Analysis of the Fragile X Trinucleotide Repeat in Basques: Association of Premutation and Intermediate Sizes, Anchoring AGGs and Linked Microsatellites with Unstable Alleles.

Fragile X Syndrome (FXS) is associated with an unstable CGG repeat sequence in the 5' untranslated region in the first exon of the FMR1 gene which resides at chromosome position Xq27.3 and is coincident with the fragile site FRAXA. The CGG sequence is polymorphic with respect to size and purity of the repeat. Interpopulation variation in the polymorphism of the FMR1 gene and consequently, in the predisposition to FXS due to the prevalence of certain unstable alleles has been observed. Spanish Basque population is distributed among narrow valleys in northeastern Spain with little migration between them until recently. This characteristic may have had an effect on allelic frequency distributions. We had previously reported preliminary data on the existence of FMR1 allele differences between two Basque valleys (Markina and Arratia). In the present work we extended the study to Uribe, Gernika, Durango, Goierri and Larraun, another five isolated valleys enclosing the whole area within the Spanish Basque region. We analyzed the prevalence of FMR1 premutated and intermediate/grey zone alleles. With the aim to complete the previous investigation about the stability of the Fragile X CGG repeat in Basque valleys, we also analyzed the existence of potentially unstable alleles, not only in relation with size and purity of CGG repeat but also in relation with DXS548 and FRAXAC1 haplotypes implicated in repeat instability. The data show that differences in allele frequencies as well as in the distribution of the mutational pathways previously identified are present among Basques. The data also suggest that compared with the analyzed Basque valleys, Gernika had increased frequency of susceptibility to instability alleles, although the prevalence of premutation and intermediate/grey zone alleles in all the analyzed valleys was lower than that reported in Caucasian populations.

Detection of survivin mRNA in urine of patients with superficial urothelial cell carcinomas.

INTRODUCTION: The aim of the present study was to assess if the presence of survivin mRNA in exfoliated cells present in urine samples can be a reliable marker of the presence of bladder tumour and recurrence. MATERIALS AND METHODS: Urine samples from 30 patients with superficial urothelial cell carcinomas (UCC) were collected prior to transurethral resection (TUR) of the tumour and in the first routine follow-up, three months after TUR. Detection of survivin mRNA was performed by reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: No correlation was observed between survivin detection and the clinicopathological variables analysed, nevertheless, when patients were grouped into low-grade (G1) and high-grade (G2+G3) tumours, statistically significant differences were found between both groups (p=0.04). When we analysed the results of survivin detection and urinary cytology together, we observed that informative cases rose from 27.8% to 44.4%. Also, Kaplan-Meier curves for patients with negative cytology in the first followup, categorised according to survivin detection, revealed that survivin mRNA positive cases recurred earlier than negative ones. CONCLUSIONS: From our results we can conclude that detection of survivin expression can be a reliable tumour marker, but more studies are needed to clarify the potential of survivin to predict recurrences. These results showed that survivin detection in combination with conventional urinary cytology can be a useful tool to increase the sensitivity in detecting the presence of a recurrence after TUR.

Dermatoglyphic analysis of autistic basque children.

We have analyzed the digital and palmar dermatoglyphics in a sample of autistic children from the Basque Country. The results have been compared with those from a control sample having the same characteristics relative to the ethnic region. We found significant differences between the digital dermatoglyphics of autistic boys and control boys. Autistic children have a higher frequency of transitional radial loops and a lower frequency of dicentric whorls; also the total finger ridge count (TFRC) and radial count are lower in autistic individuals. There were no significant differences in the girls. In palmar dermatoglyphics, autistic girls have a lower frequency of radial loops in the hypothenar area, and the value of the "atd" angle is higher than in control girls. These differences were significant. The a-b interdigital ridge count is significantly lower in autistic boys. Autistic children of both sexes have a higher frequency of aberrant palmar creases. The results obtained in the present study do not contradict the hypothesis that genetic factors may be important in autism of unknown cause.

Angelman syndrome caused by loss of a marker chromosome: cytogenetic and fluorescence in situ hybridization analysis.

We report a cytogenetic and fluorescence in situ hybridization study of a family in which a female child showed all the main characteristics of Angelman syndrome. Her karyotype revealed a translocation between chromosomes 5 and 15 with a partial deletion from 15pter to the Angelman region. Several members of her family appeared to be carriers of the same translocation, but showed no symptoms. The karyotypes showed a marker chromosome, that was not present in the female with Angelman syndrome. Fluorescence in situ hybridization revealed that the marker chromosome corresponded to material from chromosome 15. The present study is in agreement with the suggestion that genomic imprinting is one of the mechanisms involved in Angelman syndrome.

Increasing levels of MYC and MET co-amplification during tumor progression of a case of gastric cancer.

The cytogenetic study of a nodal metastasis from a gastric carcinoma, after two passages in nude mice, revealed a large number of double minutes. Comparative genomic in situ hybridization (CGH) analysis using DNA extracted from this xenograft revealed the existence of three clear amplification units that originated from the chromosomal subregions 6q24-25, 7q31-32, and 8q24 in the xenograft DNA. Similar, though less prominent, CGH results were found with DNAs extracted from the primary tumor and its metastasis, implying that the same amplicons were also present, albeit less abundantly, in the DNAs of these neoplastic tissues. Southern analysis of the second-passage xenograft detected 18- and 10-fold amplification of MET (located at 7q31) and MYC (located at 8q24), respectively. The retrospective study of the first passage of the xenograft, as well as of the metastatic and primary tumors before xenografting, showed amplification levels of MET of, respectively, 12-, 9-, and 5-fold and MYC of, respectively, 8-, 7-, and 5-fold. Our results suggest that increased levels of co-amplification of MYC and MET correlate with enhanced growth potential in this case of gastric carcinoma.

Expression of cell-cycle regulatory proteins and their prognostic value in superficial low-grade urothelial cell carcinoma of the bladder.

AIMS: Cell-cycle regulatory proteins are important indicators in determining progression trough the cell-cycle and progression to invasive cancer in patients presenting with superficial bladder cancer. We performed an immunohistochemical study in order to evaluate the prognostic value of the expression of p16, p27, pRb, p53 and Ki-67 in superficial grade I and II papillary urothelial cell carcinoma of the bladder. METHODS: p16, p27, p53, pRb and Ki-67 immunoexpression was studied in 14 pTa, 35 pT1a and 7 pT1b bladder tumours at presentation and at recurrence of their tumours. The recurrence-free survival and the progression-free survival were analysed according to these regulatory cell-cycle proteins expression. RESULTS: For survival in univariate analysis a high Ki-67 labelling index was a poor prognostic factor for recurrence-free and progression-free survival (P=0.0014 and P=0.012, respectively). Ki-67 labelling index was also an independent recurrence-free survival prognostic factor (P=0.0005). The p16, p27, p53 and pRb immunoreactivity was not significantly associated with recurrence or progression rate in this group of bladder carcinomas. CONCLUSIONS: These data suggest that the Ki-67 labelling index can be a reliable marker in predicting recurrence and/or progression in superficial low-grade bladder carcinomas and may be relevant in planning adjuvant therapy.

Cytogenetics of autosomal fragile sites: A Basque population study.

Population cytogenetic data on autosomal fragile sites show differences among different ethnic groups. The Basques are an ancient population; their origin is not exactly known and many studies using several traits have shown peculiarities in the Basques. This is the first study about the incidence of autosomal fragile sites in a healthy Basque sample. The results show interindividual variability, no sex differences at a global level, but differences for some fragile sites. Compared with other populations, a higher incidence of rare autosomal fragile sites has been demonstrated (8%). © 1996 Wiley-Liss, Inc.

Twin study of digital dermatoglyphic traits: Investigation of heritability.

Digital patterns of a sample of monozygotic and dizygotic twins were analyzed to obtain heritability values for the four basic types of patterns: arch, tented arch, loops, and whorls. Loops have been separated according to their orientation radial or ulnar. To carry out this study, we used the Holzinger and Clark indices. The results show highest concordances for monozygotic twins except for ulnar loops of the left hand and radial ones of the right hand. Different values of heritability were found for the right and left hands, with finger I having the highest values.

Identification of the Fungal Endophyte Epichloe festucae in the Fine Fescue Festuca ampla.

Festuca ampla is native to the Iberian Peninsula (4). Endophytic mycelium was observed by microscopy (2) in stem pith samples of two of eight asymptomatic plants of F. ampla collected in one population from a natural grassland in Salamanca, Spain. The fungus could be isolated (2) only from these two plants, and conidiophores and reniform conidia typical of Epichloe species (3) were observed in pure cultures. The two infected plants maintained in pots outside, developed ectostromata in some reproductive stems (choke disease) the year after the field sampling. Six seeds collected from an infected plant were germinated, and all six seedlings were found to be infected based on microscopy (2), implying seed transmission of the endophyte. These observations suggest that this is a pleiotropic symbiont, having both mutualistic and pathogenic states in its host. An ergovaline concentration of 120 ng/g dry weight was detected in a sample of leaves and leaf sheaths of an infected plant. All of the above characteristics are typical of the genus Epichloe, and in particular of the fine fescue endophyte E. festucae (1,3). To determine the species, internal transcribed spacer and 5.8-rDNA sequences as well as a partial sequence of the ß-tubulin gene were obtained. These two sequences (EMBL Accession Nos. AJ488497 and AJ488498) showed 100% sequence homology to the corresponding sequences in E. festucae. To our knowledge, this is the first report of this endophyte species in the grass F. ampla. References: (1) L. P. Bush et al. Plant Physiol. 114:1, 1997. (2) E. M. Clark et al. J. Microbiol. Methods 1:149, 1983. (3) A. Leuchtmann et al. Mycologia 86:802, 1994. (4) I. Markgraff-Dannenberg. Festuca. Pages 125-153 in: Flora Europaea, Vol 5. Cambridge University Press, Cambridge, 1980.

First Report of Choke Disease Caused by Epichloë baconii in the Grass Agrostis castellana.

Agrostis castellana is common in semiarid natural grasslands of the province of Salamanca, Spain. In this area, plants showing fungal stromata in their stems were observed in July of 2001. These symptoms are typical of choke disease, caused by Epichloë species in several grasses (3). In this disease, external fungal stromata develop around the leaf sheath of the flag leaf during the reproductive cycle of the plant host. As a result, the inflorescence does not emerge. In natural populations of A. castellana, less than 1% of plants showed disease symptoms, and all the stems of infected plants were sterilized by stromata. Intercellular endophytic mycelium was observed by microscopy in stem pith of diseased plants, but not on samples of 30 apparently healthy plants (1). Ergovaline, a fungal alkaloid, was not detected in lyophilized samples of infected plant tissue (2). In a fungal culture obtained from surface-disinfected leaf sheaths of a diseased plant (1), reniform conidia and conidiophores characteristic of the genus Epichloë were observed (4). To determine the fungal species, the nucleotide sequence of the ITS1-5.8SrRNA-ITS2 region and the three first introns of the beta-tubulin gene were obtained (EMBL Accession Nos. AJ490938 and AJ490939). When compared to those of other Epichloë species, these sequences identified the fungus from A. castellana as E. baconii (3). This fungus has been previously described as a pathogenic fungal endophyte in other Agrostis and Calamagrostis species (3,4). The fact that all stems of infected plants were diseased, infection incidence was low, and no alkaloids were detected in plants suggests that this grass-endophyte interaction is pathogenic and not mixed or mutualistic. References: (1) E. Clark et al. J. Microbiol. Methods 1:149, 1983. (2) N. Hill et al. Crop Sci. 33:331, 1993. (3) A. Leuchtmann et al. Mycol. Res. 102:1169, 1998. (4) J. White Jr. Mycologia 85:444, 1993.

Fragile X gene stability in Basque Valleys: prevalence of premutation and intermediate alleles.

Fragile X syndrome is the most common form of inherited mental retardation. The molecular basis is usually the unstable expansion of a CGG repeat in the FMR1 gene. We previously analyzed a sample of two Basque valleys. In the present work we extend the study to another five isolated valleys. The results show that differences in factors implicated in CGG repeat instability--CGG repeat size, XS548/FRAXAC1 haplotypes, and AGG interspersion pattern-are present in the Basque populations analyzed.

Near-infrared reflectance spectroscopy as a fast and non-destructive tool to predict foliar organic constituents of several woody species.

Near-infrared reflectance spectroscopy (NIRS) was used to estimate N, neutral detergent fibre (NDF), acid detergent fibre (ADF), lignin and cellulose contents in leaves of a heterogeneous group of 17 woody species from the Central Western region of the Iberian Peninsula. The sample set consisted of 182 samples of leaves of deciduous and evergreen species, showing a wide range of concentrations determined by reference methods: 6.60-35.2 g kg-1 (N), 15.5-66.0% (NDF), 10.2-57.3% (ADF), 3.45-27.4% (lignin) and 5.79-31.3% (cellulose). Reflectance spectra, obtained for samples of dried and ground leaves, were recorded as log1/R (R=reflectance) from 1,100 to 2,500 nm. NIRS calibrations were developed using multiple linear (MLR) and partial least-squares (PLSR) regressions, and tested by external validation. Spectral data were transformed to the first and second derivative (1D, 2D). The PLSR method and derivative transformations provided the best statistics and showed lower standard errors of calibration (SEC) and higher coefficients of multiple determination (R2). In the external validation the standard errors of prediction (SEP) were 0.76 g kg-1 (N), 2.11% (NDF), 1.47% (ADF), 0.85% (lignin) and 0.86% (cellulose). The results obtained show that NIRS is very effective for the estimation of these organic constituents in leaf tissue of woody species. This technique can be used in ecological or ecophysiological studies as an alternative to the more time-consuming standard methods.

Use of near-infrared reflectance spectroscopy in predicting nitrogen, phosphorus and calcium contents in heterogeneous woody plant species.

Near-infrared reflectance spectroscopy was applied to determine nitrogen (N), phosphorus (P) and calcium (Ca) content in leaf samples of 18 woody species. A total of 183 samples from mountain, riparian and dry areas from the Central-Western Iberian Peninsula were collected for this purpose. The wide intervals of variation observed in nutrient concentrations (6.6-45.0 g kg(-1) for N, 0.24-2.97 g kg(-1) for P, and 1.00-20.06 g kg(-1) for Ca) were due to the great heterogeneity of the samples. To develop calibration equations, multiple linear regression, and partial least-squares regression (PLSR) were used. In both cases, three mathematical transformations of the data were applied: log1/R and first and second derivatives. The best calibration statistics were obtained using PLSR and derivative transformations (second derivative for N and first derivative for P and Ca). The following coefficients of multiple determination (R2) and standard errors of cross validation were obtained: 0.99 and 0.93 for N, 0.94 and 0.15 for P, and 0.95 and 0.88 for Ca. In the external validation the standard errors of prediction obtained were 0.76 (N), 0.11 (P) and 0.60 (Ca).

Comparative mutagenicity of structurally related aliphatic epoxides in a modified Salmonella/microsome assay.

Four structurally related aliphatic epoxides (1,2-epoxypropane, 1,2-epoxyisobutane, cis- and trans-2,3-epoxybutane) have been tested in the Salmonella/microsome assay, modified for volatile substances, using the strains TA1535 and TA100. The aim of the study was to evaluate the effect of methylation on the mutagenicity of 1,2-epoxypropane in this vaporization assay, with and without exogenous metabolization. All substances induced a significant increase of revertants in the strains TA1535 and TA100. In terms of mutagenic potency, the following hierarchy was observed in the standard tester strain TA1535 and in the absence of rat S9: 1,2-epoxy-propane >> cis-2,3-epoxybutane > 1,2-epoxyisobutane > trans-2,3- epoxybutane. After exogenous metabolization, the mutagenic response of 1,2-epoxyisobutane was substantially reduced, while a moderate decrease of cis-2,3-epoxybutane was observed in the presence of S9, as compared with the response without S9. No influence of the S9 on the mutagenic response of trans-2,3-epoxybutane was noticed in both strains TA1535 and TA100, while an increased response with 1,2-epoxypropane was observed in TA100 but not in TA1535. The results suggest that the vaporization assay may provide more relevant information concerning mutagenic potencies of gaseous or volatile compounds than the common treat-and-plate or preincubation assays. Moreover, it appears that mutagenicity theories, based only upon inductive effects of side groups, may not suffice to explain differences in mutagenicity. Sterical factors or differential interactions with metabolizing enzymes could also be important in the evaluation of mutagenic effects.

Effects of genetic and environmental factors on the a-b, b-c and c-d interdigital ridge counts.

A study of 100 MZ (55 female and 45 male) and 97 DZ (50 male and 47 female) same-sexed twin pairs was carried out to analyse the genetic component of the variance of the a-b, b-c and c-d interdigital ridge counts by means of the Christian method. Especially for the a-b interdigital ridge count, we found it important to analyse both sexes separately. Our results suggest that the a-b count in males seems to be more influenced by environmental factors than the other counts. For females, the three interdigital counts seem to have a strong genetic component influencing their phenotypic expression. Factor analysis with VARIMAX rotation showed each interdigital ridge count to be genetically independent.

Genetic and dermatoglyphic distances among Basque Valleys.

Palmar dermatoglyphics of a sample including 552 males and 701 females from 8 Basque valleys were analyzed. We studied the frequency of palmar pattern types and compared them using correspondence the frequency of palmar pattern types and compared them using correspondence analysis. The results of this comparative study show that there is diversity among valleys and also that this diversity depends on the trait and on sex. Genetic drift could explain this variability found in the Basque population.

Genetic structure of natural populations of the grass endophyte Epichloë festucae in semiarid grasslands.

Plants of red fescue (Festuca rubra), a commercially important turf grass, are infected by the fungal endophyte Epichloë festucae in semiarid natural grasslands, known as dehesas, in western Spain. We used amplified fragment length polymorphism (AFLP) markers to analyse the genetic polymorphism existing in two natural populations of Epichloë festucae. Linkage disequilibrium and the presence of clonal lineages indicated that nonrecombinant asexual reproduction predominates in both populations. However, most genetic variation detected was found to occur within populations, with only a moderate amount of genetic differentiation between populations (F(ST): 0.197). Overall, the study suggests that dehesa grasslands are useful reservoirs of Epichloë festucae endophytes, and provides information on population structure which is relevant to design sampling strategies.

Quantitative and qualitative finger dermatoglyphics in the Basque Valley of Urola, Spain.

Digital dermatoglyphics of an indigenous sample of 87 males and 101 females from the Urola Valley in the Spanish Basque Country are compared with those from the nine other Basque valleys previously analyzed. In both sexes of the Urola Valley, there is a very high frequency of radial loops; the mean found in this valley extends the range of variation for South European-Mediterranean populations, and it is in the superior limit of all Caucasian populations. There are bimanual and sex differences in the frequencies of whorls and loops. Contrary to what occurs normally in populations, in the Urola Valley the frequency of whorls is higher in females and the quantitative value of digital patterns is lower in males. The results of this study show the existence of heterogeneity among valleys for digital trait frequencies and for finger ridge count, and this heterogeneity is more marked in females.

Analysis of digital patterns in the Basque valley of Deba: multivariate comparison with other populations.

Eighty-six females and 79 males from the Basque valley of Deba were analyzed with respect to their digital patterns using correspondence analysis. We found that there was a significant sexual difference for only one type of pattern, tented arch. Also, this population was compared with other Basque valley populations and with other Spanish populations. We found great variability among Basque subpopulations, despite their supposed common origin. Dermatoglyphic distances for some traits can be interpreted as genetic distances because there is high heritability of these traits. The results of the comparison between the Deba valley population and other Spanish populations showed that the Deba population is markedly distant from the other populations.