Symbiont diversity in scleractinian corals from tropical reefs and subtropical non-reef communities in Taiwan

We examined zooxanthellae diversity in scleractinian corals from southern Taiwan and the Penghu Archipelago, a tropical coral reef and a subtropical non-reefal community, respectively. Zooxanthellae diversity was investigated in 52 species of scleractinian corals from 26 genera and 13 families, using restriction fragment length polymorphism (RFLP), and phylogenetic analyses of the nuclear small-subunit ribosomal DNA (nssrDNA) and large-subunit ribosomal DNA (nlsrDNA). RFLP and phylogenetic analyses of nuclear-encoded ribosomal RNA genes showed that Symbiodinium clade C was the dominant zooxanthellae in scleractinian corals in the seas around Taiwan; Symbiodinium clade D was also found in some species. Both Symbiodinium clade C and D were found in colonies of seven species of scleractinian corals. Symbiodinium clade D was associated with corals that inhabit either shallow water or the reef edge in deep water, supporting the hypothesis that Symbiodinium clade D is a relatively stress-tolerant zooxanthellae found in marginal habitats.Communicated by Biological Editor H.R. Lasker     

Continuous monitoring of phytoplankton dynamics in Lake Balaton (Hungary) using on-line delayed fluorescence excitation spectroscopy

1. This study introduces delayed fluorescence (DF) excitation spectroscopy as an on‐line tool for in situ monitoring of the composition and biomass of various colour classes of phytoplankton when they are photosynthetically active (cyanobacteria, chlorophytes, chromophytes and cryptophytes). The DF data are validated by comparison with those from conventional methods (weekly microscopic counts and the measurement of chlorophyll concentration). 2. The composition of phytoplankton as assessed by DF agreed reasonably well with the results from microscopic counts, particularly when differences in chlorophyll‐specific DF integrals of the various colour classes were taken into account. 3. Integrals of DF spectra were converted into concentration of chlorophyll a using empirical factors derived from field data. The value of the conversion factor was nearly twice as high when the relative abundance of cyanobacteria was low (<15%) than when it was high. The converted DF‐chl time series agreed well with chlorophyll measurements particularly when blooms were developing. As the DF method is inherently free of the interference caused by pigment degradation products, the discrepancy between the two data sets increased during the collapse of blooms and when sediment resuspension was intense. 4. Fourier spectrum analysis of the time series of DF‐chl indicated that samples must be taken, at a minimum, every 2–3 days to capture the dynamics of phytoplankton. As a consequence, the dynamics of various algal blooms, including their timing, duration and net growth rate, could be estimated with greater confidence than by using conventional methods alone. 5. On‐line DF spectroscopy is an advanced technique for monitoring daily the biomass and composition of the photosynthetically active phytoplankton in aquatic environments, including turbid shallow lakes. At present, the detection limit is around 1 mg DF‐chl a m^?3 in terms of total biomass but confidence in estimates of phytoplankton composition declines sharply below about 5 mg chl a m^?3. 6. On‐line DF spectroscopy represents a promising approach for monitoring phytoplankton. It will be useful in water management where it can act as an early‐warning system of declines in water quality. In basic ecological research it can supplement manual methods. While default calibration spectra may be acceptable for routine monitoring, we suggest a careful individual calibration of the DF spectrometer for basic research. The statistical methods developed here help to assess the adequacy of various calibration sets.     

An information measure of the quality of protein secondary structure prediction.

We describe an information-theory-based measure of the quality of secondary structure prediction (RELINFO). RELINFO has a simple yet intuitive interpretation: it represents the factor by which secondary structure choice at a residue has been restricted by a prediction scheme. As an alternative interpretation of secondary structure prediction, RELINFO complements currently used methods by providing an information-based view as to why a prediction succeeds and fails. To demonstrate this score's capabilities, we applied RELINFO to an analysis of a large set of secondary structure predictions obtained from the first five rounds of the Critical Assessment of Structure Prediction (CASP) experiment. RELINFO is compared with two other common measures: percent correct (Q3) and secondary structure overlap (SOV). While the correlation between Q3 and RELINFO is approximately 0.85, RELINFO avoids certain disadvantages of Q3, including overestimating the quality of a prediction. The correlation between SOV and RELINFO is approximately 0.75. The valuable SOV measure unfortunately suffers from a saturation problem, and perhaps has unfairly given the general impression that secondary structure prediction has reached its limit since SOV hasn't improved much over the recent rounds of CASP. Although not a replacement for SOV, RELINFO has greater dispersion. Over the five rounds of CASP assessed here, RELINFO shows that predictions targets have been more difficult in successive CASP experiments, yet the predictions quality has continued to improve measurably over each round. In terms of information, the secondary structure prediction quality has almost doubled from CASP1 to CASP5. Therefore, as a different perspective of accuracy, RELINFO can help to improve prediction of protein secondary structure by providing a measure of difficulty as well as final quality of a prediction.     

Lactobacillus acidophilus LAP5 able to inhibit the Salmonella choleraesuis invasion to the human Caco-2 epithelial cell

The mechanisms for lactic acid bacteria (LAB) to inhibit Salmonella invasion appear to be multifactorial and include the adhesion of LAB to host intestine epithelium, the production of organic acids, or bacteriocin by LAB cells. Previously, we found a strain of Lactobacillus acidophilus isolated from swine, i.e. strain LAP5, was with antagonistic effect against Salmonella typhimurium. This strain LAP5 was also found to meet the requirements for probiotic use. In this study, we evaluate the potential of LAP5 strain to protect the human or swine from infection by Salmonella choleraesuis. We present evidence that the culture of LAP5 was able to inhibit the invasion of S. choleraesuis to human Caco-2 cell line. The LAP5 cell culture showed a higher inhibitory effect on the invasion of S. choleraesuis to Caco-2 cells than the spent culture supernatant (SCS) of LAP5 did. Also, the pH, organic acids or the bacteriocin, which act at low pH conditions, may play the role of antagonistic effect. The addition, adhesion of LAP5 cells to Caco-2 cell line may also play roles to reduce the invasion of S. choleraesuis.     

Atypical protein kinase C regulates dual pathways for degradation of the oncogenic coactivator SRC-3/AIB1

SRC-3/AIB1 is a steroid receptor coactivator with potent growth-promoting activity, and its overexpression is sufficient to induce tumorigenesis. Previous studies indicate that the cellular level of SRC-3 is tightly regulated by both ubiquitin-dependent and ubiquitin-independent proteasomal degradation pathways. Atypical protein kinase C (aPKC) is frequently overexpressed in cancers. In the present study, we show that aPKC phosphorylates and specifically stabilizes SRC-3 in a selective ER-dependent manner. We further demonstrate that an acidic residue-rich region in SRC-3 is an important determinant for aPKC-mediated phosphorylation and stabilization. The mechanism of the aPKC-mediated stabilization appears due to a decreased interaction between SRC-3 and the C8 subunit of the 20S core proteasome, thus preventing SRC-3 degradation. Our results demonstrate a potent signaling mechanism for regulating SRC-3 levels in cells by coordinate enzymatic inhibition of both ubiquitin-dependent and ubiquitin-independent proteolytic pathways.     

Effect of exercise training on calpain systems in lean and obese Zucker rats

Exercise training plays a major role in the improving physiology of diabetes. Herein we aimed to investigate the influence of exercise upon the calcium-dependent calpain-isoform expressions of lean or obese Zucker rats, a model of obesity and type II diabetes (NIDDM). Five-month-old rats were divided: (1) obese sedentary (OS, n=7); (2) obese exercise (OE, n=7); (3) lean sedentary (LS, n=7); (4) lean exercise (LE, n=7). After 2-month exercise (treadmill running), the body weight (BW) and expression of calpain 10, μ-calpain, and m-calpain in skeletal muscles were determined by RT-PCR, using β-actin as internal standard. We found exercise is useful for BW lossing, especially in the obese rats. The BW difference between OS and OE rats (69 g vs. 18.2 g) was more significantly than that between LS and LE rats (41.8 g vs. 28.7g). The calpain 10 expression of LS rats (0.965) was lower than that of LE rats (1.006), whereas those of OS and OE were comparable. The μ- or m-calpain expressions of sedentary groups (OS, LS) was significantly higher than those of exercise groups (OE, LE). The μ-calpain expression (1.13/0.92) and m-calpain expression (1.01/0.99) of OS/LS rats was significantly higher than those of OE/LE rats [1.07/0.9 (μ-calpain); 0.97/0.95 (m-calpain)]. We concluded that the μ- or m-calpains in skeletal muscle are regulated by exercise in both lean and obese Zucker rats. Exercise and BW controlling might improve the physiopathology of obesity and diabetes. Both μ- or m-calpains might become useful markers for prognoses of diabetes.     

Pioglitazone retrieves hepatic antioxidant DNA repair in a mice model of high fat diet

Background  

Pioglitazone was reported to improve hepatic steatosis and necroinflammation in human studies. To investigate whether the hepato-protective effect of pioglitazone was associated with an improvement of antioxidant defense mechanism, oxidative DNA damage and repair activity were determined in a high fat diet model. Male C57BL/6 mice were respectively fed with a 30% fat diet, the same diet with pioglitazone 100 mg/kg/day, or a chow diet as control for 8 weeks. Tissue oxidative stress was indicated by malondialdehyde concentration. Oxidative DNA damage was detected by immunohistochemical 8-oxoG staining. Enzymatic antioxidant defense was detected by the real-time PCR of superoxide dismutase (Sod1, Sod2) and DNA glycosylase (Ogg1, MutY). Oxidative DNA repair was detected by immunohistochemical staining and western blotting of OGG1 expression.