Towards precise classification of cancers based on robust gene functional expression profiles

Background

Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method.

Results

We performed experimental evaluation by RT-PCR of three different computational gene finders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was computed and each component of it was evaluated. The results showed that de novo comparative methods can identify up to about 700 chicken genes with no previous evidence of expression, and can correctly extend about 40% of homology-based predictions at the 5' end.

Conclusions

De novo comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.     

Coadministration of interleukin 2 plasmid DNA with combined DNA vaccines significantly enhances the protective efficacy against Mycobacterium tuberculosis

Coadministration of interleukin 2(IL-2) plasmid DNA with combined DNA vaccines enhanced Th1-type cellular responses by producing higher amounts of IFN-gamma with a higher ratio of antigen-specific IgG2a/IgG1. The IFN-gamma specific for Ag85B, MPT64, and MPT83 in this group was 415, 267, and 255 U/ml, respectively, and was 1.6-, 1.8-, and 2.5-fold higher than that of the same vaccine without adding IL-2. The IgG2a/IgG1 ratio for Ag85B, MPT64, and MPT83 was 4, 8, and 4, respectively, upon addition of the genetic adjuvant in the DNA vaccine, which was four times higher for every antigen when IL-2 was not included. Fluorescence activated cell sorter (FACS) analysis showed that, in the presence of IL-2, CD8+ and CD4+ T cells increased significantly, whereas in the absence of the genetic adjuvant, only a mild increase was observed for CD8+ T cells compared to the vector DNA-treated group. Bacterial CFU was reduced to less than 1/100 in the lung and to about 1/10 in the spleen relative to the same combined DNA vaccine without IL-2. The lungs of this group of mice showed much less damage due to an influx of epithelioid macrophages and less lymphocytes. RT-PCR showed that antigen genes could be detected in more organs and for a longer period of time when treated with combined DNA vaccine formulated in IL-2. We suggest that IL-2 enhanced the immunigencity and protective efficacy in immunized mice by improving the Th1-type response and also by prolonging the antigen gene expression in different organs.     

Methyl lucidenate F isolated from the ethanol-soluble-acidic components of <Emphasis Type="Italic">Ganoderma lucidum</Emphasis> is a novel tyrosinase inhibitor

Tyrosinase is a key enzyme in the biosynthesis of melanin, and the use of inhibitors against tyrosinase can prevent hyperpigmentation by inhibiting enzymatic oxidation. However, the current use of tyrosine inhibitors is limited by their low activities and high toxicities. The aim of the present research was to develop novel whitening agents, or tyrosinase-targeted medicine, from a submerged culture of the fungus Ganoderma lucidum. Methyl lucidenate F was isolated from the ethanol-soluble-acidic components (ESACs) of G. lucidum, with the structure of ESACs elucidated via UV, LC-MS, and ¹³C-NMR spectral analysis. The tyrosinase inhibitory activity was measured using catechol as a substrate. Methyl lucidenate F displayed uncompetitive inhibition of the potato tyrosinase activity, for which Lineweaver-Burk plots revealed a maximum reaction rate (V _max) of 0.4367/min, Michaelis constant (K _m) of 6.765 mM and uncompetitive inhibition constant (K _i) of 19.22 μM. Meanwhile, methyl lucidenate F (tetra cyclic triterpenoid) exhibited high tyrosinase inhibitory activity, with an IC₅₀ of 32.23 μM. These results suggest that methyl lucidenate F may serve as a potential candidate for skin-whitening agents.     

A transversely isotropic viscoelastic constitutive equation for brainstem undergoing finite deformation

The objective of this study was to define the constitutive response of brainstem undergoing finite shear deformation. Brainstem was characterized as a transversely isotropic viscoelastic material and the material model was formulated for numerical implementation. Model parameters were fit to shear data obtained in porcine brainstem specimens undergoing finite shear deformation in three directions: parallel, perpendicular, and cross sectional to axonal fiber orientation and determined using a combined approach of finite element analysis (FEA) and a genetic algorithm (GA) optimizing method. The average initial shear modulus of brainstem matrix of 4-week old pigs was 12.7 Pa, and therefore the brainstem offers little resistance to large shear deformations in the parallel or perpendicular directions, due to the dominant contribution of the matrix in these directions. The fiber reinforcement stiffness was 121.2 Pa, indicating that brainstem is anisotropic and that axonal fibers have an important role in the cross-sectional direction. The first two leading relative shear relaxation moduli were 0.8973 and 0.0741, respectively, with corresponding characteristic times of 0.0047 and 1.4538 s, respectively, implying rapid relaxation of shear stresses. The developed material model and parameter estimation technique are likely to find broad applications in neural and orthopaedic tissues.     

Cutting edge: induction of B7-H4 on APCs through IL-10: novel suppressive mode for regulatory T cells

Multiple modes of suppressive mechanisms including IL-10 are thought to be implicated in CD4+CD25+ regulatory T (Treg) cell-mediated suppression. However, the cellular source, role, and molecular mechanism of IL-10 in Treg cell biology remain controversial. We now studied the interaction between Treg cells and APCs. We demonstrate that Treg cells, but not conventional T cells, trigger high levels of IL-10 production by APCs, stimulate APC B7-H4 expression, and render APCs immunosuppressive. Initial blockade of B7-H4 reduces the suppressive activity mediated by Treg cell-conditioned APCs. Further, APC-derived, rather than Treg cell-derived, IL-10 is responsible for APC B7-H4 induction. Therefore, Treg cells convey suppressive activity to APCs by stimulating B7-H4 expression through IL-10. Altogether, our data provide a novel cellular and molecular mechanism for Treg cell-mediated immunosuppression at the level of APCs, and suggest a plausible mechanism for the suppressive effect of IL-10 in Treg cell-mediated suppression.     

提高胞外钾引起的蛙骨骼肌咖啡因挛缩增强

用蛙胫前肌小束为材料, 研究了提高胞外钾[K+]O对咖啡因挛缩的作用.[K+]O从2 mmol/L提高到10或25 mmol/L, 由3 mmol/L咖啡因引起的挛缩明显增强.以PKC/PC (PKC和PC分别为在高钾和正常钾条件下的咖啡因挛缩)表示的咖啡因挛缩增强, 依赖[K+]O和高钾作用时间.随着10 mmol/L [K+]O作用时间延长, 直至10 min, 增强逐渐增加.但是, 25 mmol/L [K+]O作用1 min时增强达到最大, 然后下降到对照.PKC/PC变化时程不能用高钾引起的去极化解释, 而与由相似[K+]O引起的胞浆自由钙变化时程相符.提示, 至少在蛙骨骼肌, 高钾引起的咖啡因挛缩增强主要是由胞浆自由钙升高引起的.     

广西壮族颅骨的测量与研究

本文以来源于壮族居民世代聚居地区,生前资料比较可靠的150例颅骨为材料并用多因素分析等6方法探索壮族的体质特征、人种地位、地区类型及可能的起源。结果表明,壮族居民属黄色人种南亚类型,中华民族的华南,与柳江人,Chen皮岩人有最接近的亲缘关系。     

鄂伦春族体质现状及其与60年前资料的比较

对内蒙古鄂伦春自治旗１９１名（男８５,女１０６）,鄂伦春族成的人进行了活体观察与测量,总结了鄂伦春的体质和类型并在城乡之间、与６０年前同一地区的资料及我国北方一些的体质数据进行了比较。     

NaCl胁迫对PSII光能利用和耗散的影响

用荧光动力学的方法研究了不同浓度的ＮａＣｌ 处理对ＰＳＩＩ光能利用和耗散的影响。结果表明,在较低的光强下,与对照、１００ｍ ｍｏｌ／Ｌ 和２００ｍ ｍｏｌ／Ｌ ＮａＣｌ 处理相比,经３００ｍ ｍｏｌ／Ｌ 和４００ｍ ｍｏｌ／Ｌ ＮａＣｌ 处理的小麦,其荧光光化学淬灭效率较低,荧光非光化学淬灭效率较高,Ｆｏ 淬灭系数较大,ＱＢ － 非还原性ＰＳＩＩ反应中心含量较大; 而在较高光强下, 其荧光非光化学淬灭效率和Ｆｏ 淬灭系数则相对较低。