Volume 28, Issue 2
March 2003, pages 135-247
pp 135-138 March 2003 Clipboard
pp 139-140 March 2003 Clipboard
pp 141-144 March 2003 Commentary
pp 145-147 March 2003 Commentary
pp 149-154 March 2003 Perspectives
pp 155-161 March 2003 Articles
The present paper discusses a general expression for determining the minimum sample size (plants) for a given number of seeds or vice versa for capturing multiple allelic diversity. The model considers sampling from a large 2 k-ploid population under a broad range of mating systems. Numerous expressions/results developed for germplasm collection/regeneration for diploid populations by earlier workers can be directly deduced from our general expression by assigning appropriate values of the corresponding parameters. A seed factor which influences the plant sample size has also been isolated to aid the collectors in selecting the appropriate combination of number of plants and seeds per plant. When genotypic multiplicity of seeds is taken into consideration, a sample size of even less than 172 plants can conserve diversity of 20 alleles from 50,000 polymorphic loci with a very large probability of conservation (0.9999) in most of the cases.
pp 163-168 March 2003 Articles
Infertility affects 15% couples attempting pregnancy and in 40–50% of these cases the male partner has qualitative or quantitative abnormalities of sperm production. Microdeletions in the azoospermia factor (AZF) region on the long arm of the Y chromosome are known to be associated with spermatogenic failure and have been used to define three regions on Yq (AZFa, AZFb and AZFc) which are critical for spermatogenesis and are recurrently deleted in infertile males. Semen analysis was carried out on one hundred and twenty five infertile males with oligozoospermia and azoospermia. Cytogenetic analysis was done for all the cases and in all cytogenetically normal cases (n = 83) microdeletion analysis was carried out on DNA extracted from peripheral blood using PCR. The sequence tagged sites (STS) primers sY84, sY86 (AZFa); sY127, sY134 (AZFb); sY254, sY255 (AZFc) were used for each case. Eight of the eighty three cases (9.63%) showed deletion of at least one of the STS markers. Correlation of phenotype with microdeletion was done in each case to determine any phenotype association with deletion of particular AZF locus. Based on the present study, the frequency of microdeletion in the Indian population is 9.63%. This study emphasizes the need for PCR analysis for determining genetic aetiology in cases with idiopathic severe testiculopathy.
pp 169-179 March 2003 Articles
Amino acid sequence analysis corresponding to the PPE proteins in H37Rv and CDC 1551 strains of theMycobacterium tuberculosis genomes resulted in the identification of a previously uncharacterized 225 amino acid-residue common region in 22 proteins. The pairwise sequence identities were as low as 18%. Conservation of amino acid residues was observed at fifteen positions that were distributed over the whole length of the region. The secondary structure corresponding to this region is predicted to be a mixture of a-helices and β-strands. Although the function is not known, proteins with this region specific to mycobacterial species may be associated with a common function. We further observed another group of 20 PPE proteins corresponding to the conserved C-terminal region comprising 44 amino acid residues with GFxGT and PxxPxxW sequence motifs. This region is preceded by a hydrophobic region, comprising 40–100 amino acid residues, that is flanked by charged amino acid residues. Identification of conserved regions described above may be useful to detect related proteins from other genomes and assist the design of suitable experiments to test their corresponding functions. Amino acid sequence analysis corresponding to the PE proteins resulted in the identification of tandem repeats comprising 41-43 amino acid residues in the C-terminal variable regions in two PE proteins (Rv0978 and Rv0980). These correspond to the AB repeats that were first identified in some proteins of theMethanosarcina mazei genome, and were demonstrated as surface antigens. We observed the AB repeats also in several other proteins of hitherto uncharacterized function inArchaea andBacteria genomes. Some of these proteins are also associated with another repeat called the C-repeat or the PKD-domain comprising 85 amino acid residues. The secondary structure corresponding to the AB repeat is predicted mainly as 4 β-strands. We suggest that proteins with AB repeats inMycobacterium tuberculosis and other genomes may be associated as surface antigens. TheM. leprae genome, however, does not contain either the AB or C-repeats and different proteins may therefore be recruited as surface antigens in theM. leprae genome compared to theM. tuberculosis genome.
pp 181-188 March 2003 Articles
Neurotrophins and their receptors of the Trk family play a critical role in proliferation, differentiation and survival of the developing neurons. There are reports on their expression in neoplasms too, namely, the primitive neuroectodermal tumours of childhood, and in adult astrocytic gliomas. The involvement of Trk receptors in tumour pathogenesis, if any, is not known. With this end in view, the present study has examined 10 tumour biopsy samples (identified as astrocytoma, pilocytic astrocytoma and glioblastoma) and peritumoral brain tissue of adult patients, for the presence of Trk A and Trk B receptors, by immunohistochemistry. The nature of the tumour samples was also confirmed by their immunoreactivity (IR) to glial fibrillary acidic protein. In the peritumoral brain tissue, only neurons showed IR for Trk A and Trk B. On the contrary, in the tumour sections, the IR to both receptors was localized in the vast majority of glia and capillary endothelium. There was an obvious pattern of IR in these gliomas: high levels of IR were present in the low-grade (type I and II) astrocytoma; whereas in the advanced malignant forms (WHO grade IV giant cell glioblastoma and glio-blastoma multiforme) the IR was very weak. These findings suggest that Trk A and Trk B are involved in tumour pathogenesis, especially in the early stage, and may respond to signals that elicit glial proliferation, and thus contribute to progression towards malignancy.
pp 189-198 March 2003 Articles
Mus terricolor I, II and III are the three chromosomal species which differ in stable autosomal short-arm heterochromatin variations established in homozygous condition. Analysis of meiosis in the laboratory-generated F1 male hybrids from crosses (both ways) betweenM. terricolor I and II and betweenM. terricolor I and III shows high frequencies of pairing abnormalities at pachytene. The backcross (N3 generation) male hybrids betweenM. terricolor I and II have meiotic abnormalities as in the F1male hybrids, though to a lesser extent. They show difference in pairing abnormalities in the different karyotypic forms; the backcross hybrids heterozygous for the heterochromatic short arms have more anomalies compared to the homokaryotypic hybrids. This suggests a negative influence of the heterochromatin heterozygosity in meiotic pairing. The results indicate a role for heterochromatin variations in the development of a reproductive barrier in the speciatingM. terricolor complex.
pp 199-203 March 2003 Articles
Embryos excised from seeds of six generations (P1, P2, F1, BC1, BC2 and F2) of a cross WH 283 x WH 533 were cultured on modified MS medium already inoculated with secondary sporidia ofNeovossia indica. Significant variations for callusing response (CR) (54.55–75.55%) were observed among generations but the presence or absence ofN. indicia did not affect callusing response. A clear inhibition zone (IZ) was formed around each embryo showing callusing. The diameter of IZ varied significantly among generations and was maximum in the resistant genotype, WH 283 (3.60 cm). Fresh weight and dry weight of calli, initiated from embryo cultured and inoculated withN. indica, varied significantly among generations. Coefficient of infection as well as percentage of infection reflected the overdominance of susceptibility. Generation mean analysis showed that the three parameter model was adequate for diameter of IZ only. Six-parameter model showed that additive (in presence ofN. indica), additive and additive x dominance (in absence ofN. indica) effects were also significant. Complementary type of epistasis for fresh weight of calli and dominance, and dominance x dominance effects for dry weight of calli were observed in the presence ofN. indica. Magnitude of additive effects was higher for diameter of IZ in three parameter model. Therefore, selection might assist in improving this trait and thus indirectly help in attaining the resistance towardsN. indica.
pp 205-213 March 2003 Articles
Exposure of bovine pulmonary artery smooth muscle plasma membrane suspension with the oxidant H2O2 (1 mM) stimulated Ca2+ATPase activity. We sought to determine the role of matrix metalloprotease-2 (MMP-2) in stimulating Ca2+ATPase activity by H2O2 in the smooth muscle plasma membrane. The smooth muscle membrane possesses a Ca2+-dependent protease activity in the gelatin containing zymogram having an apparent molecular mass of 72 kDa. The 72 kDa protease activity was found to be inhibited by EGTA, 1: 10-phenanthroline, a2-macroglobulin and tissue inhibitor of metalloprotease-2 (TIMP-2) indicating that the Ca2+-dependent 72 kDa protease is the MMP-2. Western immunoblot studies of the membrane suspension with polyclonal antibodies of MMP-2 and TIMP-2 revealed that MMP-2 and TIMP-2, respectively, are the ambient matrix metalloprotease and the corresponding tissue inhibitor of metalloprotease in the membrane.
In addition to increasing the Ca2+ATPase activity, H2O2 also enhanced the activity of the smooth muscle plasma membrane associated protease activity as evidenced by its ability to degrade14C-gelatin. The protease activity and the Ca2+ATPase activity were prevented by the antioxidant, vitamin E, indicating that the effect produced by H2O2 was due to reactive oxidant species(es). Both basal and H2O2 stimulated MMP-2 activity and Ca2+ATPase activity were inhibited by the general inhibitors of matrix metalloproteases: EGTA, 1: 10-phenanthroline, α2-macroglobulin and also by TIMP-2 (the specific inhibitor of MMP-2) indicating that H2O2 increased MMP-2 activity and that subsequently stimulated Ca2+ATPase activity in the plasma membrane. This was further confirmed by the following observations: (i) adding low doses of MMP-2 or H2O2 to the smooth muscle membrane suspension caused submaximal increase in Ca2+ATPase activity, and pretreatment with TIMP-2 prevents the increase in Ca2+ATPase activity; (ii) combined treatment of the membrane with low doses of MMP-2 and H2O2 augments further the Ca2+ATPase activity caused by the respective low doses of either H2O2 or MMP-2; and (iii) pretreatment with TIMP-2 prevents the increase in Ca2+ATPase activity in the membrane caused by the combined treatment of MMP-2 and H2O2.
pp 215-221 March 2003 Articles
In order to evaluate the modulatory effects of manganese, high fat diet fed and alloxan diabetic rats were taken and the changes in the glucose oxidation, glycerol release and effects of manganese on these parameters were measured from adipose tissue. An insulin-mimetic effect of manganese was observed in the adipose tissue in the controls and an additive effect of insulin and manganese on glucose oxidation was seen when Mn2+ was addedin vitro. The flux of glucose through the pentose phosphate pathway and glycolysis was significantly decreased in high fat fed animals. Although thein vitro addition of Mn2+ was additive with insulin when14CO2 was measured from control animals, it was found neither in young diabetic animals (6–8 weeks old) nor in the old (16 weeks old). Both insulin and manganese caused an increased oxidation of carbon-1 of glucose and an increase of its incorporation into14C-lipids in the young control animals; the additive effect of insulin and manganese suggests separate site of action. This effect was decreased in fat fed animals, diabetic animals and old animals. Manganese alone was found to decrease glycerol in both the control and diabetic adipose tissue inin vitro incubations. The results of the effects of glucose oxidation, lipogenesis, and glycerol release in adipose tissue of control and diabetic animals of different ages are presented together with the effect of manganese on adipose tissue from high fat milk diet fed animals.
pp 223-233 March 2003 Articles
We have demonstrated the presence of a Ca2+-dependent/calmodulin-stimulated protein kinase (PK) in chloronema cells of the mossFunaria hygrometrica. The kinase, with a molecular mass of 70,000 daltons (PK70), was purified to homogeneity using ammonium sulphate fractionation, DEAE-cellulose chromatography, and calmodulin (CaM)-agarose affinity chromatography. The kinase activity was stimulated at a concentration of 50 (AM free Ca2+, and was further enhanced 3–5-fold with exogenously added 3–1000 nm moss calmodulin (CaM). Autophosphorylation was also stimulated with Ca2+ and CaM. Underin vitro conditions, PK70 phosphorylated preferentially lysine-rich substrates such as HIIIS and HVS. This PK shares epitopes with the maize Ca2+-dependent/calmodulin-stimulated PK (CCaMK) and also exhibits biochemical properties similar to the maize, lily, and tobacco CCaMK. We have characterized it as a moss CCaMK.
pp 235-242 March 2003 Articles
An anaerobic methylotrophic methanogenic enrichment culture, with sustained metabolic characteristics, including that of methanation for over a decade, was the choice of the present study on interspecies interactions. Growth and methanation by the enrichment were suppressed in the presence of antibiotics, and no methanogen grown on methanol could be isolated using stringent techniques. The present study confirmed syntrophic metabolic interactions in this enrichment with the isolation of a strain ofPseudomonas sp. The organism had characteristic metabolic versatility in metabolizing a variety of substrates including alcohols, aliphatic acids, amino acids, and sugars. Anaerobic growth was favoured with nitrate in the growth medium. Cells grown anaerobically with methanol, revealed maximal nitrate reductase activity. Constitutive oxidative activity of the membrane system emerged from the high-specific oxygen uptake and nitrate reductase activities of the aerobically and anerobically grown cells respectively. Cells grown anaerobically on various alcohols effectively oxidized methanol in the presence of flavins, cofactor FAD and the methanogenic cofactor F420, suggesting a constitutive alcohol oxidizing capacity. In cells grown anaerobically on methanol, the rate of methanol oxidation with F420 was three times that of FAD. Efficient utilization of alcohols in the presence of F420 is a novel feature of the present study. The results suggest that utilization of methanol by the mixed culture would involve metabolic interactions between thePseudomonas sp. and the methanogen(s). Methylotrophic, methanogenic partnership involving an aerobe is a novel feature hitherto unreported among anaerobic syntrophic associations and is of ecological significance.
pp 243-247 March 2003 Articles
This study examines mycelial colonization of common soil fungi by bradyrhizobia and an azorhizobial strain, resulting in the forming of biofilms. The effects of the fungal exudates on a bradyrhizobial strain have also been investigated. Bradyrhizobia gradually colonized the mycelia for about 18 days, after which the biofilm structures collapsed with the release of the rhizobial cell clusters to the culture medium. The azorhizobial strain showed differential colonization of the mycelia. In general, there were no considerable mycotoxin effects of the fungal exudates on the bradyrhizobial strain used, instead the rhizobial strain utilized the exudates as a source of nutrition. This study indicates that the present microbial association with biofilm formation has important implications in the survival of rhizobia under adverse soil conditions devoid of vegetation. Further, it could have developed an as yet unidentified nitrogen fixing system that could have contributed to the nitrogen economy of soils.