IntergenicDB: a database for intergenic sequences

A whole genome contains not only coding regions, but also non-coding regions. These are located between the end of a given coding region and the beginning of the following coding region. For this reason, the information about gene regulation process underlies in intergenic regions. There is no easy way to obtain intergenic regions from current available databases. IntergenicDB was developed to integrate data of intergenic regions and their gene related information from NCBI databases. The main goal of INTERGENICDB is to offer friendly database for intergenic sequences of bacterial genomes.

Availability

http://intergenicdb.bioinfoucs.com/     

GI-POP: A combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects

Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project.     

Thermodynamics and Kinetics of Single-Chain Monellin Folding with Structural Insights into Specific Collapse in the Denatured State Ensemble

Proteins, which behave as random coils in high denaturant concentrations undergo collapse transition similar to polymers on denaturant dilution. We study collapse in the denatured ensemble of single-chain monellin (MNEI) using a coarse-grained protein model and molecular dynamics simulations. The model is validated by quantitatively comparing the computed guanidinium chloride and pH-dependent thermodynamic properties of MNEI folding with the experiments. The computed properties such as the fraction of the protein in the folded state and radius of gyration (R_g) as function of [GuHCl] are in good agreement with the experiments. The folded state of MNEI is destabilized with an increase in pH due to the deprotonation of the residues Glu24 and Cys42. On decreasing [GuHCl], the protein in the unfolded ensemble showed specific compaction. The R_g of the protein decreased steadily with [GuHCl] dilution due to increase in the number of native contacts in all the secondary structural elements present in the protein. MNEI folding kinetics is complex with multiple folding pathways and transiently stable intermediates are populated in these pathways. In strong stabilizing conditions, the protein in the unfolded ensemble showed transition to a more compact unfolded state where R_g decreased by ≈ 17% due to the formation of specific native contacts in the protein. The intermediate populated in the dominant MNEI folding pathway satisfies the structural features of the dry molten globule inferred from experiments.     

东北地区蒙古栎群落区系成分

根据吴征镒、王荷生区系分析方法, 分析了东北地区蒙古栎群落中２６１ 种维管植物的区系成分, 其中温带成分占４７－４７ ％ , 东亚成分占４２－０２ ％ , 中国特有成分占１０－５１ ％ （ 世界分布不统计在内） 。并分析了种所在属的分布区类型, 温带分布属占９０－３％ 。还分别分析了蒙古栎群落的乔木层、灌木层、草本层以及层间植物的区系成分。     

Characterization of hypoglycemiant plants by total reflection X-ray fluorescence spectrometry

In this work, synchrotron radiation total reflection X-ray fluorescence spectrometry (SRTXRF) was used to determine trace elements in eight hypoglycemiant plants (Trigonella foenum graecum, Panax ginseng, Pfaffia paniculata, Myrcia speciosa, Zea mays, Harpagophytum procumbens, Syzygium jambolona, and Bauhinia forficate). The elements P, K, Ca, Ti, Mn, Fe, Cu, Zn, Rb, and Sr were detected in all medicinal plants investigated, whereas Si, S, Sc, V, Cr, Co, Ni, Se, Nb, Mo, Sn, Sb, Ba, Hg, and Pb were detected only in some of the samples. The concentration of elements in hypoglycemiant plants varied from 0.15 μg/g of Co to 3.0×10⁴ μg/g of K and the mean of experimental limit of detection for these elements were 0.14 and 3.6 μg/g, respectively.     

Distribution patterns of trace metals and of lipid peroxidation in plasma and erythrocytes of rat exposed to aluminum

Significant decreases of the hematocrit, hemoglobin, and plasma iron levels were observed in rats receiving daily intraperitoneal injections of aluminum at a dose of 27 mg Al/kg body wt for 3 wk, as compared to untreated controls. The activity of alkaline phosphatase was also significantly lower in the treated animals as a result of the accumulation of aluminum in the liver (p<0.05). Following aluminum administration, the plasma concentrations of aluminum and copper were also significantly increased, whereas the plasma zinc levels and oxidative stress measured through thiobarbituric acid reaction products showed nonsignificant differences between the two groups (p>0.05). The erythrocyte concentrations of aluminum, copper, zinc, and iron and of superoxide dismutase activity were found to be significantly higher in the study group as compared to controls. The treated animals also showed evidence of higher oxidative stress in comparison to controls. These results suggest that erythrocyte aluminum accumulation could result in abnormal trace element homeostasis and increasing oxidative stress, which might be a mechanism of aluminum-induced anemia.     

昆虫的NF-kB信号通路

昆虫NF-kB信号通路由toll和imd两条通路组成,通过转录因子NF-kB作用于靶标基因kB位点,而调节抗菌活性物质的表达。大量实验表明它能够被细菌、真菌和病毒的侵染所激活,在昆虫体液免疫中发挥着主要作用。现就昆虫的NF-kB信号通路的主要信号元件等进行综述。     

A novel rice C2H2-type zinc finger protein lacking DLN-box/EAR-motif plays a role in salt tolerance

A cDNA for the gene ZFP182, encoding a C2H2-type zinc finger protein, was cloned from rice by RT-PCR. ZFP182 codes an 18.2 kDa protein with two C2H2-type zinc finger motifs, one nuclear localization signal and one Leu-rich domain. The DLN-box/EAR-motif, which exists in most of plant C2H2-type zinc finger proteins, does not exist in ZFP182. The expression analysis showed that ZFP182 gene was constitutively expressed in leaves, culms, roots and spikes at the adult rice plants, and markedly induced in the seedlings by cold (4 °C), 150 mM NaCl and 0.1 mM ABA treatments. The approximate 1.4 kb promoter region of ZFP182 gene was fused into GUS reporter gene and transformed into tobacco. The histochemical analysis revealed that GUS expression could not be detected in transformed tobacco seedlings under normal conditions, but strongly observed in tobacco leaf discs and the vascular tissue of roots treated with NaCl or KCl. Expression of ZFP182 in transgenic tobacco and overexpression in rice increased plant tolerance to salt stress. These results demonstrated that ZFP182 might be involved in plant responses to salt stress.     

Trace elements in human milk: Correlation with blood levels, inter-element correlations and changes in concentration during the first month of lactation

Using inductively coupled plasma mass spectrometry (ICP-MS) based analytical procedures, the concentration of several trace elements (Mn, As, Pb, Co, Ni, Cu, Zn and Se) was determined in human milk samples collected from a group of healthy lactating Portuguese women (n=44), both on the 2nd day postpartum (i.e., colostrum; n=34) and at 1 month postpartum (i.e., mature milk; n=19). Blood samples (n=44), collected on the 2nd day after parturition, were also analyzed for the same trace elements. No major correlations were observed between the levels of the analyzed trace elements in blood and colostrum samples. All the studied elements, except for Co, Pb and Ni, showed a significant trend for a decrease in concentration in milk during the first month of lactation. This trend was more pronounced for Zn and Se, whose levels decreased to approximately 23% and 44% of their initial mean concentration, respectively. With the exception of Co (r=0.607) and Zn (r=0.487), no significant correlations were observed when comparing the levels of each trace element between samples of colostrum and mature milk. Several inter-element correlations were found within each type of milk sample. The most significant were: (i) Se vs Cu (r=0.828) and Se vs Co (r=0.605) in colostrum samples and (ii) Ni vs Pb (r=0.756), Ni vs Mn (r=0.743) and Se vs Co (r=0.714) in mature milk samples. An inverse correlation between Zn and Se was also found in both types of milk sample; however, it only reached statistical significance for mature milk (r=-0.624).