Molecular evolution and nucleotide diversity of nuclear plastid phosphoglycerate kinase (PGK) gene in Triticeae (Poaceae)

Levels of nucleotide divergence provide key evidence in the evolution of polyploids. The nucleotide diversity of 226 sequences of pgk1 gene in Triticeae species was characterized. Phylogenetic analyses based on the pgk1 gene were carried out to determine the diploid origin of polyploids within the tribe in relation to their A^u, B, D, St, Ns, P, and H haplomes. Sequences from the Ns genome represented the highest nucleotide diversity values for both polyploid and diploid species with π = 0.03343 and θ = 0.03536 for polyploid Ns genome sequences and π = 0.03886 and θ = 0.03886 for diploid Psathyrostachys sequences, while Triticum urartu represented the lowest diversity among diploid species at π = 0.0011 and θ = 0.0011. Nucleotide variation of diploid Aegilops speltoides (π = 0.2441, presumed the B genome donor of Triticum species) is five times higher than that (π = 0.00483) of B genome in polyploid species. Significant negative Tajima's D values for the St, A^u, and D genomes along with high rates of polymorphisms and low sequence diversity were observed. Origins of the A^u, B, and D genomes were linked to T. urartu, A. speltoides, and A. tauschii, respectively. Putative St genome donor was Pseudoroegneria, while Ns and P donors were Psathyrostachys and Agropyron. H genome diploid donor is Hordeum.     

A marsupial phosphoglycerate kinase (PGK) processed pseudogene

A clone that cross-hybridized with a full-length human cDNA PGK probe was isolated from a hill kangaroo (Macropus robustus: Marsupialia) lambda EMBL4 EcoRI genomic library. The clone was sequenced and demonstrated to be a pseudogene, with two deletions (one of 3 bases, the other 24 bases long), one single base insertion, and a nonsense mutation with respect to the functional human X-linked gene. It is flanked by terminal repeats in the 5' and 3' noncoding regions, but it has no 3' poly(A) remnant. The 3' untranslated region has a 34-bp sequence, with 29 bp homologous to the human 3' untranslated region. The overall percentage homology with the mouse and human X-linked PGK indicates that this pseudogene is probably more closely related to eutherian X-linked PGK genes than to the autosomal form. The results also suggest that pseudogenes are of considerable antiquity (greater than 100 MYr) in the mammalian lineage.     

藏鸡心脏高海拔低氧适应相关酶的研究

目的：研究藏鸡心脏对高海拔低氧适应性的生理特征。方法：本研究将藏鸡、矮小隐性白和寿光鸡分别饲养在低海拔和高海拔环境,测定10周龄时心脏重量、心肌乳酸（LA）和乳酸脱氢酶（LDH）、琥珀酸脱氢酶（SDH）活性。结果：结果显示藏鸡在高海拔环境中,心脏相对重量未明显增加,心肌LA低于对照鸡,LDH与对照鸡差异不显著,而SDH活性明显高于对照鸡。结论：结果说明了藏鸡对高海拔低氧环境的适应,不是通过增加心脏器官的重量,也不是通过提高无氧代谢的水平,较高的SDH活力对藏鸡心肌低氧适应有一定的意义。SDH是藏鸡适应低氧的一种标志酶。     

Differential gene expression of chloroplast and cytosolic phosphoglycerate kinase in tobacco

Northern blot analysis of RNA extracted from leaves of increasing age and different organs, indicates that genes encoding both isoenzymes of tobacco phosphoglycerate kinase (PGK, EC 2.7.2.3) are differentially expressed in a developmental and tissue-specific manner. The genes for both chloroplast PGK (chl-PGK) and cytosolic PGK (cyt-PGK) also show light-modulated gene expression in vivo. In dark-grown developing cotyledonary leaves of tobacco both PGK mRNAs are present, but only the concentration of the chl-PGK mRNA increased on illumination. In contrast, on transfer to darkness, the concentration of both mRNAs decreased in light-grown seedlings and then increased again on resumption of illumination.     

Differential expression of genes important for adaptation in Capsella bursa-pastoris (Brassicaceae)

Understanding the genetic basis of natural variation is of primary interest for evolutionary studies of adaptation. In Capsella bursa-pastoris, a close relative of Arabidopsis (Arabidopsis thaliana), variation in flowering time is correlated with latitude, suggestive of an adaptation to photoperiod. To identify pathways regulating natural flowering time variation in C. bursa-pastoris, we have studied gene expression differences between two pairs of early- and late-flowering C. bursa-pastoris accessions and compared their response to vernalization. Using Arabidopsis microarrays, we found a large number of significant differences in gene expression between flowering ecotypes. The key flowering time gene FLOWERING LOCUS C (FLC) was not differentially expressed prior to vernalization. This result is in contrast to those in Arabidopsis, where most natural flowering time variation acts through FLC. However, the gibberellin and photoperiodic flowering pathways were significantly enriched for gene expression differences between early- and late-flowering C. bursa-pastoris. Gibberellin biosynthesis genes were down-regulated in late-flowering accessions, whereas circadian core genes in the photoperiodic pathway were differentially expressed between early- and late-flowering accessions. Detailed time-series experiments clearly demonstrated that the diurnal rhythm of CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) and TIMING OF CAB EXPRESSION1 (TOC1) expression differed between flowering ecotypes, both under constant light and long-day conditions. Differential expression of flowering time genes was biologically validated in an independent pair of flowering ecotypes, suggesting a shared genetic basis or parallel evolution of similar regulatory differences. We conclude that genes involved in regulation of the circadian clock, such as CCA1 and TOC1, are strong candidates for the evolution of adaptive flowering time variation in C. bursa-pastoris.     

高原鼠兔脑红蛋白基因的克隆与组织表达

克隆高原鼠兔脑红蛋白(Neuroglobin,NGB)基因编码区并检测其在成年高原鼠兔脑组织和其他组织中的表达,同时探讨高原鼠兔低氧适应的分子生物学机制。从高原鼠兔脑组织中提取总RNA,通过RT - PCR 获得高原鼠兔NGB cDNA,将其与pGEM - T Easy 载体连接,构建重组质粒,蓝白斑筛选阳性克隆并进行鉴定和测序;制备地高辛标记的RNA 探针并采用原位杂交法(In suit hybridization,ISH) 分析脑红蛋白基因在高原鼠兔脑组织中的分布;采用RT - PCR 和蛋白印记(Western blot)检测高原鼠兔不同组织中脑红蛋白的表达含量。将含有目的片段的阳性克隆经测序和Blast 分析,显示其部分编码序列与GenBank 中绵羊、大鼠等同源性很高(大于84% ),表明本实验所克隆的序列为脑红蛋白基因;原位杂交结果显示NGB 在青藏高原土著动物高原鼠兔脑部分布较为广泛;高原鼠兔不同组织中都有NGB mRNA 表达,NGB 基因并不是中枢神经系统所特有的,睾丸和肾上腺也有较高的表达。NGB 基因在高原鼠兔脑组织和其他组织中分布较为广泛,推测NGB mRNA 可能在高原鼠兔机体较为广泛的区域中发挥着作用,同时为高原低氧适应相关基因的研究提供了实验依据。     

Nucleotide sequence of the 3' nuclease-sensitive region of the human phosphoglycerate kinase 1 (PGK1) gene.

Many genes are known to have nuclease-sensitive sites and/or control sequences in their 3' flanking regions, but for very few genes has this region been sequenced. Previously, we mapped specific, gene activity-dependent DNAase I- and MspI-sensitive sites at the 3' end of the human X-linked housekeeping gene phosphoglycerate kinase (PGK1). Sequence information presented here shows that the 3' nuclease-sensitive site maps precisely to an Alu sequence and near a "BKM" repeat. This is the first report of an Alu sequence that has alternative chromatin configurations depending on gene activity.     

Characterization of the expression profiles of calpastatin (CAST) gene in chicken

The calpain system, a Ca²⁺-activated protease family, plays an important role in postmortem tenderization of skeletal muscle due to its involvement in the degradation of important myofibrillar and associated proteins, as well as in cytoskeletal remodeling and regulation of muscle growth. In this study, we quantified the expression of calpastatin (CAST) in two Chinese chicken breeds (mountainous black-bone chicken breed (MB) and a commercial meat type chicken breed (S01)), to discern the tissue and age-related specific expression pattern and its potential role on muscle tissue metabolism. Real-time quantitative PCR (RT-qPCR) assay was developed for accurate measurement of CAST mRNA levels in various tissues from chicken with different ages (0, 2, 4, 6, 8, 10, and 12 week). CAST mRNA was detected in collected organs. The heart and leg muscle tissues had the highest expression of CAST than other tissues from the same chicken (P < 0.01). Age-related expression pattern of CAST gene was evident in breast muscle, liver, and brain tissues (P < 0.05), but not in heart and leg muscle tissues (P > 0.05). Overall, the CAST mRNA level exhibited a “rise-decline-rise-decline” developmental change in breast muscle and liver, with the highest expression at 2 weeks and the lowest expression at 8 weeks. The S01 chicken had significantly higher expression of CAST in breast muscle and heart than the MB chicken (P < 0.05) at 10 weeks. Our results suggested the CAST expression may be related to muscle fiber development.     

Cloning and expression of chicken granulocyte-macrophage colony stimulating factor (GMCSF) gene

Granulocyte-macrophage colony stimulating factor (GMCSF), a multifunctional cytokine can enhance immune responses when administered along with DNA vaccine. Aim of the present study was to clone and express the chicken GMCSF cytokine for use as 'genetic adjuvant'. Chicken GMCSF gene 435bp was amplified using specific primers in which restriction sites of BamHI and HindIII were at forward and reverse primers respectively. The PCR product was cloned into eukaryotic expression vector pcDNA 3.1(+) and clones were confirmed by restriction digestion and nucleotide sequencing. Functional activity of recombinant GMCSF was checked by expression of GMCSF specific mRNA in transfected Vero cells by RT-PCR of total RNA isolated from transfected Vero cells. The recombinant plasmid can be used as genetic adjuvant in chicken.     

Differential sensitivity of chicken MM-creatine kinase to trypsin and proteinase-K

Under several conditions of SDS-PAGE, the chicken MM-creatine kinase (MM-CK) monomer migrated as a approximately 50,000 dalton polypeptide, approx 25% larger than usually reported. Characterization by sedimentation equilibrium indicated that the anomalous molecular weight was an artifact of electrophoresis. Digestion with trypsin caused only moderate reductions in CK activity, despite extensive degradation of the denatured enzyme revealed by SDS-PAGE. Characterization of trypsinized MM-CK under non-denaturing conditions of electrophoresis and HPLC revealed no fragmentation of the native enzyme, suggesting that MM-CK quaternary structure was maintained despite extensive tryptic nicking. In contrast, much lower concentrations of proteinase-K generated only a single fragment in SDS-PAGE while causing a nearly total loss of enzyme activity.     

A single nucleotide substitution in the phosphoglycerate kinase (PGK)-1 gene occurred after the separation of PGK-1 and PGK-2

Summary The mammalian genome contains two functional loci for the production of phosphoglycerate kinase, PGK-1, an X-linked gene expressed in all somatic cells, and PGK-2, an autosomal intron-less gene expressed exclusively in late spermatogenesis. A nucleotide substitution from guanine to thymine was recently found at position 473 of PGK-1 mRNA in PGK Shizuoka. The mutation was not found in the PGK-2 gene and might have occurred after separation of PGK-1 and PGK-2.     

Maternal diet influences gene expression in intestine of offspring in chicken (Gallus gallus)

The diet of the mother during pregnancy influences the onset of different diseases and health-related traits in the offspring. We investigated the influence of the mother hen diet on the intestinal gene expression pattern in the offspring. Hens received for 11 weeks either a commercial feed or a commercial feed supplemented with vitamins and minerals. The offspring of the two groups showed no changes in growth rate or feed conversion. Of this offspring, gene expression patterns in the intestine were measured at 3 and 14 days of age with an intestinal cDNA-microarray. Between the two groups, 11 genes were found to be differentially expressed both at 3 and 14 days of age. Thus, these genes were differently regulated when the intestine is developing as well as when the intestine is more mature. Genes that are differentially expressed at day 3 and/or day 14 affect intestinal turnover, proliferation and development, metabolism and feed absorption. To confirm that differences in gene expression are related to intestinal development, we investigated intestinal proliferation. This indeed also showed differences in proliferation between the two groups at day 3 and day 14 of age. The gene expression and proliferation results indicate that feed of the hens influences the functionality of intestine of the offspring at day 3 and 14 of age.