Accurate Prediction of Protein Catalytic Residues by Side Chain Orientation and Residue Contact Density

Prediction of protein catalytic residues provides useful information for the studies of protein functions. Most of the existing methods combine both structure and sequence information but heavily rely on sequence conservation from multiple sequence alignments. The contribution of structure information is usually less than that of sequence conservation in existing methods. We found a novel structure feature, residue side chain orientation, which is the first structure-based feature that achieves prediction results comparable to that of evolutionary sequence conservation. We developed a structure-based method, Enzyme Catalytic residue SIde-chain Arrangement (EXIA), which is based on residue side chain orientations and backbone flexibility of protein structure. The prediction that uses EXIA outperforms existing structure-based features. The prediction quality of combing EXIA and sequence conservation exceeds that of the state-of-the-art prediction methods. EXIA is designed to predict catalytic residues from single protein structure without needing sequence or structure alignments. It provides invaluable information when there is no sufficient or reliable homology information for target protein. We found that catalytic residues have very special side chain orientation and designed the EXIA method based on the newly discovered feature. It was also found that EXIA performs well for a dataset of enzymes without any bounded ligand in their crystallographic structures.     

Suppression of Extensive Neurofilament Phosphorylation Rescues α-Internexin/Peripherin-Overexpressing PC12 Cells from Neuronal Cell Death

Intermediate filament (IF) overproduction induces abnormal accumulation of neuronal IF, which is a pathological indicator of some neurodegenerative disorders. In our study, α-Internexin- and peripherin-overexpressing PC12 cells (pINT-EGFP and pEGFP-peripherin) were used as models to study neuropathological pathways responsible for neurodegenerative diseases. Microarray data revealed that Cdk5-related genes were downregulated and Cdk5 regulatory subunit-associated protein 3 (GSK-3α and GSK-3β) were upregulated in pINT-EGFP cells. Increased expression of phosphorylated neurofilament and aberrant activation of Cdk5 and GSK-3β were detected in both pEGFP-peripherin and pINT-EGFP cells by Western blotting. In addition, pharmacological approaches to retaining viability of pINT-EGFP and pEGFP-peripherin cells were examined. Treatment with Cdk5 inhibitor and GSK-3β inhibitor significantly suppressed neuronal death. Dynamic changes of disaggregation of EGFP-peripherin and decrease in green fluorescence intensity were observed in pEGFP-peripherin and pINT-EGFP cells by confocal microscopy after GSK-3β inhibitor treatment. We conclude that inhibition of Cdk5 and GSK-3β suppresses neurofilament phosphorylation, slows down the accumulation of neuronal IF in the cytoplasm, and subsequently avoids damages to cell organelles. The results suggest that suppression of extensive neurofilament phosphorylation may be a potential strategy for ameliorating neuron death. The suppression of hyperphosphorylation of neuronal cytoskeletons with kinase inhibitors could be one of potential therapeutic treatments for neurodegenerative diseases.     

Asian Dust Storm Elevates Children's Respiratory Health Risks: A Spatiotemporal Analysis of Children's Clinic Visits across Taipei (Taiwan)

Concerns have been raised about the adverse impact of Asian dust storms (ADS) on human health; however, few studies have examined the effect of these events on children's health. Using databases from the Taiwan National Health Insurance and Taiwan Environmental Protection Agency, this study investigates the documented daily visits of children to respiratory clinics during and after ADS that occurred from 1997 to 2007 among 12 districts across Taipei City by applying a Bayesian structural additive regressive model controlled for spatial and temporal patterns. This study finds that the significantly impact of elevated children's respiratory clinic visits happened after ADS. Five of the seven lagged days had increasing percentages of relative rate, which was consecutively elevated from a 2-day to a 5-day lag by 0.63%～2.19% for preschool children (i.e., 0～6 years of age) and 0.72%～3.17% for school children (i.e., 7～14 years of age). The spatial pattern of clinic visits indicated that geographical heterogeneity was possibly associated with the clinic's location and accessibility. Moreover, day-of-week effects were elevated on Monday, Friday, and Saturday. We concluded that ADS may significantly increase the risks of respiratory diseases consecutively in the week after exposure, especially in school children.     

The POU-domain protein Pdm3 regulates axonal targeting of R neurons in the Drosophila ellipsoid body

The ability of axons to project correctly to the target is essential for the formation of complex neural networks. The intrinsic regulation of this process is still unclear. Here, we show that POU domain motif 3 (Pdm3) is required in ring (R) neurons to control precise axon targeting to the Drosophila ellipsoid body (EB). Pdm3 is expressed in neurons of the central nervous system in larvae and adults and required for the normal development of the EB of the central complex in the adult brain. The normal EB structure is abolished in pdm3 mutants, and this phenotype is rescued by pdm3 expression in R neurons, suggesting that the defect in axonal targeting of R neurons is the major cause in EB malformation in pdm3 mutants. We show that cell fate determination, dendritic arborization, and initial axon projection of R neurons are normal while the axonal targeting to the EB is defective in pdm3 mutants. © 2011 Wiley Periodicals, Inc. Develop Neurobiol, 2012     

Induction of TRAIL- and TNF-alpha-dependent apoptosis in human monocyte-derived dendritic cells by microfilariae of Brugia malayi

Dysregulation of professional APC has been postulated as a major mechanism underlying Ag-specific T cell hyporesponsiveness in patients with patent filarial infection. To address the nature of this dysregulation, dendritic cells (DC) and macrophages generated from elutriated monocytes were exposed to live microfilariae (mf), the parasite stage that circulates in blood and is responsible for most immune dysregulation in filarial infections. DC exposed to mf for 24-96 h showed a marked increase in cell death and caspase-positive cells compared with unexposed DC, whereas mf exposure did not induce apoptosis in macrophages. Interestingly, 48-h exposure of DC to mf induced mRNA expression of the proapoptotic gene TRAIL and both mRNA and protein expression of TNF-alpha. mAb to TRAIL-R2, TNF-R1, or TNF-alpha partially reversed mf-induced cell death in DC, as did knocking down the receptor for TRAIL-R2 using small interfering RNA. The mf also induced gene expression of BH3-interacting domain death agonist and protein expression of cytochrome c in DC; mf-induced cleavage of BH3-interacting domain death agonist could be shown to induce release of cytochrome c, leading to activation of caspase 9. Our data suggest that mf induce DC apoptosis in a TRAIL- and TNF-alpha-dependent fashion.     

Sex identification of owls (family Strigidae) using oligonucleotide microarrays

Molecular sexing of the diversified avian family Strigidae is difficult. Sex identification using the intron length difference between W and Z chromosomal CHD1 genes, as visualized by agarose gel electrophoreses, often produces ambiguous results. Here we describe a simple method for sexing a variety of Strigidae species using oligonucleotide microarrays, on which several sex-specific probes operated complementarily or in concert. The sex of 8 owl species was identified clearly on the microarrays through sequence recognition. This sequence-directed method can be easily applied to a wider range of Strigidae species.     

Explaining the optimality of U-shaped age-specific mortality

Mortality is U-shaped with age for many species, declining from birth to sexual maturity, then rising in adulthood, sometimes with postreproductive survival. We show analytically why the optimal life history of a species with determinate growth is likely to have this shape. An organism allocates energy among somatic growth, fertility and maintenance/survival at each age. Adults may transfer energy to juveniles, who can then use more energy than they produce. Optimal juvenile mortality declines from birth to maturity, either to protect the increasingly valuable cumulative investments by adults in juveniles or to exploit the compounding effects of early investment in somatic growth, since early growth raises subsequent energy production, which in turn supports further growth. Optimal adult mortality rises after maturity as expected future reproduction declines as in Hamilton, but intergenerational transfers lead to postreproductive survival as in Lee. Here the Hamilton and transfer effects are divided by probabilities of survival in contrast to the fitness impact measures, which are relevant for mutation-selection balance. If energetic efficiency rises strongly with adult experience, then adult mortality could initially be flat or declining.     

New bioactive clerodane diterpenoids from the roots of Casearia membranacea

Bioassay-guided fractionation of the acetone extract of the roots of Casearia membranacea furnished three new clerodane diterpenes, caseamembrins S-U (1-3) and the known caseamembrin Q (4). Their structures were established by extensive spectroscopic analyses, especially 2D-NMR. Compounds 1-4 were tested against human tumor cells, including HeLa (cervical epitheloid carcinoma), DLD-1 (colon carcinoma), Daoy (medulloblastoma), and KB (oral epidermoid carcinoma) cell lines. Caseamembrin T (2) exhibited the most potent activity against Daoy cells (ED(50)=10 ng/ml), superior to that of the standard drug mitomycin.     

地萼苔科锡金裂萼苔(Chiloscyphus sikkimensis)在中国大陆的新记录

报道产于云南的中国苔类植物地萼苔科大陆新记录种: 锡金裂萼苔(Chiloscyphus sikkimensis(Steph.) J.J. Engel &; R.M. Schust.)。本种的主要区别特征有：茎叶倾斜或近横向着生,近轴端凸起,近似圆形,叶边全缘,卵形,先端圆钝或微凹;腹叶心形或肾形,先端圆钝或微凹,一侧或两侧基部与茎叶腹边联生。报道于台湾的Heteroscyphus acutangulus(Schiffn.) Schiffn. 实为Chiloscyphus sikkimensis,应被移出中国苔藓植物区系。     

The proto-oncogene Int6 is essential for neddylation of Cul1 and Cul3 in Drosophila

Int6 is a proto-oncogene implicated in various types of cancer, but the mechanisms underlying its activity are not clear. Int6 encodes a subunit of the eukaryotic translation initiation factor 3, and interacts with two related complexes, the proteasome, whose activity is regulated by Int6 in S. pombe, and the COP9 signalosome. The COP9 signalosome regulates the activity of Cullin-Ring Ubiquitin Ligases via deneddylation of their cullin subunit. We report here the generation and analysis of two Drosophila mutants in Int6. The mutants are lethal demonstrating that Int6 is an essential gene. The mutant larvae accumulate high levels of non-neddylated Cul1, suggesting that Int6 is a positive regulator of cullin neddylation. Overexpression in Int6 in cell culture leads to accumulation of neddylated cullins, further supporting a positive role for Int6 in regulating neddylation. Thus Int6 and the COP9 signalosome play opposing roles in regulation of cullin neddylation.