Synthesis of Cuprous Oxide (Cu2O) Nanoparticles – a Review

Cuprous Oxide (Cu2O) a semiconductor material oxide; with unique optoelectronic properties; gains significant importance for its synthesis in view of its various technological and industrial applications. A few liquid phase methods for the synthesis of Cu2O nanoparticles are reviewed on the basis of materials, methodology, synthesis conditions and key findings. A comparative study of these methods is also performed following criteria of repeatability, safety, cost, time span and simplicity. Contextual to the above mentioned criteria, three liquid phase synthesis techniques were shortlisted and actually experimented (as reported) to synthesize the Cu2O nanoparticles. This was done to investigate the effectiveness, repeatability and stability of the synthesized Cu2O product as a function of ageing time. The synthesized Cu2O using all these techniques are prone to be unstable and undergo the rapid phase change to CuO phase which was ascertained from the shift of absorbance peak in UV-VIS spectra. The results have highlighted the urgent need to develop a facile, economical, scalable and safe method to synthesize stable Cu2O nanoparticles at room temperature

Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI

Hydrolytic deamination of cytosines in DNA creates uracil and, if unrepaired, these lesions result in C to T mutations. We have suggested previously that a possible way in which cells may prevent or reduce this chemical reaction is through the binding of proteins to DNA. We use a genetic reversion assay to show that a restriction enzyme, PspGI, protects cytosines within its cognate site, 5′-CCWGG (W is A or T), against deamination under conditions where no DNA cleavage can occur. It decreases the rate of cytosine deamination to uracil by 7-fold. However, the same protein dramatically increases the rate of deaminations within the site 5′-CCSGG (S is C or G) by ∼15-fold. Furthermore, a similar increase in cytosine deaminations is also seen with a catalytically inactive mutant of the enzyme showing that endonucleolytic ability of the protein is dispensable for its mutagenic action. The sequences of the mutants generated in the presence of PspGI show that only one of the cytosines in CCSGG is predominantly converted to thymine. Our results are consistent with PspGI ‘sensitizing’ the cytosine in the central base pair in CCSGG for deamination. Remarkably, PspGI sensitizes this base for damage despite its inability to form stable complexes at CCSGG sites. These results can be explained if the enzyme has a transient interaction with this sequence during which it flips the central cytosine out of the helix. This prediction was validated by modeling the structure of PspGI–DNA complex based on the structure of the related enzyme Ecl18kI which is known to cause base-flipping

Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB

BACKGROUND: Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH2 and hABH3. This discovery was based on the prediction made by Aravind and Koonin that AlkB is a member of the 2OG-Fe(2+ )oxygenase superfamily. RESULTS: In this article, we report identification and sequence analysis of five human members of the (2OG-Fe(2+)) oxygenase superfamily designated here as hABH4 through hABH8. These experimentally uncharacterized and poorly annotated genes were not associated with the AlkB family in any database, but are predicted here to be phylogenetically and functionally related to the AlkB family (and specifically to the lineage that groups together hABH2 and hABH3) rather than to any other oxygenase family. Our analysis reveals the history of ABH gene duplications in the evolution of vertebrate genomes. CONCLUSIONS: We hypothesize that hABH 4–8 could either be back-up enzymes for hABH1-3 or may code for novel DNA or RNA repair activities. For example, enzymes that can dealkylate N3-methylpurines or N7-methylpurines in DNA have not been described. Our analysis will guide experimental confirmation of these novel human putative DNA repair enzymes

Synthesis of Cuprous Oxide (Cu2O) Nanoparticles – a Review

Cuprous Oxide (Cu2O) a semiconductor material oxide; with unique optoelectronic properties; gains significant importance for its synthesis in view of its various technological and industrial applications. A few liquid phase methods for the synthesis of Cu2O nanoparticles are reviewed on the basis of materials, methodology, synthesis conditions and key findings. A comparative study of these methods is also performed following criteria of repeatability, safety, cost, time span and simplicity. Contextual to the above mentioned criteria, three liquid phase synthesis techniques were shortlisted and actually experimented (as reported) to synthesize the Cu2O nanoparticles. This was done to investigate the effectiveness, repeatability and stability of the synthesized Cu2O product as a function of ageing time. The synthesized Cu2O using all these techniques are prone to be unstable and undergo the rapid phase change to CuO phase which was ascertained from the shift of absorbance peak in UV-VIS spectra. The results have highlighted the urgent need to develop a facile, economical, scalable and safe method to synthesize stable Cu2O nanoparticles at room temperature

Central base pair flipping and discrimination by PspGI

PspGI is a representative of a group of restriction endonucleases that recognize a pentameric sequence related to CCNGG. Unlike the previously investigated Ecl18kI, which does not have any specificity for the central base pair, PspGI prefers A/T over G/C in its target site. Here, we present a structure of PspGI with target DNA at 1.7 Å resolution. In this structure, the bases at the center of the recognition sequence are extruded from the DNA and flipped into pockets of PspGI. The flipped thymine is in the usual anti conformation, but the flipped adenine takes the normally unfavorable syn conformation. The results of this and the accompanying manuscript attribute the preference for A/T pairs over G/C pairs in the flipping position to the intrinsically lower penalty for flipping A/T pairs and to selection of the PspGI pockets against guanine and cytosine. Our data show that flipping can contribute to the discrimination between normal bases. This adds a new role to base flipping in addition to its well-known function in base modification and DNA damage repair

Stability of resistance to sorghum shoot fly, Atherigona soccata

Sorghum shoot fly, Atherigona soccata is one of the most important pests of dual-purpose sorghums during the postrainy season in India. Therefore, it is important to identify stable sources of resistance to develop cultivars with shoot fly resistance and adaptation to postrainy season. We evaluated 190 lines adapted to the postrainy season across five locations, of which 30 lines were identified with resistance to A. soccata. These lines were further evaluated for three seasons across five locations to identify lines with stable resistance to this pest across seasons and locations. Data were recorded on oviposition non-preference, deadheart incidence, recovery resistance, morphological traits (leaf glossiness, seedling vigor, plant height and days to 50% flowering), and grain yield. The sorghum genotypes CSV 22, ICSB 422, ICSB 425, ICSB 428, ICSB 432, ICSB 458, ICSB 463, IS 2312, IS 5480, IS 18662, Phule Chitra, RSV 1093, IS 18551, and RSV 1235 exhibited resistance to shoot fly damage across seasons, of which ICSB 425, ICSB 428, ICSB 432, IS 2312, IS 5480, and IS 18551 showed non-preference for oviposition. Six genotypes (ICSB 425, IS 2312, IS 18662, RSV 1090, RSV 1093, and IS 18551) also showed good recovery resistance following shoot fly damage. Principal coordinate analysis placed the maintainer lines (B-lines) with shoot fly resistance in two clusters with ICSB 422, ICSB 432, ICSB 435, ICSB 456 and ICSB 458 in one cluster and ICSB 425, ICSB 428 and ICSB 463 in the other; the open pollinated varieties/germplasm lines (restorers) were placed in a different group (CSV 22, IS 5480, IS 2312 and RSV 1093), suggesting the possibilities for developing hybrids with adaptation to the postrainy season. Based on regression coefficient and deadheart incidence, the genotypes IS 2312, ICSB 425, RSV 1090 and ICSB 428 were stable in expression of resistance to shoot fly across seasons and locations. The genotypes CSV 22 and RSV 1093 exhibited high grain yield potential and resistance to shoot fly damage, while Phule Yashoda, IS 2312, RSV 1235, and ICSV 574 were moderately resistant to shoot fly damage, but had high grain yield potential. These genotypes can be used in sorghum improvement for developing cultivars with shoot fly resistance, high grain yield and adaptation to postrainy season

A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes

A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing endonucleases and related genes and gene products. It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genome

The COMBREX Project: Design, Methodology, and Initial Results

© 2013 Brian P. et al.Prior to the “genomic era,” when the acquisition of DNA sequence involved significant labor and expense, the sequencing of genes was strongly linked to the experimental characterization of their products. Sequencing at that time directly resulted from the need to understand an experimentally determined phenotype or biochemical activity. Now that DNA sequencing has become orders of magnitude faster and less expensive, focus has shifted to sequencing entire genomes. Since biochemistry and genetics have not, by and large, enjoyed the same improvement of scale, public sequence repositories now predominantly contain putative protein sequences for which there is no direct experimental evidence of function. Computational approaches attempt to leverage evidence associated with the ever-smaller fraction of experimentally analyzed proteins to predict function for these putative proteins. Maximizing our understanding of function over the universe of proteins in toto requires not only robust computational methods of inference but also a judicious allocation of experimental resources, focusing on proteins whose experimental characterization will maximize the number and accuracy of follow-on predictions.COMBREX is funded by a GO grant from the National Institute of General Medical Sciences (NIGMS) (1RC2GM092602-01).Peer Reviewe