Search Results

Advanced search parameters have been applied.
open access

Illumina Unamplified Indexed Library Construction: An Automated Approach

Description: Manual library construction is a limiting factor in Illumina sequencing. Constructing libraries by hand is costly, time-consuming, low-throughput, and ergonomically hazardous, and constructing multiple libraries introduces risk of library failure due to pipetting errors. The ability to construct multiple libraries simultaneously in automated fashion represents significant cost and time savings. Here we present a strategy to construct up to 96 unamplified indexed libraries using Illumina TruSeq … more
Date: March 21, 2011
Creator: Hack, Christopher A.; Sczyrba, Alexander & Cheng, Jan-Fang
Partner: UNT Libraries Government Documents Department
open access

Carboxysomal carbonic anhydrases: Structure and role in microbial CO2 fixation

Description: Cyanobacteria and some chemoautotrophic bacteria are able to grow in environments with limiting CO2 concentrations by employing a CO2-concentrating mechanism (CCM) that allows them to accumulate inorganic carbon in their cytoplasm to concentrations several orders of magnitude higher than that on the outside. The final step of this process takes place in polyhedral protein microcompartments known as carboxysomes, which contain the majority of the CO2-fixing enzyme, RubisCO. The efficiency of CO2… more
Date: June 23, 2010
Creator: Cannon, Gordon C.; Heinhorst, Sabine & Kerfeld, Cheryl A.
Partner: UNT Libraries Government Documents Department
open access

Microbial co-habitation and lateral gene transfer: what transposases can tell us

Description: Determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change over time. In this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with? All currently sequenced microbial genomes were surveyed to identify pairs of taxa that share a transposase that… more
Date: March 1, 2009
Creator: Hooper, Sean D.; Mavromatis, Konstantinos & Kyrpides, Nikos C.
Partner: UNT Libraries Government Documents Department
open access

Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates

Description: Massively parallel pyrosequencing of the small subunit (16S) ribosomal RNA gene has revealed that the extent of rare microbial populations in several environments, the 'rare biosphere', is orders of magnitude higher than previously thought. One important caveat with this method is that sequencing error could artificially inflate diversity estimates. Although the per-base error of 16S rDNA amplicon pyrosequencing has been shown to be as good as or lower than Sanger sequencing, no direct assessme… more
Date: August 1, 2009
Creator: Kunin, Victor; Engelbrektson, Anna; Ochman, Howard & Hugenholtz, Philip
Partner: UNT Libraries Government Documents Department
open access

Multiple Whole Genome Alignments Without a Reference Organism

Description: Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorit… more
Date: January 16, 2009
Creator: Dubchak, Inna; Poliakov, Alexander; Kislyuk, Andrey & Brudno, Michael
Partner: UNT Libraries Government Documents Department
open access

Evolutionary Genomics of Life in (and from) the Sea

Description: High throughput genome sequencing centers that were originally built for the Human Genome Project (Lander et al., 2001; Venter et al., 2001) have now become an engine for comparative genomics. The six largest centers alone are now producing over 150 billion nucleotides per year, more than 50 times the amount of DNA in the human genome, and nearly all of this is directed at projects that promise great insights into the pattern and processes of evolution. Unfortunately, this data is being produce… more
Date: January 9, 2006
Creator: Boore, Jeffrey L.; Dehal, Paramvir & Fuerstenberg, Susan I.
Partner: UNT Libraries Government Documents Department
open access

Bacterial Microcompartments

Description: Bacterialmicrocompartments (BMCs) are organelles composed entirely of protein. They promote specific metabolic processes by encapsulatingand colocalizing enzymes with their substrates and cofactors, by protecting vulnerable enzymes in a defined microenvironment, and bysequestering toxic or volatile intermediates. Prototypes of the BMCsare the carboxysomes of autotrophic bacteria. However, structures of similarpolyhedral shape are being discovered in an ever-increasing number of heterotrophi… more
Date: June 5, 2010
Creator: Kerfeld, Cheryl A.; Heinhorst, Sabine & Cannon, Gordon C.
Partner: UNT Libraries Government Documents Department
open access

Phylogeny and comparative genome analysis of a Basidiomycete fungi

Description: Fungi of the phylum Basidiomycota, make up some 37percent of the described fungi, and are important from the perspectives of forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, plant pathogenic rusts and smuts, and some human pathogens. To better understand these important fungi, we have undertaken a comparative genomic analysis of the Basidiomycetes with available sequenced genomes. We report a phylogeny that sheds light on previously unclear … more
Date: March 14, 2011
Creator: Riley, Robert W.; Salamov, Asaf; Grigoriev, Igor & Hibbett, David
Partner: UNT Libraries Government Documents Department
open access

The Carboxysome and Other Bacterial Microcompartments

Description: - Carboxysomes are part of the carbon concentrating mechanism in cyanobacteria and chemoautotrophs. - Carboxysomes are a subclass of bacterial microcompartments (BMCs); BMCs can encapsulate a range of metabolic processes. - Like some viral particles, the carboxysome can be modeled as an icosahedron-in its case, having 4,000-5,000 hexameric shell subunits and 12 surface pentamers to generate curvature. - The threefold axis of symmetry of the CsoS1D protein in carboxysomes forms a pore that can o… more
Date: June 23, 2010
Creator: Kerfeld, Cheryl A.; Greenleaf, William B. & Kinney, James N.
Partner: UNT Libraries Government Documents Department
open access

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

Description: Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganism… more
Date: December 1, 2009
Creator: Morgan, Jenna L.; Darling, Aaron E. & Eisen, Jonathan A.
Partner: UNT Libraries Government Documents Department
open access

A Bioinformatician's Guide to Metagenomics

Description: As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe step-by-step the chain of decisions accompanying a metagenomic project from the viewpoint of a bioinformatician. We guide the reader through a standard workflow for a metagenomic project beginning with pre-sequencing con… more
Date: August 1, 2008
Creator: Kunin, Victor; Copeland, Alex; Lapidus, Alla; Mavromatis, Konstantinos & Hugenholtz, Philip
Partner: UNT Libraries Government Documents Department
open access

Ancient nature of alternative splicing and functions of introns

Description: Using four genomes: Chamydomonas reinhardtii, Agaricus bisporus, Aspergillus carbonarius, and Sporotricum thermophile with EST coverage of 2.9x, 8.9x, 29.5x, and 46.3x respectively, we identified 11 alternative splicing (AS) types that were dominated by intron retention (RI; biased toward short introns) and found 15, 35, 52, and 63percent AS of multiexon genes respectively. Genes with AS were more ancient, and number of AS correlated with number of exons, expression level, and maximum intron l… more
Date: March 21, 2011
Creator: Zhou, Kemin; Salamov, Asaf; Kuo, Alan; Aerts, Andrea & Grigoriev, Igor
Partner: UNT Libraries Government Documents Department
open access

Agave: a biofuel feedstock for arid and semi-arid environments

Description: Efficient production of plant-based, lignocellulosic biofuels relies upon continued improvement of existing biofuel feedstock species, as well as the introduction of newfeedstocks capable of growing on marginal lands to avoid conflicts with existing food production and minimize use of water and nitrogen resources. To this end, specieswithin the plant genus Agave have recently been proposed as new biofuel feedstocks. Many Agave species are adapted to hot and arid environments generally unsuitabl… more
Date: May 31, 2011
Creator: Gross, Stephen; Martin, Jeffrey; Simpson, June; Wang, Zhong & Visel, Axel
Partner: UNT Libraries Government Documents Department
open access

The complete mitochondrial sequence of the"living fossil" Tricholepidion gertschi: structure, phylogenetic implications, and the description of a novel A/T asymmetrical bias

Description: Traditionally, the 'Apterygota' has been thought to consist of five orders of wingless hexapods (Protura, Collembola, Diplura, Microcoryphia and Zygentoma) believed to be collectively basal to insects (i.e., the Pterygota). However, some studies have questioned this affinity with insects (Dallai, Abele, Spears, Nardi). Further, within these groups are hotly debated issues, including the monophyly of Entognata (Koch, 1997; Kukalova Peck, 1987), the monophyly of Diplura (Bilinski, 1993; Stys and … more
Date: June 23, 2002
Creator: Nardi, F.; Frati, F.; Carapelli, A.; Dallai, R. & Boore, J.
Partner: UNT Libraries Government Documents Department
open access

The First Complete Mitochondrial Genome Sequences for Stomatopod Crustaceans: Implications for Phylogeny

Description: We report the first complete mitochondrial genome sequences of stomatopods and compare their features to each other and to those of other crustaceans. Phylogenetic analyses of the concatenated mitochondrial protein-coding sequences were used to explore relationships within the Stomatopoda, within the malacostracan crustaceans, and among crustaceans and insects. Although these analyses support the monophyly of both Malacostraca and, within it, Stomatopoda, it also confirms the view of a paraphyl… more
Date: September 7, 2005
Creator: Swinstrom, Kirsten; Caldwell, Roy; Fourcade, H. Matthew & Boore, Jeffrey L.
Partner: UNT Libraries Government Documents Department
open access

Reenacting the birth of an intron

Description: An intron is an extended genomic feature whose function requires multiple constrained positions - donor and acceptor splice sites, a branch point, a polypyrimidine tract and suitable splicing enhancers - that may be distributed over hundreds or thousands of nucleotides. New introns are therefore unlikely to emerge by incremental accumulation of functional sub-elements. Here we demonstrate that a functional intron can be created de novo in a single step by a segmental genomic duplication. This e… more
Date: July 1, 2011
Creator: Hellsten, Uffe; Aspden, Julie L.; Rio, Donald C. & Rokhsar, Daniel S.
Partner: UNT Libraries Government Documents Department
open access

Scaling up the 454 Titanium Library Construction and Pooling of Barcoded Libraries

Description: We have been developing a high throughput 454 library construction process at the Joint Genome Institute to meet the needs of de novo sequencing a large number of microbial and eukaryote genomes, EST, and metagenome projects. We have been focusing efforts in three areas: (1) modifying the current process to allow the construction of 454 standard libraries on a 96-well format; (2) developing a robotic platform to perform the 454 library construction; and (3) designing molecular barcodes to allow… more
Date: March 23, 2009
Creator: Phung, Wilson; Hack, Christopher; Shapiro, Harris; Lucas, Susan & Cheng, Jan-Fang
Partner: UNT Libraries Government Documents Department
open access

Comparative analysis of twelve Dothideomycete plant pathogens

Description: The Dothideomycetes are one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops grown for biofuel, food or feed. Most Dothideomycetes have only a single host and related Dothideomycete species can have very diverse host plants. Twelve Dothideomycete genomes have currently been sequenced by the Joint Genome Institute and other sequencing centers. They can be accessed via Mycocosm which has tools for comparative analysis
Date: March 11, 2011
Creator: Ohm, Robin; Aerts, Andrea; Salamov, Asaf; Goodwin, Stephen B. & Grigoriev, Igor
Partner: UNT Libraries Government Documents Department
open access

Genomic Sequencing of Single Microbial Cells from Environmental Samples

Description: Recently developed techniques allow genomic DNA sequencing from single microbial cells [Lasken RS: Single-cell genomic sequencing using multiple displacement amplification, Curr Opin Microbiol 2007, 10:510-516]. Here, we focus on research strategies for putting these methods into practice in the laboratory setting. An immediate consequence of single-cell sequencing is that it provides an alternative to culturing organisms as a prerequisite for genomic sequencing. The microgram amounts of DNA re… more
Date: February 1, 2008
Creator: Ishoey, Thomas; Woyke, Tanja; Stepanauskas, Ramunas; Novotny, Mark & Lasken, Roger S.
Partner: UNT Libraries Government Documents Department
open access

Bacillus anthracis genome organization in light of whole transcriptome sequencing

Description: Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess corre… more
Date: March 22, 2010
Creator: Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas & Borodovsky, Mark
Partner: UNT Libraries Government Documents Department
open access

Gap Closing/Finishing by Targeted Genomic Region Enrichment and Sequencing

Description: Gap Closing/Finishing of draft genome assemblies is a labor and cost intensive process where several rounds of repetitious amplification and sequencing are required. Here we demonstrate a high throughput procedure where custom primers flanking gaps in draft genomes are designed. Primer libraries containing up to 4,000 unique pairs in independent droplets are merged with a fragmented genomic template. From this millions of picoliter scale droplets are formed, each one being the functional equ… more
Date: May 27, 2010
Creator: Singh, Kanwar; Froula, Jeff; Trice, Hope; Pennacchio, Len A. & Chen, Feng
Partner: UNT Libraries Government Documents Department
open access

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

Description: The Genomes On Line Database (GOLD) is a comprehensive resource of information for genome and metagenome projects world-wide. GOLD provides access to complete and ongoing projects and their associated metadata through pre-computed lists and a search page. The database currently incorporates information for more than 2900 sequencing projects, of which 639 have been completed and the data deposited in the public databases. GOLD is constantly expanding to provide metadata information related to th… more
Date: December 31, 2007
Creator: Fenner, Marsha W; Liolios, Konstantinos; Mavromatis, Konstantinos; Tavernarakis, Nektarios & Kyrpides, Nikos C.
Partner: UNT Libraries Government Documents Department
open access

Sequencing the Black Aspergilli species complex

Description: The ~15 members of the Aspergillus section Nigri species complex (the "Black Aspergilli") are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as food processing and spoilage agents and agricultural toxigens. Despite their utility and ubiquity, the morphological and metabolic distinctiveness of the complex's members, and thus their taxonomy, is poorly defined. We are using short read pyroseq… more
Date: March 11, 2011
Creator: Kuo, Alan; Salamov, Asaf; Zhou, Kemin; Otillar, Robert; Baker, Scott & Grigoriev, Igor
Partner: UNT Libraries Government Documents Department
open access

A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower

Description: Asteraceae is the second largest family of plants, with over 20,000 species. For the past few decades, numerous phylogenetic studies have contributed to our understanding of the evolutionary relationships within this family, including comparisons of the fast evolving chloroplast gene, ndhF, rbcL, as well as non-coding DNA from the trnL intron plus the trnLtrnF intergenic spacer, matK, and, with lesser resolution, psbA-trnH. This culminated in a study by Panero and Funk in 2002 that used over 13… more
Date: January 20, 2006
Creator: Timme, Ruth E.; Kuehl, Jennifer V.; Boore, Jeffrey L. & Jansen, Robert K.
Partner: UNT Libraries Government Documents Department
Back to Top of Screen