P12.06.A Relationship between ascorbate and DNA methylation markers in clinical glioma tumours

Background

Members of the 2-oxoglutarate-dependent dioxygenase (OGDD) enzyme family play an important role in gliomas as they regulate epigenetic modifications and response to hypoxia. The OGDDs require 2-OG and O2 as substrates, and ferrous iron and ascorbate as cofactors. Both hypoxia and aberrant DNA methylation are prognostic indicators for gliomas. The ten-eleven translocase (TET) DNA demethylases are OGDDs that convert 5-methyl cytosine (5mC) to 5-hydroxymethylcytosine (5hmC), with 5hmC levels related to better prognosis. Despite this, there is limited data on the OGDD enzymes and their substrates/cofactors in glioma tissues. Our previous study showed an association between ascorbate content and markers of the hypoxic response in glioblastoma tissue. Here we determine whether there is an association between ascorbate and DNA methylation in glioma. In addition, we assess whether methylation of the methylguanine-DNA methyltransferase (DNA repair enzyme MGMT) promoter is associated with ascorbate content.

Materials and methods

Frozen clinical glioma samples from 37 patients (n=11 WHO grade I-III, n=26 glioblastoma) were obtained from the Cancer Society Tissue Bank (Ethics approval H19/163). Isocitrate dehydrogenase 1 (IDH1) mutation status was determined by sequencing. Samples were processed on dry ice in liquid nitrogen and analysed for ascorbate (high-performance liquid chromatography), global DNA methylation (mass spectrometry) and MGMT promoter analyses (methylation specific PCR).

Results

Many grade I-III tumours were IDH1 R132H mutant (6/11), and most glioblastomas were not (2/26). Glioblastoma had significantly lower ascorbate content than grade I-III tumours (p=0.026). Glioblastoma also had lower global 5hmC levels (p=0.0013). IDH1 R132H tumours tended to have a lower ascorbate content (p=0.09). Ascorbate and 5hmC levels were directly correlated (Spearman r= 0.466, p=0.004). However, cytosine and 5mC showed no association with grade or ascorbate. MGMT promoter methylation status was not associated with global methylation or ascorbate content (p=0.97, p=0.96, respectively).

Conclusion

Our data suggests that ascorbate supports TET activity in clinical glioma. It also appears that site-specific (promoter) methylation was not affected by ascorbate availability. These findings may have clinical implications, as higher 5hmC levels are associated with improved outcome, whilst continued MGMT suppression suggests chemotherapy responsiveness. However, evidence that raising tumour ascorbate leads to increased 5hmC levels, or an associated improvement in survival, requires intervention trials.

Cytotaxonomical analysis of Momordica L. (Cucurbitaceae) species of Indian occurrence

Somatic chromosome number and detailed karyotype analysis were carried out in six Indian Momordica species viz. M. balsamina, M. charantia, M. cochinchinensis, M. dioica, M. sahyadrica and M. cymbalaria (syn. Luffa cymbalaria; a taxon of controversial taxonomic identity). The somatic chromosome number 2n = 22 was reconfirmed in monoecious species (M. balsamina and M. charantia). Out of four dioecious species, the chromosome number was reconfirmed in M. cochinchinensis (2n = 28), M. dioica (2n = 28) and M. subangulata subsp. renigera (2n = 56), while in M. sahyadrica (2n = 28) somatic chromosome number was reported for the first time. A new chromosome number of 2n = 18 was reported in M. cymbalaria against its previous reports of 2n = 16, 22. The karyotype analysis of all the species revealed significant numerical and structural variations of chromosomes. It was possible to distinguish chromosomes of M. cymbalaria from other Momordica species and also between monoecious and dioecious taxa of the genus. Morphology and crossability among the dioecious species was also studied. Evidence from morphology, crossability, pollen viability and chromosome synapsis suggests a segmental allopolyploid origin for M. subangulata subsp. renigera. The taxonomic status of the controversial taxon M. cymbalaria was also discussed using morphological, karyological and crossability data.

Identification of RAPD markers, in situ DNA content and structural chromosomal diversity in some legumes of the mangrove flora of Orissa

Randomly amplified polymorphic DNA (RAPD) markers, karyotypes and 4C DNA content were analyzed in five legume mangroves belonging to the sub-family Papilinoideae (Dalbergia spinosa, Derris heterophylla and D. indica) and Caesalpinioideae (Caesalpinia crista, Cynometra ramiflora) of the family Fabaceae to establish the genetic variability and phylogenetic affinities. Somatic chromosome numbers were reported for the first time in D. spinosa (2n = 20), C. ramiflora (2n = 26) and D. heterophylla (2n = 24) with reconfirmation of the somatic chromosome number in D. indica (2n = 22) and C. crista (2n = 24). Significant intergeneric and interspecific variation of 4C DNA content was observed and that varied from 8.970 pg in C. ramiflora to 28.730 pg in D. indica. From the RAPD analysis, the dendogram showed clustering of Caesalpinia crista and Cynomitra ramiflora into one group (81.80). In the second groups Derris indica and Derris heterophylla were more similar (83.10) than Dalbergia spinosa (85.80). Species-specific DNA markers (900 bp) obtained in D. spinosa from OPN15; 700 and 2000 bp in C. ramiflora from OPN4 and 400 and 800 bp in D. heterophylla and 500 bp DNA fragment in C. crista obtained from OPN-11 were found characteristic RAPD markers of these species. C. crista found more closer affinity to C. ramiflora of the sub-family Caesalpinioideae [genetic distance (1-F) = 0.847]. Derris indica showed closer genetic relation with D. heterophylla [genetic distance (1-F) = 0.856] than D. spinosa [genetic distance (1-F) = 0.876] where Derris and Dalbergia belongs to the sub-family Papilionoideae. By employing these markers the present study has helped to resolve the relationship between the taxonomically diverse leguminous mangroves and study their ability to coexist with mangroves that would shed light on the evolution of mangroves from terrestrial species.

Karyotype analyses and studies on the nuclear DNA content in 30 genotypes of potato (Solanum tuberosum) L

The cytophotometric estimation of 4C DNA content, and karyotypic and somatic chromosome number analyses were carried out in 30 genotypes comprising seven cultivars and 23 advanced breeding lines of Solanum tuberosum. Detailed karyotype analysis revealed genotype specific chromosomal characteristics and structural alterations in chromosomes of the genome, with a rare phenomenon of aneusomatic (2n = 4x + 2 = 50) condition in cv.K. Chandramukhi. The origin of this variation could be attributed to mitotic non-disjunction in the shoots giving rise to aneusomatic roots. Highly significant variations in the genome length, volume and total form percentage were noted at the cultivar level. The total chromosome length varied from 84.56 microm in cv.K. Pukhraj to 127.62 microm in MS/89-60, with an average value of 100.94 microm +/- 1.82. Total chromosome volume varied from 57.22 microm3 in MS/92-1090 to 132.64 microm3 in JW-160. Significant variations in the 4C DNA content (7.28-15.83 pg) were recorded at the cultivar level, with an exceptionally high DNA content (22.24 pg) in cv.K. Chandramukhi. This could be due to the aneusomatic condition of this genotype. Correlation studies revealed interdependence between the chromosomal and nuclear parameters of the genotypes. Structural alterations in the chromosomes, as well as loss or addition of highly repetitive sequences in the genome, caused variations in DNA content at the cultivar level. Variations in genomic structure and nuclear DNA content of the 48-chromosome genotypes suggest a genetic drift during microevolution, leading to the development of new cultivars.

Effect of NaCl on leaf salt secretion and antioxidative enzyme level in roots of a mangrove, Aegiceras corniculatum

Short-term salt (NaCl) treatment on Aegiceras corniculatum in roots and leaves showed no change in fresh and dry weight of leaves, roots and leaf area. There was no significant change in total soluble root protein, photosynthetic pigments of leaves and spectral characteristics of thylakoids. However, the activity of antioxidative enzymes (catalase, ascorbate peroxidase and guaiacol peroxidase) in roots decreased by 72, 58 and 80% respectively after 96 hr of treatment (300 mM of NaCl). Secretion of salts from the leaf salt glands and salt accumulation on upper surface of the leaves were quantified that revealed linear increase of salt secretion of leaf with increase in period of salt treatment. It was concluded that loss of activities of antioxidative enzymes at high salt treatment, caused leaf senescence in spite of high rates of salt secretion by Aegiceras corniculatum.

Seasonal dynamics of the tissue levels of total protein, free amino acid and ribonucleic acid in an Indian air-breathing teleost, Channa punctatus

The tropical freshwater air-breathing teleost, Channa punctatus, reveals a seasonal metabolic reorganization with reference to its biochemical tissue compositions. The summer-adapted and winter-adapted C. punctatus seem to be two biochemically distinct populations. Besides, the different reproductive phases viz. prespawning, spawning, post-spawning, preparatory-I and preparatory-II are also biochemically distinct.

Regulation of membrane lipid bilayer structure during seasonal variation: a study on the brain membranes of Clarias batrachus

(1) A significant seasonal variation in the membrane fluidity (as sensed by DPH-fluorescence polarization), membrane lipid components (phospholipid and neutral lipid), fatty acid composition of membrane phospholipid (phosphatidylcholine, phosphatidylethanolamine and sphingomyelin), positional distribution of fatty acids at Sn-1 and Sn-2 position of phosphatidyl-choline and -ethanolamine is noticed in the brain membranes (myelin, synaptosomes, and mitochondria) of a tropical air breathing teleost, Clarias batrachus. (2) A 'partial compensation' of membrane fluidity during seasonal adaptation is observed in myelin and mitochondria membrane fractions. Synaptosomes membrane fraction exhibits a different response. Depletion (about 15-70%) of membrane lipid components (phospholipid, cholesterol, diacylglycerol and triacylglycerol) per unit of membrane protein is the characteristic feature of summer adaptation. An increase (about 20-100%) in the level of oleic acid and decrease (about 20-60%) in the level of stearic acid are almost common features in membrane phospholipid fractions of winter-adapted Clarias (3) From the tissue slice experiment it is evident that there is an activation of cellular phospholipase A2 at lower growth temperature and of cellular phospholipase A1 at higher growth temperature and this suggests the reorganization of molecular architecture of the membrane during seasonal adaptation. (4) Accumulation of oleic acid in Sn-1 position and polyunsaturated fatty acids in Sn-2 position of phosphatidylcholine and -ethanolamine during winter indicates an increase in the concentration of 1-monoenoic, 2-polyenoic molecular species of phospholipid in order to maintain the stability of membrane lipid bilayer.

Solitary thyroid nodule: a study of 100 cases

One hundred cases of solitary thyroid nodules attending the thyroid clinic, Institute of Postgraduate Medicine & Research, Dhaka (IPGMR) and the Institute of Nuclear Medicine (INM) were included in a prospective study. Thyroid ultrasonography (USG), scintiscanning, radioactive iodine (I131) uptake (RAIU), estimation of serum total T3, T4 & TSH and Fine Needle Aspiration Cytology (FNAC) were performed in all cases. Surgical resection with histopathologic study was performed in selected cases. Extra-nodular part of the thyroid gland was normal in 68 and diffusely enlarged in 32, RAIU was normal in 62, high in 36 and very low in two subjects. Nodules were solid at USG in 67 subjects, cystic in 16 subjects and of mixed consistency in 17 subjects. Goitrous subjects had significantly lower T4 (p < 0.001) and higher T3 (p < 0.01) and TSH (p < 0.001) than non-goitrous ones. Colloid nodule was the commonest pathology occurring in 41 cases, followed by thyroid cysts (26), follicular adenoma (23), adenoma with cystic change (7), subacute thyroiditis (2) and papillary carcinoma (1). Colloid nodules were more common in goitrous subjects which could hint at iodine deficiency as the major cause of such nodules. Hyperfunctioning follicular adenomas occurred exclusively in non-goitrous subjects. Carcinoma appeared to be uncommon in patients with solitary nodules. It gives an opportunity to our physicians to be more conservative in selecting patients with solitary thyroid nodules for surgical treatment.

In vitro somatic embryogenesis from callus culture of the timber yielding treeHardwickia binata Roxb

Somatic embryogenesis was achieved in callus cultures derived from immature cotyledonary explants ofHardwickia binata Roxb., a multipurpose leguminous tree, on semisolid modified Murashige and Skoog's (mMS) medium containing 2900 mg/l potassium nitrate (KNO3) supplemented with 4.64 µM kinetin (Kn) and 5.37µM a-naphthaleneacetic acid (NAA). Somatic embryos proliferated rapidly after transfer to MS basal medium supplemented with 2052.6 µM L-glutamine and 0.084 µM gibberellic acid (GA3). Maturation of somatic embryos was achieved on half-strength MS basal medium supplemented with 1.23 µM IBA and 2% (w/v) sucrose. Histological studies confirmed different developmental stages of somatic embryogenesis inHardwickia binata.

Purification, pore-forming ability, and antigenic relatedness of the major outer membrane protein of Shigella dysenteriae type 1

The major outer membrane protein (MOMP), the most abundant outer membrane protein, was purified to homogeneity from Shigella dysenteriae type 1. The purification method involved selective extraction of MOMP with sodium dodecyl sulfate in the presence of 0.4 M sodium chloride followed by size exclusion chromatography with Sephacryl S-200 HR. MOMP was found to form hydrophilic diffusion pores by incorporation into artificial liposome vesicles composed of egg yolk phosphatidylcholine and dicetylphosphate, indicating that MOMP of S. dysenteriae type 1 exhibited significant porin activity. However, the liposomes containing heat-denatured MOMP were barely active. The molecular weight of MOMP found by size exclusion chromatography was 130,000, and in sodium dodecyl sulfate-10% polyacrylamide gel it moved as an oligomer of 78,000 molecular weight. Upon boiling, fully dissociated monomers of 38,000 molecular weight were seen for S. dysenteriae type 1. However, among the four Shigella spp., the monomeric MOMP generated upon boiling ranged from 38,000 to 35,000 in molecular weight. Antibody raised in BALB/c mice immunized with MOMP of S. dysenteriae type 1 reacted strongly with purified MOMP of S. dysenteriae type 1 in an enzyme-linked immunosorbent assay (ELISA). The antibody reacted with whole-cell preparations of S. dysenteriae type 1 in an ELISA, suggesting that MOMP possessed surface components. Moreover, MOMP could be visualized on the bacterial surface by immunoelectron microscopy with anti-MOMP antibody. S. dysenteriae type 1 MOMP-specific immunoglobulin eluted from MOMP bound to a nitrocellulose membrane was found to cross-react with MOMP preparations of S. flexneri, S. boydii, and S. sonnei, indicating that MOMPs were antigenically related among Shigella species. The strong immunogenicity, surface exposure, and antigenic relatedness make MOMP of Shigella species an immunologically significant macromolecule for study.

Modulation of fish liver fructose-1, 6-bis phosphatase by ammonia stress

Hepatic fructose 1, 6 bisphosphatase (Fru-P2ase) from Channa punctatus exhibits 100% and 60% elevations of its maximal catalytic rates (Vmax) at pH 7.5 and 9.5 respectively in summer over those in winter. Both the neutral and alkaline activities of the enzyme are enhanced remarkably (100%) in the winter-adapted fish due to exposure to 10 mg N/1 of unionized ammonia for three weeks. While the neutral activity of the purified enzyme is increased in vitro by NH+4 ions in dose-dependent manner upto about 150 mM NH4, the alkaline activity is found to be activated at a very low concentration of NH4+ (25 mM) and inhibited at 100-150 mM NH4+. The enzyme also shows a characteristics potentiation of 5'-AMP inhibition by NH4+ (125 mM).

Compensations for temperature in the activities of digestive enzymes of Periplaneta americana (L.)

1. Differential thermal acclimatory responses of maximal catalytic rates (Vmax) of digestive enzymes have been measured in both sexes of Periplaneta americana adapted to 16 and 32 degrees C. 2. Salivary amylase of females and gastric protease of males exhibit "translational" acclimation, the former showing a "complete" but the latter only a "partial" compensation. The value of Q10 is not altered in the adaptive response. 3. An alteration of the thermal coefficient is evidenced by the "translational-cum-rotational" compensation of gastric amylolytic activity, with significant warm acclimation but no cold acclimation in both sexes. 4. Gastric protease of female cockroaches and gastric lipase of both sexes are characterized by the lack of an adaptive compensation to temperature, while salivary amylase of male appears to manifest an "inverse" acclimation. 5. Sexual dimorphism in the levels of the activities and in the patterns of thermal acclimation of the digestive enzymes is indicated.