Constructing structural networks of signaling pathways on the proteome scale

Proteins function through their interactions, and the availability of protein interaction networks could help in understanding cellular processes. However, the known structural data are limited and the classical network node-and-edge representation, where proteins are nodes and interactions are edges, shows only which proteins interact; not how they interact. Structural networks provide this information. Protein-protein interface structures can also indicate which binding partners can interact simultaneously and which are competitive, and can help forecasting potentially harmful drug side effects. Here, we use a powerful protein-protein interactions prediction tool which is able to carry out accurate predictions on the proteome scale to construct the structural network of the extracellular signal-regulated kinases (ERK) in the mitogen-activated protein kinase (MAPK) signaling pathway. This knowledge-based method, PRISM, is motif-based, and is combined with flexible refinement and energy scoring. PRISM predicts protein interactions based on structural and evolutionary similarity to known protein interfaces.     

Olfactory sensitivity and odor structure-activity relationships for aliphatic carboxylic acids in CD-1 mice

Using a conditioning paradigm, the olfactory sensitivity of CD-1 mice for a homologous series of aliphatic n-carboxylic acids (ethanoic acid to n-octanoic acid) and several of their isomeric forms was investigated. With all 14 odorants, the animals significantly discriminated concentrations as low as 0.03 ppm (parts per million) from the solvent, and with four odorants the best-scoring animals even detected concentrations as low as 3 ppt (parts per trillion). Analysis of odor structure-activity relationships showed that the correlation between olfactory detection thresholds of the mice for the unbranched carboxylic acids and carbon chain length can best be described as a U-shaped function with the lowest threshold values at n-butanoic acid. A significant positive correlation between olfactory detection thresholds and carbon chain length of the carboxylic acids with their branching next to the functional carboxyl group was found. In contrast, no such correlation was found for carboxylic acids with their branching at the distal end of the carbon chain relative to the functional carboxyl group. Finally, a significant correlation was found between olfactory detection thresholds and the position of the branching of the carboxylic acids. Across-species comparisons suggest that mice are more sensitive for short-chained (C(2) to C(4)) aliphatic n-carboxylic acids than other mammalian species, but not for longer-chained ones (C(5) to C(8)). Further comparisons suggest that odor structure-activity relationships are both substance class- and species-specific.     

Comparison of 6q25 Breast Cancer Hits from Asian and European Genome Wide Association Studies in the Breast Cancer Association Consortium (BCAC)

The 6q25.1 locus was first identified via a genome-wide association study (GWAS) in Chinese women and marked by single nucleotide polymorphism (SNP) rs2046210, approximately 180 Kb upstream of ESR1. There have been conflicting reports about the association of this locus with breast cancer in Europeans, and a GWAS in Europeans identified a different SNP, tagged here by rs12662670. We examined the associations of both SNPs in up to 61,689 cases and 58,822 controls from forty-four studies collaborating in the Breast Cancer Association Consortium, of which four studies were of Asian and 39 of European descent. Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI). Case-only analyses were used to compare SNP effects in Estrogen Receptor positive (ER+) versus negative (ER−) tumours. Models including both SNPs were fitted to investigate whether the SNP effects were independent. Both SNPs are significantly associated with breast cancer risk in both ethnic groups. Per-allele ORs are higher in Asian than in European studies [rs2046210: OR (A/G) = 1.36 (95% CI 1.26–1.48), p = 7.6×10⁻¹⁴ in Asians and 1.09 (95% CI 1.07–1.11), p = 6.8×10⁻¹⁸ in Europeans. rs12662670: OR (G/T) = 1.29 (95% CI 1.19–1.41), p = 1.2×10⁻⁹ in Asians and 1.12 (95% CI 1.08–1.17), p = 3.8×10⁻⁹ in Europeans]. SNP rs2046210 is associated with a significantly greater risk of ER− than ER+ tumours in Europeans [OR (ER−) = 1.20 (95% CI 1.15–1.25), p = 1.8×10⁻¹⁷ versus OR (ER+) = 1.07 (95% CI 1.04–1.1), p = 1.3×10⁻⁷, p_{heterogeneity} = 5.1×10⁻⁶]. In these Asian studies, by contrast, there is no clear evidence of a differential association by tumour receptor status. Each SNP is associated with risk after adjustment for the other SNP. These results suggest the presence of two variants at 6q25.1 each independently associated with breast cancer risk in Asians and in Europeans. Of these two, the one tagged by rs2046210 is associated with a greater risk of ER− tumours.     

Ethnic Differences in the Prevalence of Metabolic Syndrome: Results from a Multi-Ethnic Population-Based Survey in Malaysia

Introduction

The prevalence of metabolic syndrome is increasing disproportionately among the different ethnicities in Asia compared to the rest of the world. This study aims to determine the differences in the prevalence of metabolic syndrome across ethnicities in Malaysia, a multi-ethnic country.

Methods

In 2004, we conducted a national cross-sectional population-based study using a stratified two-stage cluster sampling design (N = 17,211). Metabolic syndrome was defined according to the International Diabetes Federation/National Heart, Lung and Blood Institute/American Heart Association (IDF/NHLBI/AHA-2009) criteria. Multivariate models were used to study the independent association between ethnicity and the prevalence of the metabolic syndrome.

Results

The overall mean age was 36.9 years, and 50.0% participants were female. The ethnic distribution was 57.0% Malay, 28.5% Chinese, 8.9% Indian and 5.0% Indigenous Sarawakians. The overall prevalence of the metabolic syndrome was 27.5%, with a prevalence of central obesity, raised triglycerides, low high density lipoprotein cholesterol, raised blood pressure and raised fasting glucose of 36.9%, 29.3%, 37.2%, 38.0% and 29.1%, respectively. Among those <40 years, the adjusted prevalence ratios for metabolic syndrome for ethnic Chinese, Indians, and Indigenous Sarawakians compared to ethnic Malay were 0.81 (95% CI 0.67 to 0.96), 1.42 (95% CI 1.19 to 1.69) and 1.37 (95% CI 1.08 to 1.73), respectively. Among those aged ≥40 years, the corresponding prevalence ratios were 0.86 (95% CI 0.79 to 0.92), 1.25 (95% CI 1.15 to 1.36), and 0.94 (95% CI 0.80, 1.11). The P-value for the interaction of ethnicity by age was 0.001.

Conclusions

The overall prevalence of metabolic syndrome in Malaysia was high, with marked differences across ethnicities. Ethnic Chinese had the lowest prevalence of metabolic syndrome, while ethnic Indians had the highest. Indigenous Sarawakians showed a marked increase in metabolic syndrome at young ages.     

Enhanced Killing Effect of Nanosecond Pulse Electric Fields on PANC1 and Jurkat Cell Lines in the Presence of Tween 80

We investigated the effects of nanosecond pulse electric fields (nsPEFs) on Jurkat and PANC1 cells, which are human carcinoma cell lines, in the presence of Tween 80 (T80) at a concentration of 0.18?% and demonstarted an enhanced killing effect. We used two biological assays to determine cell viability after exposing cells to nsPEFs in the presence of T80 and observed a significant increase in the killing effect of nsPEFs. We did not see a toxic effect of T80 when cells were exposed to surfactant alone. However, we saw a synergistic effect when cells exposed to T80 were combined with the nsPEFs. Increasing the time of exposure for up to 8?h in T80 led to a significant decrease in cell viability when nsPEFs were applied to cells compared to control cells. We also observed cell type–specific swelling in the presence of T80. We suggest that T80 acts as an adjuvant in facilitating the effects of nsPEFs on the cell membrane; however, the limitations of the viability assays were addressed. We conclude that T80 may increase the fragility of the cell membrane, which makes it more susceptible to nsPEF-mediated killing.     

Male flowers are better fathers than hermaphroditic flowers in andromonoecious Passiflora incarnata

? The diversity of plant breeding systems provides the opportunity to study a range of potential reproductive adaptations. Many mechanisms remain poorly understood, among them the evolution and maintenance of male flowers in andromonoecy. Here, we studied the role of morphologically male flowers ('male morph') in andromonoecious Passiflora incarnata. ? We measured morphological differences between hermaphroditic and male morph flowers in P.?incarnata and explored the fruiting and siring ability of both flower types. ? Male morph flowers in P.?incarnata were of similar size to hermaphroditic flowers, and there was little evidence of different resource allocation to the two flower types. Male morph flowers were less capable of producing fruit, even under ample pollen and resource conditions. By contrast, male morph flowers were more successful in siring seeds. On average, male morph flowers sired twice as many seeds as hermaphroditic flowers. This difference in male fitness was driven by higher pollen export from male morph flowers as a result of greater pollen production and less self-pollen deposition. ? The production of male morph flowers in P.?incarnata appears to be a flexible adaptive mechanism to enhance male fitness, which might be especially beneficial when plants face temporary resource shortages for nurturing additional fruits.     

Chiral Sulfur Compounds Studied by Raman Optical Activity: tert-Butanesulfinamide and its Precursor tert-Butyl tert-Butanethiosulfinate

Two chiral sulfur compounds, tert-butyl tert-butanethiosulfinate (1) and tert-butanesulfinamide (2), with inversion of configuration, have been studied by Raman optical activity (ROA) and electronic circular dichroism combined with density functional theory calculation. With the S-S linkage in 1, the couplings between the two tertiary carbon atoms often generate large ROA signals, whereas the tertiary carbon atom itself generally makes a large contribution to ROA signals in 2 for similar vibrational modes. The conformational dependence of ROA parameters provides probing conformation around the S-S bond from a new perspective. The simultaneous use of electronic circular dichroism and ROA is warranted to extract reliable conformational information. ROA provides a suitable candidate for the stereochemical study of chiral sulfur compounds, especially its capability of sensing the conformation around the S-S bond. Chirality 24:731-740, 2012. ? 2012 Wiley Periodicals, Inc.     

鱼类细胞自噬研究进展

自噬是广泛存在于真核生物中的生命现象,对于细胞的生长、分化、发育和维持细胞内环境稳态等方面具有重要意义。尽管对于作为低等脊椎动物的鱼类细胞自噬研究起步较晚,但近几年围绕其自噬的诱导、自噬相关基因表达及调控、鱼类病原诱导的自噬,特别是以斑马鱼为试验模型开展的自噬与发育调控关系等研究都取得了一些进展,就此进行综述。     

Finite element analysis of stress distribution on modified retentive tips of bar clasp

This study used finite element analysis to evaluate the retentive tips of bar clasps made from different alloys and using different designs in order to determine whether or not different materials and tip forms are suitable for bar clasp applications. Co-Cr, Ti and Type IV Au alloys were selected based on their physical and mechanical properties. The 3D finite element models of three different bar clasp retentive tip geometries prepared from Co-Cr, Ti and Type IV Au alloys were constructed using the finite element software package MSC.Marc. Analysis of a concentrated load of 5?N applied to the removable partial denture approach arms in an occlusal direction was performed. Although stress distribution and localisation within bar clasps with different retentive tips were observed to be similar and were concentrated in the approach arm, stress intensities differed in all models.     

Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes

Apoptosis is a matter of life and death for cells and both inhibited and enhanced apoptosis may be involved in the pathogenesis of human diseases. The structures of protein-protein complexes in the apoptosis signaling pathway are important as the structural pathway helps in understanding the mechanism of the regulation and information transfer, and in identifying targets for drug design. Here, we aim to predict the structures toward a more informative pathway than currently available. Based on the 3D structures of complexes in the target pathway and a protein-protein interaction modeling tool which allows accurate and proteome-scale applications, we modeled the structures of 29 interactions, 21 of which were previously unknown. Next, 27 interactions which were not listed in the KEGG apoptosis pathway were predicted and subsequently validated by the experimental data in the literature. Additional interactions are also predicted. The multi-partner hub proteins are analyzed and interactions that can and cannot co-exist are identified. Overall, our results enrich the understanding of the pathway with interactions and provide structural details for the human apoptosis pathway. They also illustrate that computational modeling of protein-protein interactions on a large scale can help validate experimental data and provide accurate, structural atom-level detail of signaling pathways in the human cell.