结核分枝杆菌H37有毒株与无毒株的代谢相关基因pabB和lpdA启动子活性分析

【目的】通过分析结核分枝杆菌无毒株H37Ra的全基因组序列,并与H37Rv基因组序列比较,发现pabB和lpdA预测的启动子区发生了突变。我们利用报告基因,确认启动子突变与其基因转录水平的关系,探索结核分枝杆菌H37Ra毒力丧失的内在原因。【方法】利用生物信息学方法预测这两对基因的启动子区,采用PCR技术克隆这两对基因的启动子,与分枝杆菌启动子探针载体pMC210相连,DNA测序证实连接片段正确后,用电穿孔法将重组质粒转化至耻垢分枝杆菌mc2155。利用Quantitative Real-Time RT-PCR检测报告基因lacZ转录水平的差异,进一步验证这两对基因启动子的突变对相应基因转录水平的影响。【结果】Quantitative Real Time PCR检测结果显示H37RapabB启动子活性是H37Rv pabB启动子活性的6倍(p0.05),而H37Rv lpdA启动子的活性是H37RalpdA启动子的2倍(p0.05)。【结论】pabB,lpdA的启动子在H37Ra中的突变对其启动子的活性产生了影响,其中lpdA启动子的突变可能与结核分枝杆菌H37Ra的毒力丧失有关。     

Water dynamics clue to key residues in protein folding

A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.     

Deletion 17q12 is a recurrent copy number variant that confers high risk of autism and schizophrenia

Autism spectrum disorders (ASD) and schizophrenia are neurodevelopmental disorders for which recent evidence indicates an important etiologic role for rare copy number variants (CNVs) and suggests common genetic mechanisms. We performed cytogenomic array analysis in a discovery sample of patients with neurodevelopmental disorders referred for clinical testing. We detected a recurrent 1.4 Mb deletion at 17q12, which harbors HNF1B, the gene responsible for renal cysts and diabetes syndrome (RCAD), in 18/15,749 patients, including several with ASD, but 0/4,519 controls. We identified additional shared phenotypic features among nine patients available for clinical assessment, including macrocephaly, characteristic facial features, renal anomalies, and neurocognitive impairments. In a large follow-up sample, the same deletion was identified in 2/1,182 ASD/neurocognitive impairment and in 4/6,340 schizophrenia patients, but in 0/47,929 controls (corrected p = 7.37 × 10⁻⁵). These data demonstrate that deletion 17q12 is a recurrent, pathogenic CNV that confers a very high risk for ASD and schizophrenia and show that one or more of the 15 genes in the deleted interval is dosage sensitive and essential for normal brain development and function. In addition, the phenotypic features of patients with this CNV are consistent with a contiguous gene syndrome that extends beyond RCAD, which is caused by HNF1B mutations only.     

Identification and characterization of 74 novel polymorphic EST-SSR markers in the tea plant, Camellia sinensis (Theaceae)

? Premise of the study: New simple sequence repeat (SSR) markers were developed in the tea plant (Camellia sinensis) using published Expressed Sequence Tag (EST) sequences for further genetic studies and breeding programs. ? Methods and Results: A total of 74 EST-based SSR markers were generated. Polymorphism and transferability validation in 45 individuals of seven species and varieties of Camellia L. sect. Thea (L.) Dyer revealed that the number of alleles (N(A)) per locus varied between one and four or five in each species or variety. The observed heterozygosity (H(O)) and expected heterozygosity (H(E)) ranged from 0.000 to 1.000 and 0.893, respectively. ? Conclusions: These new polymorphic and transferable EST-SSR markers will have potential for applications in genetic diversity evaluation, molecular fingerprinting identification, comparative genomics analysis, and genetic mapping in the tea plant.     

Quantification of soil organic carbon sequestration potential in cropland: A model approach

Agroecosystems have a critical role in the terrestrial carbon cycling process. Soil organic carbon (SOC) in cropland is of great importance for mitigating atmospheric carbon dioxide increases and for global food security. With an understanding of soil carbon saturation, we analyzed the datasets from 95 global long-term agricultural experiments distributed across a vast area spanning wide ranges of temperate, subtropical and tropical climates. We then developed a statistical model for estimating SOC sequestration potential in cropland. The model is driven by air temperature, precipitation, soil clay content and pH, and explains 58% of the variation in the observed soil carbon saturation (n=76). Model validation using independent data observed in China yielded a correlation coefficient R ² of 0.74 (n=19, P<0.001). Model sensitivity analysis suggested that soils with high clay content and low pH in the cold, humid regions possess a larger carbon sequestration potential than other soils. As a case study, we estimated the SOC sequestration potential by applying the model in Henan Province. Model estimations suggested that carbon (C) density at the saturation state would reach an average of 32 t C ha⁻¹ in the top 0–20 cm soil depth. Using SOC density in the 1990s as a reference, cropland soils in Henan Province are expected to sequester an additional 100 Tg C in the future.     

ANMM4CBR: a case-based reasoning method for gene expression data classification

Background  

Accurate classification of microarray data is critical for successful clinical diagnosis and treatment. The "curse of dimensionality" problem and noise in the data, however, undermines the performance of many algorithms.     

Protective effect of supplemental anthocyanins on Arabidopsis leaves under high light

Ten anthocyanin components have been detected in roots of purple sweet potato (Ipomoea batatas Lam.) by high‐performance liquid chromatography coupled to diode array detection and electrospray ionization tandem mass spectrometry. All the anthocyanins were exclusively cyanidins or peonidin 3‐sophoroside‐5‐glucosides and their acylated derivatives. The total anthocyanin content in purple sweet potato powder obtained by solid‐phase extraction was 66 mg g^?1. A strong capacity of purple sweet potato anthocyanins (PSPA) to scavenge reactive oxygen species (superoxide, hydroxyl radical) and the stable 1,1‐diphenyl‐2‐picrylhydrazyl organic free radical was found in vitro using the electron spin resonance technique. To determine the functional roles of anthocyanins in leaves in vivo, for the first time, supplemental anthocyanins were infiltrated into leaves of Arabidopsis thaliana double mutant of the ecotype Landsberg erecta (tt3tt4) deficient in anthocyanin biosynthesis. Chlorophyll fluorescence imaging showed that anthocyanins significantly ameliorated the inactivation of photosystems II during prolonged high‐light (1300 µmol m^?2 s^?1) exposure. Comet assay of DNA revealed an obvious role of supplemental PSPA in alleviating DNA damage by high light in leaves. Our results suggest that anthocyanins could function in vitro and in vivo to alleviate the direct or indirect oxidative damage of the photosynthetic apparatus and DNA in plants caused by high‐light stress.     

Plio-Pleistocene vegetation changes in the North China Plain: Magnetostratigraphy, oxygen and carbon isotopic composition of pedogenic carbonates

The Plio-Pleistocene history of C₄ plant biomass in northwestern China has been documented from the loess-soil sequences of the Loess Plateau region. However, how C₄ plants evolved in the warmer and low-elevation eastern China monsoon zone is still poorly known mainly because of the unavailability of well-dated geological records. In this study, a 203.6-m core of floodplain deposits was recovered from the North China Plain near Tianjin and dated magnetostratigraphically. The results define a chronosequence for the last 3.3 Ma. The late Quaternary portion of the core consists of fluvio-marine sediments while the rest of the section (3.3-0.6 Ma) contains abundant paleosols formed on the floodplain, as confirmed by soil micromorphological evidence. The stable carbon and oxygen isotopic composition of pedogenic carbonates was measured to document vegetation and climate changes. The results reveal mixed C₃ and C₄ vegetation with an estimated C₄ abundance of ~ 40-60% from ~ 3.1 to ~ 2.2 Ma, and a subsequent gradual decline to ~ 25% until ~ 0.6 Ma. This trend is consistent with the data from the loess-soil sequences further west on the Loess Plateau, suggesting they are regionally significant changes. The lowering of growing-season temperature and/or drier conditions induced by global cooling would explain this overall decline.     

Structural characterization of a pectic polysaccharide from Nerium indicum flowers

A polysaccharide fraction, J6, was isolated from the hot-water extract of flowers of oleander Nerium indicum Mill., using ethanol precipitation, cetyltrimethylammonium bromide (CTAB) complexing, anion-exchange chromatography and gel permeation chromatography. J6 was found to contain l-rhamnose, l-arabinose, d-galactose, and d-galacturonic acid, in the ratio of 10.1:49.8:30.1:10.0. Its structure was investigated by methylation analysis, periodate oxidation, Smith degradation, partial acid hydrolysis, electrospray ionization mass spectrometry and NMR spectroscopic methods. It was found that J6 is an RG-I type polysaccharide, which contains a rhamnogalacturonan backbone, with various branches attached to O-4 of l-rhamnose. The branches probably involve (1 → 4)-β-d-galactan, branched l-arabino-(1 → 3)(1 → 6)-β-d-galactan, and (1 → 5)-α-l-arabinan. J6 stimulated NO production of macrophage RAW264.7 cells in a preliminary test.