Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins

Background  

We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8 and 12 Angstrom; coarse protein topology. The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non-redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of C _α traces for short proteins (up to 200 amino acids).     

Competitive relationships between two contrasting but coexisting grasses

Leymus chinensis (Trin.) Tzvelev and Phragmites communis Trin. are co-dominant grasses in both nutrient-poor and rich steppes in the Songnen Plains of northeastern China. A replacement series experiment was conducted along a five-level nutrient gradient to test for changes in the competitive relationships of the species with nutrient availability. There were significant effects of nutrient level and species proportion on mean plant height, biomass and rhizome length. Facilitation was found in these plant attributes for both species when grown in mixture compared with monoculture, especially at high nutrient levels. For example, L. chinensis grew taller and intercepted more light when in mixture. The aboveground dominance of P. communis did not decrease in mixture, possibly because it benefited from belowground interactions with L. chinensis. Biomass allocation was apparently influenced by both above and belowground competition. For example, L. chinensis allocated much more biomass to shoots and less to roots when neighbor number was increased, suggesting that aboveground competition occurred. Root: shoot ratios of L. chinensis in monoculture decreased gradually with increasing nutrient availability, whereas the ratio in mixture declined rapidly, implying intense competition for light at high levels. Our results support the hypothesis that nutrient competition is more important than light competition when soil nutrients are scarce. Although the interactions between these species benefit both, P. communis is more likely to displace L. chinensis at high nutrient availability.     

B cell-activating factor of the tumor necrosis factor family (BAFF) is expressed under stimulation by interferon in salivary gland epithelial cells in primary Sjögren's syndrome

B cell-activating factor (BAFF) has a key role in promoting B-lymphocyte activation and survival in primary Sj?gren's syndrome (pSS). The cellular origin of BAFF overexpression in salivary glands of patients with pSS is not fully known. We investigated whether salivary gland epithelial cells (SGECs), the main targets of autoimmunity in pSS, could produce and express BAFF. We used quantitative RT-PCR, ELISA and immunocytochemistry in cultured SGECs from eight patients with pSS and eight controls on treatment with IL-10, tumor necrosis factor alpha (TNF-alpha), IFN-alpha and IFN-gamma. At baseline, BAFF expression in SGECs was low in pSS patients and in controls. Treatment with IFN-alpha, IFN-gamma and TNF-alpha + IFN-gamma increased the level of BAFF mRNA in pSS patients (the mean increases were 27-fold, 25-fold and 62-fold, respectively) and in controls (mean increases 19.1-fold, 26.7-fold and 17.7-fold, respectively), with no significant difference between patients and controls. However, in comparison with that at baseline, stimulation with IFN-alpha significantly increased the level of BAFF mRNA in SGECs of pSS patients (p = 0.03) but not in controls (p = 0.2), which suggests that SGECs of patients with pSS are particularly susceptible to expressing BAFF under IFN-alpha stimulation. Secretion of BAFF protein, undetectable at baseline, was significantly increased after IFN-alpha and IFN-gamma stimulation both in pSS patients (40.8 +/- 12.5 (+/- SEM) and 47.4 +/- 18.7 pg/ml, respectively) and controls (24.9 +/- 8.0 and 9.0 +/- 3.9 pg/ml, respectively), with no significant difference between pSS and controls. Immunocytochemistry confirmed the induction of cytoplasmic BAFF expression after stimulation with IFN-alpha and IFN-gamma. This study confirms the importance of resident cells of target organs in inducing or perpetuating autoimmunity. Demonstrating the capacity of SGECs to express and secrete BAFF after IFN stimulation adds further information to the pivotal role of these epithelial cells in the pathogenesis of pSS, possibly after stimulation by innate immunity. Our results suggest that an anti-BAFF therapeutic approach could be particularly interesting in pSS.     

Diagnostic scintigraphy and effectiveness of 131I radioiodine therapy in differentiated thyroid carcinoma (DTC)

INTRODUCTION: Since the effect of pre-therapeutic scintigraphy on the outcome of DTC treatment is debated, we evaluated factors affecting the effectiveness of (131)I therapy with respect to the delay between diagnostic scintigraphy and the application of radioiodine. MATERIAL AND METHODS: In the studied group of 60 patients with DTC, mean age 54.6 +/- 13.0 years, four weeks prior to the planned diagnostics, L-thyroxine was withdrawn and the following tests performed: (131)I (4 MBq) uptake above the neck, thyroid volume by USG, TSH and hTg level. Wholebody scintigraphy (37 MBq) was performed. The time between this diagnostic scintigraphy and application of (131)I (3657 MBq) was calculated. Based on whole-body 131I scintigraphy (74 MBq) performed 1 year after radioiodine treatment, the patients were divided into: group I - 42 patients with no tracer accumulation, and group II--18 patients who continued to accumulate (131)I in the neck. RESULTS: The differences between the median values of (131)I uptake and of thyroid volumes, and between the TSH and hTg median values in the two groups of patients were found not to be statistically significant. The average times between diagnostic scintigraphy and (131)I treatment in group I and II (9.4 vs. 8.3 weeks, respectively) were not significantly different either. CONCLUSION: Despite the different effectiveness of supplementary (131)I treatment, patients in group I and group II showed no statistically significant differences in the studied parameters. It appears that the diagnostic (131)I activity of 37 MBq and the time between diagnostic scintigraphy and application of (131)I did not have any effect on the results of the treatment in our group of patients.     

Overexpression of the Saccharomyces cerevisiae RER2 gene in Trichoderma reesei affects dolichol dependent enzymes and protein glycosylation

Protein secretion in Trichoderma reesei could be stimulated by overexpression of the yeast Saccharomyces cerevisiae DPM1 gene encoding dolichyl phosphate mannose synthase (DPMS) a key enzyme in the O-glycosylation pathway. The secreted proteins were glycosylated to the wild type level. On the other hand, the elevated concentration of GDP-mannose, a direct substrate for DPMS, resulting from overexpression in T. reesei of the mpg1 gene coding for guanyltransferase, did not affect secretion of proteins but did affect the degree of their O- and N-glycosylation. In this paper, we examined the effects of dolichol, an indispensable carrier of sugar residues in protein glycosylation, on the synthesis of glycosylated proteins. An increase in dolichol synthesis was obtained by overexpression of the yeast gene encoding cis-prenyltransferase, the first enzyme of the mevalonate pathway committed to dolichol biosynthesis. We observed that, an increased concentration of dolichol resulted in an increased expression of the dpm1 gene and DPMS activity and in overglycosylation of secreted proteins.     

Impact de la varicocélectomie chez les patients ayant une azoospermie non obstructive ou une oligozoospermie sévère

Objective

To evaluate the changes induced by retroperitoneal varicocelectomy on infertile men with nonobstructive azoospermia or severe oligozoospermia.

Patients and methods

The records were retrospectively evaluated for 46 infertile men with severe oligozoospermia (group I) and 15 infertile men with non-obstructive azoospermia (group II). The parameters of sperm before and after surgery and unassisted pregnancy rate were comparatively analysed.

Results

In the severe oligozoospermia group, the mean age of patients was 35.5 ± 6.4 (23–47 years). The mean duration of infertility was 4.9 ± 3.4 years (1–13 years). Of these patients, 41(89.1%) had bilateral varicocele and five (10.9%) had unilateral left-side varicocele. The varicocele was classified as grade I in two cases (4.3%), grade II in 39 cases (84.7%) and grade III in five cases (10.9%). After surgery, the mean sperm count increased from 1.85 ± 1.4 to 8.3 ± 10.3 millions/ml and mean sperm normal motility from 43.3 ± 21.5 to 47.6 ± 29.2%. The mean sperm abnormal morphology decreased from 65.05 ± 21.6 to 50.08 ± 26.9%. After a mean follow-up of 26.2 ± 11.6 months, the unassisted pregnancy rate in this group was 26.1%. In the non-obstructive azoospermia group (N = 15), the mean age of patients was 40.8 ± 7.2 (27–47 years). The mean duration of infertility was 6 ± 3.1 years (3–15 years). After varicocelectomy, an induction of spermatogenesis was observed in three patients (20%) with presence of motile sperm in the ejaculate. In this group, only one of the 15 men achieved unassisted pregnancy.

Conclusion

Retroperitoneal varicocele repair resulted in spermatogenesis induction with presence of motile ejaculated spermatozoa for some men with non-obstructive azoospermia. It induced spermatogenesis and fertility enhancement in men with severe oligozoospermia. Varicocele repair should be considered in men with non-obstructive azoospermia or severe oligozoospermia.     

Effects of paclobutrazol on Botrytis cinerea isolates obtained from potted plants

The growth of different isolates of Botrytis cinerea, collected from potted plants affected by Botrytis blight in southern Spain during recent years, was studied. These isolates, which show wide phenotypic differences when grown in vitro, are differentially affected by growth temperature, gibberellic acid, and paclobutrazol--an efficient plant growth retardant used widely in nursery potted plants to reduce plant size, favouring compactness, a more intense green foliage and increased stress tolerance to maintain quality prior to sale. In addition, paclobutrazol may have a fungicidal effect since it belongs to the triazole chemical group. However, paclobutrazol is only used as a plant growth retardant in Spain. In this work, we evaluate the effect of paclobutrazol dose (0, 0.05, 0.25, 1.25, and 6.25 mg/plate) on the growth of a collection of different B. cinerea isolates obtained from the following potted plants: Cyclamen persicum, Hydrangea macrophylla, Lantana camara and Lonicera japonica. Mycelial growth curves and growth rates assessed from difference in colony areas during the linear phase, conidiation (measured as time of appearance), conidial length (microm), and sclerotia production (number/plate) were evaluated in the isolates, which were grown at 26 degrees C on Petri dishes containing potato dextrose agar for up to 36 days. Mycelial growth curves fitted a typical kinetic equation of fungus grown on solid media. The B. cinerea isolates showed a high degree of variability in their growth kinetics, depending on the isolate and paclobutrazol dose. This triazole delayed mycelial growth during the linear phase in an isolate-dependent manner, and isolates from C. persicum and L. japonica were more affected by paclobutrazol than H. macrophylla. On the other hand, 0.25 mg of paclobutrazol was the critical dose to significantly reduce the growth rate in all isolates. 6.25 mg paclobutrazol inhibited conidiation in isolates from C. persicum, and reduced the conidial length in isolates from H. macrophylla and L. camara. The sclerotia production process was blocked at paclobutrazol doses higher than 1.25 mg, while no sclerotia were produced in isolates from C. persicum and L. japonica with 0.25 mg. H. macrophylla was the isolate in which sclerotia production was most influenced by paclobutrazol. It was concluded that the exact effect of paclobutrazol on B. cinerea growth depends on the isolate, and new strategies should be considered for evaluating its use as retardant and fungicide.     

Responses of Wheat Roots to Exogenous Selenium Supply Under Enhanced Ultraviolet-B

Effects of selenium (Se) on growth and some physiological traits of roots in wheat (Triticum aestivum L. cv Han NO.7086) seedlings exposed to enhanced ultraviolet-B (UV-B) stress are reported. Responses of roots were different depending on the Se concentration. Compared with the control, root weight of wheat seedlings treated with 1.0 and 2.0 mg Se kg⁻¹ soil increased by 39.47% and 16.28%, respectively. The lower amount Se (0.5 mg kg⁻¹) and the higher amount Se treatments (3.0 mg kg⁻¹) did not significantly affect on root weight. Se treatments significantly increased root activity, flavonoids and proline content, and activities of peroxidase and superoxide dimutase in wheat roots exposed to enhanced UV-B. In addition, the treatments with 0.5, 1.0, and 2.0 mg Se kg⁻¹ significantly reduced malondialdehyde content and the rate of superoxide radical (O₂⁻) production of roots, whereas the higher amount Se treatment only induced a decrease in the rate of O₂⁻ production. The results of this study demonstrated that optimal Se supply promoted roots growth of wheat seedlings, and that optimal Se supply could reduce oxidative stress in wheat roots under enhanced UV-B radiation.     

Antioxidant Responses of Wheat Seedlings to Exogenous Selenium Supply Under Enhanced Ultraviolet-B

The paper reports the effects of selenium (Se) supply on growth and antioxidant traits of wheat (Triticum aestivum L. cv Han NO.7086) seedlings exposed to enhanced ultraviolet-B (UV-B) stress. Antioxidant responses of seedlings were different depending on the Se concentration. Compared with the control, the lower amount used (0.5 mg Se kg⁻¹ soil) had no significant effect on biomass accumulation. The treatments with 1.0, 2.0, and 3.0 mg Se kg⁻¹ promoted biomass accumulation of wheat seedlings, and the increased amount in biomass was the most at 1.0 mg Se kg⁻¹ treatment. Se treatments with 1.0, 2.0, and 3.0 mg kg⁻¹ also significantly increased activities of peroxidase (POD) and superoxide dismutase (SOD) and reduced the rate of superoxide radical (O₂⁻) production and malondialdehyde (MDA) content of wheat seedlings. In addition, anthocyanins and phenolic compounds content in wheat seedlings evidently increased by the treatments with 1.0 and 2.0 mg Se kg⁻¹. The lower Se treatment had no significant effect on MDA content, although it increased activities of antioxidant enzymes (POD, SOD, and catalase activities) and reduced the rate of O₂⁻ production in wheat seedlings. These results suggest that optimal Se supply is favorable for the growth of wheat seedlings and that optimal Se supply can reduce oxidative stress of seedlings under enhanced UV-B radiation.