Deciphering genetic diversity analysis of saffron (Crocus sativus L.) using RAPD and ISSR markers

The existence of genetic diversity in Crocus sativus has globally remained a mystery till date. The study investigated PCR based DNA amplification profile of saffron using ISSR and RAPD based primers. A total of 38 amplicons were generated by ISSR primers in the range from 7 to 12 with an average of 9.50 bands per primer. 20 bands were found to be polymorphic and 18 were monomorphic with an average percentage of polymorphism as 52.48%. RAPD based amplification revealed a total 161 amplicons, 107 as polymorphic and 54 as monomorphic with an average percentage of polymorphism as 66.44%. Cumulative results of RAPD and ISSR demonstrated that Nei-Li’s similarity index ranged between 0.70 and 0.97. The results of AMOVA has revealed 9% of variance among populations and 91% of variance within populations, Φ PT was found as 0.089, which indicates existence of genetic differences though limited. In conclusion, the results indicate that saffron accessions are minimally genetically differentiated, which could be capitalized in future breeding programmes to ameliorate this precious crop.     

Pseudogenization in pathogenic fungi with different host plants and lifestyles might reflect their evolutionary past

Pseudogenes are genes with significant homology to functional genes, but contain disruptive mutations (DMs) leading to the production of non‐ or partially functional proteins. Little is known about pseudogenization in pathogenic fungi with different lifestyles. Here, we report the identification of DMs causing pseudogenes in the genomes of the fungal plant pathogens Botrytis cinerea, Cladosporium fulvum, Dothistroma septosporum, Mycosphaerella fijiensis, Verticillium dahliae and Zymoseptoria tritici. In these fungi, we identified 1740 gene models containing 2795 DMs obtained by an alignment‐based gene prediction method. The contribution of sequencing errors to DMs was minimized by analyses of resequenced genomes to obtain a refined dataset of 924 gene models containing 1666 true DMs. The frequency of pseudogenes varied from 1% to 5% in the gene catalogues of these fungi, being the highest in the asexually reproducing fungus C. fulvum (4.9%), followed by D. septosporum (2.4%) and V. dahliae (2.1%). The majority of pseudogenes do not represent recent gene duplications, but members of multi‐gene families and unitary genes. In general, there was no bias for pseudogenization of specific genes in the six fungi. Single exceptions were those encoding secreted proteins, including proteases, which appeared more frequently pseudogenized in C. fulvum than in D. septosporum. Most pseudogenes present in these two phylogenetically closely related fungi are not shared, suggesting that they are related to adaptation to a different host (tomato versus pine) and lifestyle (biotroph versus hemibiotroph).     

Cloning and characterization of Na+/H+ antiporter (LfNHX1) gene from a halophyte grass Leptochloa fusca for drought and salt tolerance

Abiotic stresses such as salinity and drought have adverse effects on plants. In the present study, a Na⁺/H⁺ antiporter gene homologue (LfNHX1) has been cloned from a local halophyte grass (Leptochloa fusca). The LfNHX1 cDNA contains an open reading frame of 1,623 bp that encodes a polypeptide chain of 540 amino acid residues. LfNHX1 protein sequence showed high similarity with NHX1 homologs reported from other halophyte plants. Amino acid and nucleotide sequence similarity, protein topology modeling and the presence of conserved functional domains in the LfNHX1 protein sequence classified it as a vacuolar NHX1 homolog. The overexpression of LfNHX1 gene under CaMV35S promoter conferred salt and drought tolerance in tobacco plants. Under drought stress, transgenic plants showed higher relative water contents, photosynthetic rate, stomatal conductance and membrane stability index as compared to wild type plants. More negative value of leaf osmotic potential was also observed in transgenic plants when compared with wild type control plants. Transgenic plants showed better germination and root growth at 2 mg L^?1 Basta herbicide and three levels (100, 200 and 250 mM) of sodium chloride. These results showed that LfNHX1 is a potential candidate gene for enhancing drought and salt tolerance in crops.     

Predicting deleterious nsSNPs: an analysis of sequence and structural attributes

Background  

There has been an explosion in the number of single nucleotide polymorphisms (SNPs) within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs), some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl.     

Tyrosinase inhibitory cycloartane type triterpenoids from the methanol extract of the whole plant of Amberboa ramosa Jafri and their structure-activity relationship

New tyrosinase inhibitory cycloartane triterpenoids have been discovered from the methanol extract of the whole plant of Amberboa ramosa (Roxb.) Jafri, which is a member from the Compositae family. Utilizing the conventional spectroscopic techniques, including 1D and 2D NMR analysis, and also by comparing the experimental with literature data, the isolated compounds proved to be cycloartane type triterpenoids. These cycloartanes are: (22R)-cycloart-20, 25-dien-2alpha3beta22alpha triol (1), (22R)-cycloart-23-ene-3beta, 22alpha, 25-triol (2), cycloartenol (3), cycloart-23-ene-3beta, 25-diol (4), cycloart-20-ene-3beta, 25-diol (5), cycloart-25-ene-3beta, (22R) 22-diol (6), 3beta, 21, 22, 23-tetrahydroxy-cycloart-24 (31), 25 (26)-diene (7), and (23R)-5alpha-cycloart-24-ene-3beta, 21, 23-triol (8). Out of these eight compounds, compound 3 did not show any activity against the enzyme tyrosinase. Among them compound 7 was found to be the most potent (1.32 microM) when compared with the standard tyrosinase inhibitors kojic acid (16.67 microM) and L-mimosine (3.68 microM). Finally in this paper, we have discussed the structure-activity relationships of these molecules.     

Anatomical adaptations to salinity in cogon grass [Imperata cylindrica (L.) Raeuschel] from the Salt Range, Pakistan

To examine anatomical adaptations in a potential forage grass, Imperata cylindrica (L.) Raeuschel, a population was collected from the natural salt-affected soils of the Salt Range, Pakistan. Using a hydroponic system, the degree of salt tolerance in terms of structural modifications in the Salt Range ecotype was compared with that in an ecotype collected from a normal non-saline habitat of the Faisalabad region. The Salt Range ecotype was superior to the Faisalabad ecotype in biomass production under saline conditions. High salt tolerance of the Salt Range ecotype was associated with increased succulence in root and leaf (mainly midrib), formation of aerenchyma in leaf sheath, increased vascular bundle area, metaxylem area and phloem area, highly developed bulliform cells on leaves and increased sclerification in root and leaf. Furthermore, both stomatal density and stomatal area were considerably reduced under high salinities in the Salt Range ecotype.     

A brief report: Yale Research Symposium on Complementary and Integrative Medicine

The 2010 Yale Research Symposium on Complementary and Integrative Medicine highlighted original research in related areas by Yale faculty and provided a forum to discuss and debate issues of evidence and plausibility. In this brief report, we describe selected presentations on such diverse foci as nutritional influences on cancer, acupuncture for low back pain, protein intake's effects on bone consumption, Chinese herb-derived adjuvant chemotherapy, and the relationship between anger and cardiac arrhythmia. This symposium demonstrated that rigorous research methods are being used to study unconventional therapies and that an integrative medicine approach requires a solid scientific foundation.     

Comparison of different methods for erythroid differentiation in the K562 cell line

Objective

To compare methods for erythroid differentiation of K562 cells that will be promising in the treatment of beta-thalassemia by inducing γ-globin synthesis.

Results

Cells were treated separately with: RPMI 1640 medium without glutamine, RPMI 1640 medium without glutamine supplemented with 1 mM sodium butyrate, RPMI 1640 medium supplemented with 1 mM sodium butyrate, 25 µg cisplatin/ml, 0.1 µg cytosine arabinoside/ml. The highest differentiation (84 %) with minimum toxicity was obtained with cisplatin at 15 µg /ml. Real-time RT-PCR showed that expression of the γ-globin gene was significantly higher in the cells differentiated with cisplatin compared to undifferentiated cells (P < 0.001).

Conclusions

Cisplatin is useful in the experimental therapy of ß-globin gene defects and can be considered for examining the basic mechanism of γ-reactivation.