Evaluation of the Relationship Between the 18S rRNA/rDNA Ratio and Population Growth in the Marine Diatom Skeletonema tropicum via the Application of an Exogenous Nucleic Acid Standard.

Ribosomal RNA (rRNA) has been regarded as a proxy for metabolic activity and population growth in microbes, but the limitations and assumptions of this approach should be better defined, particularly in eukaryotic microalgae. In this study, the 18S rRNA/rDNA ratio of a marine diatom, Skeletonema tropicum, was examined in batch and semi-continuous cultures subjected to low nitrogen and phosphorus treatments at a temperature of 20 °C. In the semi-continuous cultures, the measured 18S rRNA/rDNA ratio ranged from 4.0 × 102 to 5.0 × 103 , and the logarithmic form of this ratio increased linearly with the population growth rate under both low nitrogen and low phosphorus conditions. In batch cultures grown under low nitrogen or low phosphorus conditions, log (rRNA/rDNA) also increased linearly with growth rate when the latter ranged between -0.4 and 1.5 day-1 . The 18S rRNA/rDNA ratios of Skeletonema sampled from in the southern East China Sea were substantially lower than measured from laboratory cultures. Among the field samples, ratios obtained at a coastal station were higher than those obtained farther offshore. These results imply higher growth rate at the coastal station, but the influences of other factors, such as cell size and temperature, cannot be ruled out.

Identification and characterization of an extracellular alkaline phosphatase in the marine diatom Phaeodactylum tricornutum.

In phosphorus-deficient conditions, Phaeodactylum tricornutum releases an alkaline phosphatase (PtAPase) to the medium that is readily detectable by activity staining. Nucleic acid and amino acid sequence of this alkaline phosphatase (APase) was identified by performing proteomic analysis and database searches. Sequence alignment suggests that PtAPase belongs to the PhoA family, and it possesses key residues at the Escherichia coli PhoA active site. Quantitative PCR results indicate that the induction of APase mRNA transcription is very sensitive to phosphorus availability and population growth. The molecular mass of native PtAPase (148 kDa) determined by gel filtration chromatography indicates that PtAPase, like most PhoA, is homodimeric. Zn and Mg ions are essential cofactors for most PhoA enzymes; however, PtAPase activity did not require Zn ions. In fact, 5 mM Zn²âº, Mo²âº, Co²âº, Cd²âº, or Cu²âº inhibited its enzymatic activity, whereas 5 mM Mn²âº, Mg²âº, or Ca²âº enhanced its enzymatic activity. The responses of PtAPase to divalent metal ions were different from those of most PhoAs, but were similar to the PhoA in a marine bacterium, Cobetia marina. Phylogenetic analysis shows that homologs of PhoA are also present in other diatom species, and that they clustered in a unique branch away from other PhoA members. PtAPase may represent a novel class of PhoA that helps diatoms to survive in the ocean. Quantification of the PtAPase mRNA may help monitor the physiological condition of diatoms in natural environments and artificial bioreactors.

Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with the physicochemical complementarity features based on the non-covalent interaction data derived from protein interiors.

Update on thalassemia treatment in Taiwan, including bone marrow transplantation, chelation therapy, and cardiomyopathy treatment effects.

Over the past few decades, Taiwan has seen striking improvements in the life expectancy of its 400 registered beta-thalassemia major (beta-TM) patients due mainly to adequate transfusion regimens and effective iron chelation therapy. Since 1995, Taiwanese citizens have enjoyed universal health care through National Health Insurance (NIH), receiving comprehensive treatment at minimal cost. In 1984, a national program for thalassemia prevention, control, and hematopoietic stem cell transplantation (HSCT) was initiated. Recent data show 1- and 2-year event-free survival rates of 85 and 78%, respectively. Chelation agents like deferoxamine (DFO), deferiprone (L1) and deferasirox (DFRA) are available in Taiwan, and therapy is tailored to individuals based on drug availability and tissue distribution of iron load. Intensive chelation regimens combining L1 and DFO are recommended in patients with cardiac complications, while DFRA has been found to be effective in reducing serum ferritin, with acceptable side effects. Here, we report advances in thalassemia treatment in Taiwan and suggest treatment guidelines.

Regression of myocardial dysfunction after switching from desferrioxamine to deferiprone therapy in beta-thalassemia major patients.

This study tries to compare the cardioprotective effects of the desferrioxamine (DFO) and deferiprone (L1) therapies on thalassemia major patients. We enrolled nine patients with thalassemia major complicated by some degree of myocardial dysfunction. These patients, recipients of >10 years of DFO injection therapy, were switched from DFO to L1. Echocardiographic measures of left ventricular systolic, diastolic and global functions, were assessed regularly every 6 months. Mean values of each parameter for the DFO and L1 treatment periods were compared using paired t-test and Wilcoxon signed-rank test. Global cardiac function improved significantly. Myocardial dysfunction in patients with thalassemia major can be reversed by regular use of the oral iron chelator L1.