Temperature response of denitrification rate and greenhouse gas production in agricultural river marginal wetland soils.

Soils are predicted to exhibit significant feedback to global warming via the temperature response of greenhouse gas (GHG) production. However, the temperature response of hydromorphic wetland soils is complicated by confounding factors such as oxygen (O2 ), nitrate (NO3-) and soil carbon (C). We examined the effect of a temperature gradient (2-25 °C) on denitrification rates and net nitrous oxide (N2 O), methane (CH4 ) production and heterotrophic respiration in mineral (Eutric cambisol and Fluvisol) and organic (Histosol) soil types in a river marginal landscape of the Tamar catchment, Devon, UK, under non-flooded and flooded with enriched NO3- conditions. It was hypothesized that the temperature response is dependent on interactions with NO3--enriched flooding, and the physicochemical conditions of these soil types. Denitrification rate (mean, 746 ± 97.3 µg m(-2)  h(-1) ), net N2 O production (mean, 180 ± 26.6 µg m(-2)  h(-1) ) and net CH4 production (mean, 1065 ± 183 µg m(-2)  h(-1) ) were highest in the organic Histosol, with higher organic matter, ammonium and moisture, and lower NO3- concentrations. Heterotrophic respiration (mean, 127 ± 4.6 mg m(-2)  h(-1) ) was not significantly different between soil types and dominated total GHG (CO2 eq) production in all soil types. Generally, the temperature responses of denitrification rate and net N2 O production were exponential, whilst net CH4 production was unresponsive, possibly due to substrate limitation, and heterotrophic respiration was exponential but limited in summer at higher temperatures. Flooding with NO3- increased denitrification rate, net N2 O production and heterotrophic respiration, but a reduction in net CH4 production suggests inhibition of methanogenesis by NO3- or N2 O produced from denitrification. Implications for management and policy are that warming and flood events may promote microbial interactions in soil between distinct microbial communities and increase denitrification of excess NO3- with N2 O production contributing to no more than 50% of increases in total GHG production.

Denitrification potential of the Northern Arabian Gulf--an experimental study.

The study aims to establish denitrification potential of the Northern Arabian Gulf (NAG), as nitrogen critically affects the ocean productivity, obliterates acidity, oxidative capacity and radiative transfer capability of atmosphere. The experimental study was conducted by taking cores from intertidal zones from two different sites in North and South, referred as sites N and S; representing two distinct environmental milieu. The experiment was conducted in controlled laboratory conditions simulating the tidal cycles. Multiple cores were taken and loaded with seawater with different N concentrations, the redox potential was established for each condition. Redox potential was significantly lower at 10 cm depth compared to the surface in all cores (P < 0.001). The redox potential at surface and at 10 cm depth was significantly lower at site S compared to site N (P < 0.001; F = 714.2), suggesting anaerobic sediments at site S. Effects of nitrate spiked seawater on denitrification under nonflooded and flooded conditions at the two sites were also studied. Three-way ANOVA analysis indicated that site, nitrate concentration, and flooding had significant main and interactive effects on the rate of denitrification. The results suggest that under ambient nitrate concentrations (0.03 mg NO(3)-N l(-1)), 6.3 ± 2.1 g NO(3)-N ha day can be denitrified by inter-tidal zone sediments. At a nitrate concentration of 1 mg NO(3)-N l(-1), 92 ± 16 g NO(3)-N ha day may be denitrified whilst at a very high nitrate load of 10 mg NO(3)-N l(-1), the sediments may attain a rate of denitrification close to 404 ± 78 g NO(3)-N ha day.

Subtypes of oligodendroglioma defined by 1p,19q deletions, differ in the proportion of apoptotic cells but not in replication-licensed non-proliferating cells.

Oligodendrogliomas may be divided into those with deletion of chromosomes 1p and 19q (Del+), and those without (Del-). Del+ tumours show better survival and chemoresponsiveness but the reason for this difference is unknown. We have investigated whether these subgroups differ in (a) apoptotic index, (b) the proportion of cells licensed for DNA replication but not in-cycle, and (c) the relative length of G1-phase. Fluorescence in situ hybridisation with probes to 1p and 19q was used to determine the deletion status of 54 oligodendrogliomas, including WHO grades II and III. The apoptotic index was determined using counts of apoptotic bodies. Replication-licensed non-proliferating cells were determined from the Mcm2 minus Ki67 labelling index, whilst the geminin to Ki67 ratio was used as a measure of the relative length of G1. Del+ oligodendrogliomas showed a higher apoptotic index than Del- tumours (P=0.037); this was not accounted for by differences in tumour grade or in proliferation. There were no differences in the Mcm2-Ki67 index or in the geminin/Ki67 ratio between the subgroups, but grade III tumours showed a higher proportion of licensed non-proliferating cells than grade II tumours (P=0.001). An increased susceptibility to apoptosis in oligodendrogliomas with 1p+/-19q deletion may be important in their improved clinical outcome compared to Del- tumours.

HER2 amplification status in breast cancer: a comparison between immunohistochemical staining and fluorescence in situ hybridisation using manual and automated quantitative image analysis scoring techniques.

AIMS: To compare the results of breast cancer sections with HercepTesttrade mark immunohistochemistry (IHC) scores ranging from 0 to 3+ with fluorescence in situ hybridisation (FISH) for HER2 amplification. The HER2 digital scoring application of the Micrometastasis Detection System (MDS) was used, together with manual scoring of FISH and HercepTest, to determine whether this system provides an accurate alternative. METHODS: Paraffin wax embedded sections were stained using HercepTest and analysed by eye and automated quantitative image analysis. FISH was performed using the PathVysion fluorescent probe and scored by eye and automated quantitative image analysis using MDS. RESULTS: Of 114 cases, 26% were amplified by FISH, whereas only 18% scored 3+; 32% of IHC 2+ cases were amplified by FISH, and one showed borderline amplification. Six percent of IHC negative cases (0 or 1+) were amplified by FISH, and one showed borderline amplification. Of IHC 3+ cases, 10% were non-amplified by FISH. Classification discrepancies were seen in 18% of HercepTest cases scored by eye and using the MDS system. MDS was consistent with visual FISH scoring and correctly differentiated most ambiguous visual IHC scores. CONCLUSIONS: FISH provides a more accurate and consistent scoring system for determining HER2 amplification than HercepTest. The MDS system provides a reliable, consistent alternative to visual IHC and FISH scoring. IHC is still a valuable technique to aid in identification of isolated or heterogeneous tumour populations for subsequent FISH analysis, and a combined FISH and HercepTest approach to all breast cancer cases may be the most efficient strategy.

An epidemiological study of Wolf-Hirschhorn syndrome: life expectancy and cause of mortality.

OBJECTIVE: Early research into Wolf-Hirschhorn syndrome (WHS) described a high mortality and no relationship between deletion size and phenotype. This may need to be revised in the light of improved cytogenetic resolution and medical care. We have collected epidemiological data to allow the calculation of birth incidence and mortality figures. In addition, we have investigated the possibility of a relationship between deletion size and mortality. METHOD: Information relating to past and present cases diagnosed in the UK was collected by multiple ascertainment. RESULTS: A total of 159 cases were collected. The status (alive or dead) was determined for 146, of whom 96 are alive, 37 had died, and 13 were detected on prenatal diagnostic tests. A minimum birth incidence of 1 in 95 896 was calculated. The crude infant mortality rate was 17% (23/132) and in the first two years of life the mortality rate was 21% (28/132). Cases with large de novo deletions (proximal to and including p15.2) were more likely to have died than those with smaller deletions (odds ratio=5.7, 95% CI=1.7-19.9) after adjusting for age. A comparison of survival curves for de novo deletions and translocations did not show a statistically significant difference (p=0.11). The median survival time for de novo deletions was 34+ years while for translocation cases it was 18+ years. CONCLUSIONS: The mortality rate is lower than previously reported. There is a statistically significant relationship between deletion size and overall risk of death in de novo deletion cases. The difference in survival curves between de novo deletions and translocations is not statistically significant.

Elevated p53 expression in benign meningiomas protects against recurrence and may be indicative of senescence.

Prediction of recurrence after resection of benign meningiomas represents a significant clinical problem. A prospective study commenced in 1984 aimed to elucidate the molecular mechanisms involved in the development of abnormal karyotype and tumour recurrence in meningiomas. Expression of key cell cycle regulators p53, p21, mdm2 and proliferating cell nuclear antigen (PCNA) were studied by immunohistochemistry in 85 tumours for which follow-up data was available. It was found that most tumours expressed p53, p21 and PCNA, with significant correlations between expression of p53 and both p21 and PCNA. As PCNA fulfils a multifunctional role its expression may be an unreliable indicator of proliferation in benign tumours. The degree of tumour excision remains the best prognostic indicator while p53 is the main predictor of abnormal karyotype. Karyotype is not however, related to prognosis. Incompletely excised tumours which expressed high levels of p53 and p21 did not recur. It is suggested that this is indicative of a fully functional p53-mediated DNA damage response mechanism. Rather than contributing to tumour progression, p53 is fulfilling its role as guardian of the genome in benign meningiomas. This study shows that induction of senescence may be an important tumour suppressor mechanism in benign tumours.

Meningiomas, dicentric chromosomes, gliomas, and telomerase activity.

Lack of telomere maintenance during cell replication leads to telomere erosion and loss of function. This can result in telomere associations which probably cause the dicentric chromosomes seen in some tumour cells. One mechanism of telomere maintenance in dividing cells is the action of telomerase, a ribonucleoprotein enzyme that adds TTAGGG repeats onto telomeres and compensates for their shortening during cell division. Over 90 per cent of extracranial malignant neoplasms have been found to have telomerase activity. This study sought to determine if there was a relationship between absence of telomerase activity and presence of dicentric chromosomes in meningiomas and to what extent the other main group of central nervous system tumours, the gliomas, expressed telomerase activity. Telomerase activity was measured on 25 meningiomas and 29 gliomas. Four of the meningiomas were atypical variants and 11 were positive for dicentric chromosomes. Twenty-five of 29 gliomas were glioblastoma multiforme tumours. Measures were taken to ensure absence of false positives due to primer-dimer interaction and false negatives due to protein degradation or the presence of Taq polymerase inhibitors. All 25 meningiomas and the four low-grade gliomas (WHO grade II) were telomerase activity-negative. Seven (28 per cent) of the 25 glioblastoma multiforme tumours showed telomerase activity. The absence of telomerase activity in meningiomas and the high frequency of telomere associations support the hypothesis that these tumours are benign, transformed but pre-crisis. The relatively low frequency of telomerase activity in the malignant glioblastoma multiforme suggests that most of these tumours may have other mechanisms of telomere maintenance and that the potentially therapeutic telomerase inhibitors will not be of great value in the future management of the majority of patients suffering from these tumours.

Cytogenetics of iris melanomas: disparity with other uveal tract melanomas.

The chromosomal alterations of iris melanomas are poorly characterized, only one report has been detailed. Cytogenetic analysis was performed on the tumors and heparinized blood samples of three patients with iris melanomas; in one case a primary tumor and its related seedling were examined. On analysis of lymphocytes, two of the patients were found to experience a low level fragility of chromosome 9, in the region of a cutaneous melanoma susceptibility gene. All iris melanoma lesions were karyotyped. Clonal abnormalities of chromosomes 3, 5, 6, 7, 8, 9, 12, 15, 17, 18, 19, and Y were found, and in one case a large number of marker chromosomes were observed. No specific chromosomal change was common to the iris melanomas, but two cases had different abnormalities of chromosomes 5 and 18. Variations between the primary tumor and its related seedling were the acquisition of an additional chromosome 15, and a polyploid form of the cell line in the seedling. This study suggests that the most common chromosomal changes of posterior uveal melanomas are less frequent in iris melanomas. Iris melanomas also appear to experience relatively high levels of chromosomal alterations, including the formation of marker chromosomes, which is perhaps reminiscent of cutaneous melanoma.

A report of a child with a deletion (9)(q34.3): a recognisable phenotype?

We report a case of a male infant who presented with congenital anomalies and was found to have a de novo deletion in the terminal region of the long arm of chromosome 9. He died at the age of 17 weeks of cardiorespiratory failure owing to RSV positive bronchiolitis. A review of previously published reports documented one previous report of a patient with a deletion of (9)(q34.3) and multiple congenital anomalies. Comparison with the previously reported case suggests that the phenotype observed constitutes a clinically recognisable pattern of malformations.

Xp21 muscular dystrophy due to X chromosome inversion.

Two brothers with Duchenne muscular dystrophy have an inversion of the X chromosome, 46, Y, inv(X) (p11.2p21.2). Because their mother is an unaffected carrier of the inversion, this confirms that maternal passage of a structurally abnormal X chromosome can cause dystrophinopathy in males. Our experience suggests that as well as molecular genetic analysis, karyotyping can be useful in Xp21 muscular dystrophy.

Down syndrome with partial duplication and del (21) syndrome: study protocol and call for collaboration. Study I: Clinical assessment.

We report on the clinical and cytogenetic assessment of five cases of Down syndrome phenotype with either a partial duplication of chromosome 21 or a normal karyotype, and we quote a case of del (21q) syndrome. Down syndromes with a partial duplication of chromosome 21 (as well as cases of del (21q), which are partly the phenotypic countertype of trisomy 21) are of paramount importance in the understanding of genes involved in the phenotype of Down syndrome. The goal is to find the relevant genes implicated in the main traits of Down syndrome (i.e. mental retardation, Alzheimer disease, and serious visceral malformations). Such a goal, in our opinion, cannot be reached just by publishing the genotype and the phenotype of a small cohort of patients: 1. a sufficient number of accurate cases is needed, and 2. data have to be computerized for definite conclusions to be reached. The main aims of this report are to present our study protocol and to invite colleagues to participate in a collaborative study in order to collect a maximum of these (rare) cases.

Detecting deletions in the critical region for lissencephaly on 17p13.3 using fluorescent in situ hybridisation and a PCR assay identifying a dinucleotide repeat polymorphism.

During a study of lissencephaly in England and Wales, 23 children were identified with this diagnosis. They were classified as follows: three children had Miller-Dieker syndrome (MDS), 13 had isolated lissencephaly sequence (ILS), two had type II lissencephaly, and five children were reclassified as focal or diffuse cortical dysplasia. Microdeletions of chromosome 17p13.3, also known as the Miller-Dieker critical region, have been associated with both MDS and ILS. We used the commercially available Oncor probe for fluorescent in situ hybridisation (FISH) studies on 14 patients and a further four were studied elsewhere. Deletions were identified in all three MDS patients and two of the ILS patients. These results are consistent with previously reported data. No deletions were found in those patients with focal or diffuse cortical dysplasia. In addition, a CA repeat polymorphism which maps to the Miller-Dieker critical region was studied in 12 families and was informative in nine; the results were consistent with the FISH data. We conclude that FISH is a reliable method to detect deletions in patients with MDS and ILS and also useful to identify chromosome rearrangements in their parents which are not detected by conventional cytogenetic analysis. The PCR assay, if informative, is also reliable and a useful alternative if only DNA is available. None of the five children with atypical radiological features had a deletion. We therefore suggest that as well as looking for other aetiologies a careful review of the diagnosis should be made of the MDS or ILS cases in whom a deletion is not found.

A case of deletion 14(q22.1-->q22.3) associated with anophthalmia and pituitary abnormalities.

An interstitial deletion of the region q22.1-->q22.3 of chromosome 14 is described in a child with bilateral anophthalmia, dysmorphic features including micrognathia, small tongue, and high arched palate, developmental and growth retardation, undescended testes with a micropenis, and hypothyroidism. Interstitial deletions of the long arm of chromosome 14 are extremely rare, but this case seems to confirm that the region q22 is specifically concerned with pituitary and eye development.

Campomelic dysplasia associated with a de novo 2q;17q reciprocal translocation.

A phenotypically female fetus with campomelic dysplasia and a de novo reciprocal translocation, 46,XY,t(2;17) (q35;q23-24), is presented. This is the second case of campomelic dysplasia in which a rearrangement involving the long arm of chromosome 17 has been identified, indicating that this is likely to be the site of the campomelic dysplasia locus.

Cytogenetic studies in 50 meningiomas.

In a series of 50 meningiomas, cytogenetic studies showed that almost half had a normal diploid karyotype. The remainder had monosomy 22, some with a normal diploid line also present. The initial monosomy was often followed by further chromosome loss, and occasionally by structural abnormalities, some with distinctive characteristics. Chromosomes most often involved in structural rearrangements were 1, 14, 10, and 19, and those most often lost were 17 and Y. The type of chromosome abnormalities seen were similar to those described for senescent human cell cultures, which suggests that common chromosomal mechanisms may be operative in benign tumors and senescent cells. Although meningiomas occur more commonly in females, the chromosomally abnormal tumors are distributed evenly between males and females. Within the group of tumors with structural chromosomal abnormality, there seems to be a bias toward meningotheliomatous histology, but otherwise the karyotype changes seen independent of the histologic type of tumor.

Folate sensitive site at 10q23 and its expression as a deletion.

A patient is reported for whom initial chromosome analysis indicated 45,X/46,XX/46,XX,10q- mosaicism. The clinical findings included hypothyroidism and a low red cell folate estimation. The deleted chromosome 10 was subsequently shown to be an extreme expression of the folate sensitive heritable fragile site at 10q23, and a possible association between this and the in vivo folate status of the patient is suggested.

Prometaphase chromosome analysis as a routine diagnostic technique.

The use of techniques for the production of prometaphase chromosomes leading to increased resolution of banding patterns has resulted in problems as well as advantages in their routine use. A simple technique utilising the folate antagonist methotrexate has been in use in this regional diagnostic cytogenetics centre for three years, and a number of chromosome abnormalities have been detected in cases previously reported as normal following G banding studies. With reference to this, the routine analysis of prometaphase-type chromosomes is discussed and assessed.