The EIM algorithm in the joint segregation analysis of quantitative traits

In this article, a new algorithm for obtaining the maximum likelihood estimators (MLEs) of parameters in the joint segregation analysis (JSA) of multiple generations of P1, F1, P2, F2 and F2:3 (MG5) for quantitative traits was set up. Firstly, owing to the fact that the component variance of the heterogeneous genotype in F2:3 included both the first-order genetic parameters (denoted by the means of distributions) and the second-order parameters, a simple closed form for the MLEs of the means of component distributions did not exist while the expectation and maximization (EM) algorithm was used. To simplify the estimation of parameters, the first partial derivative of the above variance on the mean in the sample log-likelihood function was omitted. However, this would be remedied by the iterated method. Then, variances of component distributions for segregating populations were partitioned into major-gene, polygenic and environmental variances so that the generally iterated formulae for estimating the means as well as polygenic and environmental variances of component distributions in the maximization step (M-step) of the EM algorithm were obtained. Therefore, the EM algorithm for estimating parameters in the JSA model for the MG5 was simplified. This is called the expectation and iterated maximization (EIM) algorithm. Finally, an example of the inheritance of the resistance of soybean to beanfly showed that the results of mixed inheritance analysis in this paper coincided with those in both Wang & Gai (2001) and Wei et al. (1989), so the EIM algorithm was appropriate.     

Development of enhancer trap lines for functional analysis of the rice genome

Enhancer trapping has provided a powerful strategy for identifying novel genes and regulatory elements. In this study, we adopted an enhancer trap system, consisting of the GAL4/VP16-UAS elements with GUS as the reporter, to generate a trapping population of rice. Currently, 31 443 independent transformants were obtained from two cultivars using Agrobacterium-mediated T-DNA insertion. PCR tests and DNA blot hybridization showed that about 94% of the transformants contained T-DNA insertions. The transformants carried, on average, two copies of the T-DNA, and 42% of the transformants had single-copy insertions. Histochemical assays of approximately 1000 T0 plants revealed various patterns of the reporter gene expression, including expression in only one tissue, and simultaneously in two or more tissues. The expression pattern of the reporter gene in T1 families corresponded well with the T0 plants and segregated in a 3 : 1 Mendelian ratio in majority of the T1 families tested. The frequency of reporter gene expression in the enhancer trap lines was much higher than that in gene trap lines reported previously. Analysis of flanking sequences of T-DNA insertion sites from about 200 transformants showed that almost all the sequences had homology with the sequences in the rice genome databases. Morphologically conspicuous mutations were observed in about 7.5% of the 2679 T1 families that were field-tested, and segregation in more than one-third of the families fit the 3 : 1 ratio. It was concluded that GAL4/VP16-UAS elements provided a useful system for enhancer trap in rice.     

A peptide mimetic of Gal-alpha 1,3-Gal is able to block human natural antibodies

The carbohydrate of Gal-alpha1,3-Gal is thought to be the major antigenic epitope present on pig vascular endothelium. The peptides that mimic the binding of antigenic epitope (Gal-alpha1,3-Gal) to lectin BS-I-B4 were identified from screening a filamentous phage-displayed random library. A phage bearing the peptide NCVSPYWCEPLAPSARA has been identified to bind the lectin strongly. Melibiose was able to inhibit the binding of the human natural anti-alpha Gal antibody to the peptide competitively. Our experiments show that the peptide mimetic of Gal-alpha1,3-Gal is able to inhibit the agglutination of pig RBCs by human natural antibody or lectin BS-I-B4. The peptide inhibitor of human natural antibodies may prove useful in pig-to-human xenotransplantation.     

Cytosolic prion protein is not toxic and protects against Bax-mediated cell death in human primary neurons

Recently, it was observed that reverse-translocated cytosolic PrP and PrP expressed in the cytosol induce rapid death in neurons (Ma, J., Wollmann, R., and Lindquist, S. (2002) Science 298, 1781-1785). In this study, we investigated whether accumulation of prion protein (PrP) in the cytosol is toxic to human neurons in primary culture. We show that in these neurons, a single PrP isoform lacking signal peptide accumulates in the cytosol of neurons treated with epoxomicin, a specific proteasome inhibitor. Therefore, endogenously expressed PrP is subject to the endoplasmic reticulum-associated degradation (ERAD) pathway and is degraded by the proteasome in human primary neurons. In contrast to its toxicity in N2a cells, reverse-translocated PrP (ERAD-PrP) is not toxic even when neurons are microinjected with cDNA constructs to overexpress either wild-type PrP or mutant PrPD178N. We found that ERAD-PrP in human neurons remains detergent-soluble and proteinase K-sensitive, in contrast to its detergent-insoluble and proteinase K-resistant state in N2a cells. Furthermore, not only is microinjection of a cDNA construct expressing CyPrP not toxic, it protects these neurons against Bax-mediated cell death. We conclude that in human neurons, ERAD-PrP is not converted naturally into a form reminiscent of scrapie PrP and that PrP located in the cytosol retains its protective function against Bax. Thus, it is unlikely that simple accumulation of PrP in the cytosol can cause neurodegeneration in prion diseases.     

Effects of Octadecanoylsucrose Derivatives on the Production of Inulinase by Apergillus niger SL-09

Summary The effect of the addition of octadecanoylsucrose esters to the growth medium on the production of inulinase by Aspergillus niger SL-09 was studied in batch culture using shake flasks. The activities of inulinase in vitro and in vivo formed by Aspergillus niger SL-09 was enhanced dramatically by the addition of sucrose ester S-770 to the medium, and it was confirmed that sucrose ester acted as a very efficient inducer for inulinase production. As a result, with the addition of 6 g sucrose ester l⁻¹ at the beginning of the culture, the enzyme activities were enhanced near 7-fold higher than that obtained in the basal medium.     

Isolation and characterization of phenanthrene-degrading <Emphasis Type="Italic">Sphingomonas paucimobilis</Emphasis> strain ZX4

Phenanthrene-degrading bacterium strain ZX4 was isolated from an oil-contaminated soil, and identified as Sphingomonas paucimobilis based on 16S rDNA sequence, cellular fatty acid composition, mol% G + C and Biolog-GN tests. Besides phenanthrene, strain ZX4 could also utilize naphthalene, fluorene and other aromatic compounds. The growth on salicylic acid and catechol showed that the strain degraded phenanthrene via salicylate pathway, while the assay of catechol 2, 3-dioxygenase revealed catechol could be metabolized through meta-cleavage pathway. Three genes, including two of meta-cleavage operon genes and one of GST encoding gene were obtained. The order of genes arrangement was similar to S-type meta-pathway operons. The phylogenetic trees based on 16S rDNA sequence and meta-pathway gene both revealed that strain ZX4 is clustered with strains from genus Sphingomonas.     

DGGE analysis of 16S rDNA of ammonia-oxidizing bacteria in chemical–biological flocculation and chemical coagulation systems

Microbial community DNA was extracted from activated sludge samples taken from a chemical bioflocculation process and a chemical coagulation process in Shanghai, China. 16S rDNA of ammonia-oxidizing bacteria (AOB)was amplified by nested polymerase chain reaction and fingerprinted by denaturing gradient gel electrophoresis for microbial structure analysis. The Shannon diversity index of each sample was determined. The results indicated that the microbial structure of AOB in chemical bioflocculation process was comparable at two operational conditions. The ammonia-oxidizing bacterial communities were similar in three channels of the chemical bioflocculation process and in three serial tanks in the chemical coagulation process at the same condition. The diversity of microbial structures in the chemical bioflocculation process was higher than in the chemical coagulation process, in which the microbial structure was similar to that in the influent. Although the microbial study provides insights to the nitrification removal, higher microbial diversity of AOB does not necessarily mean higher ammonia oxidization. Molecular analysis should be combined with chemical assays to optimize operational conditions.     

近岸污染指示半知菌灰黄青霉(Penicillium griseo fulvum)的分子检测

【目的】通过分子方法检测近海污染环境优势种灰黄青霉,并为由此而推断污染程度做准备。【方法】根据GenBank中青霉属不同种和相近属种的ITS序列差异和灰黄青霉特有的IAO序列,设计了污染区优势种灰黄青霉的特异性引物AS1/RS4和IAO1/IAO2,建立相应的特异探针检测体系。通过PCR和套式PCR技术,分析比较两对特异序列检测灰黄青霉的差异。【结果】建立的分子检测体系可以排除其它近似或相关菌株干扰,从环境中扩增到目的基因片段。利用引物AS1/RS4作为核酸探针,通过套式PCR菌株DNA的检测灵敏度可达到10fg/μL,当仅有10个数量级分生孢子时即可检测出,从沉积物中检测灵敏度为102个数量级孢子/0.25g。特异酶基因IAO1/IAO2检测灵敏度较前者稍低。【结论】利用特异序列作为探针检测污染环境优势种灰黄青霉的方法可行,在一定范围内,灰黄青霉的出现频率及数量对污染程度有较好的指示作用。     

Evolution of selenium utilization traits

Background

The essential trace element selenium is used in a wide variety of biological processes. Selenocysteine (Sec), the 21st amino acid, is co-translationally incorporated into a restricted set of proteins. It is encoded by an UGA codon with the help of tRNA^Sec (SelC), Sec-specific elongation factor (SelB) and a cis-acting mRNA structure (SECIS element). In addition, Sec synthase (SelA) and selenophosphate synthetase (SelD) are involved in the biosynthesis of Sec on the tRNA^Sec. Selenium is also found in the form of 2-selenouridine, a modified base present in the wobble position of certain tRNAs, whose synthesis is catalyzed by YbbB using selenophosphate as a precursor.

Results

We analyzed completely sequenced genomes for occurrence of the selA, B, C, D and ybbB genes. We found that selB and selC are gene signatures for the Sec-decoding trait. However, selD is also present in organisms that do not utilize Sec, and shows association with either selA, B, C and/or ybbB. Thus, selD defines the overall selenium utilization. A global species map of Sec-decoding and 2-selenouridine synthesis traits is provided based on the presence/absence pattern of selenium-utilization genes. The phylogenies of these genes were inferred and compared to organismal phylogenies, which identified horizontal gene transfer (HGT) events involving both traits.

Conclusion

These results provide evidence for the ancient origin of these traits, their independent maintenance, and a highly dynamic evolutionary process that can be explained as the result of speciation, differential gene loss and HGT. The latter demonstrated that the loss of these traits is not irreversible as previously thought.     

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.