酸性和碱性土壤新分离的放线菌中线型和环型质粒的检测

从湖南、云南采集的19份酸性土壤样品分离到50株放线菌,在pH4.5和pH7.0的培养基上都能生长.从新疆、青海、云南的14份碱性土壤样品中分离到38株放线菌,在pH10.0和pH7.0的培养基上均能生长.因此,这些菌株属于中度嗜酸或中度嗜碱放线菌.利用脉冲电泳技术和普通凝胶电泳在其中12株放线菌中检测到线型质粒,其中3株放线菌中检测到环型质粒.这是首次在中度嗜酸和中度嗜碱的放线菌中报道线型和环型质粒.     

RAGE upregulation and nuclear factor-kappaB activation associated with ageing rat cardiomyocyte dysfunction

Evidence suggests that ageing is a major risk factor for cardiac dysfunction. Interactions between advanced glycation endproducts (AGEs) and the receptor for AGEs (RAGE) are known to cause chronic cellular activation, including activation of nuclear factor-kappaB (NF-kappaB), which has been implicated as a causal factor in the ageing process. To assess whether cardiomyocyte contractile function and the interaction of AGEs with RAGE in the heart are altered in ageing, 25- and 2-month-old male rats were compared. Mechanical properties were assessed in ventricular myocytes using an edge-detection system, including peak twitch amplitude (PTA), time-to-PTA (TPS), time-to-75% relengthening (TR75) and maximal velocity of shortening/relengthening (+/-dL/dt) in ventricular myocytes. AGEs were detected by using a fluorescence assay. The expression of RAGE and NF-kappaB was assessed through a Western blot analysis. Compared with young myocytes, aged myocytes displayed a prolonged TR75 at 1 Hz. With increasing stimulus frequency (from 2 to 4 Hz), aged myocytes' PTA was significantly reduced relative to young myocytes. Aged rat hearts displayed high level of AGEs, RAGE upregulation and NF-kappaB activation. These findings demonstrate impaired cardiomyocyte relaxation and reduced tolerance to increased stimulus frequency in aged rats, which might be associated with enhanced AGEs, RAGE expression, and NF-kappaB activation.     

Association of single-nucleotide polymorphisms in RHOB and TXNDC3 with knee osteoarthritis susceptibility: two case-control studies in East Asian populations and a meta-analysis

Introduction

Conflicting findings on the association of single nucleotide polymorphisms (SNPs) in RHOB and TXNDC3 with susceptibility to knee osteoarthritis (OA) have been reported in European Caucasians. To examine the associations of these SNPs with OA in East Asian populations and to evaluate their global significance, we conducted two case-control studies in 955 Chinese and 750 Japanese patients.

Methods

We genotyped the previously implicated SNPs rs585017 (in RHOB) and rs4720262 (in TXNDC3) in patients with primary symptomatic knee OA with radiographic confirmation and in matched control individuals, and analyzed their associations. We further conducted a meta-analysis of the study findings together with those of previously reported European studies using the DerSimonian-Laird procedure.

Results

A significant association of RHOB with knee OA was observed in male Chinese patients (P = 0.02). No significant associations were found for RHOB in any other comparisons in the East Asian populations. The association of TXNDC3 was replicated in Chinese female (P = 0.04) and Japanese (P = 0.03) patients, although none of these associations persisted after Bonferroni correction. Significant association (P = 0.02 for the allelic frequency) with nonsignificant heterogeneity was found in the East Asian replication study. No significant association was found in any comparison in the meta-analysis for all studies.

Conclusion

Our study replicates the association, previously reported in European Caucasians, of TXNDC3 with knee OA susceptibility in an East Asian population.     

Disruption of Smad4 in neural crest cells leads to mid-gestation death with pharyngeal arch, craniofacial and cardiac defects

TGFβ/BMP signaling pathways are essential for normal development of neural crest cells (NCCs). Smad4 encodes the only common Smad protein in mammals, which is a critical nuclear mediator of TGFβ/BMP signaling. In this work, we sought to investigate the roles of Smad4 for development of NCCs. To overcome the early embryonic lethality of Smad4 null mice, we specifically disrupted Smad4 in NCCs using a Cre/loxP system. The mutant mice died at mid-gestation with defects in facial primordia, pharyngeal arches, outflow tract and cardiac ventricles. Further examination revealed that mutant embryos displayed severe molecular defects starting from E9.5. Expression of multiple genes, including Msx1, 2, Ap-2α, Pax3, and Sox9, which play critical roles for NCC development, was downregulated by NCC disruption of Smad4. Moreover, increased cell death was observed in pharyngeal arches from E10.5. However, the cell proliferation rate in these areas was not substantially altered. Taken together, these findings provide compelling genetic evidence that Smad4-mediated activities of TGFβ/BMP signals are essential for appropriate NCC development.     

Transcriptome differences in the hypopharyngeal gland between Western Honeybees (Apis mellifera) and Eastern Honeybees (Apis cerana)

Background

Apis mellifera and Apis cerana are two sibling species of Apidae. Apis cerana is adept at collecting sporadic nectar in mountain and forest region and exhibits stiffer hardiness and acarid resistance as a result of natural selection, whereas Apis mellifera has the advantage of producing royal jelly. To identify differentially expressed genes (DEGs) that affect the development of hypopharyngeal gland (HG) and/or the secretion of royal jelly between these two honeybee species, we performed a digital gene expression (DGE) analysis of the HGs of these two species at three developmental stages (newly emerged worker, nurse and forager).

Results

Twelve DGE-tag libraries were constructed and sequenced using the total RNA extracted from the HGs of newly emerged workers, nurses, and foragers of Apis mellifera and Apis cerana. Finally, a total of 1482 genes in Apis mellifera and 1313 in Apis cerana were found to exhibit an expression difference among the three developmental stages. A total of 1417 DEGs were identified between these two species. Of these, 623, 1072, and 462 genes showed an expression difference at the newly emerged worker, nurse, and forager stages, respectively. The nurse stage exhibited the highest number of DEGs between these two species and most of these were found to be up-regulated in Apis mellifera. These results suggest that the higher yield of royal jelly in Apis mellifera may be due to the higher expression level of these DEGs.

Conclusions

In this study, we investigated the DEGs between the HGs of two sibling honeybee species (Apis mellifera and Apis cerana). Our results indicated that the gene expression difference was associated with the difference in the royal jelly yield between these two species. These results provide an important clue for clarifying the mechanisms underlying hypopharyngeal gland development and the production of royal jelly.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-744) contains supplementary material, which is available to authorized users.     

鼎湖山季风常绿阔叶林小气候特征分析

阐述了鼎湖山季风常绿阔叶林小气候特征与空旷地的差异 ,并分析了这些差异产生的原因。结果表明 :季风常绿阔叶林冠层顶部的太阳总辐射量年平均为 3488.8MJ·m- 2 ,由辐射强度和辐射总量计算出的反射率分别为 1 0 .5%、1 1 .4% ,年平均气温为 1 9.9℃ ,此 3项都比空旷地低 ,而年平均相对湿度高于空旷地 ,其值为 87% ;季风常绿阔叶林年蒸散力为987.50 mm,湿润指数为 0 .96;季风常绿阔叶林土壤表层温度日变化不及空旷地显著 ;无论是季风常绿阔叶林 ,还是空旷地 ,土壤温度在春、夏季节自上而下逐步降低 ,在秋、冬季节自上而下逐步升高。     

Changes of primary sequence and secondary structure proximal to the 5′ end of the stop codon substantially increases the expression of the variable region of an antibody in <Emphasis Type="Italic">E. coli</Emphasis>

The sequence context at the 5 end of the stop codon may influence the efficiency of termination and translation. To increase the expression of a designed variable region of an antibody (named as VH5) against tumor necrosis factor (TNF), two nucleotides (TC) at 25 and 26 nucleotides (nt) upstream of termination codon were substituted with AG, respectively. The free energy of 70 nt (arbitrarily defined from the 32 nt upstream of termination codon to 38 nt downstream) was changed from –13.5 kcal mol^-1 to –17.3 kcal mol^-1. The expression level was increased from 1 ± 0.3% to 10 ± 1.2% of total cellular protein. Although the precise mechanism of this phenomenon remains to be elucidated, this report provides an alternative means to increase the expression of a foreign gene in E. coli. Revisions requested 18 October 2004; Revisions received 26 November 2004     

High throughput screening of co-expressed gene pairs with controlled false discovery rate (FDR) and minimum acceptable strength (MAS).

Many exploratory microarray data analysis tools such as gene clustering and relevance networks rely on detecting pairwise gene co-expression. Traditional screening of pairwise co-expression either controls biological significance or statistical significance, but not both. The former approach does not provide stochastic error control, and the later approach screens many co-expressions with excessively low correlation. We have designed and implemented a statistically sound two-stage co-expression detection algorithm that controls both statistical significance (false discovery rate, FDR) and biological significance (minimum acceptable strength, MAS) of the discovered co-expressions. Based on estimation of pairwise gene correlation, the algorithm provides an initial co-expression discovery that controls only FDR, which is then followed by a second stage co-expression discovery which controls both FDR and MAS. It also computes and thresholds the set of FDR p-values for each correlation that satisfied the MAS criterion. Using simulated data, we validated asymptotic null distributions of the Pearson and Kendall correlation coefficients and the two-stage error-control procedure; we also compared our two-stage test procedure with another two-stage test procedure using the receiver operating characteristic (ROC) curve. We then used yeast galactose metabolism data to illustrate the advantage of our method for clustering genes and constructing a relevance network. The method has been implemented in an R package "GeneNT" that is freely available from the Comprehensive R Archive Network (CRAN): www.cran.r-project.org/.     

Phospholipid capture combined with non-linear chromatographic correction for improved serum metabolite profiling

Serum analysis with LC/MS can yield thousands of potential metabolites. However, in metabolomics, biomarkers of interest will often be of low abundance, and ionization suppression from high abundance endogenous metabolites such as phospholipids may prevent the detection of these metabolites. Here a cerium-modified column and methyl-tert-butyl-ether (MTBE) liquid–liquid extraction were employed to remove phospholipids from serum in order to obtain a more comprehensive metabolite profile. XCMS, an in-house developed data analysis software platform, showed that the intensity of existing endogenous metabolites increased, and that new metabolites were observed. This application of phospholipid capture in combination with XCMS non-linear data processing has enormous potential in metabolite profiling, for biomarker detection and quantitation.