Identification of vip3A-type genes from Bacillus thuringiensis strains and characterization of a novel vip3A-type gene

AIMS

To search for novel Vip3A proteins for controlling insect pests.

METHODS AND RESULTS

A pair of universal primers was designed based on the conserved regions of five vip3A genes. Amplified products were digested with the HindIII and EcoR enzymes so as to confirm different restriction fragment length polymorphism (RFLP) patterns used to identify vip3A-type genes. The vip3A gene types of 606 Bacillus thuringiensis strains were screened and three patterns of RFLP were successfully identified. Two novel vip3A genes were found and one of these, vip3Aa19, was further characterized and its product was confirmed toxic to Spodoptera exigua, Helicoverpa armigera and Plutella xylostella larvae. Partial sequences of another novel vip3A-type gene were obtained that shared 83% homology with that of the vip3Af1 gene.

CONCLUSIONS

A polymerase chain reaction (PCR)-RFLP system we developed could be used for identifying novel vip3A-genes from B. thuringiensis strains. A novel Vip3A protein was found to have a broader insecticidal spectrum.

SIGNIFICANCE AND IMPACT OF THE STUDY

The reported method is a powerful tool to find novel Vip3A proteins from large-scale B. thuringiensis strains. The novel Vip3A protein may be used to control insect pests or resistant insect pests by constructing genetically engineered strains or transgenic plants.

Improving toxicity of Bacillus thuringiensis strain contains the cry8Ca gene specific to Anomala corpulenta larvae

The cry8C-type gene designated cry8Ca2, which was cloned and sequenced from a Bacillus thuringiensis isolate HBF-1 in China, consisted of an open reading frame of 3483 bp encoding a protein of 1160 amino-acid residues. Sequence analysis showed that the Cry8Ca2 protoxin of 130.5 kDa had 99.9% sequence homology with the previously reported Cry8Ca1 protein, with one mismatch between the two amino-acid sequences. When the Cry8Ca2 toxin was expressed in a crystal-negative strain of B. thuringiensis (HD-73(-)), elliptical crystals were produced. Cell extracts from this recombinant strain showed insecticidal activity against Anomala corpulenta larva. Mutant cry8Ca2 genes, produced by polymerase chain reaction amplification with Taq DNA polymerase, were used to develop recombinant B. thuringiensis strains. Mutants producing higher levels of insecticidal activity were identified by bioassay. Thirty-five mutants forming crystals were characterized, and two of them showed significantly increased insecticidal activity against A. corpulenta larva. The 50% lethality concentrations (LC(50)) of the two mutants were 0.2334 x 10(8) and 0.2591 x 10(8) colony-forming units g(-1), considerably lower than the LC(50) of the wild-type strain HBF-1 (0.9583 x 10(8) CFU g(-1)) and that of B. thuringiensis serovar japonensis strain Buibui (1.0752 x 10(8) CFU g(-1)).

Effective gene selection method with small sample sets using gradient-based and point injection techniques

Microarray gene expression data usually consist of a large amount of genes. Among these genes, only a small fraction is informative for performing cancer diagnostic test. This paper focuses on effective identification of informative genes. We analyze gene selection models from the perspective of optimization theory. As a result, a new strategy is designed to modify conventional search engines. Also, as overfitting is likely to occur in microarray data because of their small sample set, a point injection technique is developed to address the problem of overfitting. The proposed strategies have been evaluated on three kinds of cancer diagnosis. Our results show that the proposed strategies can improve the performance of gene selection substantially. The experimental results also indicate that the proposed methods are very robust under all the investigated cases.

Degree of angle closure and extent of peripheral anterior synechiae: an anterior segment OCT study

AIMS

To evaluate the relationship between angle width as determined by anterior segment optical coherence tomography (AS-OCT) and the presence of peripheral anterior synechiae (PAS).

METHODS

This was a prospective observational case series in which 203 subjects with primary angle closure or open angles were recruited. Images of the nasal, temporal and inferior angles were obtained with AS-OCT in dark conditions. Subjects then underwent gonioscopy by an independent examiner who was masked to the AS-OCT findings. PAS were identified by gonioscopy and defined as abnormal adhesions of the iris to the angle that were at least half a clock hour in width and present to the level of the anterior trabecular meshwork or higher. The total clock hours of PAS were recorded.

RESULTS

Sixty-eight subjects (33.5%) were PACS, 76 subjects (37.4%) had PAC/PACG, 14 (6.9%) had primary open angle glaucoma, and 45 (22.2%) subjects were normal with open angles. There was a weak but significant correlation between the angle opening distance (AOD), trabecular iris space area (TISA) and angle recess area (ARA) with clock hours of PAS (Spearman's correlation coefficients = -0.30, -0.32 and -0.32, respectively, p<0.001). The mean values of the AOD, TISA and ARA in the nasal, temporal and inferior quadrants were significantly less in eyes with PAS compared with those without (p<0.001, Mann-Whitney U test). Analysis by quadrant showed that these parameters were smaller in the nasal and temporal quadrants in eyes with PAS (p<0.01).

CONCLUSIONS

Angle width determined by AS-OCT and the extent of PAS were weakly correlated, and angle width was significantly smaller in eyes with PAS.

Validation of quantitative fluorescence imaging analysis (QFIA) of β-catenin in archived prostate tissues for cancer biomarker discovery

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Background: The objective of this study was to develop a sensitive tissue proteomic assay for quantifying proteins (e.g. β- catenin) in tissues and prostate core biopsies by QFIA. A second objective was to apply the validated methodology to quantify other biomarkers for prostate cancer risk assessment, and to study oxidative stress in BPH, prostate cancer, the cancer field, and in inflammatory prostatitis in animals and human prostatitis. Methods: Biopsies from controls and cancer patients were depariffinized, the antigen retrieved, and labeled with a robotic BioGenex Stainer with a primary mouse monoclonal antibody (1/100) to β-catenin. A secondary goat anti-mouse IgG antibody (2° Ab 1/100) coupled with Alexa Fluor 568 was used as the indicator system. The Leica Fluorescence Microscope was calibrated and standardized with fluorescence beads, LNCAP cells, and BPH tissue sections. QFIA of β-catenin was validated by RPPA methacarn fixed tissues. Adjacent 4-micron tissue sections were analyzed by QFIA for total β-catenin content by RPPA. Results: Reproducibility was 10% or less for the LNCAP cells and BPH tissue controls. Adjacent tissue sections assayed by QFIA and RPPA exhibited a strong linear correlation (r=.97) as did tissues fixed in methacarn vs.10% buffered-formalin and assayed by QFIA (r=0.84). For the core biopsy specimens the average MPI (AMPI) from 40 to 200 acini was quantified. The AMPI of cancerous acini (CA) compared to nomal acini (NA) was reduced in 37 of 42 cases p<.02. ROC plots revealed that β-catenin expression in NAA identified 42% (95%CI 25 - 52%) of cancer cases, with 88% (95% CI 80%-96%) specificity. The tissue QFIA method was used to quantify oxidative stress biomarkers (MnSOD, HNE, 8-OHdG) and other field disease biomarkers (Connexin42, and UDP-glucose dehydrogenase (UGDH) in BPH, prostate cancer, and in prostatitis. Conclusions: A tissue based QFIA method has been developed for the quantification of β-catenin in prostate core biopsy specimens, and the method has been validated by RPPA. Assay of β-catenin in prostate core biopsy specimens shows promise as a potential biomarker for a profile defining individuals at risk for prostate cancer and studying oxidative stress in relation to the pathogenesis of disease.

No significant financial relationships to disclose.

Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer

MOTIVATION

Most gene-expression based studies aim to identify genes with the capability of distinguishing different phenotypes. Although analysis at the genomic level is important, results of the molecular/cellular level are essential for understanding biological mechanisms. To deliver molecular/cellular-level results, a two-stage scheme is widely employed. This scheme just evaluates biological processes/molecular activities individually, totally overlooking the relationship between processes/activities. This treatment conflicts with the fact that most biological processes/molecular activities do not work alone. In order to deliver improved results, this shortcoming should be addressed.

RESULTS

We design a selection model from a novel perspective to directly detect important gene functional categories (each category represents a cellular process or a molecular activity). More importantly, the correlations between gene categories are considered. Contributed by this capability, the proposed method shows its advantages over others.

AVAILABILITY

the source code in Matlab is accessible via http://www.ee.cityu.edu.hk/~twschow/category_selection/category_selection.htm

Association of variants in theIL12Bgene with leprosy and tuberculosis

There is a great range in outcomes after mycobacterial infections, and this is probably due to individual variation in immune responses. One of the key cytokine regulators of the immune response is interleukin (IL-) 12. The IL12B gene encodes the p40 chain of both IL-12 and IL-23 and it has two major variant sites at which different alleles are associated with increased levels of gene expression and with susceptibility to a range of immune-related diseases. We hypothesized that IL12B variants associated with increased expression would be as associated with susceptibility to persistent mycobacterial infection. We tested this hypothesis by genotyping Indian subjects, having either leprosy or tuberculosis (TB), as well as ethnically matched controls. Subjects with leprosy were less likely to have the 3'UTR genotype associated with lower IL12B expression (P= 0.001). Subjects with TB were not only more likely to have the high-expressing IL12B promoter genotype (P= 0.01) but also more likely to have this in the same haplotype with the high expressing 3'UTR allele (P= 0.0009). These results suggest these infectious diseases may be improved by modulating IL-l2p40 production.

Feature extraction using recursive cluster-based linear discriminant with application to face recognition

A novel recursive procedure for extracting discriminant features, termed recursive cluster-based linear discriminant (RCLD), is proposed in this paper. Compared to the traditional Fisher linear discriminant (FLD) and its variations, RCLD has a number of advantages. First of all, it relaxes the constraint on the total number of features that can be extracted. Second, it fully exploits all information available for discrimination. In addition, RCLD is able to cope with multimodal distributions, which overcomes an inherent problem of conventional FLDs, which assumes uni-modal class distributions. Extensive experiments have been carried out on various types of face recognition problems for Yale, Olivetti Research Laboratory, and JAFFE databases to evaluate and compare the performance of the proposed algorithm with other feature extraction methods. The resulting improvement of performances by the new feature extraction scheme is significant.

Altered expression of β-catenin and UDP-glucose dehydrogenase in normal appearing acini of cancer-bearing prostate glands, detected by quantitative fluorescence imaging analysis

14540

Background: Expression of β-catenin and UDP-glucose dehydrogenase (UGDH) is markedly altered in prostate adenocarcinomas. The objective of this work was to evaluate expression of these proteins in normal appearing acini (NAA) of cancer-bearing prostate glands, as potential biomarkers of PC field disease. Methods: Archived core biopsies of 42 pairs of PC cases and controls were labeled for β-Catenin, and a tissue microarray of 10 prostatectomy specimens of cancer cases and controls were labeled for UGDH. A fluorophore-conjugated secondary antibody was incorporated into the staining protocol. Fluorescence in prostatic acini was measured with an automated Leica microscope and Image Pro Plus software and expressed as mean pixel intensity (MPI) per acinus and average MPI (AMPI) per case or control. Results: Mean AMPI of β-catenin in NAA of 33 cases (545 ± 93) was lower (p < 0.01) than that of normal acini (NA) in age-matched controls (684 ± 90), whereas mean AMPI of NAA in the remaining 9 cases (712 ± 111) was higher (p = 0.003) than that of the matched controls (634 ± 95). Twelve cases under-expressing β-catenin in NAA had AMPIs below the lowest AMPI (506 ± 83) of all controls. Mean AMPI of UGDH in NAA of 7 cases (372 ± 169) was lower (p < 0.05) in comparison to both NA (558 ± 119) and cancerous acini (CA) (645 ± 88). The difference between CA and NA did not achieve statistical significance. Conclusions: Reduced expression of β-catenin is a cancer-associated event in NAA. A cut-off AMPI (506) for β-catenin detected 29% of PC cases with 100% specificity. Altered expression of UGDH in NAA is a potential biomarker of PC. Funded by DoD grant DAMD17–02–1-0121.

No significant financial relationships to disclose.