Lanthionine Synthetase C-like Protein 1 Interacts with and Inhibits Cystathionine β-Synthase: A TARGET FOR NEURONAL ANTIOXIDANT DEFENSE*

The finding that eukaryotic lanthionine synthetase C-like protein 1 (LanCL1) is a glutathione-binding protein prompted us to investigate the potential relationship between LanCL1 and cystathionine β-synthase (CBS). CBS is a trans-sulfuration enzyme critical for the reduced glutathione (GSH) synthesis and GSH-dependent defense against oxidative stress. In this study we found that LanCL1 bound to CBS in mouse cortex and HEK293 cells. Mapping studies revealed that the binding region in LanCL1 spans amino acids 158–169, and that in CBS contains N-terminal and C-terminal regulatory domains. Recombinant His-LanCL1 directly bound endogenous CBS from mouse cortical lysates and inhibited its activity. Overexpression of LanCL1 inhibited CBS activity in HEK293 cells. CBS activity is reported to be regulated by oxidative stress. Here we found that oxidative stress induced by H₂O₂ or glutamate lowered the GSH/GSSG ratio, dissociated LanCL1 from CBS, and elevated CBS activity in primary rat cortical neurons. Decreasing the GSH/GSSG ratio by adding GSSG to cellular extracts also dissociated LanCL1 from CBS. Either lentiviral knockdown of LanCL1 or specific disruption of the LanCL1-CBS interaction using the peptide Tat-LanCL1_153–173 released CBS activity in neurons but occluded CBS activation in response to oxidative stress, indicating the major contribution of the LanCL1-CBS interaction to the regulation of CBS activity. Furthermore, LanCL1 knockdown or Tat-LanCL1_153–173 treatment reduced H₂O₂ or glutamate-induced neuronal damage. This study implies potential therapeutic value in targeting the LanCL1-CBS interaction for neuronal oxidative stress-related diseases.     

重组鼠疫菌F1抗原的纯化及其在ELISA检测鼠疫免疫中的应用

从表达rF1抗原的大肠杆菌中以Superdex-200凝胶过滤层析纯化rF1抗原,电泳扫描显示纯化率>90%。SDS-PAGE及琼脂免疫双扩散结果显示纯化的rF1抗原具天然F1抗原的活性。将此纯化的rF1抗原用于间接ELISA分析免疫动物血清中抗F1抗体的水平,并与天然F1抗原相比较,证明rF1抗原优于天然F1抗原分析结果,可用于鼠疫的血清学检测。     

Overexpression of SmLEA enhances salt and drought tolerance in Escherichia coli and Salvia miltiorrhiza

Salinity and drought are important abiotic stresses limiting plant growth and development. Late embryogenesis abundant (LEA) proteins are a group of proteins associated with tolerance to water-related stress. We previously cloned an LEA gene, SmLEA, from Salvia miltiorrhiza Bunge. Phylogenetic analysis indicated that SmLEA belongs to Group LEA14, which is involved in the dehydration response. To determine its function in detail, we have now overexpressed SmLEA in Escherichia coli and S. miltiorrhiza. The logarithmic increase in accumulations of SmLEA proteins in E. coli occurred earlier under salinity than under standard conditions. SmLEA-transformed S. miltiorrhiza plants also showed faster root elongation and a lower malondialdehyde concentration than the empty vector control plants did when cultured on MS media supplemented with 60 mM NaCl or 150 mM mannitol. Moreover, SmLEA-overexpressing transgenics experienced a less rapid rate of water loss. Under either salinity or drought, overexpressing plants had greater superoxide dismutase activity and a higher glutathione concentration. These results suggest that SmLEA may be useful in efforts to improve drought and salinity tolerance in S. miltiorrhiza. Our data also provide a good foundation for further studies into the stress resistance mechanism and molecular breeding of this valuable medicinal plant.     

Integrating 'omic' information: a bridge between genomics and systems biology

The availability of genome sequences for several organisms, including humans, and the resulting first-approximation lists of genes, have allowed a transition from molecular biology to 'modular biology'. In modular biology, biological processes of interest, or modules, are studied as complex systems of functionally interacting macromolecules. Functional genomic and proteomic ('omic') approaches can be helpful to accelerate the identification of the genes and gene products involved in particular modules, and to describe the functional relationships between them. However, the data emerging from individual omic approaches should be viewed with caution because of the occurrence of false-negative and false-positive results and because single annotations are not sufficient for an understanding of gene function. To increase the reliability of gene function annotation, multiple independent datasets need to be integrated. Here, we review the recent development of strategies for such integration and we argue that these will be important for a systems approach to modular biology.     

An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

Background

Gene expression microarray has been the primary biomarker platform ubiquitously applied in biomedical research, resulting in enormous data, predictive models, and biomarkers accrued. Recently, RNA-seq has looked likely to replace microarrays, but there will be a period where both technologies co-exist. This raises two important questions: Can microarray-based models and biomarkers be directly applied to RNA-seq data? Can future RNA-seq-based predictive models and biomarkers be applied to microarray data to leverage past investment?

Results

We systematically evaluated the transferability of predictive models and signature genes between microarray and RNA-seq using two large clinical data sets. The complexity of cross-platform sequence correspondence was considered in the analysis and examined using three human and two rat data sets, and three levels of mapping complexity were revealed. Three algorithms representing different modeling complexity were applied to the three levels of mappings for each of the eight binary endpoints and Cox regression was used to model survival times with expression data. In total, 240,096 predictive models were examined.

Conclusions

Signature genes of predictive models are reciprocally transferable between microarray and RNA-seq data for model development, and microarray-based models can accurately predict RNA-seq-profiled samples; while RNA-seq-based models are less accurate in predicting microarray-profiled samples and are affected both by the choice of modeling algorithm and the gene mapping complexity. The results suggest continued usefulness of legacy microarray data and established microarray biomarkers and predictive models in the forthcoming RNA-seq era.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0523-y) contains supplementary material, which is available to authorized users.     

结缔组织生成和肿瘤

肿瘤的发生并不只是由肿瘤细胞本身恶化引起的,肿瘤基质也发挥了非常重要的作用,肿瘤发生是肿瘤细胞和围绕它的肿瘤基质相互作用的产物。肿瘤细胞可以通过各种途径激活与其相邻的间质,促进成纤维细胞的增生、细胞外基质的沉积、免疫细胞浸润和血管生成,这种现象被称为结缔组织生成。结缔组织生成形成了一个支持肿瘤发展的微环境,通过多种途径促进了肿瘤的发生、发展和转移。针对结缔组织生成进行肿瘤治疗可以为肿瘤的临床治疗提供新的思路。     

Seasonal variation in the mating system of a selfing annual with large floral displays

Background and Aims Flowering plants display considerable variation in mating system, specifically the relative frequency of cross- and self-fertilization. The majority of estimates of outcrossing rate do not account for temporal variation, particularly during the flowering season. Here, we investigated seasonal variation in mating and fertility in Incarvillea sinensis (Bignoniaceae), an annual with showy, insect-pollinated, ‘one-day’ flowers capable of delayed selfing. We examined the influence of several biotic and abiotic environmental factors on day-to-day variation in fruit set, seed set and patterns of mating.Methods We recorded daily flower number and pollinator abundance in nine 3 × 3-m patches in a population at Mu Us Sand land, Inner Mongolia, China. From marked flowers we collected data on daily fruit and seed set and estimated outcrossing rate and biparental inbreeding using six microsatellite loci and 172 open-pollinated families throughout the flowering period.Key Results Flower density increased significantly over most of the 50-d flowering season, but was associated with a decline in levels of pollinator service by bees, particularly on windy days. Fruit and seed set declined over time, especially during the latter third of the flowering period. Multilocus estimates of outcrossing rate were obtained using two methods (the programs MLTR and BORICE) and both indicated high selfing rates of ∼80 %. There was evidence for a significant increase in levels of selfing as the flowering season progressed and pollinator visitation declined. Biparental inbreeding also declined significantly as the flowering season progressed.Conclusions Temporal variation in outcrossing rates may be a common feature of the mating biology of annual, insect-pollinated plants of harsh environments but our study is the first to examine seasonal mating-system dynamics in this context. Despite having large flowers and showy floral displays, I. sinensis attracted relatively few pollinators. Delayed selfing by corolla dragging largely explains the occurrence of mixed mating in I. sinensis, and this mode of self-fertilization probably functions to promote reproductive assurance when pollinator service is limited by windy environmental conditions and competition from co-occurring flowering plants.     

Artificial synthesis of interspecific chimeras between tuber mustard (Brassica juncea) and cabbage (Brassica oleracea) and cytological analysis

Interspecific chimeras between tuber mustard and red cabbage were obtained by in vitro graft-culture method. Before grafting, 6-day-old seedlings of tuber mustard and red cabbage were vertically half-cut and treated with different concentrations of 6-BA and NAA for 1 min, then, they were symmetrically fit together. As a result, sectorial chimeras were initially produced from the united shoot tips. The maximum frequency of chimeral bud formation reached 6.33% when the vertical sections of tuber mustard and cabbage were treated with 2 mg/l 6-BA and 1 mg/l NAA. When sectorial chimeras were propagated on MS medium containing 1 mg/l 6-BA, periclinal and mericlinal chimeras gradually developed. Chimeral shoots were rooted on half-strength MS medium containing 0.1 mg/l NAA. The rooted chimeras were acclimatized and transferred to the field for cytological and morphological analysis. The results showed that stomata density in the chimeras was significantly higher than that of their parents, while chloroplast size, starch grain size and number were intermediate between the two parents. The chimeras were further analyzed by flow cytometry, and the results indicated that they contained both sets of parental chromosomes. Moreover, chimeral plants possessed valuable characters from the two parents.     

Inhibition of Hypoxia Inducible Factor 1α by siRNA‐Induced Apoptosis in Human Retinoblastoma Cells

Hypoxia, which activates the hypoxia inducible factor 1α (HIF‐1α), is an essential feature of retinoblastoma (RB) and contributes to poor prognosis and resistance to conventional therapy. In this study, the effect of HIF‐1α knockdown by small interfering RNA (siRNA) on cell proliferation, apoptosis, and apoptotic pathways of human Y‐79 RB cells was first investigated. Exposure to hypoxia induced the increased expression of HIF‐1α both in mRNA and protein levels. Then, knockdown of HIF‐1α by siRNA_HIF‐1α resulted in inhibition of cell proliferation and induced cell apoptosis in human Y‐79 RB cells under both normoxic and hypoxic conditions, with hypoxic conditions being more sensitive. Furthermore, knockdown of HIF‐1α could enhance hypoxia‐induced slight increase of Bax/Bcl‐2 ratio and activate caspase‐9 and caspase‐3. These results together indicated that suppression of HIF‐1α expression may be a promising strategy for the treatment of human RB in the future.