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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>This demonstrates the applicability of next-generation sequencing technology and comparative genomic analysis in the development of CHO genomic resources.</p

A 12 GHz satellite video receiver: Low noise, low cost prototype model for TV reception from broadcast satellites

A 12-channel synchronous phase lock video receiver consisting of an outdoor downconverter unit and an indoor demodulator unit was developed to provide both low noise performance and low cost in production quantities of 1000 units. The prototype receiver can be mass produced at a cost under $1540 without sacrificing system performance. The receiver also has the capability of selecting any of the twelve assigned satellite broadcast channels in the frequency range 11.7 to 12.2 GHz

Genetic variation exists for telomeric array organization within and among the genomes of normal, immortalized, and transformed chicken systems

This study investigated telomeric array organization of diverse chicken genotypes utilizing in vivo and in vitro cells having phenotypes with different proliferation potencies. Our experimental objective was to characterize the extent and nature of array variation present to explore the hypothesis that mega-telomeres are a universal and fixed feature of chicken genotypes. Four different genotypes were studied including normal (UCD 001, USDA-ADOL Line 0), immortalized (DF-1), and transformed (DT40) cells. Both cytogenetic and molecular approaches were utilized to develop an integrated view of telomeric array organization. It was determined that significant variation exists within and among chicken genotypes for chromosome-specific telomeric array organization and total genomic-telomeric sequence content. Although there was variation for mega-telomere number and distribution, two mega-telomere loci were in common among chicken genetic lines (GGA 9 and GGA W). The DF-1 cell line was discovered to maintain a complex derivative karyotype involving chromosome fusions in the homozygous and heterozygous condition. Also, the DF-1 cell line was found to contain the greatest amount of telomeric sequence per genome (17%) as compared to UCD 001 (5%) and DT40 (1.2%). The chicken is an excellent model for studying unique and universal features of vertebrate telomere biology, and characterization of the telomere length variation among genotypes will be useful in the exploration of mechanisms controlling telomere length maintenance in different cell types having unique phenotypes

Supplemental Immobilization Cast Stone Technology Development and Waste Form Qualification Testing Plan

The Hanford Tank Waste Treatment and Immobilization Plant (WTP) is being constructed to treat the 56 million gallons of radioactive waste stored in 177 underground tanks at the Hanford Site. The WTP includes a pretreatment facility to separate the wastes into high-level waste (HLW) and low-activity waste (LAW) fractions for vitrification and disposal. The LAW will be converted to glass for final disposal at the Integrated Disposal Facility (IDF). The pretreatment facility will have the capacity to separate all of the tank wastes into the HLW and LAW fractions, and the HLW Vitrification Facility will have the capacity to vitrify all of the HLW. However, a second immobilization facility will be needed for the expected volume of LAW requiring immobilization. A number of alternatives, including Cast Stone—a cementitious waste form—are being considered to provide the additional LAW immobilization capacity

Letter Report: LAW Simulant Development for Cast Stone Screening Test

More than 56 million gallons of radioactive and hazardous waste are stored in 177 underground storage tanks at the U.S. Department of Energy’s (DOE’s) Hanford Site in southeastern Washington State. The Hanford Tank Waste Treatment and Immobilization Plant (WTP) is being constructed to treat the wastes and immobilize them in a glass waste form. The WTP includes a pretreatment facility to separate the wastes into a small volume of high-level waste (HLW) containing most of the radioactivity and a larger volume of low-activity waste (LAW) containing most of the nonradioactive chemicals. The HLW will be converted to glass in the HLW vitrification facility for ultimate disposal at an offsite federal repository. At least a portion (~35%) of the LAW will be converted to glass in the LAW vitrification facility and will be disposed of onsite at the Integrated Disposal Facility (IDF). The pretreatment and HLW vitrification facilities will have the capacity to treat and immobilize the wastes destined for each facility. However, a second facility will be needed for the expected volume of additional LAW requiring immobilization. A cementitious waste form known as Cast Stone is being considered to provide the required additional LAW immobilization capacity. The Cast Stone waste form must be acceptable for disposal in the IDF. The Cast Stone waste form and immobilization process must be tested to demonstrate that the final Cast Stone waste form can comply with waste acceptance criteria for the IDF disposal facility and that the immobilization processes can be controlled to consistently provide an acceptable waste form product. Further, the waste form must be tested to provide the technical basis for understanding the long term performance of the waste form in the IDF disposal environment. These waste form performance data are needed to support risk assessment and performance assessment (PA) analyses of the long-term environmental impact of the waste disposal in the IDF. A testing program was developed in fiscal year (FY) 2012 describing in some detail the work needed to develop and qualify Cast Stone as a waste form for the solidification of Hanford LAW (Westsik et al. 2012). Included within Westsik et al. (2012) is a section on the near-term needs to address Tri-Party Agreement Milestone M-062-40ZZ. The objectives of the testing program to be conducted in FY 2013 and FY 2014 are to: • Determine an acceptable formulation for the LAW Cast Stone waste form. • Evaluate sources of dry materials for preparing the LAW Cast Stone. • Demonstrate the robustness of the Cast Stone waste form for a range of LAW compositions. • Demonstrate the robustness of the formulation for variability in the Cast Stone process. • Provide Cast Stone contaminant release data for PA and risk assessment evaluations. The first step in determining an acceptable formulation for the LAW Cast Stone waste form is to conduct screening tests to examine expected ranges in pretreated LAW composition, waste stream concentrations, dry-materials sources, and mix ratios of waste feed to dry blend. A statistically designed test matrix will be used to evaluate the effects of these key parameters on the properties of the Cast Stone as it is initially prepared and after curing. The second phase of testing will focus on selection of a baseline Cast Stone formulation for LAW and demonstrating that Cast Stone can meet expected waste form requirements for disposal in the IDF. It is expected that this testing will use the results of the screening tests to define a smaller suite of tests to refine the composition of the baseline Cast Stone formulation (e.g. waste concentration, water to dry mix ratio, waste loading)

Interaction Analysis between HLA-DRB1 Shared Epitope Alleles and MHC Class II Transactivator CIITA Gene with Regard to Risk of Rheumatoid Arthritis

HLA-DRB1 shared epitope (SE) alleles are the strongest genetic determinants for autoantibody positive rheumatoid arthritis (RA). One of the key regulators in expression of HLA class II receptors is MHC class II transactivator (CIITA). A variant of the CIITA gene has been found to associate with inflammatory diseases

Feeding behavior of the ctenophore Thalassocalyce inconstans : revision of anatomy of the order Thalassocalycida

© 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Marine Biology 156 (2009): 1049-1056, doi:10.1007/s00227-009-1149-6.Behavioral observations using a remotely operated vehicle (ROV) in the Gulf of California in March, 2003, provided insights into the vertical distribution, feeding and anatomy of the rare and delicate ctenophore Thalassocalyce inconstans. Additional archived ROV video records from the Monterey Bay Aquarium Research Institute of 288 sightings of T. inconstans and 2,437 individual observations of euphausiids in the Gulf of California and Monterey Canyon between 1989 and 2005 were examined to determine ctenophore and euphausiid prey depth distributions with respect to temperature and dissolved oxygen concentration [dO]. In the Gulf of California most ctenophores (96.9%) were above 350 m, the top of the oxygen minimum layer. In Monterey Canyon the ctenophores were more widely distributed throughout the water column, including the hypoxic zone, to depths as great as 3,500 m. Computer-aided behavioral analysis of two video records of the capture of euphausiids by T. inconstans showed that the ctenophore contracted its bell almost instantly (0.5 s), transforming its flattened, hemispherical resting shape into a closed bi-lobed globe in which seawater and prey were engulfed. Euphausiids entrapped within the globe displayed a previously undescribed escape response for krill (‘probing behavior’), in which they hovered and gently probed the inner surfaces of the globe with antennae without stimulating further contraction by the ctenophore. Such rapid bell contraction could be effected only by a peripheral sphincter muscle even though the presence of circumferential ring musculature was unknown for the Phylum Ctenophora. Thereafter, several live T. inconstans were collected by hand off Barbados and microscopic observations confirmed that assumption.Supported by the David and Lucile Packard Foundation and NOAA Grant #NA06OAR4600091

Photoemission analysis of chemically modified TlBr surfaces for improved radiation detectors

Abstract not provide

Reciprocal co-regulation of EGR2 and MECP2 is disrupted in Rett syndrome and autism

Mutations in MECP2, encoding methyl-CpG-binding protein 2 (MeCP2), cause the neurodevelopmental disorder Rett syndrome (RTT). Although MECP2 mutations are rare in idiopathic autism, reduced MeCP2 levels are common in autism cortex. MeCP2 is critical for postnatal neuronal maturation and a modulator of activity-dependent genes such as Bdnf (brain-derived neurotropic factor) and JUNB. The activity-dependent early growth response gene 2 (EGR2), required for both early hindbrain development and mature neuronal function, has predicted binding sites in the promoters of several neurologically relevant genes including MECP2. Conversely, MeCP2 family members MBD1, MBD2 and MBD4 bind a methylated CpG island in an enhancer region located in EGR2 intron 1. This study was designed to test the hypothesis that MECP2 and EGR2 regulate each other’s expression during neuronal maturation in postnatal brain development. Chromatin immunoprecipitation analysis showed EGR2 binding to the MECP2 promoter and MeCP2 binding to the enhancer region in EGR2 intron 1. Reduction in EGR2 and MeCP2 levels in cultured human neuroblastoma cells by RNA interference reciprocally reduced expression of both EGR2 and MECP2 and their protein products. Consistent with a role of MeCP2 in enhancing EGR2, Mecp2-deficient mouse cortex samples showed significantly reduced EGR2 by quantitative immunofluorescence. Furthermore, MeCP2 and EGR2 show coordinately increased levels during postnatal development of both mouse and human cortex. In contrast to age-matched Controls, RTT and autism postmortem cortex samples showed significant reduction in EGR2. Together, these data support a role of dysregulation of an activity-dependent EGR2/MeCP2 pathway in RTT and autism

Phylogenetic Relationships and Evolutionary Patterns of the Order Collodaria (Radiolaria)

Collodaria are the only group of Radiolaria that has a colonial lifestyle. This group is potentially the most important plankton in the oligotrophic ocean because of its large biomass and the high primary productivity associated with the numerous symbionts inside a cell or colony. The evolution of Collodaria could thus be related to the changes in paleo-productivity that have affected organic carbon fixation in the oligotrophic ocean. However, the fossil record of Collodaria is insufficient to trace their abundance through geological time, because most collodarians do not have silicified shells. Recently, molecular phylogeny based on nuclear small sub-unit ribosomal DNA (SSU rDNA) confirmed Collodaria to be one of five orders of Radiolaria, though the relationship among collodarians is still unresolved because of inadequate taxonomic sampling. Our phylogenetic analysis has revealed four novel collodarian sequences, on the basis of which collodarians can be divided into four clades that correspond to taxonomic grouping at the family level: Thalassicollidae, Collozoidae, Collosphaeridae, and Collophidae. Comparison of the results of our phylogenetic analyses with the morphological characteristics of each collodarian family suggests that the first ancestral collodarians had a solitary lifestyle and left no silica deposits. The timing of events estimated from molecular divergence calculations indicates that naked collodarian lineages first appeared around 45.6 million years (Ma) ago, coincident with the diversification of diatoms in the pelagic oceans. Colonial collodarians appeared after the formation of the present ocean circulation system and the development of oligotrophic conditions in the equatorial Pacific (ca. 33.4 Ma ago). The divergence of colonial collodarians probably caused a shift in the efficiency of primary production during this period