Computer Algorithm-Based Hydroxyurea Dosing Facilitates Titration to Maximum Tolerated Dose in Sickle Cell Anemia.

Adults with sickle cell disease (SCD) experience acute and chronic complications and die prematurely. When taken at maximum tolerated dose (MTD), hydroxyurea prolongs survival; however, it has not consistently reversed organ dysfunction. Patients also frequently do not take hydroxyurea, at least in part because of physician discomfort with prescribing hydroxyurea. We sought to develop a computer program that could easily titrate hydroxyurea to MTD. This was a single-arm, open-label pilot study. Fifteen patients with homozygous SCD were enrolled in the protocol, and 10 patients were followed at baseline and then for 1 year after hydroxyurea initiation or dose titration. Fetal hemoglobin significantly increased in all 10 patients from 8.3% to 25.1% (P < .001). Nine patients were titrated to MTD in an average of 7.9 months, and the tenth patient's hydroxyurea dose was increased to 33 mg/kg/day. Computer program dosing recommendations were the same as manual dosing decisions made using the same algorithm for all patients and at all times. We also evaluated markers of cardiopulmonary, liver and renal damage. Although cardiopulmonary function did not significantly improve, direct bilirubin and alanine aminotransferase levels significantly decreased (P < .001 and P < .01, respectively). Last, although kidney function did not improve, degree of proteinuria was significantly reduced (P < .05). We have developed a computer program that reliably titrates hydroxyurea to MTD. A larger study is indicated to test the program either as a computer program or a downloadable application.

Chinese hamster genome database: an online resource for the CHO community at www.CHOgenome.org.

The Chinese hamster genome database (http://www.chogenome.org/) is an online resource for the Chinese hamster (Cricetulus griseus) and Chinese hamster ovary (CHO) cell communities. CHO cells are important for biomedical research and are widely used in industry for the production of biopharmaceuticals. The genome of the CHO-K1 cell line was recently sequenced and the CHO community has developed an online resource to facilitate accessibility of the genomic data and the development of genomic tools.

Genomic sequencing and analysis of a Chinese hamster ovary cell line using Illumina sequencing technology.

BACKGROUND: Chinese hamster ovary (CHO) cells are among the most widely used hosts for therapeutic protein production. Yet few genomic resources are available to aid in engineering high-producing cell lines. RESULTS: High-throughput Illumina sequencing was used to generate a 1x genomic coverage of an engineered CHO cell line expressing secreted alkaline phosphatase (SEAP). Reference-guided alignment and assembly produced 3.57 million contigs and CHO-specific sequence information for ~ 18,000 mouse and ~ 19,000 rat orthologous genes. The majority of these genes are involved in metabolic processes, cellular signaling, and transport and represent attractive targets for cell line engineering. CONCLUSIONS: This demonstrates the applicability of next-generation sequencing technology and comparative genomic analysis in the development of CHO genomic resources.

EnGenIUS -- Environmental Genome Informational Utility System.

Short-insert shotgun sequencing approaches have been applied in recent years to environmental genomic libraries. In the case of complex multispecies microbial communities, there can be many sequence reads that are not incorporated into assemblies, and thus need to be annotated and accessible as single reads. Most existing annotation systems and genome databases accommodate assembled genomes containing contiguous gene-encoding sequences. Thus, a solution is required that can work effectively with environmental genomic annotation information to facilitate data analysis. The Environmental Genome Informational Utility System (EnGenIUS) is a comprehensive environmental genome (metagenome) research toolset that was specifically designed to accommodate the needs of large (> 250 K sequence reads) environmental genome sequencing efforts. The core EnGenIUS modules consist of a set of UNIX scripts and PHP programs used for data preprocessing, an annotation pipeline with accompanying analysis tools, two entity relational databases, and a graphical user interface. The annotation pipeline has a modular structure and can be customized to best fit input data set properties. The integrated entity relational databases store raw data and annotation analysis results. Access to the underlying databases and services is facilitated through a web-based graphical user interface. Users have the ability to browse, upload, download, and analyze preprocessed data, based on diverse search criteria. The EnGenIUS toolset was successfully tested using the Alvinella pompejana epibiont environmental genome data set, which comprises more than 300 K sequence reads. A fully browsable EnGenIUS portal is available at (http://ocean.dbi.udel.edu/) (access code: "guest"). The scope of this paper covers the implementation details and technical aspects of the EnGenIUS toolset.

Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility.

Hydrothermal vent ecosystems support diverse life forms, many of which rely on symbiotic associations to perform functions integral to survival in these extreme physicochemical environments. Epsilonproteobacteria, found free-living and in intimate associations with vent invertebrates, are the predominant vent-associated microorganisms. The vent-associated polychaete worm, Alvinella pompejana, is host to a visibly dense fleece of episymbionts on its dorsal surface. The episymbionts are a multispecies consortium of Epsilonproteobacteria present as a biofilm. We unraveled details of these enigmatic, uncultivated episymbionts using environmental genome sequencing. They harbor wide-ranging adaptive traits that include high levels of strain variability analogous to Epsilonproteobacteria pathogens such as Helicobacter pylori, metabolic diversity of free-living bacteria, and numerous orthologs of proteins that we hypothesize are each optimally adapted to specific temperature ranges within the 10-65 degrees C fluctuations characteristic of the A. pompejana habitat. This strategic combination enables the consortium to thrive under diverse thermal and chemical regimes. The episymbionts are metabolically tuned for growth in hydrothermal vent ecosystems with genes encoding the complete rTCA cycle, sulfur oxidation, and denitrification; in addition, the episymbiont metagenome also encodes capacity for heterotrophic and aerobic metabolisms. Analysis of the environmental genome suggests that A. pompejana may benefit from the episymbionts serving as a stable source of food and vitamins. The success of Epsilonproteobacteria as episymbionts in hydrothermal vent ecosystems is a product of adaptive capabilities, broad metabolic capacity, strain variance, and virulent traits in common with pathogens.