Orthologous gene-expression profiling in multi-species models: search for candidate genes

Microarray-driven gene-expression profiles are generally produced and analyzed for a single specific experimental model. We have assessed an analytical approach that simultaneously evaluates multi-species experimental models within a particular biological condition using orthologous genes as linkers for the various Affymetrix microarray platforms on multi-species models of ventilator-associated lung injury. The results suggest that this approach may be a useful tool in the evaluation of biological processes of interest and selection of process-related candidate genes.     

Database searching by flexible protein structure alignment

We have recently developed a flexible protein structure alignment program (FATCAT) that identifies structural similarity, at the same time accounting for flexibility of protein structures. One of the most important applications of a structure alignment method is to aid in functional annotations by identifying similar structures in large structural databases. However, none of the flexible structure alignment methods were applied in this task because of a lack of significance estimation of flexible alignments. In this paper, we developed an estimate of the statistical significance of FATCAT alignment score, allowing us to use it as a database-searching tool. The results reported here show that (1) the distribution of the similarity score of FATCAT alignment between two unrelated protein structures follows the extreme value distribution (EVD), adding one more example to the current collection of EVDs of sequence and structure similarities; (2) introducing flexibility into structure comparison only slightly influences the sensitivity and specificity of identifying similar structures; and (3) the overall performance of FATCAT as a database searching tool is comparable to that of the widely used rigid-body structure comparison programs DALI and CE. Two examples illustrating the advantages of using flexible structure alignments in database searching are also presented. The conformational flexibilities that were detected in the first example may be involved with substrate specificity, and the conformational flexibilities detected in the second example may reflect the evolution of structures by block building.     

次声暴露对大鼠脾、肝脏某些酶活性的影响

目的:观察8 Hz,130 dB次声暴露不同时间对大鼠脾、肝脏某些酶活性的影响.方法:35只SD大鼠随机分为5组,即对照组,1周,2周,3周,4周组.每天次声暴露1次,每次2 h.实验后,观察大鼠脾、肝脏组织中MAO,GSH-px,SOD活性和MDA含量的变化.结果:大鼠脾脏MAO活性1周,2周时显著增高(P＜0.01),3周下降,4周时又显著增加(P＜0.05).肝脏组织MAO活性变化不明显(P＞0.05).脾脏组织中GSH-px活性在4周时明显增高(P＜0.05),肝脏组织中GSH-px活性在1周时就有显著性增高(P＜0.05).脾脏SOD活性在1周至4周均有显著性增高(P＜0.05).肝脏组织在实验期变化不明显(P＞0.05).脾脏组织中MDA含量在3周至4周时有显著性增高(P＜0.05).肝脏组织在1至2周时有非常显著的增高(P＜0.01),在3周时下降,到4周时又显著高于对照组(P＜0.05).结论:8Hz,130 dB次声暴露,大鼠脾、肝脏组织活性氧自由基、脂质过氧化物增高,抗氧化能力降低,造成对组织的损伤.     

白细胞介素-2降低缺氧/复氧心肌细胞对细胞内钙的处理能力

目的 :研究在正常和缺氧 /复氧过程中白细胞介素 2 (IL 2 )对心肌细胞收缩和细胞内钙的处理能力的影响。方法 :采用酶解分离大鼠心室肌细胞化学缺氧模型 ,用视频跟踪系统和细胞内双波长钙荧光系统检测单个心肌细胞收缩和细胞内钙的变化。结果 :①缺氧过程中 ,心肌细胞收缩被抑制 ,钙瞬变幅度降低、静息钙水平增高 ,咖啡因诱导的钙释放减少 ,但对细胞膜L -型钙通道活性无明显影响 ;复氧期间 ,各指标不能恢复到对照水平。②IL 2 (2× 10 5U/L)抑制心肌细胞收缩 ,使钙瞬变幅度降低、静息钙水平增高 ,使咖啡因诱导的钙释放减少。③在缺氧期间加入IL 2 (2× 10 5U/L)后 ,复氧期间各参数回复均减慢。结论 :缺氧时同时存在IL 2 ,可加剧复氧时心肌细胞收缩功能和钙处理能力的降低 ,这可能与心肌细胞肌浆网内贮钙释放减少有关。     

DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments

The phosphatidylinositol (PI) metabolic pathway is considered critical in plant responses to many environmental factors, and previous studies have indicated the involvement of multiple PI-related gene families during cellular responses.Through a detailed analysis of the Arabidopsis thaliana genome, 82 polypeptides were identified as being involved in PI signaling. These could be grouped into different families including PI synthases (PIS), PI-phosphate kinases (PIPK),phospholipases (PL), inositol polyphosphate phosphatases (IPPase), inositol polyphosphate kinases (IPK), PI transfer proteins and putative inositol polyphosphate receptors. The presence of more than 10 isoforms of PIPK, PLC, PLD and IPPase suggested that these genes might be differentially expressed during plant cellular responses or growth and development. Accordingly, DNA chip technology was employed to study the expression patterns of various isoforms.In total, 79 mRNA clones were amplified and used for DNA chip generation. Expression profile analysis was performed using samples that represented multiple tissues or cellular responses. Tested samples included normal leaf, stem and flower tissues, and leaves from plants treated with various hormones (auxin, cytokinin, gibberellin, abscisic acid and brassinosteroid) or environmental factors (temperature, calcium, sodium, drought, salicylic acid and jasmonic acid).Results showed that many PI pathway-related genes were differentially expressed under these experimental conditions.In particular, the different isoforms of each family were specifically expressed in many cases, suggesting their involvement in tissue specificity and cellular responses to environmental conditions. This work provides a starting point for functional studies of the relevant PI-related proteins and may help shed light onto the role of PI pathways in development and cellular responses.     

FRAGILE FIBER3, an Arabidopsis gene encoding a type II inositol polyphosphate 5-phosphatase, is required for secondary wall synthesis and actin organization in fiber cells

Type II inositol polyphosphate 5-phosphatases (5PTases) in yeast and animals have been known to regulate the level of phosphoinositides and thereby influence various cellular activities, such as vesicle trafficking and actin organization. In plants, little is known about the phosphatases involved in hydrolysis of phosphoinositides, and roles of type II 5PTases in plant cellular functions have not yet been characterized. In this study, we demonstrate that the FRAGILE FIBER3 (FRA3) gene of Arabidopsis thaliana, which encodes a type II 5PTase, plays an essential role in the secondary wall synthesis in fiber cells and xylem vessels. The fra3 mutations caused a dramatic reduction in secondary wall thickness and a concomitant decrease in stem strength. These phenotypes were associated with an alteration in actin organization in fiber cells. Consistent with the defective fiber and vessel phenotypes, the FRA3 gene was found to be highly expressed in fiber cells and vascular tissues in stems. The FRA3 protein is composed of two domains, an N-terminal localized WD-repeat domain and a C-terminal localized 5PTase catalytic domain. In vitro activity assay demonstrated that recombinant FRA3 exhibited phosphatase activity toward PtdIns(4,5)P2, PtdIns(3,4,5)P3, and Ins(1,4,5)P3, with the highest substrate affinity toward PtdIns(4,5)P2. The fra3 missense mutation, which caused an amino acid substitution in the conserved motif II of the 5PTase catalytic domain, completely abolished the FRA3 phosphatase activity. Moreover, the endogenous levels of PtdIns(4,5)2 and Ins(1,4,5)P3 were found to be elevated in fra3 stems. Together, our findings suggest that the FRA3 type II 5PTase is involved in phosphoinositide metabolism and influences secondary wall synthesis and actin organization.     

Association between PCR-SSCP of growth differentiation factor 9 gene and high prolificacy in Small Tail Han sheep

Small Tail Han sheep that has significant characteristics of high prolificacy and nonseasonal ovulatory activity is an excellent local sheep breed in P.R. China. The lambing percentage averaged 260% in Small Tail Han sheep. Growth differentiation factor 9 (GDF9) gene, which was essential for growth and differentiation of early ovarian follicles, was considered as a possible candidate gene for litter size in Small Tail Han sheep. The genetic polymorphism of a part of the GDF9 gene was detected in 130 ewes of Small Tail Han sheep by PCR-SSCP. The results indicated that there were two genotypes (AA and AB) detected by two primer pairs. In both exon 1 and exon 2 of the GDF9 gene in Small Tail Han sheep, frequencies of AA genotype were 0.846 and 0.908, frequencies of AB genotype were 0.154 and 0.092, frequencies of A allele were 0.923 and 0.954, and frequencies of B allele were 0.077 and 0.046, respectively. The results of chi2 fitness test indicated that both exon 1 and exon 2 of the GDF9 gene were in Hardy-Weinberg equilibrium (p > 0.05) in Small Tail Han sheep. Least squares means of litter size in the first and the second parity for genotype AA were 0.30 (p <0.05) and 0.77 (p <0.0001) more than those for genotype AB detected in exon 1 of the GDF9 gene in Small Tail Han sheep, respectively. Fragments detected in exon 2 of the GDF9 gene had no significant effect (p > 0.05) on litter size in both the first and the second parity in Small Tail Han sheep. Litter size in sheep is lowly heritable, expressed only in females, and manifested relatively late in life. Access to genetic markers would thus be advantageous in selection programs.     

Crystal structure of the putative adapter protein MTH1859

MTH1859 from Methanobacterium thermoautotrophicum is a 77 residue protein representing a conserved family of functionally uncharacterized proteins. We solved the crystal structure of MTH1859 by single wavelength anomalous diffraction phasing using selenomethionine labeled protein. MTH1859 adopts a mainly anti-parallel all-beta-fold. The beta-sheet is heavily bent to form a U-structure that is closed through a loop. The monomer structure possesses similarities to the photoreaction center (PRC) domain fold, but the protein employs a unique oligomerization scheme. Two monomers of MTH1859 occupy the asymmetric unit and dimerize in a head-to-head fashion. Crystal packing interactions identify a second protein-protein interaction interface at the MTH1859 tails which can simultaneously bind two partner molecules. These interactions lead to the formation of a honeycomb structure and suggest that the family of MTH1859-like proteins might function as adapters for protein complex assembly.     

白细胞介素-2对大鼠心肌Ca2+ATPase和Na+ /K+ATPase的影响

为了探讨IL－2对心肌细胞内钙影响的可能机制,用光学法检测心肌肌浆网Ca^2 ATPase的活性,以及细胞膜Ca^2 ATPase和Na^ /K^ ATPase的活性。结果：（1）用IL－2（10、40、200、800U/ml）灌流心脏后,其肌浆网Ca^2 ATPase的活性随IL－2浓度的升高而增强;（2）在ATP浓度为0.1-4mmol/L时,Ca^2 ATPase的活性随ATP浓度的升庙则增强,由IL－2（200U／ml）灌流后的心脏获得肌浆网（SR）,其Ca^2 ATPase的活性对ATP的反应强于对照组;（3）在[Ca^2 ]为1－40μmol/L时,心脏SR Ca^2 ATPase的活性随[Ca^2 ]增加而增强,而IL－2灌流心脏后分离的SR,其Ca^2 ATPase活性在[Ca^2 ]升高时没有明显改变;（4）用nor-BNI(10nmol/L）预处理5min后,IL－2（200U／ml）灌流后不再使SR Ca^2 ATPase的活性增强;（5）用PTX（5mg/L）预处理后,IL－2对SR Ca^2 ATPase的影响减弱;（6）用磷脂酶C（PLC）抑制剂U73122（5μmol/L）处理后,IL－2不再使SR Ca^2 ATPase活性增高;（7）用IL－2直接处理从正常大鼠分离的SR后,对SR Ca^2 ATPase活性无明显影响;（8）IL－2灌流后,对心肌细胞膜Ca^2 ATPase和Na^ /K^ ATPase活性没有显著。上述结果表明,IL－2灌流心脏后使心肌肌浆网Ca^2 ATPase的活性增加,心肌细胞膜上的κ－阿片受体及其下游的G蛋白和PLC介导了IL－2的作用。尽管IL－2提高SR Ca^2 ATPase对ATP的反应性,但却抑制SR Ca^2 ATPase对钙离子的敏感性。IL－2对心肌细胞膜Ca^2 ATPase和Na^ /K^ ATPase的活性无明显影响。