotransposons. However, losses of all classes of DNA sequence through unequal homologous recombination and illegitimate recombination have attenuated the growth of the rice genome. Small deletions have been particularly frequent throughout the genome. In >1 Mb of orthologous regions that we analyzed, no cases of complete gene acquisition or loss from either indica or japonica were found, nor was any example of precise transposon excision detected. The sequences between genes were observed to have a very high rate of divergence, indicating a molecular clock for transposable elements that is at least 2-fold more rapid than synonymous base substitutions within genes. We found that regions prone to frequent insertions and deletions also exhibit higher levels of point mutation. These results indicate a highly dynamic rice genome with competing processes for the generation and removal of genetic variation.