Characterisation of hepcidin response to holotransferrin treatment in CHO TRVb-1 cells.

Iron overload coupled with low hepcidin levels are characteristics of hereditary haemochromatosis. To understand the role of transferrin receptor (TFR) and intracellular iron in hepcidin secretion, Chinese hamster ovary transferrin receptor variant (CHO TRVb-1) cells were used that express iron-response-element-depleted human TFRC mRNA (TFRC∆IRE). Results showed that CHO TRVb-1 cells expressed higher basal levels of cell-surface TFR1 than HepG2 cells (2.2-fold; p < 0.01) and following 5 g/L holotransferrin treatment maintained constitutive over-expression at 24h and 48 h, contrasting the HepG2 cells where the receptor levels significantly declined. Despite this, the intracellular iron content was neither higher than HepG2 cells nor increased over time under basal or holotransferrin-treated conditions. Interestingly, hepcidin secretion in CHO TRVb-1 cells exceeded basal levels at all time-points (p < 0.02) and matched levels in HepG2 cells following treatment. While TFRC mRNA expression showed expected elevation (2h, p < 0.03; 4h; p < 0.05), slc40a1 mRNA expression was also elevated (2 h, p < 0.05; 4 h, p < 0.03), unlike the HepG2 cells. In conclusion, the CHO TRVb-1 cells prevented cellular iron-overload by elevating slc40a1 expression, thereby highlighting its significance in the absence of iron-regulated TFRC mRNA. Furthermore, hepcidin response to holotransferrin treatment was similar to HepG2 cells and resembled the human physiological response.

Application repository and science gateway for running molecular docking and dynamics simulations.

Molecular docking and dynamics studies are of considerable importance in a range of disciplines including molecular biology, drug design, environmental studies, psychology, etc. Using in silico tools to support or even to substitute wet laboratory work could help better focusing the laboratory experiments resulting not only in considerable saving of resources but also increasing the number of molecules and scenarios investigated. There are several software packages that support in silico modeling. However, these tools require lot of compute resources and special technical knowledge. As a result, many bio-scientists cannot use them. The paper describes a science gateway based solution which provides access to Distributed Computing Infrastructures such as clouds, desktop and service grids. This environment enables bio-scientists to execute simple molecular modeling scenarios or build more complex use-cases from existing building blocks while hiding the technical details of the infrastructure. Four scenarios have been defined and deconstructed in order to identify common building blocks supporting a large number of complex use-cases. A reference implementation for the first scenario regarding the impact on indicator species of pharmaceuticals released into water courses has been implemented on the EDGI infrastructure, demonstrating the feasibility of the approach.

The lectin Helix pomatia agglutinin recognizes O-GlcNAc containing glycoproteins in human breast cancer.

There has been considerable interest in understanding the epitopes that bind the lectin Helix pomatia agglutinin (HPA) in breast cancer as the lectin has been shown to identify glycosylation changes associated with the development of metastatic disease. HPA has previously been shown to recognize aberrant O-linked α-N-acetylgalactosamine (GalNAcα)/mucin glycosylation in cancer, including exposed Tn epitopes. However, recent glycan-array analysis reported that diverse epitopes are also recognized by the lectin, e.g. consortium for functional glycomics (CFG) data: GalNAcα1,3Gal; ß-GalNAc; GlcNAcß1,4Gal. The intriguing observations from the CFG array led to this study, in which HPA-binding epitopes were localized and characterized in an in vitro model of breast cancer metastasis. HMT3522 (benign disease), BT474 (primary cancer) and T47D/MCF7 (metastatic cancer) cells were assessed in confocal microscopy-based co-localization studies and a glycoproteomic analysis based on 2-dimensional electrophoresis (2DE), western blotting and mass spectrometry was adopted. HPA binding correlated with levels of integrin α6, transcription factors heterogeneous nuclear ribonuclear protein (HnRNP) H1, HnRNP D-like, HnRNP A2/B1 as well as heat shock protein 27 (Hsp27), glial fibrillary acidic protein and enolase 1 (ENO1). These glycoproteins were non-detectable in the non-metastatic breast cancer cell lines. The recognition of HnRNPs, Hsp27 and ENO1 by HPA correlated with O-GlcNAcylation of these proteins. Integrin α6 was the most abundant HPA glycoprotein in the breast cancer cells with a metastatic phenotype; this concurred with previous findings in colorectal cancer. This is the first report in which HPA has been shown to bind O-GlcNAcylated transcription factors. This class of proteins represents a new means by which HPA differentiates cancer cells with an aggressive metastatic phenotype.

The N-glycans of Trichomonas vaginalis contain variable core and antennal modifications.

Trichomonad species are widespread unicellular flagellated parasites of vertebrates which interact with their hosts through carbohydrate-lectin interactions. In the past, some data have been accumulated regarding their lipo(phospho)glycans, a major glycoconjugate on their cell surfaces; on the other hand, other than biosynthetic aspects, few details about their N-linked oligosaccharides are known. In this study, we present both mass spectrometric and high-performance liquid chromatography data about the N-glycans of different strains of Trichomonas vaginalis, a parasite of the human reproductive tract. The major structure in all strains examined is a truncated oligomannose form (Man(5)GlcNAc(2)) with α1,2-mannose residues, compatible with a previous bioinformatic examination of the glycogenomic potential of T. vaginalis. In addition, dependent on the strain, N-glycans modified by pentose residues, phosphate or phosphoethanolamine and terminal N-acetyllactosamine (Galß1,4GlcNAc) units were found. The modification of N-glycans by N-acetyllactosamine in at least some strains is shared with the lipo(phospho)glycan and may represent a further interaction partner for host galectins, thereby playing a role in binding of the parasite to host epithelia. On the other hand, the variation in glycosylation between strains may be the result of genetic diversity within this species.

siRNA-mediated inhibition of Na(+)-K(+)-2Cl- cotransporter (NKCC1) and regulatory volume increase in the chondrocyte cell line C-20/A4.

The Na(+)-K(+)-2Cl(-) cotransporter (NKCC1) is an essential membrane transporter and has been linked to the regulation of volume, matrix synthesis and bone growth in chondrocytes; the sole resident cell type of articular cartilage. Despite the integral nature of NKCC1, its regulation is currently poorly understood, and therefore here we describe a NKCC1 knockdown technique that will permit the easier study of this transporter. Small interfering RNA (siRNA), designed to knock down NKCC1, was transfected into the chondrocyte cell line C-20/A4 and the efficacy determined at the message, protein and functional levels. NKCC1 expression was analyzed by reverse-transcriptase polymerase chain reaction, where NKCC1 expression declined to 25.10 ± 1.08% after 12 h of transfection and did not show any rise in the following 36 h. The efficacy of the designed siRNA molecules was confirmed by both Western blot and immunocytochemistry. The effect of the knockdown on regulatory volume increase (RVI, a novel assay for NKCC1 function) was investigated by confocal laser scanning microscopy in response to a 43% hypertonic challenge, whereby control chondrocytes underwent a decrease in volume to 67.38 ± 1.70%, followed by volume restoration to 82.17 ± 2.23 at 20 min (t½ = 22.11 ± 3.23 min). Conversely, upon knockdown, chondrocytes exhibited a slower rate of RVI (t½ = 43.26 ± 5.64 min), thus suggesting that NKCC1 plays an important and yet partial role in RVI in C-20/A4 chondrocytes. Together, these data provide a robust protocol for the study of NKCC1 in chondrocytes and suggest a mechanism for C-20/A4 chondrocyte RVI.

Cation-π interactions induce kinking of a molecular hinge in the RNA polymerase bridge-helix domain.

RNAPs (RNA polymerases) are complex molecular machines that contain a highly conserved catalytic site surrounded by conformationally flexible domains. High-throughput mutagenesis in the archaeal model system Methanocaldococcus jannaschii has demonstrated that the nanomechanical properties of one of these domains, the bridge-helix, exert a key regulatory role on the rate of the NAC (nucleotide-addition cycle). Mutations that increase the probability and/or half-life of kink formation in the BH-HC (bridge-helix C-terminal hinge) cause a substantial increase in specific activity ('superactivity'). Fully atomistic molecular dynamics simulations show that kinking of the BH-HC appears to be driven by cation-π interactions and involve amino acid side chains that are exceptionally highly conserved in all prokaryotic and eukaryotic species.

Purification and analysis of DNases of Tritrichomonas foetus: evidence that these enzymes are glycoproteins.

Tritrichomonas foetus is the causative agent of trichomoniasis. In cattle, infection results in economic losses to the beef and dairy industries due to abortion and infertility. Soluble DNases of T. foetus that play a role in pathogenesis and are potential therapeutic targets, were extracted and purified utilising lectin affinity chromatography. The DNases were bound to and eluted from Concanavalin A (Con A)-sepharose indicating that they are glycoproteins with alpha-linked mannose or glucose residues. The nature of the glycans carried on the eluted proteins in the fraction containing DNase activity was assessed using an enzyme-linked lectin assay. The lectin binding studies predict the presence of both N- and O-type glycans. Manganese was a potent (33%) activator of the DNase(s) whereas zinc inhibited enzyme activity by approximately 66%. The DNase(s) had a pH optimum of 4 and a molecular weight of 160 kDa. The DNase(s) were able to completely degrade DNA from animal, plant, fungal, yeast and bacterial sources, but did not significantly degrade RNA.

Proteome analysis of metastatic colorectal cancer cells recognized by the lectin Helix pomatia agglutinin (HPA).

The lectin from Helix pomatia (HPA) binds to adenocarcinomas with a metastatic phenotype but the glycoconjugates of cancer cells that bind to the lectin have yet to be characterized in detail. We used a model of metastatic (HT29) and nonmetastatic (SW480) human colorectal cancer cells and a proteomic approach to identify HPA binding glycoproteins. Cell membrane proteins purified by HPA affinity chromatography, were separated by 2-DE and analyzed by MS. Competitive inhibition experiments with N-acetylgalactosamine, N-acetylglucosamine, and sialic acid confirmed that HPA binding was via a glycan-mediated interaction. Western blot analysis showed that HPA binds to proteins not recognized by an antibody against blood group A epitope. The proteomic study showed the main HPA binding partners include integrin alphav/alpha6 and annexin A2/A4. These proteins were found complexed with microfilament proteins alpha and beta tubulin, actin, and cytokeratins 8 and 18. HPA also bound to Hsp70, Hsp90, TRAP-1, and tumor rejection factor 1. This study revealed that the prognostic utility of HPA lies in its ability to bind simultaneously to many glycoproteins involved in cell migration and signaling, in addition, the proteins recognized by HPA are glycosylated with structures distinct from the blood group A epitope.

Identification and elimination of false-positives in an ELISA-based system for qualitative assessment of glycoconjugate binding using a selection of plant lectins.

Systematic optimization of a lectin-based enzyme-linked immunosorbent assay (ELISA) procedure using a panel of 21 biotinylated plant lectins and a glycoprotein with defined glycosylation (i) identified blocking as a limiting step in solid phase sugar binding analysis and (ii) found Synblock to be a better alternative to bovine serum albumin (BSA) as blocking agent.

Detection of human papillomavirus from archival tissues in cervical cancer patients in Mauritius.

BACKGROUND: Around half a million new cases of cervical cancer are diagnosed worldwide each year, accounting for almost 300,000 deaths. Development of cervical cancer can be multi-factorial, but high-risk human papillomaviruses (HPV) have been associated with the aetiology of cervical cancer. It is believed that HPV DNA integrates into the host DNA causing abnormal cell growth with cells becoming carcinogenic and spreading metastatically. In Mauritius, cervical cancer account for 65% of gynaecological cancers and 3.4% of the cervical cancers are diagnosed at the stage of carcinoma in situ. OBJECTIVES: To determine the prevalence of HPV in histological samples from patients with cervical cancer in Mauritius. STUDY DESIGN: DNA from archival cervical samples from a cohort of 65 patients suffering from cervical cancer and controls from Mauritius were tested for the presence of HPV using MY09/11 and GP5+/6+ primer sets. RESULTS: In a cohort of 65 patients from Mauritius, diagnosed with cervical cancer in the year 2000, 19% of cervical histology sections were found to be positive for the presence of high-grade HPV, exclusively HPV18 using MY09 and MY11 primers. Only 15% of the Mauritian population is over 50 years of age, whereas 66% (35) of the diagnosed cases of cervical cancer were seen in patients above 50 years with 50% (5) affected with HPV. These findings suggest that for an infection with HPV to develop into cancer may take years if not decades. Differences were noted using two different primer sets, MY09/11 and GP5+/6+. The latter produce a much smaller amplicon (150bp) compared to the former ( approximately 450bp). Seven additional positive cases were detected with the GP5+/6+ primer set, resulting in an apparent prevalence of 32% as compared to the 19% seen with the MY09/11 primer set. This may indicate that some degradation of the target DNA has occurred during processing and storage of histological samples. CONCLUSION: Using primer sets MY09/11 and GP5+/6+, only HPV type 18 was found in the Mauritian cohort with a prevalence of 32%.

Application of recombinant phage display antibody system in study of Codakia orbicularis gill proteins.

We used the recombinant phage display antibody system (RPAS) to obtain chimeric single-chain fragment variable (ScFv) antibodies to gill proteins of the white clam Codakia orbicularis (Linné, 1758). After three rounds of selection on immunotubes loaded with total gill protein extract, recombinant phages exhibiting antibodies to gill proteins were isolated and tested by enzyme-linked immunosorbent assay (ELISA). Clones exhibiting a high affinity for the mollusk proteins were selected for production of soluble ScFv antibodies, which were purified for subsequent analysis. ScFv antibodies exhibited a reaction specific for a protein whose molecular mass was about 15,000 Daltons and that was detected by the antigen capture technique followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis and Western blotting.