E. Abeln

A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These isolates, which were found in slightly acidic dune soils in the Netherlands, were strictly aerobic, Gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili. A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. DNA G+C contents were 57–62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (>98·6 % sequence similarity) and could be assigned to the β-Proteobacteria, family ‘Oxalobacteraceae’, order ‘Burkholderiales’. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiti...

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 i...

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.

TNO is searching for partners for a consortium research project aiming at the identification of novel solutions for controlling pathogenic Clostridia such as Clostridium difficile and C. perfringens. These are a serious threat for human and animal health and a major reason for using antibiotics. Novel solutions preventing disease development will lead to a reduction in antimicrobial resistance development and fit with global One Health goals.

TNO’s intestinal screening model (TNO i-screen) helps to quickly identify food ingredients that modulate the intestinal microbiota composition. For manufacturers, searching for health-promoting ingredients is a complex and time-consuming process. Large numbers of substances have to be screened, while for some components almost no proper identification methods are available. When a functional ingredient has finally been selected, extensive in vitro and human volunteer studies are required to demonstrate its safety and to validate its efficacy prior to marketing it as beneficial to health.

TNO combines state of the art technologies, such as organoids, high throughput sequencing and computational modelling to gain insight and discover functionalities in complex biological systems, to unlock our microbiome for your applications. Our microbiome analysis and modelling techniques can help in solving questions, such as: How does this ingredient influence the microbiome composition? Can my ingredient suppress outgrowth of pathogens? Will these fibers be metabolized by our microbiome?

TNO recently developed InTESTine™ in order to study the absorption and translocation of pharmaceutical, biological and nutritional compounds across the intestinal wall in a physiologically relevant model. This system uses fresh ex vivo intestinal tissue mounted into a two compartment model. So far, this has been the missing link in our toolbox to accurately predict absorption, oral bioavailability and PK of compounds.

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 indi...

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.

We identified an open reading frame (ORF) which is located closely behind the gene encoding granulebound 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 ß-1,3-glucanases and ß-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.

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.

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.