Tracing of particulate organic C sources across the terrestrial-aquatic continuum, a case study at the catchment scale (Carminowe Creek, southwest England).

Soils deliver crucial ecosystem services, such as climate regulation through carbon (C) storage and food security, both of which are threatened by climate and land use change. While soils are important stores of terrestrial C, anthropogenic impact on the lateral fluxes of C from land to water remains poorly quantified and not well represented in Earth system models. In this study, we tested a novel framework for tracing and quantifying lateral C fluxes from the terrestrial to the aquatic environment at a catchment scale. The combined use of conservative plant-derived geochemical biomarkers n-alkanes and bulk stable δ13C and δ15N isotopes of soils and sediments allowed us to distinguish between particulate organic C sources from different land uses (i.e. arable and temporary grassland vs. permanent grassland vs. riparian woodland vs. river bed sediments) (p<0.001), showing an enhanced ability to distinguish between land use sources as compared to using just n-alkanes alone. The terrestrial-aquatic proxy (TAR) ratio derived from n-alkane signatures indicated an increased input of terrestrial-derived organic matter (OM) to lake sediments over the past 60years, with an increasing contribution of woody vegetation shown by the C27/C31 ratio. This may be related to agricultural intensification, leading to enhanced soil erosion, but also an increase in riparian woodland that may disconnect OM inputs from arable land uses in the upper parts of the study catchment. Spatial variability of geochemical proxies showed a close coupling between OM provenance and riparian land use, supporting the new conceptualization of river corridors (active river channel and riparian zone) as critical zones linking the terrestrial and aquatic C fluxes. Further testing of this novel tracing technique shows promise in terms of quantification of lateral C fluxes as well as targeting of effective land management measures to reduce soil erosion and promote OM conservation in river catchments.

Patterns of chromosomal imbalances in invasive breast cancer.

Invasive breast carcinomas are characterized by a complex pattern of chromosomal alterations. We applied comparative genomic hybridization (CGH) to analyze 105 primary breast carcinomas using histograms to indicate the incidence of DNA imbalances of tumor subgroups and difference histograms to compare invasive ductal carcinomas (IDC) with lobular carcinomas (ILC), well and poorly differentiated carcinomas (G1/G3) and estrogen receptor-positive and -negative tumors (ER(+)/ER(-)). Only single imbalances showed a higher incidence in ILC compared with IDC, i.e., gains on chromosomes 4 and 5q13-q23 as well as deletions on chromosomes 6q, 11q14-qter, 12p12-pter, 16q, 17p, 18q, 19, and 22q. Of these, particularly gains of 4 and losses at 16q21-q23, and 18q12-q21 were statistically significant. For most loci, IDC showed more alterations providing a genetic correlate to the fact that ductal carcinoma overall is associated with a worse prognosis than ILC. Of these, many imbalances showing statistical significance were also observed in G3 and ER(-) tumors, i.e., deletions at 2q35-q37, 3p12-p14, 4p15-p16, 5q, 7p15, 8p22-p23, 10q, 11p, 14q21-q31, 15q, and gains at 2p, 3q21-qter, 6p, 8q21-qter, 10p, 18p11-q11, and 20q, suggesting that they contribute to a more aggressive tumor phenotype. By contrast, gains on chromosome 5q13-q23 as well as deletions at 6q, 16q and 22q were more prevalent in G1 and ER(+) tumors. The ratio profiles of all cases as well as histograms are accessible at our CGH online tumor database at http://amba.charite.de/cgh. Our results highlight distinct chromosomal subregions for cancer-associated genes. In addition, these imbalances may serve as markers for a genetic classification of invasive breast cancer.

Unbalanced chromosomal aberrations in neuroendocrine lung tumors as detected by comparative genomic hybridization.

Typical and atypical carcinoids (TC, ATC) and small (SCLC) and large cell neuroendocrine carcinomas (LCNEC) constitute the spectrum of neuroendocrine lung tumors. Chromosomal aberrations have not been studied in LCNEC and only rarely in carcinoids. Only SCLCs have been investigated frequently for chromosomal aberrations. We compared three typical and four atypical carcinoids, one atypical carcinoid/SCLC mixed type, three SCLC, and three LCNEC for chromosomal gains and losses using comparative genomic hybridization. Typical carcinoids showed either no changes or only few chromosomal gains. Atypical carcinoids appeared genetically heterogeneous: One case had no aberrations, and three cases had few aberrations; two of them showed a deletion of 11q. SCLC and LCNEC were characterized by many gains and losses, especially similar changes of 3p, 5q, 5p, and 13q. Although ATC resemble LCNEC morphologically, there were no similarities at the genetic level. We have found a reciprocal relationship of prognosis and the amount of aberrations. TCs and ATCs with few chromosomal changes have the best prognosis, whereas SCLCs and LCNECs were generally characterized by a great amount of aberrations and worst prognosis. There was no unbalanced aberration common in all types of neuroendocrine tumors of the lung.

Chromosome alterations in breast carcinomas: frequent involvement of DNA losses including chromosomes 4q and 21q.

Comparative genomic hybridization was applied to map DNA gains and losses in 39 invasive ductal breast carcinomas. Frequent abnormalities included gains on chromosomal regions 1q, 8q, 11q12-13, 16p, 19, 20q and X as well as frequent losses on 1p, 5q, 6q, 9p, 11q, 13q and 16q. Furthermore, frequent losses on 4q (20 cases) and 21q (14 cases) were found for the first time in this tumour type. High copy number amplifications were observed at 8q12-24, 11q11-13 and 20q13-ter. Highly differentiated tumours were associated with gains on 1q and 11q12-13 along with losses on 1p21-22, 4q, 13q, 11q21-ter. Undifferentiated breast carcinomas were characterized by additional DNA imbalances, i.e. deletions of 5q13-23, all of chromosome 9, the centromeric part of chromosome 13 including band 13q14 and the overrepresentation of chromosome X. We speculate that these changes are associated with tumour progression of invasive ductal breast cancer.

Genomic alterations associated with malignancy in head and neck cancer.

BACKGROUND: Comparative genomic hybridization (CGH) was performed on 50 primary head and neck squamous cell carcinomas (HNSCC) to discover molecular genetic alterations underlying the progression of these tumors. METHODS: In CGH, equal amounts of differently labeled tumor deoxyribonucleic acid (DNA) and normal reference DNA were hybridized simultaneously to normal metaphase chromosomes. They were visualized by different fluorochromes, and the signal intensities were quantitated separately as gray levels along the single chromosomes. The over- and underrepresented DNA segments were determined by computation of ratio images and average ratio profiles. RESULTS: Prevalent changes observed in more than 50% of the HNSCC included deletions of chromosomes 1p, 4, 5q, 6q, 8p, 9p, 11, 13q, 18q, and 21q and DNA overrepresentations of 11q13 as well as 3q, 8q, 16p, 17q, 19, 20q, and 22q. The calculation of ratio profiles of tumor subgroups revealed that well differentiated carcinomas (G1) were defined by the deletions of chromosomes 3p, 5q, and 9p together with the overrepresentation of 3q, suggesting the association with early tumor development. Accordingly, the undifferentiated tumors (G3) were characterized by additional deletions of chromosomes 4q, 8p, 11q, 13q, 18q, 21q, and overrepresentations of 1p, 11q13, 19, and 22q. CONCLUSION: Our data indicate that the CGH patterns of chromosomal imbalances may help to define the malignant potential of head and neck squamous cell carcinomas.

Models for the regulation of purine metabolism in rat hepatocytes: evaluation of tracer kinetic experiments.

Metabolic pathways are characterized by numerous regulatory mechanisms. Their study calls for the determination of the metabolite concentrations as well as the flux rates. Corresponding experiments using purified enzymes and an artificial environment frequently yield results that differ from findings for in vivo systems. To be more realistic, the tracer kinetic experiments presented here involved intact isolated hepatocytes. It is necessary to establish mathematical models to deduce the flux rates. With the presumption of metabolic steady-state conditions, the flux rates are determined by a possibly stiff system of linear differential equations. For the first time, the flux rate determination in the purine metabolism of rat hepatocytes was accomplished by applying a combination of a nonlinear least-square fit and a numerical integration. Because of the complexity of this pathway, it was necessary to use three different tracers requiring three partial models. By ensuring their compatibility and using a fit of high statistical quality, the experimental situation could be described adequately. Our flux rate analysis confirmed earlier experimental findings and also allows much more insight into the regulatory mechanisms of the metabolism studied.

Patterns of chromosomal imbalances in adenocarcinoma and squamous cell carcinoma of the lung.

Comparative genomic hybridization was used to screen 25 adenocarcinomas and 25 squamous cell carcinomas of the lung for chromosomal imbalances. DNA copy number decreases common to both entities were observed on chromosomes 1p, 3p, 4q, 5q, 6q, 8p, 9p, 13q, 18q, and 21q. Similarly, DNA gains were observed for chromosomes 5p, 8q, 11q13, 16p, 17q, and 19q. Adenocarcinomas showed more frequently DNA overrepresentations of chromosome 1q and DNA losses on chromosomes 3q, 9q, 10p, and 19, whereas squamous cell carcinomas were characterized by increased overrepresentations of chromosome 3q and 12p as well as deletions of 2q. For the first time, we used a histogram representation and statistical analysis to evaluate the differences between both tumor groups. In particular, the overrepresentation of the chromosomal band 1q23 and the deletion at 9q22 were significantly associated with adenoid differentiation, whereas the DNA loss of chromosomal band 2q36-37 and the overrepresentations at 3q21-22 and 3q24-qter were statistically significant markers for the squamous cell type. The study strengthens the notion that different tumor subgroups of the respiratory tract are characterized by distinct patterns of chromosomal alterations.

Primary small-cell lung carcinomas and their metastases are characterized by a recurrent pattern of genetic alterations.

Small-cell lung cancer (SCLC) represents a group of highly malignant tumors giving rise to early and widespread metastases. We used comparative genomic hybridization in autoptic tumor specimens from 10 patients to discover genetic alterations that are associated with tumor progression and potentially with the metastatic phenotype. Ten primary SCLC and 16 corresponding metastases were investigated with a maximum of 4 tumors per case. Prevalent changes observed in more than 60% of the primary tumors and their metastases included deletions on chromosomes 3p, 4q, 5q, 10q, 13q and 17p, and DNA over-representations on chromosomes 3q and 5p. The number of common alterations in the primary tumors and the related metastases outnumbered the differences, indicating a clonal relationship. Within the lesions of the same patient, differences were found between the primary tumor and the metastases as well as between metastases of distinct organ sites. However, no specific alteration was significantly associated with the metastatic phenotype. We suggest that the high malignancy of SCLC is defined by the above-mentioned pattern of aberrations.

[Comparative genomic hybridization of bronchial carcinomas and their metastases]. / Comparative Genomische Hybridisierung an Bronchialkarzinomen und ihren Metastasen.

We analysed 150 carcinomas of the respiratory tract and their metastases by Comparative Genomic Hybridization (CGH), a screening method for the detection of chromosomal imbalances in solid tumors. Small cell lung carcinomas (SCLC) and non-small cell lung carcinomas (NSCLC) revealed characteristic patterns of chromosomal alterations with overlapping and specific lesions in both tumor groups. SCLC were defined by a pattern of deletions on chromosomes 3p, 4q, 5q, 10q, 13q and 17p along with overrepresentations of chromosomes 3q and 5p. In contrast, NSCLC carried frequently deletions on chromosomes 1p, 3p, 4q, 5q, 6q, 8p, 9p, 13q, 18q and 21q along with overrepresentations of chromosomes 5p and 11q13. The deletions of the chromosomal band 2q36-q37 together with amplifications of chromosome 3q were statistically significant lesions of squamous cell carcinomas (SCC) whereas adenocarcinomas were characterized in particular by the overrepresentation of chromosome 1q23 and the deletion on chromosome 9q22. The comparison of primary and metastatic tumors revealed that the deletion of chromosome 10q was a statistically significant marker of tumor progression and metastatic phenotype in SCC and SCLC. In conclusion, the data indicate that tumor histotypes and phenotypes are associated with patterns of chromosomal alterations which give important additional information for the classification of human lung carcinomas.

Small-cell lung cancer is characterized by a high incidence of deletions on chromosomes 3p, 4q, 5q, 10q, 13q and 17p.

The genetic mechanisms that define the malignant behaviour of small-cell lung cancer (SCLC) are poorly understood. We performed comparative genomic hybridization (CGH) on 22 autoptic SCLCs to screen the tumour genome for genomic imbalances. DNA loss of chromosome 3p was a basic alteration that occurred in all tumours. Additionally, deletions were observed on chromosome 10q in 94% of tumours and on chromosomes 4q, 5q, 13q and 17p in 86% of tumours. DNA loss was confirmed by loss of heterozygosity (LOH) analysis for chromosomes 3p, 5q and 10q. Simultaneous mutations of these six most abundant genetic changes were found in 12 cases. One single tumour carried at least five deletions. DNA under-representations were observed less frequently on chromosome 15q (55%) and chromosome 16q (45%). The prevalent imbalances were clearly indicated by the superposition of the 22 tumours to a CGH superkaryogram. In our view, the high incidence of chromosomal loss is an indication that SCLC is defined by a pattern of deletions and that the inactivation of multiple growth-inhibitory pathways contributes in particular to the aggressive phenotype of that type of tumour.

Distinct patterns of chromosomal alterations in high- and low-grade head and neck squamous cell carcinomas.

Comparative genomic hybridization was performed on 30 primary head and neck squamous cell carcinomas. Fractional or entire DNA loss of chromosome 3p was a basic finding that occurred in 29 cases (97%). Additional DNA underrepresentations were observed in more than 50% of the cases on chromosomes 1p, 4, 5q, 6q, 8p, 9p, 11q, 13q, 18q, and 21q. Deletions on chromosomes 3p, 13q, and 17p were confirmed by loss of heterozygosity analysis. Entire or partial DNA copy number increases were identified for chromosome 3q in 26 cases (87%) with high-level amplifications at 3q24 and 3q27-qter. Overrepresentations were found in decreasing order of frequency at 11q13 (70%), 8q (57%), 19q (50%), 19p (47%), and 17q (47%). The use of comparative genomic hybridization superkaryograms of the group of well-differentiated carcinomas (G1) indicated that the deletions on chromosomes 3p and 9p along with the overrepresentation of 3q are associated with early tumor development. Accordingly, the undifferentiated tumors (G3) were characterized by additional deletions on chromosomes 4q, 8p, 11q, 13q, 18q, and 21q and overrepresentations on 1pter, 11q13, 19, and 22q, suggesting that these changes are preferentially associated with tumor progression.

[Comparative genomic hybridization. A screening method in genetic tumor diagnosis]. / Die komparative genomische Hybridisierung. Eine Screeningmethode in der genetischen Tumordiagnostik.

Comparative genomic hybridization (CGH) is a new method of screening a tumor for genetic changes. The alterations are classified as DNA gains and losses and reveal a characteristic pattern that includes mutations at the chromosomal and subchromosomal levels. Although DNA from fresh-frozen tissue is recommended as the starting material, archival specimens can also be analyzed. Various examples are presented that illustrate the changes that occur in different tumor entities, and preneoplastic lesions, the differentiation of primary tumors from metastases, and the investigation of tumor cell lines that are resistant to cytostatic drugs. These examples emphasize that CGH can extend the possibilities for genetic diagnosis in tumor pathology.

[Genetic screening of head-neck carcinomas using comparative genomic hybridization (CGH)]. / Genetisches Screening von Kopf-Hals-Karzinomen mittels der Komparativen Genomischen Hybridisierung (CGH).

BACKGROUND: Comparative Genomic Hybridization (CGH) is a novel cytogenetic method that allows the comprehensive analysis of a tumor genome for DNA gains and losses. METHODS: CGH was performed on genomic DNA extracted from 14 primary head and neck squamous cell carcinomas. Equal amounts of biotin-labeled tumor DNA and digoxigenin-labeled normal reference DNA were hybridized to normal metaphase chromosomes. The tumor DNA was visualized with fluorescein (FITC) and the normal DNA with rhodamine (TRITC) and detected in a fluorescence microscope. The signal intensities of the different fluorochromes were quantitated as gray levels along the single chromosomes. The over-and underrepresented DNA segments were quantified by computation of FITC/TRITC ratio images and average ratio profiles. RESULTS: Consensus deletion regions were most frequently observed on chromosome arms 3p (14 cases), 9p (11), 13q (10), 18q (10), 5q (9), 4q (9), 4p (7), 11q (7), 6q (6), 8p (6), and 11p (6). Copy number increases were identified for chromosomes 3q (11), 16p (9), 17q (9), 19p (8), 19q (7), 22 (7), 1p (6), 8q (6), 9q (6), and 20q (6). Particularly, the 3q isochromosome formation (3p loss/3q amplification), found in 10 cases, was a basic alteration. In addition, 11 tumors showed a 11 q13 amplification. CONCLUSION: CGH analysis allows the identification of recurrent genetic alterations in head and neck squamous cell carcinomas that will be associated with specific tumor phenotypes like metastatic behavior and prognosis.

Transitions of hepatic purine metabolism of Ehrlich ascites tumor bearing mice in different phases of tumor growth.

The concentrations of purine nucleotides, nucleosides and nucleobases in hepatocytes taken from healthy control mice and from Ehrlich ascites tumor bearing mice have been measured. The level of adenine nucleotides in the hepatocytes was higher during the proliferating phase in comparison with the resting phase of tumor growth and with control mice hepatocytes. The tracerkinetic studies on purine catabolism have been carried out on liver cells at different periods of tumor growth. The dynamics of radioactive tracers was mathematically modelled by a system of differential equations for both the concentrations and the specific radioactivities of the metabolites. Large differences in metabolic flux rates between control hepatocytes and hepatocytes in different phases of tumor growth were observed. The final purine degradation of hepatocytes was found to be accelerated in the resting phase but not in the proliferating phase of tumor growth. This result is in accordance with increased ATP concentration of liver itself in the proliferating phase of tumor growth. A conclusion is possible that the liver does not supply nucleosides and nucleobases for the Ehrlich ascites tumor cells during the proliferating phase of tumor growth.

Estimation of metabolic flux rates in liver purine catabolism of tumour-bearing mice by computer simulation of radioactive tracer experiments.

Mouse hepatocytes from healthy control mice and from Ehrlich ascites tumour-bearing mice were used for tracer-kinetic studies of purine catabolism of liver cells during different periods of tumour growth. The dynamics of the radioactive tracers were modelled mathematically by a system of differential equations. Computer simulations, i.e. direct fitting of numerical solutions of these equations to the observed time-courses of metabolites and specific radioactivities, enables one to estimate unknown kinetic parameters of a simplified model of pathways of hepatic purine catabolism in tumour-bearing mice. There occurred great differences of metabolic flux rates between control hepatocytes, hepatocytes of mice during the proliferating period of tumour growth (6th day after inoculation of the tumour) and hepatocytes of mice during the resting period of tumour growth (12th day after inoculation of the tumour). The final purine degradation of hepatocytes prepared during the proliferating period was lower in comparison with that of control hepatocytes, but it was markedly higher in hepatocytes prepared during the resting period of tumour growth. The changes in hepatocyte purine catabolism during the proliferating period of tumour growth argue for transitions which aim at the maintenance of high purine nucleotide levels in the liver itself rather than for an increased nucleoside and nucleobase supply for the tumour. This suggestion is in accordance with the increased ATP level of the liver during the proliferating phase of tumour growth.(ABSTRACT TRUNCATED AT 250 WORDS)

Estimation of steady-state flux rates in metabolic systems by computer simulations of radioactive tracer experiments.

The dynamics of radioactive tracers in metabolic systems can be mathematically modelled by coupled systems of differential equations for both the concentrations and the specific radioactivities of the metabolites involved. Computer simulations, i.e. direct fitting of numerical solutions of these equations to observed time-courses of metabolites and specific radioactivities, enables one to estimate unknown kinetic parameters of the system. The theoretical fundamentals of this approach and the main steps towards the quantitative assessment of flux rates in stationary metabolic systems are outlined. An application of the method to the purine nucleotide metabolism of Ehrlich ascites tumor cells is given based on a simplified model of this pathway. The obtained steady-state flux rates indicate a marked increase in the metabolism of the adenine nucleotides during the proliferating phase in comparison to the resting phase of tumor growth.