Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs

Background

Annotations that describe the function of sequences are enormously important to researchers during laboratory investigations and when making computational inferences. However, there has been little investigation into the data quality of sequence function annotations. Here we have developed a new method of estimating the error rate of curated sequence annotations, and applied this to the Gene Ontology (GO) sequence database (GOSeqLite). This method involved artificially adding errors to sequence annotations at known rates, and used regression to model the impact on the precision of annotations based on BLAST matched sequences.

Results

We estimated the error rate of curated GO sequence annotations in the GOSeqLite database (March 2006) at between 28% and 30%. Annotations made without use of sequence similarity based methods (non-ISS) had an estimated error rate of between 13% and 18%. Annotations made with the use of sequence similarity methodology (ISS) had an estimated error rate of 49%.

Conclusion

While the overall error rate is reasonably low, it would be prudent to treat all ISS annotations with caution. Electronic annotators that use ISS annotations as the basis of predictions are likely to have higher false prediction rates, and for this reason designers of these systems should consider avoiding ISS annotations where possible. Electronic annotators that use ISS annotations to make predictions should be viewed sceptically. We recommend that curators thoroughly review ISS annotations before accepting them as valid. Overall, users of curated sequence annotations from the GO database should feel assured that they are using a comparatively high quality source of information.     

First report of the benthic dinoflagellate,Gambierdiscus belizeanus (Gonyaulacales: Dinophyceae) for the east coast of Sabah,Malaysian Borneo

Species of the genus Gambierdiscus Adachi & Fukuyo, in particular G. toxicus Adachi & Fukuyo are known producers of neurotoxins associated with ciguatera fish poisoning (CFP). In this study live samples were collected from seaweed beds of the east coast of Sabah, Malaysian Borneo and a strain of Gambierdiscus was isolated and cultured. Examination of the thecal fine morphology was undertaken using light, epifluorescence, and scanning electron microscopy. Observed morphological features and their associated morphometric information enabled identification to Gambierdiscus belizeanus Faust. This represents the first report for the occurrence of G. belizeanus in the Asia Pacific region.     

Cancer risk associated with insulin glargine among adult type 2 diabetes patients--a nationwide cohort study

Background

Preclinical and observational studies raise the concern about the safety of insulin glargine in terms of cancer initiation and promotion. This study is designed to examine cancer incidence associated with use of insulin glargine vs. intermediate/long-acting human insulin (HI).

Methodology

A retrospective cohort study using the Taiwan National Health Insurance claims database was conducted to identify adult patients with type 2 diabetes mellitus and without a history of cancer who initiated insulin glargine (n = 10,190) or intermediate/long-acting HI (n = 49,253) during 2004–2007. Exclusive users were followed from the date of insulin initiation to the earliest of cancer diagnosis, death, disenrollment, or December 31 2007. We estimated adjusted hazard ratios and 95% confidence intervals (CIs) with Cox proportional hazards models adjusting for baseline propensity score.

Findings

The incidence rate of all cancer per 1,000 person-years was 13.8 for insulin glargine initiators (179 cases) and 16.0 for intermediate/long-acting HI initiators (1,445 cases) during an average follow-up of 2 years. No significant difference in overall cancer risk between insulin glargine initiators and HI initiators was found. For men, however, the adjusted hazard ratio of insulin glargine use as compared with intermediate/long-acting HI was 2.15 (95% CI 1.01–4.59) for pancreatic cancer, and 2.42 (95% CI 1.50–8.40) for prostate cancer. The increased risk was not observed among women.

Conclusions

Insulin glargine use did not increase the risk of overall cancer incidence as compared with HI. The positive associations with pancreatic and prostate cancer need further evaluation and validation.     

Scalable encapsulation of hepatocytes by electrostatic spraying

Encapsulating cells by polyelectrolyte complex coacervation can be accomplished at physiological temperature and buffer conditions. One of the oppositely charged polyelectrolytes in the microcapsule core can be collagen or any other natural extra-cellular matrices suitable for cellular support while the other polyelectrolyte forms the ultra-thin shell to ensure efficient mass transfer. These microcapsules with ultra-thin shell are difficult to produce in large quantities due to their fragility. In this study, electrostatic spraying technique was used to achieve a scalable production of one such type of microcapsules formed by complex coacervation between the cationic methylated collagen and anionic terpolymer of hydroxylethyl methacrylate, methyl methacrylate and methylacrylic acid (HEMA-MMA-MAA). It was found that the microcapsule sizes were dependent on several important operational parameters, such as the diameter of the spraying needle, the flow rate of the hepatocytes-collagen mixture and the voltage of the electrical field. The microcapsules with diameters of 200-800 microm and a narrow size distribution (standard deviation of 5-28%) were successfully produced. The above parameters also influenced the hepatocyte viability and functions. With a practical encapsulation rate of up to 55 ml/h per orifice required in bio-artificial liver-assisted device applications, we have produced large quantities of microcapsules maintaining comparable cell viability (>87%), mechanical stability and bio-functions to the manually extruded microcapsules.     

Biodegradation of phenanthrene by the indigenous microbial biomass in a zinc amended soil

AIMS: To study the effect of zinc on the biodegradation of phenanthrene by the microbial biomass in soil. METHODS AND RESULTS: Uncontaminated soil was amended with zinc and phenanthrene as single or co-contaminants, and microbial metabolic activity was measured using an intracellular dehydrogenase enzyme bioassay over 37 days. Contaminants were amended at optimum, action and double the action level specified in 'The New Dutch List' (Ministry of Housing, Spatial Planning and Environment, the Netherlands, 2000). Microbial activity in soils with zinc or phenanthrene alone indicated the presence of tolerant, albeit inhibited soil micro-organisms. A zinc concentration at the optimum level of 140 mg kg(-1) in the co-contaminated soil (phenanthrene at 40 mg kg(-1)) resulted in marginal stimulation of the rate of phenanthrene biodegradation. However, Zn2+ concentrations at the action and double the action level of zinc (720 and 1440 mg kg(-1)) inhibited phenanthrene degradation. CONCLUSIONS: Biodegradation of phenanthrene in soils co-contaminated with zinc at concentrations above the action value is impeded. SIGNIFICANCE AND IMPACT OF THE STUDY: Bioremediation efforts to remove polycyclic aromatic hydrocarbon in zinc co-contaminated soils are likely to be constrained.     

Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein

Background  

A large number of papers have been published on analysis of microarray data with particular emphasis on normalization of data, detection of differentially expressed genes, clustering of genes and regulatory network. On other hand there are only few studies on relation between expression level and composition of nucleotide/protein sequence, using expression data. There is a need to understand why particular genes/proteins express more in particular conditions. In this study, we analyze 3468 genes of Saccharomyces cerevisiae obtained from Holstege et al., (1998) to understand the relationship between expression level and amino acid composition.     

Loss of viability during freeze–thaw of intact and adherent human embryonic stem cells with conventional slow-cooling protocols is predominantly due to␣apoptosis rather than cellular necrosis

Summary A major challenge in the widespread application of human embryonic stem (hES) cells in clinical therapy and basic scientific research is the development of efficient cryopreservation protocols. Conventional slow-cooling protocols utilizing standard cryoprotectant concentrations i.e. 10% (v/v) DMSO, yield extremely low survival rates of <5% as reported by previous studies. This study characterized cell death within frozen–thawed hES colonies that were cryopreserved under standard conditions. Surprisingly, our results showed that immediately after post-thaw washing, the overwhelming majority of hES cells were viable (≈98%), as assessed by the trypan blue exclusion test. However, when the freshly-thawed hES colonies were incubated within a 37 °C incubator, there was observed to be a gradual reduction in cell viability over time. The kinetics of cell death was drastically slowed-down by keeping the freshly-thawed hES colonies at 4 °C, with >90% of cells remaining viable after 90 min of incubation at 4 °C. This effect was reversible upon re-exposing the cells to physiological temperature. The vast majority of low temperature-exposed hES colonies gradually underwent cell death upon incubation for a further 90 min at 37 °C. Terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end-labeling (TUNEL) assay confirmed apoptosis-induced nuclear DNA fragmentation in frozen–thawed hES cells after incubation at 37 °C for 90 min. Expression of active caspase-3 enzyme, which is another prominent marker of apoptosis, was confirmed by immunocytochemical staining, while transmission electron microscopy showed typical ultrastructural features of apoptosis such as chromatin condensation and margination to the nuclear membrane. Hence, our results demonstrated that apoptosis instead of cellular necrosis, is the major mechanism of the loss of viability of cryopreserved hES cells during freeze–thawing with conventional slow-cooling protocols.