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.     

A parallel coiled-coil tetramer with offset helices

Specific helix-helix interactions are fundamental in assembling the native state of proteins and in protein-protein interfaces. Coiled coils afford a unique model system for elucidating principles of molecular recognition between alpha helices. The coiled-coil fold is specified by a characteristic seven amino acid repeat containing hydrophobic residues at the first (a) and fourth (d) positions. Nonpolar side chains spaced three and four residues apart are referred to as the 3-4 hydrophobic repeat. The presence of apolar amino acids at the e or g positions (corresponding to a 3-3-1 hydrophobic repeat) can provide new possibilities for close-packing of alpha-helices that includes examples such as the lac repressor tetramerization domain. Here we demonstrate that an unprecedented coiled-coil interface results from replacement of three charged residues at the e positions in the dimeric GCN4 leucine zipper by nonpolar valine side chains. Equilibrium circular dichroism and analytical ultracentrifugation studies indicate that the valine-containing mutant forms a discrete alpha-helical tetramer with a significantly higher stability than the parent leucine-zipper molecule. The 1.35 A resolution crystal structure of the tetramer reveals a parallel four-stranded coiled coil with a three-residue interhelical offset. The local packing geometry of the three hydrophobic positions in the tetramer conformation is completely different from that seen in classical tetrameric structures yet bears resemblance to that in three-stranded coiled coils. These studies demonstrate that distinct van der Waals interactions beyond the a and d side chains can generate a diverse set of helix-helix interfaces and three-dimensional supercoil structures.     

Divergent regulation of 1,25-dihydroxyvitamin D3 on human bone marrow osteoclastogenesis and myelopoiesis

The physiologically active form of vitamin D3, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) has influence over osteoclastogenesis and myelopoiesis, but the regulational mechanism is not well-defined. In this report, formation of osteoclast-like (OCL) cells from primitive myeloid colony-forming cells (PM-CFC) as mediated by 1,25(OH)2D3 was examined. Our results present in this report clearly show that 1,25(OH)2D3 dose-dependently stimulated OCL cell formation when added to suspension cultures of individually replated PM-CFC colonies. Marrow cells were plated with either granulocyte-macrophage colony-stimulating factor (GM-CSF) or the human bladder carcinoma cell line 5637 conditioned medium (5637 CM) as the source of colony-stimulating activity. The 1,25(OH)2D3 effect of osteoclast differentiation was associated with a concomitant decrease in clonogenic growth of myelopoietic progenitors in response to colony-stimulating activity. Secondly, the effect of adding the known stimulator of hematopoiesis, interleukin-1beta (IL-1beta) and/or 1,25(OH)2D3 on human myeloid colony growth was assessed. IL-1beta enhanced the formation of primitive myeloid colonies in response to GM-CSF by 160%. On the other hand, 1,25(OH)2D3 dose-dependently inhibited both GM-CSF- and 5637 CM-driven myeloid colony formation by as much as 90% at 100 nM. Addition of IL-1beta to GM-CSF-stimulated cultures dampened the inhibitory effect of 1,25(OH)2D3. The inhibition of myeloid clonogenic growth by 1,25(OH)2D3 was almost abolished (89%) by simultaneously adding anti-tumor necrosis factor-alpha monoclonal antibody (anti-TNF-alpha MoAb) to the culture medium. These results collectively suggest divergent roles for 1,25(OH)2D3 in osteoclastogenesis and myelopoiesis, promoting the differentiation of OCL cells from primitive myeloid cells but inhibiting the proliferation of later myeloid progenitor cells. This inhibition of myeloid progenitors may be mediated by TNF-alpha.     

植酸对红豆杉细胞悬浮培养影响作用的研究

针对红豆杉细胞培养中经常遇到的褐变问题,以植酸做抗氧化剂,添加到悬浮细胞培养基中,能提高细胞鲜重,明显抑制细胞多酚氧化酶和过氧化物酶活性,从而有效地控制细胞褐变,促进红豆杉悬浮细胞生长。以005%浓度的添加效果最好。     

由不同细胞核背景引起的小麦细胞质雄性不育系(CMS)叶绿体蛋白质组的变化(简报)

叶绿体和线粒体是高等植物细胞内2种重要的细胞器。由于细胞质雄性不育(CMS)被认为是一种由线粒体基因编码的性状,因此,近10多年来,国内外研究者对线粒体基因组结构与功能、由线粒体基因编码的与CMS相关蛋白的研究积累了大量的资料。与线粒体相比,叶绿体与CMS关系的研究相对滞后。虽然一些研究者在核不育水稻中,观     

土壤健康的生物学表征与调控

如何有效判定土壤健康状态是实现农业绿色发展的基本问题。在现有的土壤健康评价体系中,很少考虑土壤生物在维持土壤健康方面的作用。基于此,本文论述了土壤健康的内涵,从土壤生物健康的角度,总结了土壤健康的生物学表征指标,阐述了土壤微生物、土壤酶活性、土壤微食物网及蚯蚓对土壤健康的指示作用。基于上述生物指标,从作物和土壤管理等方面探讨了不同农田管理措施对土壤健康状况的调控途径,并对土壤生物健康的未来发展趋势进行了展望。本文旨在增强科学家和决策者对维护土壤生物健康的认识,充分发挥土壤生物在生态系统服务中的重要作用。     

Bt rice expressing Cry1Ab does not stimulate an outbreak of its non-target herbivore, Nilaparvata lugens

In this study, the non-target effects of Bt rice “KMD2” expressing a Cry1Ab protein on the performance of the brown planthopper (BPH), Nilaparvata lugens, over multiple generations were evaluated under laboratory and field conditions. In the laboratory, BPH was reared to observe the impact of the Bt rice as compared to its parental non-Bt cultivar Xiushui 11, while the population dynamics and oviposition performance of BPH were investigated in the field. The survival of BPH nymphs fed Bt and non-Bt rice did not differ significantly. The nymph developmental duration of BPH was significantly delayed by the Bt rice by comparison with the non-Bt rice for the 1st and 2nd but not the 4th generation. Most importantly, the fecundity of BPH on the Bt rice was significantly decreased in every generation when compared with the non-Bt rice. In the field investigations, the population density of BPH nymphs was significantly lower in the Bt rice field. However, the temporal pattern of population dynamics of BPH adults was similar between the Bt and non-Bt rice, presumably due to migratory interference of the adults. In the Bt rice field, the percentage of tillers with eggs and the number of eggs per tiller were also significantly lower from tillering to mature stage. Additionally, Cry1Ab protein could not be detected in guts from single BPH adults. In general, our results suggest that the Bt rice “KMD2” could not stimulate an outbreak of BPH.     

Can mobile sandy land be vegetated in the cold and dry Tibetan Plateau in China?

Desertification has taken place in the overgrazed grassland of the Tibetan Plateau,China,and the area of mobile sandy land has increased in recent decades.The challenging problem about desertification control is how to restore the vegetation of mobile sandy lands caused by severe desertification.Sand drifting is now regarded as the limiting factor of vegetation restoration in such lands.The initial phase of vegetation restoration is plant colonization,but it is often aborted due to sand drifting,and then vegetation restoration fails to proceed.For the sake of revegetation,the first step is to stop sand drifting to ensure plant colonization.In the northeastern Tibetan Plateau,China,feasible approaches have been found through long-term experiments,and the vegetation is being restored satisfactorily with these approaches in experimental sandy lands.The approaches comprise three types:enclosure,mechanical barriers and biological barriers.Different sandy lands require dissimilar combinations of these approaches.Enclosures may be adequate to revegetate inter-dunes or degraded grassland even in cold regions like the Tibetan Plateau,China,but it is deficient for revegetation of the shifting sand dunes unless mechanical and biological barriers are established simultaneously.     

Assessing indica-japonica differentiation of improved rice varieties using microsatellite markers

To assess the indica-japonica differentiation of improved rice varieties, a total of 512 modem varieties including 301 indica and 211 japonica accessions were analyzed using 36 microsatellites. The Fst coefficients ranged from 0.002 to 0.730 among the loci with an average of 0.315. Significant differentiation was detected at 94.4% of the loci studied （P 〈 0.05, pairwise Fst tests）, indicating that there was a high level of indica-japonica differentiation within the improved varieties. At 18 loci, about 74%-98% of the alleles of indica and japonica accessions were distributed in two ranges of amplicon length. Linkage disequilibrium analysis showed that the distribution trends were significantly nonrandomly associated. Using the differentiation trends at the 18 loci, microsatellite index （MI） was proposed for discrimination of the two subspecies. When rice accessions with MI value greater than zero were classified as indica, and those with MI value smaller than zero were classified as japonica, about 96.1% of the accessions could be classified. This result agrees with the classification based on morphological-physiological characters, indicating that this method is feasible and effective.