WormBase 2007.

WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research.

Analysis of pooled data from two pivotal controlled trials on the efficacy of topiramate in the prevention of migraine.

Context: A substantial proportion of the patient population with migraine headache should be considered for preventive treatment based on the frequency and disability associated with this disorder. Use of the anticonvulsant topiramate was previously examined in two large, double-blind, randomized, placebo-controlled clinical trials of a subset of patients who have 3 to 12 migraine episodes per month.

Objective: To better characterize the efficacy of topiramate for prevention of migraine, with or without aura, by pooling and analyzing data from the two large clinical trials.

Overexpression of cold-inducible RNA-binding protein increases interferon-gamma production in Chinese-hamster ovary cells.

Culturing recombinant CHO (Chinese-hamster ovary) cells at low temperatures (30-33 degrees C) increases specific recombinant protein productivity by 2-5-fold. However, even though the specific productivity is increased, cell growth is decreased in low-temperature culture such that the final recombinant protein titre remains unchanged or is even diminished, owing to the lower cell density. Exposing mammalian cells to low temperatures results in a change in the expression of many 'cold-stress' genes.

A GFP-based screen for growth-arrested, recombinant protein-producing cells.

The growth of anchorage-dependent Chinese hamster ovary (CHO) cells is arrested upon serum deprivation; however, a portion of these cells remain viable for extended time periods in serum-free culture. This work presents a strategy to both rapidly generate a heterogeneous population of CHO cells as well as to select for subpopulations that remain robust and continue to produce recombinant protein when their growth is arrested. Stable expression of recombinant proteins in mammalian cells is often a tedious and time-consuming process because only a small percentage of transfected cells will express sufficient quantities of protein.

Application of destabilizing sequences on selection marker for improved recombinant protein productivity in CHO-DG44.

We have developed a systematic and generic way to improve recombinant protein productivities in stable transfections by applying mRNA and protein destabilizing elements to reduce selection marker expression strength. Interferon-gamma (IFNgamma) expression vectors containing different combinations of AU-rich elements (ARE) and mouse ornithine decarboxylase (MODC) PEST region on the amplifiable dihydrofolate reductase (dhfr) selection marker were stably transfected into CHO-DG44 cells. Improvements in specific IFNgamma productivities were 1.

Identification of active biomolecules in the high-yield synthesis of single-crystalline gold nanoplates in algal solutions.

In this work, single-crystalline gold nanoplates were produced by treating an aqueous solution of chloroauric acid with the extract of the unicellular green alga Chlorella vulgaris at room temperature. The results suggest proteins as the primary biomolecules involved in providing the dual function of Au(III) reduction and the size- and shape-controlled synthesis of the nanogold crystals. A protein with a molecular weight of approximately 28 kDa was isolated and purified by reversed-phase HPLC; this protein tested positive for the reduction of chloroauric acid in aqueous solution.

Comparative oxidation studies of methionine residues reflect a structural effect on chemical kinetics in rhG-CSF.

The effect of protein conformation on the rate of chemical degradation is poorly understood. To address the role of structure on chemical degradation kinetics, comparative oxidation studies of methionine residues in recombinant human granulocyte colony-stimulating factor (rhG-CSF) were performed. The kinetics of oxidation of methionine residues by hydrogen peroxide (H2O2) in rhG-CSF and corresponding chemically synthesized peptides thereof was measured at different temperatures.

WormBase: new content and better access.

WormBase (http://wormbase.org), a model organism database for Caenorhabditis elegans and other related nematodes, continues to evolve and expand. Over the past year WormBase has added new data on C.

High-avidity antitumor T-cell generation by toll receptor 8-primed, myeloid- derived dendritic cells is mediated by IL-12 production.

Background: High-level production of heterodimeric p70 interleukin (IL)-12 by myeloid-derived dendritic cells (DCs) requires 2 signals: interferon gamma (IFN-gamma) and a maturation signal provided by CD40 ligation (CD40L) or lipopolysaccharide (LPS).

Methods: In the current study we demonstrate that signaling through toll-like receptor (TLR) 8, but not TLR3, TLR2, or TLR4, provides a priming signal to myeloid-derived DC for high IL-12 p70 heterodimer production.

Results: All the TLR agonists induced maturation of DC as evidenced by increased expression of CD83, CD80, and CD86.

Ion-exchange purification of proteins using magnetic nanoclusters.

Polymer-coated magnetic nanoclusters were used for recovery and purification of proteins from both model systems and cell-free Pichia pastoris fermentation broth. The nanoclusters exhibited extremely high capacity for proteins, up to 900 mg/mL adsorbent, and were recovered by high gradient magnetic separation (HGMS) at flow rates of up to 3,600 cm(3)/cm(2) h (flow rates up to 15,000 cm(3)/cm(2) h are possible). The nanoclusters were coated with a primary coating of poly(acrylic acid-co-styrenesulfonic acid-co-vinylsulfonic acid), which allowed both electrostatic and hydrophobic interactions with the protein to be used to enhance specificity for targeted products.

RNA interference of sialidase improves glycoprotein sialic acid content consistency.

An important challenge facing therapeutic protein production in mammalian cell culture is the cleavage of terminal sialic acids on recombinant protein glycans by the glycosidase enzymes released by lysed cells into the supernatant. This undesired phenomenon results in a protein product which is rapidly cleared from the plasma by asialoglycoprotein receptors in the liver. In this study, RNA interference was utilized as a genetic approach to silence the activity of sialidase, a glycosidase responsible for cleaving terminal sialic acids on IFN-gamma produced by Chinese Hamster Ovary (CHO) cells.

Affinity-tagged green fluorescent protein (GFP) extraction from a clarified E. coli cell lysate using a two-phase aqueous micellar system.

Green fluorescent protein (GFP) has been proposed as an ideal choice for a protein-based biological indicator for use in the validation of decontamination or disinfection treatments. In this article, we present a potentially scalable and cost-effective way to purify recombinant GFP, produced by fermentation in Escherichia coli, by affinity-enhanced extraction in a two-phase aqueous micellar system. Affinity-enhanced partitioning, which improves the specificity and yield of the target protein by specific bioaffinity interactions, has been demonstrated.

Enhancing recombinant glycoprotein sialylation through CMP-sialic acid transporter over expression in Chinese hamster ovary cells.

Glycosylation engineering strategies that are currently used to improve quality of recombinant glycoproteins involve the manipulation of glycosyltransferase and/or glycosidase expression. We explored the possibility that over expressing nucleotide sugar transporters, particularly the CMP-sialic acid transporter (CMP-SAT) would improve the sialylation process in Chinese hamster ovary cells (CHO). Our hypothesis was that increasing CMP-SAT in the cells through recombinant means would increase the transport of CMP-sialic acid into the Golgi, resulting in an increased CMP-sialic acid intra-lumenal pool and increased sialylation of the proteins produced.

Co-expression of estrogen receptor-alpha and targets of estrogen receptor action in proliferating monkey mammary epithelial cells.

Introduction: Failure to detect co-expression of estrogen receptor-alpha (ERalpha) and proliferation 'markers' such as Ki67 in human mammary epithelium led to the view that estrogen acts indirectly to stimulate mammary epithelial proliferation. The mitotic index was so low in prior studies, however, that transient co-expression of ERalpha and Ki67 during the cell cycle could have been below detection limits.

Methods: Immunohistochemistry was used on mammary tissue sections from estrogen treated rhesus monkeys to investigate co-expression of ERalpha and the proliferation antigen Ki67.

WormBase: better software, richer content.

WormBase (http://wormbase.org), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content. Performance was improved by accelerating the loading of central data pages such as the omnibus Gene page, by rationalizing internal data structures and software for greater portability, and by making the Genome Browser highly customizable in how it views and exports genomic subsequences.

Determination of volatile organic compounds in different microenvironments by multibed adsorption and short-path thermal desorption followed by gas chromatographic-mass spectrometric analysis.

A multiphase assurance approach was developed for the accurate and precise determination of volatile organic compounds (VOCs) in different microenvironments. This approach includes (i) development of a method including adsorption of VOCs onto a multisorbent media followed by short-path thermal desorption (SPTD) pre-concentration and gas chromatography (GC) coupled to a mass spectrometry (MS) quantification, (ii) validation of the sampling and analytical method and (iii) validation of the data using a multidimensional procedure. Tenax TA and Carbopack B sorbent combinations were used to collect 102 individual VOCs ranging from C5 to C12.

Cutting on triangle mesh: local model-based haptic display for dental preparation surgery simulation.

A new method to realize stable and realistic cutting simulation using an impedance display haptic device and microcomputer is presented in this paper. Material removal or cutting simulation is a critical task in dental preparation surgery simulation. In this paper, a piecewise contact force model is proposed to approximately describe the cutting process.

Toll-like receptor 8-mediated reversal of CD4+ regulatory T cell function.

CD4+ regulatory T (Treg) cells have a profound ability to suppress host immune responses, yet little is understood about how these cells are regulated. We describe a mechanism linking Toll-like receptor (TLR) 8 signaling to the control of Treg cell function, in which synthetic and natural ligands for human TLR8 can reverse Treg cell function. This effect was independent of dendritic cells but required functional TLR8-MyD88-IRAK4 signaling in Treg cells.

Tau is hyperphosphorylated in the insulin-like growth factor-I null brain.

IGF action has been implicated in the promotion of oxidative stress and aging in invertebrate and murine models. However, some in vitro models suggest that IGF-I specifically prevents neuronal oxidative damage. To investigate whether IGF-I promotes or retards brain aging, we evaluated signs of oxidative stress and neuropathological aging in brains from 400-d-old Igf1-/- and wild-type (WT) mice.

Controlled clustering and enhanced stability of polymer-coated magnetic nanoparticles.

The clustering and stability of magnetic nanoparticles coated with random copolymers of acrylic acid, styrenesulfonic acid, and vinylsulfonic acid has been studied. Clusters larger than 50 nm are formed when the coatings are made using too low or too high molecular weight polymers or using insufficient amounts of polymer. Low-molecular-weight polymers result in thin coatings that do not sufficiently screen van der Waals attractive forces, while high-molecular-weight polymers bridge between particles, and insufficient polymer results in bare patches on the magnetite surface.