Multiple gene genealogies and phenotypic characters differentiate several novel species of Mycosphaerella and related anamorphs on banana.

Three species of Mycosphaerella, namely M. eumusae, M. fijiensis, and M. musicola are involved in the Sigatoka disease complex of bananas. Besides these three primary pathogens, several additional species of Mycosphaerella or their anamorphs have been described from Musa. However, very little is known about these taxa, and for the majority of these species no culture or DNA is available for study. In the present study, we collected a global set of Mycosphaerella strains from banana, and compared them by means of morphology and a multi-gene nucleotide sequence data set. The phylogeny inferred from the ITS region and the combined data set containing partial gene sequences of the actin gene, the small subunit mitochondrial ribosomal DNA and the histone H3 gene revealed a rich diversity of Mycosphaerella species on Musa. Integration of morphological and molecular data sets confirmed more than 20 species of Mycosphaerella (incl. anamorphs) to occur on banana. This study reconfirmed the previously described presence of Cercospora apii, M. citri and M. thailandica, and also identified Mycosphaerella communis, M. lateralis and Passalora loranthi on this host. Moreover, eight new species identified from Musa are described, namely Dissoconium musae, Mycosphaerella mozambica, Pseudocercospora assamensis, P. indonesiana, P. longispora, Stenella musae, S. musicola, and S. queenslandica.

Newly isolated Bacillus clausii GMBAE 42: an alkaline protease producer capable to grow under higly alkaline conditions.

AIMS: The isolation and identification of new Bacillus sp. capable of growing under highly alkaline conditions as alkaline protease producers. METHODS AND RESULTS: A Bacillus strain capable of growing under highly alkaline conditions was isolated from compost. The strain is a Gram-positive, spore-forming, motile, aerobic, catalase- and oxidase-positive, alkaliphilic bacterium and designated as GMBAE 42. Good growth of the strain was observed at pH 10. The strain was identified as Bacillus clausii according to the physiological properties, cellular fatty acid composition, G + C content of genomic DNA and 16S rRNA gene sequence analyses. The result of 16S rRNA sequence analyses placed this bacterium in a cluster with B. clausii. The G + C content of the genomic DNA of the isolate GMBAE 42 was found to be 49 mol%. The crude extracellular alkaline protease produced by the isolate showed maximal activity at pH 11.0 and 60 degrees C. CONCLUSIONS: The results suggest that isolated strain GMBAE 42 is a new type of B. clausii capable of growing at pH 10.0 and produce extracellular alkaline protease very active at pH 11.0. SIGNIFICANCE AND IMPACT OF THE STUDY: Isolated strain could be used in commercial alkaline protease production and its enzyme can be considered as a candidate as an additive for commercial detergents.

The use of AFLP to relate cheese-contaminating Penicillium strains to specific points in the production plants.

Amplified fragment length polymorphism (AFLP) analysis was performed on isolates of Penicillium commune and Penicillium palitans originating from cheese and indoor environment in four cheese factories. The AFLP method was found to be a useful tool for identification of P. commune and P. palitans on, as well as below, species level. However, AFLP in combination with M13 fingerprinting described in a previous paper provided better resolution at the intraspecific level than either of the methods alone. Specific P. commune and P. palitans strains were found in the same factories over a period of more than a year and showed that the cheese factories have contaminating strains that are well established. The majority of the P. commune and P. palitans strains were found only within a single factory, but several were found in different cheese factories. The combined fingerprinting data could relate strains isolated from cheese to specific points in the production plants. Several of cheese-contaminating Penicillium strains could be related to air in the wrapping room, which must be considered to be a critical point for contamination of cheese.

Molecular genetic analysis of flow-sorted and microdissected ovarian tumor cells improved detection of loss of heterozygosity.

Study of loss of heterozygosity (LOH) is widely used to identify chromosomal locations of putative tumor suppressor genes. In this type of analysis, DNA extracted from tumor tissue is compared with constitutive DNA from the same patient by the use of polymorphic DNA markers (1). This approach has two intrinsic limitations. First, tumor specimens with a high fraction of nonneoplastic cells have to be excluded from this analysis because LOH in tumor cells may be undetectable, because of the low concentration of tumor DNA. This may lead to a selection bias, which affects the representativity of the results. A second limitation is that the analysis of DNA extracted from homogenized tumor samples may obscure the presence of intratumor genetic heterogeneity.

Molecular identification of a partial hydatidiform mole.

Specimens of a vacuum curettage were microscopically indicated for a hydatidiform mole. The combination of three different approaches identified the specimen as a partial mole caused by the fertilization of a haploid ovum by sperm containing a haploid or diploid nucleus with one or two sets of paternal genetic material. Interphase fluorescence in situ hybridization identified three chromosome 1 centromeres, and DNA flow cytometry revealed a peak with a DNA index of 1.50. The combination of flow cytometric cell sorting and microsatellite marker polymerase chain reaction proved that in this case two alleles were from paternal origin. Because it is known that partial hydatidiform moles have a tendency for recurrence, specimens from the same patient of an earlier executed vacuum curettage were investigated. Microdissection of the villi was performed before DNA isolation in this case as too few villi were present for DNA flow cytometry and cell sorting. In this case, no evidence was fond for additional alleles. This study shows the diagnostic potential of microsatellite markers for genetic typing of hydatidiform moles.

Molecular genetic evidence for the conversion hypothesis of the origin of malignant mixed müllerian tumours.

The origin of malignant mixed Müllerian tumours (MMMTs) has long been debated, due to the indefinite relationship between epithelial and mesenchymal malignant cells. In order to obtain insight into the clonal relationship between the two components of these tumours, molecular genetic changes were investigated at the level of loss of heterozygosity (LOH) in both cells types. LOH was studied in a series of six cases with 74 polymorphic microsatellite markers mapping to 19 different chromosomes. The epithelial and the mesenchymal neoplastic cells were separately microdissected from formalin-fixed, paraffin-embedded tissue, prior to DNA isolation. LOH was observed for 35 different markers mapping to chromosomes 3, 6, 8, 11, 15, 16, 17, 18, 21, and X. The most frequently involved chromosomes were 17p, 17q, 11q, 15q, and 21q. LOH was observed in five out of six cases and identical alleles were lost in the epithelial and in the mesenchymal cells. No genetic differences were observed between the two cell types for any of the informative markers. Immunohistochemistry (IHC) and TP53 mutation analysis revealed involvement of TP53 in all cases. Mutations were identified in five MMMTs. In four tumours, of which three had a missense mutation, strong nuclear staining for p53 was observed. In the remaining two cases, the mutation resulted in a stop codon, with no nuclear staining for p53 by IHC. The results support a monoclonal origin of MMMTs, with the absence of genetic changes uniquely associated with either of the phenotypes. The latter finding is compatible with current opinion that these neoplasms should be considered as metaplastic carcinomas and supports the conversion hypothesis.

One-tube triple staining method for flow cytometric analysis of DNA ploidy and phenotypic heterogeneity of human solid tumors using single laser excitation.

We have developed a "one-tube" triple staining procedure that allows the identification of intratumor phenotypic subpopulations by FCM. Solid tumors were dissociated by a combined mechanical/ enzymatic method. Ovarian ascites tumor cell aggregates were enzymatically dissociated using trypsin. An antikeratin 8/18 MAb was used to label the epithelial fraction of these tumor samples. A second MAb directed against the leukocyte common antigen (LCA) was applied to identify nonneoplastic DNA-diploid cells. Other MAbs used as a second marker were directed against a tumor-associate surface, a cytoplasmic, or a nuclear antigen. Cells were stained using subclass-specific fluorescein-isothiocyanate (FITC) or R-phycoerythrin (PE)-conjugated antibodies. DNA was stained with propidium iodide (PI). Triply stained samples were measured on a standard bench-top flow cytometer (FACScan). Keratin 8/18-positive cells, LCA-positive cells, and DNA could be simultaneously detected in dissociated breast carcinomas, mixed Müllerian tumors, and ovarian ascites specimen for refining DNA index (DI) calculations and S phase fraction (SPF) determination. Coefficients of variation (CV) of the G0G1 peak of the DNA histograms obtained ranged from 2.55% to 4.64% and from 2.71% to 4.71% for the DNA-diploid and -aneuploid fractions, respectively. In DNA-diploid tumors, antigen expression (HER-2/Neu, proliferating cell nuclear antigen) could be analyzed without interference of fluorescence signals from nonneoplastic cells. Neoplastic tumor subpopulations were clearly identified based on both DNA-ploidy status and heterogeneity of antigen expression. The present method offers new possibilities for multiparameter DNA FCM on clinical samples and enables the identification of intratumor neoplastic subpopulations based on antigen expression and DNA-ploidy status.

Rapid identification of mixed up bladder biopsy specimens using polymorphic microsatellite markers.

During standard registration of incoming surgery specimens, loss of registration numbers may occur. In our laboratory two series of small bladder biopsies (numbered I-V and I-VI, respectively), obtained from two patients, were given the same laboratory registration number. The biopsies were of similar size and embedded in paraffin. Thus, five pairs of Roman-numbered paraffin blocks had the same laboratory registration numbers. The histological findings in several biopsies were similar, some showing carcinoma in situ. Only from biopsy number VI was the identity retained, and this specimen could be used as a reference. We used polymerase chain reaction (PCR)-driven microsatellite marker analysis to identify the specimens using five different microsatellite markers. Within 48 h, two different banding patterns were revealed, allowing us to distinguish the two series. In addition, in one biopsy which showed carcinoma in situ of the bladder, microsatellite instability was observed while in none of this patient's other biopsies containing carcinoma in situ could this phenomenon be detected, which may indicate intratumor heterogeneity or multifocality. In conclusion, it is possible to solve the problem of mixing up small paraffin-embedded biopsies by using microsatellite marker PCR.

Molecular genetic evidence for unifocal origin of advanced epithelial ovarian cancer and for minor clonal divergence.

Detection of loss of heterozygosity (LOH) and DNA flow cytometry (FCM) were used to trace the origin of bilateral ovarian cancer from 16 patients. From each tumour the DNA index (DI) and LOH patterns for chromosomes 1, 3, 6, 11, 17, 18, 22 and X were determined with 36 microsatellite markers. Formalin-fixed, paraffin-embedded as well as frozen specimens were used. Flow cytometric cell sorting was used to enrich tumour cells for polymerase chain reaction (PCR)-driven LOH analysis. Analysis of the LOH data showed that in 12 of the 16 cases concordance was observed for all informative markers, namely retention of heterozygosity (ROH) or loss of identical alleles in both tumour samples. In four cases discordant LOH patterns were observed. In two cases the discordant LOH was found for one of the chromosomes tested while other LOH patterns clearly indicated a unifocal origin. This suggests limited clonal divergence. In the other two cases all LOH patterns were discordant, most likely indicating an independent origin. The number of chromosomes showing LOH ranged from 0 to 6. Comparison of DNA FCM and the LOH data showed that the latter technique has a higher sensitivity for the detection of a unifocal origin. In 14/16 cases evidence was found for a unifocal origin, while in two cases clonal divergence was found at LOH level and in two other cases clonal divergence at DNA ploidy level. In 12 cases the complete observed allelotype had developed before the formation of metastases, including the two cases showing a large DNA ploidy difference.

Molecular genetic analysis of flow-sorted ovarian tumour cells: improved detection of loss of heterozygosity.

Detection of loss of heterozygosity (LOH) is usually performed on homogenised tumour specimens. In this type of analysis samples with a low percentage of tumour cells have to be excluded and possible intra-tumour heterogeneity is obscured. In this study we report the application of polymerase chain reaction (PCR)-driven LOH detection with in total 22 microsatellite markers for chromosome 1q, 3p, 3q, 4p, 6p, 6q, 11p, 11q, 17p, 17q, 18p, 18q, Xp and Xq on flow-sorted cells from fresh and paraffin-embedded ovarian tumour tissue. Titration experiments showed that LOH can be detected with as few as 100 cell equivalents of DNA. Clear examples of LOH could be detected in the sorted aneuploid fractions from one unilateral and two bilateral ovarian tumours from three patients. In two samples the sorted fraction was less than 10% of the total sample. The bilateral tumours from the same patient showed loss of identical alleles for one marker (case OV64) and two markers (case OV69), indicative of their monoclonal origin. Multiparameter flow cytometry using two different ovarian tumour markers (MOv18 and BMA180), an anti-cytokeratin monoclonal antibody (MAb) (M9), an anti-vimentin MAb (V9) and a MAb against the panepithelial antigen 17-1A on the fresh ascites cells of the fourth ovarian cancer patient was used to investigate possible intra-tumour heterogeneity. We showed the presence of at least three phenotypically different populations, of which the diploid, keratin-positive, vimentin-negative population showed a similar LOH pattern as the aneuploid population (DNA index = 1.7), indicative of its neoplastic origin. The same LOH pattern was shown in an omentum metastasis from this patient also having the same aneuploid DNA index of 1.7. The sharing of the same LOH pattern by the diploid and aneuploid tumour cell populations suggests that the observed allele loss events occurred before the development of aneuploidy. PCR on flow-sorted cells is thus an important tool to study clonal diversity in tumours.

PCR-based microsatellite polymorphisms in the detection of loss of heterozygosity in fresh and archival tumour tissue.

PCR-based microsatellite polymorphisms have proved their power in genetic linkage analysis and other identification methods, due to their high information content and even distribution over the chromosomes. In the present study we applied microsatellite polymorphisms to detect loss of heterozygosity in fresh (snap-frozen) and in archival ovarian tumour tissue. Clear allele losses were found in fresh and paraffin embedded tumour samples. Conventional Southern analysis of flanking markers on the same tumour DNA samples confirmed the observed losses detected by microsatellite polymorphisms. Titration experiments suggest that loss of heterozygosity remains detectable in tumour samples despite 60% contamination with normal DNA. This technique provides a fast and reproducible alternative to conventional Southern blotting in the detection of loss of heterozygosity, with the crucial additional advantages of minimal sample requirements, making archival material available for genetic investigation.

A putative beta-glucanase pseudogene behind the potato GBSS gene.

We identified an open reading frame (ORF) which is located closely behind the gene encoding granule-bound starch synthase (GBSS) of potato (Solanum tuberosum L.). The ORF ends with a perfect 43 bp direct repeat, which carries the stop triplet precisely at the beginning of the second repeat. The deduced protein shows homology with all known isoforms of plant beta-1,3-glucanases and beta-1,3-1,4-glucanases. Although the DNA sequence is unique in potato and tomato (Lycopersicon esculentum L.), no expression of the gene was found in these species. Taken together with the unusual codon usage and length of the predicted protein, this sequence could be a pseudogene.