5-Hydroxypyrimidine deoxynucleoside triphosphates are more efficiently incorporated into DNA by exonuclease-free Klenow fragment than 8-oxopurine deoxynucleoside triphosphates.

Recent studies with 8-oxodeoxyguanosine triphosphate (8-oxodGTP) have suggested that incorporation of oxidized nucleotides from the precursor pool into DNA may have deleterious effects. Here we show that 5-hydroxydeoxycytosine triphosphate (5-OHdCTP) and 5-hydroxydeoxyuridine triphosphate (5-OHdUTP) are more efficient substrates than 8-oxodGTP for Escherichia coli DNA polymerase I Klenow fragment lacking proofreading activity, while 8-oxodeoxyadenosine triphosphate (8-oxodGTP, 5-OHdCTP can mispair with dA in DNA but with lower efficiency. Since the 5-hydroxypyrimidines are present in normal and oxidized cellular DNA in amounts similar to the 8-oxopurines, these data suggest that enzymatic mechanisms might exist for removing them from the DNA precursor pools.     

DNA-like duplexes with repetitions. III. Efficient template-guided chemical polymerization of d(TGGCCAAGCTp).

Self-association of a decanucleotide d(TGGCCAAGCTp) in an aqueous solution is shown by UV spectroscopy, CD and sedimentation analysis to yield a pseudopolymeric (concatemeric) duplex having a geometry similar to that of DNA B-type. It is demonstrated that in conditions when the concatemeric duplex is stable a water-soluble carbodiimide induces efficient polymerization of the 3'- or 5'-phosphorylated decanucleotide, and the resulting polymers d(TGGCCAAGCTp)2-10 contain only natural phosphodiester bonds. In conditions optimal for template-guided polymerization of d(TGGCCAAGCTp) the overall yield of 20-100-member polynucleotides exceeds 90%. The obtained polymeric duplexes are cleaved by restriction endonuclease Alu II, Bsu RI, and Hind III to corresponding decamers which were isolated and sequenced.     

Photoinduced electron transfer reactions of pyranine with benzoquinone and titanium dioxide

The fluorescence quenching of pyranine by benzoquinone in acetonitrile medium was studied using steady‐state and time‐resolved fluorescence techniques. The quenching process was characterized by a Stern–Volmer plot, which displayed a linear aspect. From the linear plot, the bimolecular quenching rate constant was obtained. The obtained rate constants are within diffused controlled limits. The results show that benzoquinone can efficiently quench the fluorescence of pyranine with dynamic quenching rate constants in the order of 10¹⁰ M^–1 s^–1, suggesting that the pyranine can act as a good electron donor for photoinduced electron transfer in artificial photosynthesis and organic solar cells. In addition, the electron injection dynamics of a pyranine/titanium dioxide semiconductor film was also investigated and electron injection from the excited state pyranine into the conduction band of titanium dioxide is suggested. These preliminary results hold promise for the possibility of using pyranine in dye‐sensitized solar cells. Copyright © 2016 John Wiley & Sons, Ltd.     

In vitro shoot propagation of Dendrocalamus strictus nees

Multiple shoots were induced from seedling and axillary buds of mature plants of Dendrocalamus strictus on Murashige and Shoog's medium supplemented with BA and kinetin. About 35–45 shoots were obtained within 20–25 days from a nodal explant of seedling and 3–8 shoots were obtained from a nodal explant of mature plants in the primary culture. The seedling derived cultures were separated into groups of 5–7 and transferred to fresh subculture medium. Rooting of the shoots was achieved under in vitro and ex vitro conditions. 85–90% of rooting was achieved by the ex vitro method using IBA. This revised version was published online in June 2006 with corrections to the Cover Date.     

Evaluation and elimination of inhibitory effects of salts and heavy metal ions on biodegradation of Congo red by Pseudomonas sp. mutant

In this study, it was attempted to evaluate the influences and also recommended some elimination methods for inhibitory effects offered by salts and heavy metal ions. Congo red dye solution treated with mutant Pseudomonas sp. was taken as a model system for study. The salts used in this study are NaCl, CaCl₂ and MgSO₄·7H₂O. Though the growth was inhibited at concentrations above 4 g/l, toleration was achieved by acclimatization process. In case of heavy metal ions, Cr (VI) showed low inhibition up to 500 mg/l of concentration, compared to Zn (II) and Cu (II). It was due to the presence of chromium reductase enzyme which was confirmed by SDS-PAGE. Zn (II) and Cu (II) ion inhibitions were eliminated by chelation with EDTA. The critical ion concentrations obtained as per Han-Levenspiel model for Cr (VI), Zn (II) and Cu (II) were 0.8958, 0.3028 and 0.204 g/l respectively.     

Class-based stratification matrix for physical leaf traits in phenetic relations of Withania somnifera (L.) Dunal accessions

Withania somnifera (L.) Dunal is a promising herb with many pharmaceutical and therapeutic uses ranging from immunomodulation to anticarcinogenicity. It is commonly known as Indian ginseng, as it is comparable to Panax ginseng, which is a widely studied and utilized herb. There are limited studies on the genetic diversity of W. somnifera from the northeastern region of the Indian Subcontinent. This paper describes the characterization of wild accessions collected from Tamil Nadu State. A total of 15 accessions collected from wild populations were studied for their physical leaf traits such as leaf fresh weight (g), dry weight (mg), leaf dry matter content (mg g^?1), specific leaf area (mm² mg^?1), leaf size (mm²), total carbon and nitrogen, and total withaferin-A content in leaves. An attempt was made to correlate physical leaf traits with withaferin-A content. The molecular traits, which were treated in a presence–absence matrix, failed to group the hyper-withaferin-A accessions. The quantified physical leaf traits were converted into a presence–absence matrix using a novel method of class-based stratification. The phenetic relations inferred from the Fitch–Margoliash algorithm applied to physical leaf trait data resulted in grouping of accessions with high withaferin-A content. These traits were used in the selection of promising accessions which can be further used for breeding programmes.     

Microsatellite markers for the native Texas perennial grass, Panicum hallii (Poaceae)

? Premise of the study: We developed microsatellites for Panicum hallii for studies of gene flow, population structure, breeding experiments, and genetic mapping. ? Methods and Results: Next-generation (454) genomic sequence data were used to design markers. Eighteen robust markers were discovered, 15 of which were polymorphic across six accessions of P. hallii var. hallii. Fourteen of the markers cross-amplified in a P. capillare accession. For the 15 polymorphic markers, the total number of alleles per locus ranged from two to 26 (mean: 11.0) across six populations (11-19 individuals per population). Observed heterozygosity (mean: 0.031) was 13.7 times lower than the expected heterozygosity (mean: 0.426). ? Conclusions: The deficit of heterozygous individuals is consistent with P. hallii having a high rate of self-fertilization. These markers will be useful for studies in P. hallii and related species.     

Power of exclusion of 19 microsatellite markers for parentage testing in river buffalo (Bubalus bubalis)

In the present study, 19 microsatellite markers were assessed for their power of exclusion to test parentage in river buffalo. Microsatellite genotypes of 216 unrelated buffaloes belonging to five different breeds were utilized for the study. The probabilities of exclusion were calculated for three hypothetical situations viz. paternity testing (PE1), one parental genotype unavailable (PE2) and exclusion of both parents i.e. substituted offspring (PE3). The mean probability of exclusion across 19 investigated markers in buffalo was 0.578 (PE1), 0.405 (PE2) and 0.764 (PE3) respectively. The probability of exclusion for paternity (PE1) ranged between 0.297 and 0.814 across different markers. The exclusion probability for the cases one parent unavailable (PE2) and substituted offspring (PE3) varied from 0.143 to 0.688 and 0.465 to 0.946 respectively. Polymorphism information content and expected heterozygosity were found to have significantly high correlation with probability of exclusion of microsatellite markers. The cumulative PE1 of nine marker loci was estimated to be 0.9999 while in case of absence of one of the parental genotypes, a minimum of 11 markers were required to achieve a cumulative PE2 of 0.999. In conclusion, the present study proposes two multiplex sets with four and five markers respectively for routine parentage testing in buffalo and an additional set of four markers for doubtful cases of paternity.     

A novel dynamic impact approach (DIA) for functional analysis of time-course omics studies: validation using the bovine mammary transcriptome

The overrepresented approach (ORA) is the most widely-accepted method for functional analysis of microarray datasets. The ORA is computationally-efficient and robust; however, it suffers from the inability of comparing results from multiple gene lists particularly with time-course experiments or those involving multiple treatments. To overcome such limitation a novel method termed Dynamic Impact Approach (DIA) is proposed. The DIA provides an estimate of the biological impact of the experimental conditions and the direction of the impact. The impact is obtained by combining the proportion of differentially expressed genes (DEG) with the log2 mean fold change and mean -log P-value of genes associated with the biological term. The direction of the impact is calculated as the difference of the impact of up-regulated DEG and down-regulated DEG associated with the biological term. The DIA was validated using microarray data from a time-course experiment of bovine mammary gland across the lactation cycle. Several annotation databases were analyzed with DIA and compared to the same analysis performed by the ORA. The DIA highlighted that during lactation both BTA6 and BTA14 were the most impacted chromosomes; among Uniprot tissues those related with lactating mammary gland were the most positively-impacted; within KEGG pathways 'Galactose metabolism' and several metabolism categories related to lipid synthesis were among the most impacted and induced; within Gene Ontology "lactose biosynthesis" among Biological processes and "Lactose synthase activity" and "Stearoyl-CoA 9-desaturase activity" among Molecular processes were the most impacted and induced. With the exception of the terms 'Milk', 'Milk protein' and 'Mammary gland' among Uniprot tissues and SP_PIR_Keyword, the use of ORA failed to capture as significantly-enriched (i.e., biologically relevant) any term known to be associated with lactating mammary gland. Results indicate the DIA is a biologically-sound approach for analysis of time-course experiments. This tool represents an alternative to ORA for functional analysis.     

A new affinity reagent for the site-specific, covalent attachment of DNA to active-site nucleophiles: application to the EcoRI and RsrI restriction and modification enzymes.

A modified oligodeoxyribonucleotide duplex containing an unnatural internucleotide trisubstituted 3' to 5' pyrophosphate bond in one strand [5'(oligo1)3'-P(OCH3)P-5'(oligo2) 3'] reacts with nucleophiles in aqueous media by acting as a phosphorylating affinity reagent. When interacted with a protein, a portion of the oligonucleotide [--P-5'(oligo2)3'] becomes attached to an amino acid nucleophilic group through a phosphate of the O-methyl-modified pyrophosphate linkage. We demonstrate the affinity labeling of nucleophilic groups at the active sites of the EcoRI and RsrI restriction and modification enzymes with an oligodeoxyribonucleotide duplex containing a modified scissile bond in the EcoRI recognition site. With the EcoRI and RsrI endonucleases in molar excess approximately 1% of the oligonucleotide becomes attached to the protein, and with the companion methyltransferases the yield approaches 40% for the EcoRI enzyme and 30% for the RsrI methyltransferase. Crosslinking proceeds only upon formation of a sequence-specific enzyme-DNA complex, and generates a covalent bond between the 3'-phosphate of the modified pyrophosphate in the substrate and a nucleophilic group at the active site of the enzyme. The reaction results in the elimination of an oligodeoxyribonucleotide remnant that contains the 3'-O-methylphosphate [5'(oligo1)3'-P(OCH3)] derived from the modified phosphate of the pyrophosphate linkage. Hydrolysis properties of the covalent protein-DNA adducts indicate that phosphoamide (P-N) bonds are formed with the EcoRI endonuclease and methyltransferase.