Predicting deleterious nsSNPs: an analysis of sequence and structural attributes

Background  

There has been an explosion in the number of single nucleotide polymorphisms (SNPs) within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs), some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl.     

Caspase activation, sialidase release and changes in sialylation pattern of recombinant human erythropoietin produced by CHO cells in batch and fed-batch cultures

The activation of caspases represents a crucial turning point during a batch or a fed-batch culture of mammalian cells. It not only affects the quantity but also the quality of the recombinant glycoprotein produced. In this study, the activation of various caspases, the release of intracellular sialidase and the changes in sialylation pattern of a recombinant product, erythropoietin (EPO), in the culture medium were analyzed in both batch and fed-batch cultures. In both setups, all caspase activities peaked at the culture time point at which decline of cell viability was most pronounced. In addition, the release of intracellular lactate dehydrogenase (LDH) was also tracked during these cultures. The increase in LDH activity in the medium coincided with the increase of intracellular caspase activities, the release of sialidase and the observed decline in cell viability, suggesting that the LDH activity in the medium can be used as an indirect indicator of apoptotic cell death in bioreactors. Isoelectric focusing (IEF) coupled with double blotting was employed to analyze the changes in sialylation pattern of the recombinant EPO. This assay resulted in a prompt resolution of secreted EPO isoforms in a time course format. IEF profile of batch culture showed relatively consistent product sialylation compared to fed-batch culture, which showed gradual band shifts towards the isoforms with fewer sialic acid as the culture progressed. These data provided a guideline for the optimal time point to terminate the culture and collect products in batch and fed-batch cultures.Kok Hwee Chuan and Sing Fee Lim contributed equally to this work.     

Antinociceptive effects of morphine and naloxone in mu-opioid receptor knockout mice transfected with the MORS196A gene

Background  

Opioid analgesics such as morphine and meperidine have been used to control moderate to severe pain for many years. However, these opioids have many side effects, including the development of tolerance and dependence after long-term use, which has limited their clinical use. We previously reported that mutations in the mu-opioid receptors (MOR) S196L and S196A rendered them responsive to the opioid antagonist naloxone without altering the agonist phenotype. In MORS196A knock-in mice, naloxone and naltrexone were antinociceptive but did not cause tolerance or physical dependence. In this study we delivery this mutated MOR gene into pain related pathway to confirm the possibility of in vivo transfecting MORS196A gene and using naloxone as a new analgesic agent.     

In <Emphasis Type="Italic">Helicobacter pylori</Emphasis> auto-inducer-2, but not LuxS/MccAB catalysed reverse transsulphuration,regulates motility through modulation of flagellar gene transcription

Background  

LuxS may function as a metabolic enzyme or as the synthase of a quorum sensing signalling molecule, auto-inducer-2 (AI-2); hence, the mechanism underlying phenotypic changes upon luxS inactivation is not always clear. In Helicobacter pylori, we have recently shown that, rather than functioning in recycling methionine as in most bacteria, LuxS (along with newly-characterised MccA and MccB), synthesises cysteine via reverse transsulphuration. In this study, we investigated whether and how LuxS controls motility of H. pylori, specifically if it has its effects via luxS-required cysteine metabolism or via AI-2 synthesis only.     

<Emphasis Type="Italic">In vivo</Emphasis> assessment of the impedance ratio method used in electronic foramen locators

Background  

The results of an in vivo study on the "ratio method" used in electronic foramen locators (EFL) are presented. EFLs are becoming widely used in the determination of the working length (WL) during the root canal treatment. The WL is the distance from a coronal reference point to the point at which canal preparation and filling should terminate. The "ratio method" was assessed by many clinicians with the aim of determining its ability to locate the apical foramen (AF). Nevertheless, in vivo studies to assess the method itself and to explain why the "ratio method" is able to locate the apical foramen and is unable to determine intermediate distances were not published so far.     

EGF-induced tyrosine phosphorylation of Endofin is dependent on PI3K activity and proper localization to endosomes

In our previous study, Endofin was validated to be a novel tyrosine phosphorylation target downstream of EGFR. Here, we attempted to map the signaling events associated with Endofin following activation of EGFR with EGF. Tyrosine phosphorylation of endogenous Endofin peaked around 15 min and was modulated within 30 min of EGF treatment. Phosphatidylinositol 3-kinase (PI3K) activity and FYVE domain-mediated localization of Endofin to EEA1-marked endosomes were shown to be necessary for the tyrosine phosphorylation of Endofin. Tyrosine 515 was mapped to be a major phosphorylation site on Endofin but disruption of phosphorylation at Y515 neither affected Endofin's localization nor its co-localization with EGFR in the endosomes. Instead, abrogation of Y515 phosphorylation and mislocalization of Endofin were found to enhance the amplitude of the MAPK cascade, suggesting a possible role of Endofin in the modulation of MAPK pathway. Our study has identified a novel signaling cascade involving EGFR, PI3K, Endofin and MAPK in the EGFR signaling network.     

The gastrointestinal microbiota affects the selenium status and selenoprotein expression in mice

Colonization of germ-free (GF) mice has been shown to induce the gastrointestinal form of the selenium-dependent glutathione peroxidases, GPx2. Since bacterial colonization of the gastrointestinal tract is associated with stress, we aimed to clarify how bacteria affect selenoprotein expression in unstressed conditions. GF and conventional (CV) FVB/NHan(TMHsd) mice were fed a selenium-poor (0.086 ppm) or a selenium-adequate (0.15 ppm) diet for 5 weeks starting from weaning. Each group consisted of five animals. Specific glutathione peroxidase (GPx) and thioredoxin reductase (TrxR) expression was measured in plasma, liver and intestinal sections by activity, protein and mRNA level as appropriate. Under selenium-adequate conditions, selenoprotein expression did not differ in GF and CV mice. Under selenium-limiting conditions, however, GF mice generally contained higher GPx and TrxR activities in the intestine and liver, higher GPx1 protein and RNA levels in the liver, higher GPx2 protein levels in the proximal and distal jejunum and colon and higher GPx1 and GPx2 RNA levels in the colon. In addition, higher selenium concentrations were estimated in plasma, liver and cecum. All differences were significant. It is concluded that bacteria may compete with the host for selenium when availability becomes limiting. A variable association with different microorganisms might influence the daily requirement of mice for selenium. Whether the microbiota also affects the human selenoprotein status appears worthy of investigation.     

The tumor-associated antigen 90K/Mac-2-binding protein secreted by human colon carcinoma cells enhances extracellular levels of promatrilysin and is a novel substrate of matrix metalloproteinases-2, -7 (matrilysin) and -9: Implications of proteolytic cleavage

Background

The tumor-associated antigen 90K (TAA90K)/Mac-2-binding protein is expressed at elevated level in cancerous tissues and associated with poor prognosis. Since TAA90K has been implicated in the restructuring of the extracellular matrix, we examined the functional relationship between colon cancer cell-derived TAA90K and the matrix metalloproteinase (MMP) promatrilysin (proMMP-7), and also tested whether TAA90K is a novel substrate for MMPs-2, -7 and -9.

Methods

The effect of TAA90K on proMMP-7 levels in HT-29 conditioned media was quantified by enzyme-linked immunosorbent assays. Binding of TAA90K to MMPs, extracellular matrix proteins and galectin-3 was measured by solid-phase binding assays. Proteolytic cleavage of TAA90K by MMPs was documented by SDS-PAGE and protein sequencing analysis.

Results

TAA90K enhanced extracellular levels of proMMP-7 in HT-29 cells. In addition, TAA90K was cleaved by MMPs-2, -7 and -9. MMP-7-mediated cleavage of TAA90K did not affect its binding to MMP-7, laminin-1, collagen IV and galectin-3 but reduced its interaction with fibronectin and laminin-10, and lowered the levels of proMMP-7 in the HT-29 medium.

Conclusion

TAA90K is a novel substrate for MMPs-2, -7 and -9 and modulates proMMP-7 levels in colon cancer cells.

General significance

Proteolytic cleavage of TAA90K may have functional implications in colon cancer.