Chromosome studies in Hippeastrum (Amaryllidaceae): variation in genome size

This paper presents the karyotype and DNA content of 12 diploid species of Hippeastrum from South America. The variation in genome size is compared with the karyotype and DNA content of Amaryllis belladonna from South Africa. The Hippeastrum species present a uniform and bimodal basic karyotype formula, but significant differences are found in the total chromosome volume (TCV) and nuclear DNA content. A positive correlation between the DNA content and TCV is also observed. The karyotype's constancy is a product of changes in DNA content occurring in the whole chromosome complement. The DNA addition to the long and short sets of chromosomes varies independently. In species with higher DNA contents, the short chromosomes add equal DNA amounts to both arms, maintaining their metacentric morphology, whereas the long chromosomes add DNA only to the short arm, increasing the chromosome symmetry. These data show that the evolutionary changes in DNA amount are proportional to chromosome length, maintaining the karyotypic uniformity. A. belladonna has a larger DNA content and possesses a karyotype different from that of Hippeastrum spp., supporting the distinction between the two genera and upholding the name Amaryllis for the South African entity against Hippeastrum for the South American genus.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 171–178.     

DNA ploidy as a prognostic factor in rhabdomyosarcoma. Analysis of 35 cases with image cytometry

OBJECTIVE: To correlate DNA ploidy in rhabdomyosarcoma (RMS) with other prognostic factors and patient survival and to search for possible reasons for inconsistent conclusions in similar, published studies. STUDY DESIGN: DNA content was measured in archival specimens obtained from 35 patients (23 children and 12 adults) with RMS. Cell suspensions were prepared by the modified Hedley technique, stained by the modified Feulgen-thionin method and analyzed by automated high-resolution image cytometry. DNA ploidy was assessed on the basis of DNA index values. We used the chi 2 test to correlate DNA ploidy with other prognostic factors, Kaplan-Meier procedure to estimate overall survival in terms of individual prognostic factors, log-rank test to calculate differences in survival between groups and Cox multivariate regression analysis to determine the independence of variables in relation to survival. RESULTS: A statistically significant correlation was found only between DNA ploidy and histologic subtype of RMS, patient sex and patient age. A hyperdiploid DNA pattern predominated among patients with embryonal RMS, and a tetraploid pattern dominated among patients with alveolar RMS. The highest 5-year survival rate was seen among patients with hyperdiploid RMS, followed by those with diploid, tetraploid and hypertetraploid RMS. Although DNA ploidy was a significant prognostic factor in univariate analysis, it did not retain its independent prognostic value in multivariate analysis, in which patient age, tumor size and histologic subtype were the only significant factors. We found 12 articles reporting on the association between DNA ploidy and survival of patients with RMS: 6 found a correlation, and 6 did not. The main reasons for the discrepancies seem to be the inclusion of chemotherapy-treated and nontreated patients, low number of patients and differences in grouping DNA histograms. CONCLUSION: The precise prognostic value of DNA ploidy in RMS remains equivocal. Larger, cooperative studies could give statistically more reliable results.     

Intra- and interspecific variations in nuclear parameters of two closely related species of Narcissus L.

Nuclear DNA amount, nuclear area, genome volume and karyotype length were analysed in different populations of two closely related species of Narcissus. There are intra- and interspecific variations in these parameters. 4C DNA amount and karyotype length, on one hand, and 2C DNA amount and telophase nuclear area, on the other, are not correlated. It seems that DNA content and chromosome length are independent parameters. However, 4C DNA content and karyotype volume are correlated, and are also correlated to different density estimations (4C DNA to Kar.length & 2C DNA to telophase area). These facts suggest that the relative length of the chromosomes is genetically controlled and that it is independent of the DNA that they contain. It seems that the interpopulational differences in DNA content are correlated with length changes of small segments in almost all chromosomes.     

Assessment of genetic diversity among 16 promising cultivars of ginger using cytological and molecular markers

Ginger (Zingiber officinale Roscoe) is an economically important plant, valued all over the world. The existing variation among 16 promising cultivars as observed through differential rhizome yield (181.9 to 477.3 g) was proved to have a genetic basis using different genetic markers such as karyotype, 4C nuclear DNA content and random amplified polymorphic DNA (RAPD). The karyotypic analysis revealed a differential distribution of A, B, C, D and E type of chromosomes among different cultivars as represented by different karyotype formulas. A significant variation of 4C DNA content was recorded in ginger at an intraspecific level with values ranging from 17.1 to 24.3 pg. RAPD analysis revealed a differential polymorphism of DNA showing a number of polymorphic bands ranging from 26 to 70 among 16 cultivars. The RAPD primers OPC02, OPA02, OPD20 and OPN06 showing strong resolving power were able to distinguish all 16 cultivars. The extent of genetic diversity among these cultivars was computed through parameters of gene diversity, sum of allele numbers per locus and Shannon's information indices. Cluster analysis, Nei's genetic similarity and genetic distances, distribution of cultivars into special distance classes and principal coordinate analysis and the analysis of molecular variance suggested a conspicuous genetic diversity among different cultivars studied. The genetic variation thus detected among promising cultivars of ginger has significance for ginger improvement programs.     

Biological characterisation of superficial bladder cancer by bivariate cytokeratin 7/DNA analysis, flow cytometric assessment of MIB- 1, and an immunohistochemical study.

A total of 238 cases of bladder carcinoma stages Ta, Tis, T1 were submitted prospectively to multiparameter flow cytometry and immunohistochemical study in order to determine the biological aggressiveness of the tumour. DNA index (DI), S-phase fraction (SPF) obtained by bivariate cytokeratin 7/DNA analyses, and the immunohistochemical evaluation of p53 and MIB-1 were studied in relation to the traditional prognostic factors in bladder cancer (stage and grade). the variance analysis results showed that DNA aneuploidy was significantly associated with high stage (p = 0.0001), high grade (p = 0.0001), high SPF value > or = 5.5% (p = 0.0001), MIB-1 positivity > or = 31% (p = 0.0001) and high expression of p53 (staining involving > 50% of cells, p = 0.0001). Even if there was no statistical significance the hypotetraploid class (1.70 < DI < 1.89) showed poor prognostic biomarkers more frequently than the other aneuploid classes. Out of 238 cases, 101 were also submitted to flow cytometric measurement of MIB-1 (fMIB-1) to study the correlation between cell proliferation and DNA content. Data obtained from fresh, 3:1 methanol/acetone fixed samples were compared with values obtained from both cell cycle analysis methods and routine application of the MIB-1 immunostaining in histological sections. fMIB-1 values were positively correlated with SPF values (r = 0.801, p < 0.01) and S+G2M fraction (percentage of cells in S and in G2M phases) (r = 0.763, p < 0.01) but no correlation with paraffin sections was found. A fMIB-1 value > 7% was strongly associated with aneuploidy (p = 0.0001). The determination of DNA content coupled with the study of the epithelial (cytokeratin 7) and proliferative (MIB-1) markers could be useful in providing important information on the biological behaviour of superficial bladder tumours.     

Tissue-type plasminogen activator (tPA) content in colorectal cancer and in surrounding mucosa: relationship with clinicopathologic parameters and prognostic significance

The aim of this study was to evaluate the cytosolic tissue-type plasminogen activator (tPA) content in colorectal cancer, its possible relationship with the clinicopathologic parameters of tumors, and its prognostic significance. We have therefore examined by immunoenzymatic assay the cytosolic tPA content in tumors and paired surrounding normal mucosa samples from 162 colorectal cancer patients. Cytosolic tPA levels were significantly higher in surrounding normal mucosa samples than in neoplastic tissues (4.01 +/- 5.07 vs 2.63 +/- 5.82 ng/mg protein; p < 0.0001). By contrast, no significant correlation was found between tPA content and clinicopathologic tumor parameters such as location, Dukes' stage, histologic grade, and DNA content or S-phase fraction. However, the results indicated that a high cytosolic tPA content (> 0.75 ng/mg protein) in tumors predicted for a shorter relapse-free and overall survival (both p < 0.05) in 123 resectable colorectal cancer patients who were prospectively evaluated during a mean follow-up period of 32.2 months. This suggests that tPA may give additional information to that provided by other biochemical markers currently used in colorectal cancer.     

Plasmodium berghei: gametocyte production, DNA content, and chromosome-size polymorphisms during asexual multiplication in vivo

In this study the DNA content and the karyotype of clones of Plasmodium berghei, which differed in the capability to produce gametocytes, were determined. The DNA content per haploid genome was established by cytofluorometric methods after staining of the haploid merozoites with DNA-specific fluorescent dyes. Field inversion gel electrophoresis was used to establish the number and size of the chromosomes. Parasites of a high gametocyte producer clone (original HP) and a low producer clone (original LP) contained 13 to 14 chromosomes in the size range of 0.5-3.8 megabase. In four independent experiments parasites of the original HP clone were maintained in mice and were mechanically transmitted for prolonged periods of time (up to 90 weeks). During the transmission period the capability to produce gametocytes decreased in all four lines. After mosquito transmission of parasites from these low producer lines, the gametocyte production returned to the level of the original HP clone. The total DNA content per haploid genome of low producer parasites was not significantly different from that of HP parasites. During prolonged periods of asexual multiplication of the HP clone in vivo, changes in the relative size of several chromosomes were detected. Mosquito transmission of the original HP clone did not result in a change of the karyotype. However, novel karyotypes were readily observed after mosquito transmission of parasites of the low producer lines. The decrease of the capability to produce gametocytes did not necessarily involve detectable changes in DNA content or in karyotype.     

DNA grading of malignancy in breast cancer. Prognostic validity, reproducibility and comparison with other classifications

The prognostic significance of the "DNA malignancy grade" (DNA-MG) was tested in a series of 104 breast cancer patients in comparison with TNM staging, histomorphologic grading according to Bloom and Richardson, mean nuclear area (MNA) and DNA-histogram classification according to Auer. The reproducibility and representativity of the grading systems were investigated, and their results in primary tumors and lymph node metastases were compared. The scalar DNA-MG was assessed on monolayer smears prepared from paraffin-embedded tissues; the smears were automatically Feulgen stained and used for rapid interactive DNA cytometric evaluation by an automated microscope and a TV image-analysis system. TNM staging showed the highest correlation with survival, followed by histomorphologic grading and DNA-MG; MNA and the DNA-histogram classification failed to give statistically significant prognostic information. Both histomorphologic grading and DNA-MG were identified as parameters adding independent prognostic information to the TNM staging. However, only DNA-MG demonstrated an acceptable reliability, with small 95% ranges between repeated measurements within the primary tumor (+/- 0.3 DNA-MG) and a strong correlation between the results in the primary tumor and its lymph node metastases. These findings show that the DNA-MG is a valid and reliable prognostic index that adds significant prognostic information to TNM staging.     

Synaptonemal complex analysis in spermatocytes and oocytes of turbot, Scophthalmus maximus (Pisces, Scophthalmidae).

A surface-spreading synaptonemal complex (SC) technique was used to analyze spermatocytes and oocytes of turbot (Scophthalmus maximus) to visualize the process of chromosome synapsis. The total SC length was 205 +/- 12 microm in males and 172 +/- 29 microm in the only female analyzed. A representative SC karyotype of turbot was obtained. Each SC showed lateral elements of equal length. No bivalent exhibiting atypical synaptic behaviour that could be associated with heteromorphic sex chromosomes was observed, either in males or in the female. The DNA content of turbot was evaluated in eight individuals of both sexes by flow cytometry analysis. The 2C mean DNA content of turbot (1.308 +/- 0.009 pg/cell) was among the lowest observed within fishes. No statistical differences in DNA content were revealed between the sexes [Wilcoxon/Mann-Whitney test; P(W(x) = 0.243)]. The SC/DNA content ratio observed in turbot was the highest reported to date in bony fishes (Osteichthyes).     

DNA content in species of Vernonia and Vernonanthura from South America: An approach to systematics and evolution of the Vernonieae (Asteraceae)

There are relatively few studies of DNA content in the Vernonieae (Asteraceae) tribe. The first studies were realized in the Lessingianthus genus and determined the DNA content of 25 species. After DNA content, ploidy level and the total karyotype were compared in 6 Chrysolaena species. The aim of this study was to present, for the first time, the DNA content values of Vernonanthura and Vernonia and to thereby expand knowledge of the Vernonieae tribe. A total of 19 natural populations belonging to the genera Vernonanthura and Vernonia were studied for the first time. The results were compared with other Vernonieae genera and with other Asteraceae tribes. Our results found that Vernonieae have the smallest range of 1C value variation in Asteraceae. Furthermore, there were differences in the DNA content of Vernonia and Vernonanthura. These results show that low DNA content and herbaceous habit in Vernonia are characters derived from the higher DNA content and woody habit present in Vernonanthura. These results could indicate a hybrid origin of one species and allow the determination of both the ploidy and chromosome number of other taxa. The results observed in Vernonanthura species showed a highly significant correlation between 1C-value and latitude.     

Flow cytometric DNA ploidy, p53, PCNA, and c-erbB-2 protein expressions as predictors of survival in surgically resected gastric cancer patients

In order to determine retrospectively the impact of some cytometric and immunohistochemical parameters on the overall survival of gastric cancer patients treated with surgery alone, paraffin-embedded tumor samples from 137 gastric carcinoma patients undergoing curative resection from 1987-1993 were analyzed by flow cytometry (FCM) and immunohistochemistry (p53, c-erbB-2, and PCNA expression). FCM-derived parameters were DNA ploidy and fraction of S-phase cells (SPF). Multiple regression analysis was applied to determine the prognostic significance of the conventional clinicopathologic findings together with the flow cytometric and immunohistochemical parameters on overall survival. When all parameters were entered simultaneously into the Cox regression model, stage and DNA ploidy (DNA index >1.35) clearly emerged as the only independent prognostic factors. When the stages were analysed separately, the independent prognostic factors resulted DNA ploidy in early stages (I-II) and grading in stage IIIA tumors. For stage IIIB tumors, no independent prognostic factor was found. These results indicate that the DNA ploidy pattern is a valuable predictor of survival in curatively resected gastric cancer patients, especially when less advanced tumors are taken into consideration.     

Genome size and numerical polymorphism for the B chromosome in races of maize (Zea mays ssp. mays, Poaceae)

Twenty-one native populations (1120 individuals) of maize from Northern Argentina were studied. These populations, which belong to 13 native races, were cultivated at different altitudes (80-3620 m). Nineteen of the populations analyzed showed B chromosome (Bs) numerical polymorphism. The frequency of individuals with Bs varied from 0 to 94%. The number of Bs per plant varied from 0 to 8 Bs, with the predominant doses being 0, 1, 2, and 3. Those populations with varying number of Bs showed a positive and statistically significant correlation of mean number of Bs with altitude. The DNA content, in plants without Bs (A-DNA)(2n = 20), of 17 populations of the 21 studied was determined. A 36% variation (5.0-6.8 pg) in A-DNA content was found. A significant negative correlation between A-DNA content and altitude of cultivation and between A-DNA content and mean number of Bs was found. This indicates that there is a close interrelationship between the DNA content of A chromosomes and doses of Bs. These results suggest that there is a maximum limit to the mass of nuclear DNA so that Bs are tolerated as long as this maximum limit is not exceeded.     

Karyological relationships among some South American species of Solanum (Solanaceae) based on fluorochrome banding and nuclear DNA amount

Fluorescent chromosome banding and measurements of nuclear DNA content by image cytometry of Feulgen-stained cells were performed in one sample each of eight diploid (2n?=?24) species of Solanum: S.?endoadenium, S.?argentinum, S.?pseudocapsicum, S.?atropurpureum, S.?elaeagnifolium, S.?sisymbriifolium, S.?chenopodioides, and S.?palustre. The species studied could be distinguished by heterochromatin amount, banding patterns, and genome size. They exhibited only GC-rich heterochromatin and showed a comparatively low heterochromatin amount (expressed as percentage of haplotype karyotype length), ranging from 2.10 in S.?argentinum to 8.37 in S.?chenopodioides. Genome size displayed significant variation between species, with 1C-values ranging from 0.75?pg (735?Mbp) in S.?palustre to 1.79?pg (1,754?Mbp) in S.?sisymbriifolium. No significant correlation between genome size and heterochromatin amount was observed, but intrachromosomal asymmetry index (A ₁) was negative and significantly correlated with heterochromatin amount. DNA content was positively and significantly correlated with karyotype length. DNA C-value distribution in the genus as well as karyotype affinities and relationships between species are discussed in relation to different infrageneric classifications of Solanum.     

Genome size in 21 Artemisia L. species (Asteraceae, Anthemideae): systematic, evolutionary, and ecological implications.

Genome size was estimated by flow cytometry in 24 populations belonging to 22 Artemisia taxa (21 species, 1 with two subspecies), which represent the distinct subgenera, life forms, basic chromosome numbers, and ploidy levels in the genus. 2C nuclear DNA content values range from 3.5 to 25.65 pg, which represents a more than sevenfold variation. DNA content per haploid genome ranges from 1.75 to 5.76 pg. DNA amount is very well correlated with karyotype length and ploidy level. Some variations in genome size have systematic and evolutionary implications, whereas others are linked to ecological selection pressures.     

A Flow Cytometric Analysis of the Nuclear 2C DNA Content in 17 Phaseolus Species (53 Genotypes)

The genus Phaseolus is characterized by a highly stable karyotype of 2n = 22. Despite this constancy, the size of the chromosomes varies, and crossing of species is possible only in a few cases. We determined the 2C nuclear DNA content of a number of Phaseolus species, cultivars and genotypes by flow cytometry, in order to realize the interspecific and intraspecific variation of the 2C value. The data range from 1.03 pg to 2.18 pg without any clear correlation to systematic relationships. The mean DNA values of wild and cultivated forms, as well as those of Andean and Mesoamerican genotypes, do not differ significantly. The variation is interpreted in terms of some nucleotypic adaptations. The data may be useful for molecular biological analyses, as well as for biotechnological and classical breeding programmes.     

Karyotypic study of Echinops (Asteraceae) in Fars Province, Iran

A karyotypic study was performed on 19 Echinops species in Fars Province, Iran. The taxa revealed chromosome counts of 2 n = 28, 30, 32 and 34. Somatic chromosome numbers of 18 species are reported for the first time. Using somatic chromosome number as a criterion for section delimitation, the transfer of E. gedrosiacus, E. cyanocephalm and E. sojakii from Sect. Oligolepis to Sect. Ritropsis is suggested. Differences in basic chromosome numbers point towards the possible role played by centric fusion/fission in the karyotypic evolution of the genus. The Karl Pearson coefficient of correlation and principal components analysis indicated the occurrence of structural changes in chromosomes. The species occupied classes 1A, 2A & 2B of Stebbins' karyotype classification, indicating the presence of a primitive symmetrical karyotype in the genus.     

Prognostic significance of proliferative activity, DNA-ploidy, p53 and Ki-ras point mutations in colorectal liver metastases

Paired colorectal liver metastases (CLM) and normal tissue samples from a consecutive series of 36 patients were studied prospectively. MIB-1 expression was studied by immunohistochemistry on paraffin-embedded sections. DNA ploidy and S-phase fraction (SPF) measurements were performed by flow cytometry on frozen tissues. Mutations within the p53 (exons 5-8) and c- Ki-ras (codons 12 and 13) genes were detected by PCR single-strand conformation polymorphism analysis followed by sequencing. A high correlation was observed between the MIB-1 LI and SPF value (rho=0.81; P <0.01). Moreover, p53 gene mutations were associated with either high MIB-1 LI and high SPF. In univariate analysis, SPF and MIB-1 levels were related to risk of death. The association between overall survival and DNA-ploidy or p53 mutations did not reach statistical significance, but a slightly better survival was observed for patients either with DNA-diploid tumours or without mutations ( P =0.05 and P =0.06, respectively). SPF was shown by multivariate Cox model analysis to be an independent prognostic variable and thus it might be a useful prognostic factor in patients with CLM.     

Clinical applications of image cytometry to human tumour analysis

Image cytometry (ICM) is widely applied to the automated screening, the detection, the diagnosis, the classification, the prognosis and the therapeutic follow-up of different types of cancers (breast, bladder, cervix,...). This review describes the analysis methods and the applications of nuclear image analysis, the determination of DNA content and the analysis of morphometry and of nuclear texture. DNA content analysis can contribute to a prognostic information in addition to other prognostic factors for breast, renal and prostate cancers. For ovarian cancer, aneuploidy seems to be related to prognosis. Bladder tumours with DNA aneuploidy were frequently of high malignancy while ploidy was significantly correlated to relapse risk. For digestive cancers, patients presenting DNA diploid tumours show a better survival than patients with aneuploid ones. Morphometry seems to be a more important criterion than other conventional prognostic factors of invasive breast and digestive carcinomas. A differential diagnosis between normal and neoplastic thyroids is more precise when based on a quantitative evaluation of texture associated to morphometry. Textural parameters permit the discrimination of two populations of patients having a different prognosis and could thus be an aid for prognosis in prostatic cancers. Morphonuclear parameters contribute to separate low and high grade bladder carcinomas. Although ICM was frequently reported, results from the reported examples were not always obvious. In conclusion, the measurements obtained with ICM could be helpful for a decision in several cancers but could not be a substitute for the classical approach of the pathologist.     

Independent prognostic value of hormone receptor expression and S-phase fraction in advanced breast cancer

OBJECTIVE: TO assess the prognostic value of immunocytochemically assessed hormone receptor expression and DNA flow cytometry data in advanced breast cancer. STUDY DESIGN: This prospective study with long-term follow-up evaluated the above parameters in relation to overall survival in 392 patients with advanced breast cancer (stages IIB, n = 106; IIIA, n = 66; IIIB, n = 174; and IV, n = 46) using fine needle aspiration cytology. RESULTS: Estrogen and progesterone receptor positivity was detected in 65.1% and 46.1% of the tumors, respectively. DNA aneuploidy was present in 70.9% of the cases, and the median S-phase fraction (SPF) was 9.4%. There was a significant correlation of aneuploidy and high SPF with lack of hormone receptors. The median SPF and SPF tertiles (cutoff values, 6.5% and 12%), applied in the whole series, showed a significant correlation with survival, whereas if SPF was used according to ploidy status, no prognostic significance was found. No differences in relation to survival among different DNA aneuploidy subclasses were verified. In univariate analysis, clinical staging, hormone receptors, DNA ploidy and SPF showed a statistically significant correlation with the overall survival. In multivariate analysis only DNA ploidy did not maintain independent prognostic significance. CONCLUSION: Hormone receptor expression and flow cytometric SPF are independent prognostic factors in advanced breast cancer.     

DNA content in South American endemic species of Lathyrus

The genome size was surveyed in 13 Notolathyrus species endemic to South America by flow cytometry and analyzed in an evolutionary and biogeographic context. A DNA content variation of 1.7-fold was registered, and four groups of species with different DNA content were determined. Although, the 2C values were correlated with the total chromosome length and intrachromosomal asymmetry index (A₁), the karyotype formula remained almost constant. The conservation of the karyotype formula is in agreement with proportional changes of DNA in the chromosome arms. Species with annual life cycle and shorter generation time had the lowest DNA content and the data suggest that changes in DNA content involved reductions of genome size in the perennial to annual transitions. The variation of 2C values was correlated with precipitation of the coldest quarter and, to some extent, with altitude. Additional correlations with other variables were observed when the species were analyzed separately according to the biogeographic regions. In general, the species with higher DNA content were found in more stable environments. The bulk of evidence suggests that changes on genome size would have been one of the most important mechanisms that drove or accompanied the diversification of Notolathyrus species.