Hepatic Oxidoreduction-Related Genes Are Upregulated by Administration of Hydrogen-Saturated Drinking Water

The effects of the administration of molecular hydrogen-saturated drinking water (hydrogen water) on hepatic gene expression were investigated in rats. Using DNA microarrays, 548 upregulated and 695 downregulated genes were detected in the liver after 4 weeks of administration of hydrogen water. Gene Ontology analysis revealed that genes for oxidoreduction-related proteins, including hydroxymethylglutaryl CoA reductase, were significantly enriched in the upregulated genes.     

大鼠再生肝中表达上调基因的筛选与鉴定

采用新发展的抑制差减杂交技术（suppression subtractive hybridization,SSH）在基因组水平筛选再生肝中高表达基因。大鼠肝部分切除后24h的再生杆组织来源的cDNA作为受检者（tester）,正常肝组织的cDNA作为驱动者（driver）,进行差减杂交,获得一900个克隆的差减杂交库,随后对差减克隆进行了差异筛选,得到50个在再生肝中高表达的强阳性克隆,序列测定和同源比较表明这些克隆代表了37个基因,其中13个与已报道的肝再生相关的基因同源,15个为忆知基因但首次发现与肝再生相关,9个为新的基因（EST）已被GenBank收录。制备了标准化RNA点杂交膜,通过对上述部分基因的RNA点杂交分析,不但确认了这些基因在再生肝中表达水平的升高,同时发现它们在肝再生过程中有不同的表达模式。实验结果提示这些基因在肝再生过程中具有重要功能。     

Expression of the Stress-Related Genes for Glutathione S-Transferase and Ascorbate Peroxidase in the Most-Glycinin-Deficient Soybean Cultivar Tousan205 during Seed Maturation

Global analysis of gene expression profiles in most-glycinin-deficient cultivar Tousan205, was performed by DNA microarray analysis. It was confirmed that Tousan205 lacks mRNA expression of three glycinin subunit precursor genes, G1 (A1aB1x), G2 (A2B1a), and G5 (A3B4), and lacks G4 (A5A4B3) protein. Most glycinin subunits were deficient in mature seeds of Tousan205. We compared the gene expression of Tousan205 with those of parent cultivar, Tamahomare, which was used for crossbreeding of Tousan205. As a result, Tousan205 exhibited higher expression of some seed maturation proteins, and stress-related genes such as glutathione S-transferase and ascorbate peroxidase. This result indicates the possibility that the decrease of main storage protein, glycinin causes stress in soybean.     

D-gal致大鼠急性肝损伤过程中肝卵圆细胞增殖及迁延

目的用D-gal建立大鼠急性肝损伤模型,观察肝损伤后再生过程中肝卵圆细胞的增殖和迁延。方法建立大鼠急性肝损伤模型,于第1、3、7和14天分别取肝组织,分别行病理、免疫组织化学,观察卵圆细胞的分布迁移情况,并取第7天肝组织进行组织电镜观察汇管区新增生细胞超微结构。结果病理切片显示肝细胞变性坏死程度以第7天和第14天为主,出现新增生的细胞。免疫组化示随时间阳性细胞明显增多,分布于汇管区,并向小叶中心迁移,形成大量的胆小管,并有部分向坏死区迁移。透射电镜有新生内源性细胞,小于成熟的肝细胞,细胞器较少,有细胞紧密连接,以数个细胞排列成小胆管,与免疫组化一致。结论在大鼠急性肝损伤时HOC被活化、增殖,并向肝小叶中心迁移,全程参与了肝再生过程。     

Diurnal expression of Dnmt3b mRNA in mouse liver is regulated by feeding and hepatic clockwork

DNA methyltransferase 3B (DNMT3B) is critically involved in de novo DNA methylation and genomic stability, while the regulatory mechanism in liver is largely unknown. We previously reported that diurnal variation occurs in the mRNA expression of Dnmt3b in adult mouse liver. The aim of this study was to determine the mechanism underlying the diurnal expression pattern. The highest level and the lowest level of Dnmt3b mRNA expression were confirmed to occur at dawn and in the afternoon, respectively, and the expression pattern of Dnmt3b closely coincided with that of Bmal1. Since the diurnal pattern of Dnmt3b mRNA expression developed at weaning and scheduled feeding to separate the feeding cycle from the light/dark cycle led to a phase-shift in the expression, it could be assumed that feeding plays a critical role as an entrainment signal. In liver-specific Bmal1 knockout (L-Bmal1 KO) mice, L-Bmal1 deficiency resulted in significantly higher levels of Dnmt3b at all measured time points, and the time when the expression was the lowest in wild-type mice was shifted to earlier. Investigation of global DNA methylation revealed a temporal decrease of 5-methyl-cytosine percentage in the genome of wild-type mice in late afternoon. By contrast, no such decrease in 5-methyl-cytosine percentage was detected in L-Bmal1 KO mice, suggesting that altered Dnmt3b expression affects the DNA methylation state. Taken together, the results suggest that the feeding and hepatic clockwork generated by the clock genes, including Bmal1, regulate the diurnal variation in Dnmt3b mRNA expression and the consequent dynamic changes in global DNA methylation.     

Diurnal expression of Dnmt3b mRNA in mouse liver is regulated by feeding and hepatic clockwork

DNA methyltransferase 3B (DNMT3B) is critically involved in de novo DNA methylation and genomic stability, while the regulatory mechanism in liver is largely unknown. We previously reported that diurnal variation occurs in the mRNA expression of Dnmt3b in adult mouse liver. The aim of this study was to determine the mechanism underlying the diurnal expression pattern. The highest level and the lowest level of Dnmt3b mRNA expression were confirmed to occur at dawn and in the afternoon, respectively, and the expression pattern of Dnmt3b closely coincided with that of Bmal1. Since the diurnal pattern of Dnmt3b mRNA expression developed at weaning and scheduled feeding to separate the feeding cycle from the light/dark cycle led to a phase-shift in the expression, it could be assumed that feeding plays a critical role as an entrainment signal. In liver-specific Bmal1 knockout (L-Bmal1 KO) mice, L-Bmal1 deficiency resulted in significantly higher levels of Dnmt3b at all measured time points, and the time when the expression was the lowest in wild-type mice was shifted to earlier. Investigation of global DNA methylation revealed a temporal decrease of 5-methyl-cytosine percentage in the genome of wild-type mice in late afternoon. By contrast, no such decrease in 5-methyl-cytosine percentage was detected in L-Bmal1 KO mice, suggesting that altered Dnmt3b expression affects the DNA methylation state. Taken together, the results suggest that the feeding and hepatic clockwork generated by the clock genes, including Bmal1, regulate the diurnal variation in Dnmt3b mRNA expression and the consequent dynamic changes in global DNA methylation.     

Stabilization of the immobilized linkers and DNA probes for DNA microarray fabrication by end-capping of the remaining unreacted silanol on the glass

High stability of the oligonucleotides immobilized on the glass is essential for the reliable DNA microarray analysis. In the present study, effect of end-capping of the unreacted silanol, remaining after the surface amine-functionalization, was explored: (1) Cy3-NHS (N-hydorxysuccinincimide) dye was spotted on the surface and change in the fluorescent intensity was measured. (2) DNA probes were immobilized by the reactivity of oxanine linked at the 5’-end, the complementary oligonucleotides with Cy5-fluorescence at the 5’-end was hybridized, and the time-dependence of the fluorescence intensity was observed. Both the systems showed improved stability of the immobilized molecules, indicative of the stabilization by end-capping.     

Effects of energy or protein restriction followed by realimentation on the composition of gain and meat quality characteristics of Musculus longissimus dorsi in pigs

The effect of realimentation of fattening pigs on gain composition and intramuscular fat content in the longissimus dorsi muscle and their relationship to meat tenderness was investigated in 60 gilts. From day 90 to 168 of age, Group C (control) was fed according to the requirements, while from day 90 to 118 of age, Group R was fed restrictively (protein and energy) and Group P was fed restrictively with protein alone. This period was followed by adequate feeding. Comparative slaughter techniques were used; animals were slaughtered at the beginning of the study (day 90), at the end of the restriction period (day 118), and after two periods of realimentation (day 146 and day 168). Interactions between experimental treatments indicated that muscle protein gain (p < 0.05), muscle fat gain (p < 0.01), and shear force (p < 0.01) differed depending on period of realimentation. Muscle protein deposition differed only during the second period of realimentation, where Group R deposited more protein compared with Groups C and P (6.0, 4.5 and 5.0 g/d, respectively). Muscle fat deposition during the first period of realimentation was lower in Groups R and P than in Group C (0.73, 0.74 and 1.20 g/d, respectively) while in the second period Group R deposited considerably more fat than Groups C and P (2.39, 1.20 and 1.23 g/d, respectively). At the end of the first period, the shear force of Groups R and P was lower when compared with Group C (2.44, 2.79 and 3.22 kg, respectively); however, at final age it did not differ between treatments.     

Hepatic Uptake of Solutes from the Preservation Solution during Hypothermic Storage: A H NMR Study in Rat Liver

The hepatic uptake of histidine and carnosine (histidyl-alanine), used as buffer agents in four preservation solutions, was studied during 24-h hypothermic storage of rat livers by use of ¹H nuclear magnetic resonance (NMR) spectroscopy. Results demonstrated that there was a progressive, concentration-linked passive diffusion of histidine into liver tissues throughout the storage period. A similar inward diffusion of carnosine was also noted. Of the carbohydrate osmotic buffers in the preservation solutions, mannitol permeated the liver tissues to a greater degree and more rapidly than raffinose after the flushing with equivalent concentrations and storage at hypothermia. In general, many solutes from preservation solutions will increasingly penetrate the hepatic inter- and intracellular spaces during extended hypothermic preservation and ¹H NMR spectroscopy is one technique that can assist in the identification of these changes.     

Large scale of identification of differentially expressed genes in the regenerating rat liver after SISPH

Extensive gene expression analysis was carried out after a 0, 4, 36, 72, 96 h short interval successive partial hepatectomy (SISPH) was performed. A total of 185 elements were identified as differing by more than two-fold in their expression levels at one or more time points. Of these 185 elements, 103 were up-regulated, 82 were down-regulated and 86 elements were unreported genes. Quite a few genes were previously unknown to be involved in liver regeneration (LR). Using cluster and general analysis, we found that the genes at five time points of the SISPH share eight different types of different expression profiles and eight distinct temporal induction or suppression patterns. A comparison of the gene expression in SISPH with that after PH found that 41 genes were specifically altered in SISPH, and 144 genes were simultaneously up-regulated or down-regulated in SISPH and after PH, but they were present in different amounts at the different time points. The conclusions are that (i) microarrays combined with suppressive subtractive hybridization (SSH) can effectively identify genes involved in LR on a large scale; (ii) more genes were up-regulated than down-regulated; (iii) there are fewer abundantly expressed genes than those with increased levels of 2–5 fold.     

应用寡核苷酸芯片筛选维甲酸诱导神经母细胞瘤细胞系SH-SY5Y分化成神经元过程中的差异表达基因

目的:应用寡核苷酸芯片筛选维甲酸(RA)诱导神经母细胞瘤细胞系SH-SY5Y分化成神经元过程中的差异表达基因。方法:从人胎脑及不同类型神经系统肿瘤组织中获取目的基因,查询相应基因mRNA序列,设计并合成探针,制备了含218种基因的神经功能相关的寡核苷酸芯片。应用RA诱导SH-SY5Y8d分化成成熟神经元,提取对照组和实验组每天的总RNA,通过逆转录荧光标记cDNA探针并与芯片杂交,洗片后扫描获取图像,数据分析获得差异表达基因,并通过RT-PCR进行验证。结果:发现13种基因表达上调,没有得到下调基因。RT-PCR验证结果基本与芯片结果一致。结论:SH-SY5Y经RA诱导分化成神经元存在一些差异表达的基因,寡核苷酸芯片技术可为研究SH-SY5Y诱导分化成神经元的分子作用机理提供技术平台。     

The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities

We developed a broad-ranging method for identifying key hydrogen-producing and consuming microorganisms through analysis of hydrogenase gene content and expression in complex anaerobic microbial communities. The method is based on a tiling hydrogenase gene oligonucleotide DNA microarray (Hydrogenase Chip), which implements a high number of probes per gene by tiling probe sequences across genes of interest at 1.67 × –2 × coverage. This design favors the avoidance of false positive gene identification in samples of DNA or RNA extracted from complex microbial communities. We applied this technique to interrogate interspecies hydrogen transfer in complex communities in (i) lab-scale reductive dehalogenating microcosms enabling us to delineate key H₂-consuming microorganisms, and (ii) hydrogen-generating microbial mats where we found evidence for significant H₂ production by cyanobacteria. Independent quantitative PCR analysis on selected hydrogenase genes showed that this Hydrogenase Chip technique is semiquantitative. We also determined that as microbial community complexity increases, specificity must be traded for sensitivity in analyzing data from tiling DNA microarrays.     

Genes for Polymorphic H1 Histones Are Linked in the Japanese Quail Genome

In a previous report (Palyga, J., Biochem.Genet. 29, 431-445, 1991), three subtypes oferythrocyte histone H1 were found to vary in a Japanesequail population. While H1.b and H1.z histones were eachrepresented by two electromorphs differing in apparentmolecular weights, a polymorphism of histone H1.a wasconnected with a lack of this protein in some birds. Asa genetic basis for this variability was demonstrated only in H1.b, here genetic data are providedwhich indicate that both H1.a and H1.z are encoded bytwo codominant alleles at a locus. A linkage analysis offamily data in 13 quail pedigrees has revealed a significant linkage between H1.a and H1.z andbetween H1.b and H1.z ( lod scores about 12 and 5,respectively). Thus, a gene for histone H1.z is locatedbetween H1.a and H1.b in the quail genome.     

Identification of genes regulating colorectal carcinogenesis by using the algorithm for diagnosing malignant state method

We studied the expression profiles of various stages of colorectal tumors (adenoma (AD), seven samples; carcinoma (CA), 16 samples) by using cDNA microarrays and developed ADMS (algorithm for diagnosing malignant state) method, selecting 335 clones characteristic of CA state. We, then, applied ADMS to 12 additional samples (five from primary lesions with metastasis and seven metastases); all 16 CAs and 12 metastatic tumors were diagnosed correctly as cancerous states. Although three of the seven ADs were diagnosed as "cancerous," the large size of two of these tumors suggested their potential malignancy. Our strategy for selecting clones characteristic of the malignant state is widely applicable to diagnosis and for predicting the stage of progression during multistep carcinogenesis. Of the 335 clones we selected, 135 were known genes. Included in the 135 genes were tumor suppressor and growth factor-related genes and were consistent with the literature. ADMS is a reliable means for identifying genes useful for the diagnosis of cancer.