Spectrum structures and biological functions of 8-mers in the human genome

The spectra of k-mer frequencies can reveal the structures and evolution of genome sequences. We confirmed that the trimodal spectrum of 8-mers in human genome sequences is distinguished only by CG2, CG1 and CG0 8-mer sets, containing 2,1 or 0 CpG, respectively. This phenomenon is called independent selection law. The three types of CG 8-mers were considered as different functional elements. We conjectured that (1) nucleosome binding motifs are mainly characterized by CG1 8-mers and (2) the core structural units of CpG island sequences are predominantly characterized by CG2 8-mers. To validate our conjectures, nucleosome occupied sequences and CGI sequences were extracted, then the sequence parameters were constructed through the information of the three CG 8-mer sets respectively. ROC analysis showed that CG1 8-mers are more preference in nucleosome occupied segments (AUC > 0.7) and CG2 8-mers are more preference in CGI sequences (AUC > 0.99). This validates our conjecture in principle.     

草酰乙酸和苹果酸对菠菜叶片和完整叶绿体光合作用的影响

观测了OAA和MA对菠菜叶片和完整叶绿体光合作用的影响.结果显示,当叶片切块在20μmol/L的OAA存在时,其叶片的光合放氧速率增加了89%,经OAA处理的离体完整叶绿体的光合放氧速率增加了72%;当反应体系中存在有较高浓度的NaHCO3时,OAA的作用不明显.叶片经20 μmol/L的MA处理后,叶片光合放氧速率比对照高127%.用CO2分析仪观测了处理后叶片的净光合速率(Pn),结果显示,OAA和MA处理后的叶片Pn值分别是对照的117%和111%.对在C3植物中建立C4微循环系统来提高光合作用效率的可能性进行了讨论.     

大黄酚体外抗白念珠菌生物膜作用的研究

目的研究大黄酚对体外白念珠菌生物膜的影响。方法采用XTT减低法评价大黄酚对白念珠菌的生物膜及黏附性的影响;镜下观察该药对白念珠菌生物膜的形态学影响;细胞毒试验检测该药的毒副作用。结果大黄酚对白念珠菌生物膜的SMIC50、SMIC80分别为125、1000μg/ml;100μg／ml及1000μg/ml含量浓度的大黄酚对自念珠菌的早期黏附及菌丝生长有抑制作用;大黄酚对人细胞毒性较弱。结论大黄酚对体外白念珠菌生物膜有较强的抑制作用。     

二倍体鲫鲤F2产生不同倍性卵子的证据

在检测到鲫鲤F2产生3种不同大小(直径分别为0.13 cm,0.17cm和0.2 cm)类型的卵子基础上,进行了F2(♀)×红鲫(♂)及F2(♀)×四倍体鲫鲤(♂)的交配实验.通过染色体计数和流式细胞仪分析,在F2(♀)×红鲫(♂)后代中获得了四倍体、三倍体、二倍体鱼;在F2(♀)×四倍体鲫鲤(♂)后代中获得了四倍体和三倍体鱼.这两个交配组合后代中出现的不同倍性的鱼类为证明鲫鲤F2能产生三倍体、二倍体和单倍体卵子提供了进一步证据.F2(♀)×红鲫(♂)中雄性四倍体鱼的存在说明在四倍体后代中存在基因型为XXXY的个体.对上述两个交配组合后代的四倍体鱼和三倍体鱼的性腺结构观察表明四倍体鱼是可育的,而三倍体鱼是不育的.作者认为鲫鲤F2能够产生二倍体和三倍体卵子与核内复制机制和生殖细胞的融合有关.     

Comparison of Newly Generated Doublecortin-immunoreactive Neuronal Progenitors in the Main Olfactory Bulb among Variously Aged Gerbils

In the present study, we investigated age-related differences in neuronal progenitors in the gerbil main olfactory bulb (MOB) using doublecortin (DCX), a marker for neuronal progenitors which differentiate into neurons in the brain. No difference in the number of neuronal nuclei (NeuN)-immunoreactive neurons was found in the MOB at variously aged gerbils. At postnatal month (PM) 1, DCX immunoreaction was detected in all layers of the MOB except for the olfactory nerve layer. At this time point, DCX-immunoreactive cells (neuronal progenitors) were very abundant; however, they did not have fully developed-processes. From PM 3, the number of DCX-immunoreactive neuronal progenitors was decreased with age. At PM 6, DCX-immunoreactive cells showed very well-developed processes. In western blot analysis, DCX protein level in the MOB was highest at PM 1. Thereafter, levels of DCX protein were decreased with age. In the subventricular zone of the lateral ventricle, the number of Ki-67-immunoractive cells (proliferating cells) was also significantly decreased with age. In addition, increases of α-synuclein-immunoreactive structures were observed in the MOB with age. These results suggest that decrease in DCX-immunoreactive neuronal progenitors and its protein levels in the MOB with age may be associated with reduction of cell proliferation in the SVZ and with an increase in α-synuclein in the MOB.     

TNF/LTA polymorphisms and risk for gastric cancer/duodenal ulcer in the Korean population

The tumor necrosis factor-alpha (TNF) and lymphotoxin-alpha (LTA) are proinflammatory cytokines with immunoregulatory effects. TNF is also known to inhibit gastric acid secretion. Previously we have shown that the known proinflammatory genotypes, IL-1B -31C/+ and IL-1RN *2/*2, were not associated with increased risks for gastric cancer/duodenal ulcer in the Korean population. In this study, we tested the association between the polymorphisms of another candidate cytokine TNF/LTA and 341 gastric cancers, 133 duodenal ulcers, and 261 healthy controls. Five TNF promoter polymorphisms (-1031, -863, -857, -308, and -238) and two LTA polymorphisms (intron 1 and Thr26Asn) were analyzed. Individual polymorphisms were not associated with the gastric cancer and/or duodenal ulcer risk. When a haplotype analysis was performed with seven polymorphisms, differences in haplotype profile between the controls and gastric cancer and/or duodenal ulcer were not statistically significant. However, the frequencies of individual haplotypes C and D, which had opposite alleles at -1031, -863, and -857, showed statistically significant differences between the gastric cancer and duodenal ulcer (P=0.005 and P=0.02, respectively), suggesting that the TNF/LTA genotypes might play an opposite role in the pathogenesis of gastric cancer and duodenal ulcer.     

Bacterial decolorization and degradation of the reactive dye Reactive Red 180 by Citrobacter sp. CK3

A bacterial strain, CK3, with remarkable ability to decolorize the reactive textile dye Reactive Red 180, was isolated from the activated sludge collected from a textile mill. Phenotypic characterization and phylogenetic analysis of the 16S rDNA sequence indicated that the bacterial strain belonged to the genus Citrobacter. Bacterial isolate CK3 showed a strong ability to decolorize various reactive textile dyes, including both azo and anthraquinone dyes. Anaerobic conditions with 4 g l^?1 glucose, pH = 7.0 and 32 °C were considered to be the optimum decolorizing conditions. Citrobacter sp. CK3 grew well in a high concentration of dye (200 mg l^?1), resulting in approximately 95% decolorization extent in 36 h, and could tolerate up to 1000 mg l^?1 of dye. UV–vis analyses and colorless bacterial cells suggested that Citrobacter sp. CK3 exhibited decolorizing activity through biodegradation, rather than inactive surface adsorption. It is the first time that a bacterial strain of Citrobacter sp. has been reported with decolorizing ability against both azo and anthraquinone dyes. High decolorization extent and facile conditions show the potential for this bacterial strain to be used in the biological treatment of dyeing mill effluents.     

Functional genomic approaches using the nematode Caenorhabditis elegans as a model system

Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cell lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology.