PQN and DQN: algorithms for expression microarrays

An ideal expression algorithm should be able to tell truly different expression levels with small false positive errors and be robust to assay changes. We propose two algorithms. PQN is the non-central trimmed mean of perfect match intensities with quantile normalization. DQN is the non-central trimmed mean of differences between perfect match and mismatch intensities with quantile normalization. The quantiles for normalization can be either empirical or theoretical. When array types and/or assay change in a study, the normalization to common quantiles at the probe set level is essential. We compared DQN, PQN, RMA, GCRMA, DCHIP, PLIER and MAS5 for the Affymetrix Latin square data and our data of two sets of experiments using the same bone marrow but different types of microarrays and different assay. We found the computation for AUC of ROC at affycomp.biostat.jhsph.edu can be improved.     

2株耐低温微生物处理污水模拟试验初报

从下水管道的污泥中分离筛选到耐冷细菌H6和耐冷酵母菌J1,采用此2菌株进行模拟污水低温(8℃)处理试验。H6和J1菌株对模拟污水COD的去除率分别为66.6%和72.2%;H6、J1菌株对有机氮去除率分别为76.9%和64.5%;H6、J1菌株对总磷去除率分别为53.9%和14.0%。说明低温微生物在低温环境的污水处理具有广阔的应用前景。     

同源四倍体高粱与约翰逊草杂交的细胞遗传学研究

对约翰逊草、人工诱变四倍体高粱品系四沈甜及二者杂交种中期Ⅰ染色体构型、后期Ⅰ染色体行为进行了观察,并对花粉育性与结实率关系进行了研究。结果表明：约翰逊草、四沈甜及杂交种的染色体构型分别是：0．49Ⅰ＋15．83Ⅱ＋0．15Ⅲ＋1．60Ⅳ、0．72Ⅰ＋15．23Ⅱ＋0．075Ⅲ十2．15Ⅳ、0．68Ⅰ＋17．00Ⅱ＋0．18Ⅲ＋0．95Ⅳ。双亲及杂交种都是不规则的四倍体遗传群体。约翰逊草与同源四倍体高粱的染色体组间存在一定程度的同源性,杂交容易成功。     

PCR-based generation of shRNA libraries from cDNAs

Background  

The use of small interfering RNAs (siRNAs) to silence target gene expression has greatly facilitated mammalian genetic analysis by generating loss-of-function mutants. In recent years, high-throughput, genome-wide screening of siRNA libraries has emerged as a viable approach. Two different methods have been used to generate short hairpin RNA (shRNA) libraries; one is to use chemically synthesized oligonucleotides, and the other is to convert complementary DNAs (cDNAs) into shRNA cassettes enzymatically. The high cost of chemical synthesis and the low efficiency of the enzymatic approach have hampered the widespread use of screening with shRNA libraries.     

TDZ对植物体细胞胚胎发生的作用

介绍了TDZ在植物体细胞胚胎发生中的作用及其可能的作用机制的研究进展。     

双侧自体腘绳肌腱一期重建前后交叉韧带损伤的临床疗效

目的:探讨关节镜辅助下使用双侧自体腘绳肌腱一期修复膝关节前后交叉韧带损伤的方法和临床疗效。方法:内窥镜微创双侧自体腘绳肌腱修复膝关节内韧带,术后用IKDC分级、影像学IKDC分级、Lysholm功能评分和KT2000TM测量进行关节机能打分。结果:11例患者获得3-5年随访,平均随访3.8年。术前Lysholm功能评分平均(46.8±5.7)分,终末随访时平均(81.3±10.5)分,差异有显著性(P<0.05)。术后关节稳定性测量,在20磅时、30磅和最大拉力时健膝和患膝分别是:6.1±0.3和6.8±0.8;6.3±0.5和7.7±1.3;7.5±0.6和9.6±2.4,统计学上差异无显著性(P>0.05)。主观IKDC分级:A级4例,B级6例,C级1例;影像学IKDC分级:A级8例,B级2例,C级1例。结论:关节镜辅助下使用双侧自体腘绳肌腱一期修复膝关节前后交叉韧带损伤是重建膝关节稳定性的良好有效方法。     

上皮性卵巢癌中Maspin蛋白与血管内皮生长因子-C的表达及其相关性

目的:探讨上皮性卵巢癌组织中maspin蛋白与血管内皮生长因子-C(VEGF-C)表达的临床意义及其相关性。方法:采用免疫组化技术检测75例上皮性卵巢癌中maspin蛋白与VEGF-C的表达情况,以卵巢良性肿瘤及正常卵巢作为对照。结果:maspin和VEGF-C在上皮性卵巢癌中的阳性表达率分别为61.3%、82.7%,均明显高于卵巢良性肿瘤(13.3%、20%)和正常卵巢组织(0%、0%),maspin蛋白在上皮性卵巢癌中的表达与FIGO分期高、组织学分级高、腹水形成和淋巴结转移有关;VEGF-C与FIGO分期高、淋巴结转移和腹水形成有关;上皮性卵巢癌中maspin蛋白与VEGF-C的表达成正相关。结论:maspin和VEGF-C在上皮性卵巢癌中表达上调,在卵巢上皮性癌的浸润、转移中起重要作用。     

约氏疟原虫Pys48核酸疫苗传播阻断效应的实验研究

探讨约氏疟原虫（Plasmodium yoelii17XL）Pys48核酸疫苗免疫BALB/c小鼠的特异性抗体产生特点及其效应。将Pys48核酸疫苗肌肉内注射免疫BALB/c小鼠,并以空质粒注射组作为对照,3次免疫后通过P.y17XL攻击小鼠;采用ELISA检测免疫后小鼠血清中特异性抗体水平;通过P.y17XL感染小鼠,取其感染后第3天含有配子体的血液进行体外培养,观察合子、动合子的形成数量。ELISA结果显示疫苗免疫组小鼠血清特异性抗体滴度明显高于对照组;而合子、动合子数量明显低于对照组。提示Pys48核酸疫苗具有良好的免疫原性,免疫小鼠后可以建立起有效的传播阻断效应。     

Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure

Objective

Animal studies suggest that regulatory T (T_reg) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T_reg cells in patients with chronic heart failure (CHF). However, the mechanisms behind T_reg-cell defects remained unknown. We here sought to elucidate the mechanism of T_reg-cell defects in CHF patients.

Methods and Results

We performed flow cytometry analysis and demonstrated reduced numbers of peripheral blood CD4⁺CD25⁺FOXP3⁺CD45RO⁻CD45RA⁺ naïve T_reg (nT_reg) cells and CD4⁺CD25⁺FOXP3⁺CD45RO⁺CD45RA⁻ memory T_reg (mT_reg) cells in CHF patients as compared with non-CHF controls. Moreover, the nT_reg/mT_reg ratio (p<0.01), CD4⁺CD25⁺FOXP3⁺CD45RO⁻ CD45RA⁺CD31⁺ recent thymic emigrant T_reg cell (RTE-T_reg) frequency (p<0.01), and T-cell receptor excision circle levels in T_reg cells (p<0.01) were lower in CHF patients than in non-CHF controls. Combined annexin-V and 7-AAD staining showed that peripheral T_reg cells from CHF patients exhibited increased spontaneous apoptosis and were more prone to interleukin (IL)-2 deprivation- and CD95 ligand-mediated apoptosis than those from non-CHF individuals. Furthermore, analyses by both flow cytometry and real-time polymerase chain reaction showed that T_reg-cell frequency in the mediastinal lymph nodes or Foxp3 expression in hearts of CHF patients was no higher than that of the non-CHF controls.

Conclusion

Our data suggested that the T_reg-cell defects of CHF patients were likely caused by decreased thymic output of nascent T_reg cells and increased susceptibility to apoptosis in the periphery.     

Increasing manganese peroxidase production and biodecolorization of triphenylmethane dyes by novel fungal consortium

A fungal consortium-SR consisting of Trametes sp. SQ01 and Chaetomium sp. R01 was developed for decolorizing three kinds of triphenylmethane dyes, which were decolorized by individual fungi with low efficiencies. The fungal consortium-SR produced 1.3 U ml(-1) of manganese peroxidase, 5.5 times higher than that produced by the monoculture of Trametes sp. SQ01, and decolorized Crystal Violet, Coomassie Brilliant Blue G250 (CBB G250) and Cresol Red. The fungal consortium-SR had a decolorization rate of 63-96%, much higher than that of the monoculture of strain SQ01 (38-72%). In consortium-SR, the higher efficiencies of decolorization of Crystal Violet and CBB G250 were obtained when they added to the culture after 4d of mixed cultivation rather than at the beginning of cultivation. Cresol Red was the exception. It is suggested that the consortium-SR has great potential for decolorizing triphenylmethane dyes.