AlkA protein is the third Escherichia coli DNA repair protein excising a ring fragmentation product of thymine

Various forms of oxidative stress lead to the formation of damaged bases including N-(2-deoxy-beta-D-erythro-pentofuranosyl)-N-3-(2R-hydroxyisobutyric acid)-urea or alphaRT, the fragmentation product of thymine formed from 5R-thymidine C5-hydrate upon hydrolysis. It was shown that alphaRT is excised by Escherichia coli Fpg and Nth proteins. Here we report that when present in DNA, alphaRT is, in addition, a substrate for the E. coli AlkA protein with an apparent K(m) value of congruent with170 nM. alphaRT positioned opposite T, dG, dC, and dA were efficiently excised by AlkA protein from duplex oligodeoxynucleotides in the following order: dA approximately T > dC approximately dG. This is the first example of the excision of a ring opened form of a pyrimidine by AlkA protein and also the first example where the same DNA base lesion is excised by three different DNA glycosylases of the base excision repair pathway. The present results suggest possible structural similarity of the active site between E. coli AlkA, Fpg, and Nth proteins.     

Effect of Tridax procumbens on liver antioxidant defense system during lipopolysaccharide-induced hepatitis in D-galactosamine sensitised rats

The present study was carried out to assess the effect of chloroform insoluble fraction of ethanolic extract of Tridax procumbens (TP) against D-Galactosamine/Lipopolysaccharide (D-GalN/LPS)-induced hepatitis in rats. Induction of rats with D-GalN/LPS (300 mg/kg body weight/30 microg/kg body weight) led to a marked increase in lipid peroxidation as measured by thiobarbituric acid reactive substances (TBARS) in liver. Further there was a decline in the activities of enzymic antioxidants such as superoxide dismutase, catalase, glutathione peroxidase, glutathione s-transferase and the levels of non-enzymic antioxidants namely reduced glutathione, vitamin C and vitamin E. These biochemical alterations were normalised upon pretreatment with TP extract. Thus, the above results suggest that TP (300 mg/kg body weight orally for 10 days) is very effective in allievating the D-GalN/LPS-induced oxidative stress suggesting its antioxidant property.     

Beyond the clause: extraction of phosphorylation information from medline abstracts

MOTIVATION: Phosphorylation is an important biochemical reaction that plays a critical role in signal transduction pathways and cell-cycle processes. A text mining system to extract the phosphorylation relation from the literature is reported. The focus of this paper is on the new methods developed and implemented to connect and merge pieces of information about phosphorylation mentioned in different sentences in the text. The effectiveness and accuracy of the system as a whole as well as that of the methods for extraction beyond a clause/sentence is evaluated using an independently annotated dataset, the Phospho.ELM database. The new methods developed to merge pieces of information from different sentences are shown to be effective in significantly raising the recall without much difference in precision.     

4,4′-Dimethoxytrityl group derived from secondary alcohols: Are they removed slowly under acidic conditions?

Removal of 4,4'-dimethoxytrityl (DMT) groups from primary and secondary hydroxyl functionality was investigated. It was observed that deblocking of DMT group from secondary hydroxyl group of molecules attached to solid support under acidic conditions occurred relatively slowly compared to primary hydroxyl group. Marginal difference in rate of detritylation was observed between DMT group attached to 5'-hydroxyl group of deoxyribonucleoside and 2'-O-methoxyethylribonucleoside when attached to one kind of support. Removal of DMT from nucleoside attached to OligoPrep solid support was found to be slow.     

Comparison of dosimetric characteristics of physical and enhanced dynamic wedges

BackgroundWedge filters can be used as missing tissue compensators or wedge pairs to alter the shape of isodose curves so that two beams can be angled with a small hinge angle at a target volume without creating a hotspot.AimIn this study the dosimetric properties of Varian Enhanced Dynamic Wedge (EDW) and physical wedges (PW) were analyzed and compared.Materials and methodsIonometric measurements of open field output factor, physical wedge output factor, physical wedge factor and EDW factor for photon beams were carried out. A 3D scanning water phantom was used to scan depth dose and profiles for open and PW fields. The 2D ionization matrix was used to measure profiles of physical and EDW wedges. The isodose curves of physical and EDW angles were obtained using a therapy verification film.Results and discussionThe PW output factors of photons were compared with the open field output factors. The physical and EDW factors were compared. The difference in percentage depth dose for open and PW fields was observed for both photon beams. The measured isodose plots for physical and EDW were compared.ConclusionThe wedge field output factor increases with field size and wedge angle compared to that of the open field output factor. The number of MU to deliver a particular dose with the EDW field is less than that of the PW field due to a change in wedge factor. The dosimetric characteristics, like profile and isodose of EDW, closely match with that of the PW.     

Pragmatic Perspective on Conservation Genetics and Demographic History of the Last Surviving Population of Kashmir Red Deer (Cervus elaphus hanglu) in India

The hangul (Cervus elaphus hanglu) is of great conservation concern because it represents the easternmost and only hope for an Asiatic survivor of the red deer species in the Indian subcontinent. Despite the rigorous conservation efforts of the Department of Wildlife Protection in Jammu & Kashmir, the hangul population has experienced a severe decline in numbers and range contraction in the past few decades. The hangul population once abundant in the past has largely become confined to the Dachigam landscape, with a recent population estimate of 218 individuals. We investigated the genetic variability and demographic history of the hangul population and found that it has shown a relatively low diversity estimates when compared to other red deer populations of the world. Neutrality tests, which are used to evaluate demographic effects, did not support population expansion, and the multimodal pattern of mismatch distribution indicated that the hangul population is under demographic equilibrium. Furthermore, the hangul population did not exhibit any signature of bottleneck footprints in the past, and Coalescent Bayesian Skyline plot analysis revealed that the population had not experienced any dramatic changes in the effective population size over the last several thousand years. We observed a strong evidence of sub-structuring in the population, wherein the majority of individuals were assigned to different clusters in Bayesian cluster analysis. Population viability analysis demonstrated insignificant changes in the mean population size, with a positive growth rate projected for the next hundred years. We discuss the phylogenetic status of hangul for the first time among the other red deer subspecies of the world and strongly recommend to upgrade hangul conservation status under IUCN that should be discrete from the other red deer subspecies of the world to draw more conservation attention from national and international bodies.     

Structural basis for the inhibition of M1 family aminopeptidases by the natural product actinonin: Crystal structure in complex with E. coli aminopeptidase N

Actinonin is a pseudotripeptide that displays a high affinity towards metalloproteases including peptide deformylases (PDFs) and M1 family aminopeptidases. PDF and M1 family aminopeptidases belong to thermolysin-metzincin superfamily. One of the major differences in terms of substrate binding pockets between these families is presence (in M1 aminopeptidases) or absence (in PDFs) of an S1 substrate pocket. The binding mode of actinonin to PDFs has been established previously; however, it is not clear how the actinonin, without a P1 residue, would bind to the M1 aminopeptidases. Here we describe the crystal structure of Escherichia coli aminopeptidase N (ePepN), a model protein of the M1 family aminopeptidases in complex with actinonin. For comparison we have also determined the structure of ePepN in complex with a well-known tetrapeptide inhibitor, amastatin. From the comparison of the actinonin and amastatin ePepN complexes, it is clear that the P1 residue is not critical as long as strong metal chelating head groups, like hydroxamic acid or α-hydroxy ketone, are present. Results from this study will be useful for the design of selective and efficient hydroxamate inhibitors against M1 family aminopeptidases.     

Biocontrol of Aspergillus Species on Peanut Kernels by Antifungal Diketopiperazine Producing Bacillus cereus Associated with Entomopathogenic Nematode

The rhabditid entomopathogenic nematode associated Bacillus cereus and the antifungal compounds produced by this bacterium were evaluated for their activity in reducing postharvest decay of peanut kernels caused by Aspergillus species in in vitro and in vivo tests. The results showed that B. cereus had a significant effect on biocontrol effectiveness in in vitro and in vivo conditions. The antifungal compounds produced by the B. cereus were purified using silica gel column chromatography and their structure was elucidated using extensive spectral analyses. The compounds were identified as diketopiperazines (DKPs) [cyclo-(L-Pro-Gly), cyclo(L-Tyr-L-Tyr), cyclo-(L-Phe-Gly) and cyclo(4-hydroxy-L-Pro-L-Trp)]. The antifungal activities of diketopiperazines were studied against five Aspergillus species and best MIC of 2 µg/ml was recorded against A. flavus by cyclo(4-hydroxy-L-Pro-L-Trp). To investigate the potential application of cyclo(4-hydroxy-L-Pro-L-Trp) to eliminate fungal spoilage in food and feed, peanut kernels was used as a food model system. White mycelia and dark/pale green spores of Aspergillus species were observed in the control peanut kernels after 2 days incubation. However the fungal growth was not observed in peanut kernels treated with cyclo(4-hydroxy-L-Pro-L-Trp). The cyclo(4-hydroxy-L-Pro-L-Trp) was nontoxic to two normal cell lines [fore skin (FS) normal fibroblast and African green monkey kidney (VERO)] up to 200 µg/ml in MTT assay. Thus the cyclo(4-hydroxy-L-Pro-L-Trp) identified in this study may be a promising alternative to chemical preservatives as a potential biopreservative agent which prevent fungal growth in food and feed. To the best of our knowledge, this is the first report demonstrating that the entomopathogenic nematode associated B. cereus and cyclo(4-hydroxy-L-Pro-L-Trp) could be used as a biocontrol agents against postharvest fungal disease caused by Aspergillus species.     

Synthesis of Dimer Phosphoramidite Synthons for Oligodeoxyribonucleotide Phosphorothioates Using Diethyldithiocarbonate disulfide as an Efficient Sulfurizing Reagent

Abstract

An efficient solution phase synthesis of deoxyribonucleoside phosphorothioate dimers utilizing phosphoramidite approach is described. Diethyldithiocarbonate disulfide (DDD) was found to be an efficient sulfurizing reagent in the conversion of phosphite triesters to phosphorothioate triesters.