Some new results on Cox–Czanner divergence and their applications in survival studies

In the present communication, we propose a quantile-based measure for the divergence between two survival functions. This can also be used in a dynamic way where the divergence between survival functions varies with time. Several new properties of the proposed measure are investigated with suitable examples. The behavior of the measure for various reliability models is also investigated. A real data analysis is employed to compare the relative efficacy of two treatment groups using the proposed divergence measure.     

The impact of a salinity barrier on the partitioning of heavy metals in sediments of a tropical backwater system

Abstract

Concentrations of heavy metals (Cd, Co, Cr, Cu and Fe) in surface sediments and their partitioning behaviour between exchangeable, reducible (Fe-Mn oxide bound) and organic/residual phases of the sediments in a typical backwater system of Kerala, viz. the southern upstream part of Cochin Estuarine System (South India), have been studied. Spatial and temporal variations of trace metals are discussed with special reference to pH, dissolved oxygen, salinity, organic carbon and texture of sediment. Metal concentrations in the tide gated part of the estuary were found to be significantly higher when compared to metal concentrations reported from the unrestricted part of the Cochin estuarine system and also those from many of the unpolluted estuaries worldwide. The higher levels of heavy metals in the study area and their characteristic distribution and partitioning behaviour in the surficial sediments were attributed to the presence of a salinity barrier across the backwater system and also by the massive use of pesticides and chemical fertilizers in the vast area of agricultural land near the backwater system.     

Absence of p53 complements defects in Abelson murine leukemia virus signaling

The v-Abl protein encoded by Abelson murine leukemia virus (Ab-MLV) induces transformation of pre-B cells via a two-stage process. An initial proliferative phase during which cells with limited tumorigenic potential expand is followed by a crisis period marked by high levels of apoptosis and erratic growth. Transformants that survive this phase emerge as fully malignant cells and usually contain mutations that disable the p53 tumor suppressor pathway. Consistent with the importance of p53 in this process, pre-B cells from p53 null animals bypass crisis. Thus, the transformation process reflects a balance between signals from the v-Abl protein that drive transformation and those coming from the cellular response to inappropriate growth. One prediction of this hypothesis is that Ab-MLV mutants that are compromised in their ability to transform cells may be less equipped to overcome the effects of p53. To test this idea, we examined the ability of the P120/R273K mutant to transform pre-B cells from wild-type, p53 null, and Ink4a/Arf null mice. The SH2 domain of the v-Abl protein encoded by this mutant contains a substitution that affects the phosphotyrosine-binding pocket, and this mutant is compromised in its ability to transform NIH 3T3 and pre-B cells, especially at 39.5 degrees C. Our data reveal that loss of p53 or Ink4a/Arf locus products complements the transforming defect of the P120/R273K mutant, but it does not completely restore wild-type function. These results indicate that one important transforming function of v-Abl proteins is overcoming the effects of a functional p53 pathway.     

Caloric restriction and genomic stability

Caloric restriction (CR) reduces the incidence and progression of spontaneous and induced tumors in laboratory rodents while increasing mean and maximum life spans. It has been suggested that CR extends longevity and reduces age-related pathologies by reducing the levels of DNA damage and mutations that accumulate with age. This hypothesis is attractive because the integrity of the genome is essential to a cell/organism and because it is supported by observations that both cancer and immunological defects, which increase significantly with age and are delayed by CR, are associated with changes in DNA damage and/or DNA repair. Over the last three decades, numerous laboratories have examined the effects of CR on the integrity of the genome and the ability of cells to repair DNA. The majority of studies performed indicate that the age-related increase in oxidative damage to DNA is significantly reduced by CR. Early studies suggest that CR reduces DNA damage by enhancing DNA repair. With the advent of genomic technology and our increased understanding of specific repair pathways, CR has been shown to have a significant effect on major DNA repair pathways, such as NER, BER and double-strand break repair.     

Antiinflammatory and antiulcer activities of phytic acid in rats

Maximum antiinflammatory activity of phytic acid (PA) was seen at an oral dose of 150 mg/kg in the carrageenan induced rat paw edema model. Although PA showed ability to prevent denaturation of proteins, it showed less antiinflammatory activity than ibuprofen. Ability of PA to bring down thermal denaturation of proteins might be a contributing factor in the mechanism of action against inflammation. PA, at all the doses tested, showed significant protection from ulcers induced by ibuprofen, ethanol and cold stress, with a maximum activity at 150 mg/kg. There was a significant increase in gastric tissue malondialdehyde levels in ethanol treated rats but these levels decreased following PA pretreatment. Moreover, pretreatment with PA significantly inhibited various effects of ethanol on gastric mucosa, such as, reduction in the concentration of nonprotein sulfhydryl groups, necrosis, erosions, congestion and hemorrhage. These results suggested that gastro-protective effect of PA could be mediated by its antioxidant activity and cytoprotection of gastric mucosa.     

Correlations between local strains and tissue phenotypes in an experimental model of skeletal healing

Defining how mechanical cues regulate tissue differentiation during skeletal healing can benefit treatment of orthopaedic injuries and may also provide insight into the influence of the mechanical environment on skeletal development. Different global (i.e., organ-level) mechanical loads applied to bone fractures or osteotomies are known to result in different healing outcomes. However, the local stimuli that promote formation of different skeletal tissues have yet to be established. Finite element analyses can estimate local stresses and strains but require many assumptions regarding tissue material properties and boundary conditions. This study used an experimental approach to investigate relationships between the strains experienced by tissues in a mechanically stimulated osteotomy gap and the patterns of tissue differentiation that occur during healing. Strains induced by the applied, global mechanical loads were quantified on the mid-sagittal plane of the callus using digital image correlation. Strain fields were then compared to the distribution of tissue phenotypes, as quantified by histomorphometry, using logistic regression. Significant and consistent associations were found between the strains experienced by a region of the callus and the tissue type present in that region. Specifically, the probability of encountering cartilage increased, and that of encountering woven bone decreased, with increasing octahedral shear strain and, to a lesser extent, maximum principal strain. Volumetric strain was the least consistent predictor of tissue type, although towards the end of the four-week stimulation timecourse, cartilage was associated with increasingly negative volumetric strains. These results indicate that shear strain may be an important regulator of tissue fate during skeletal healing.     

Bioactivity-guided fractionation of Coronopus didymus: A free radical scavenging perspective

The whole plant aqueous extract of Coronopus didymus Linn. was fractionated on the basis of polarity and resulting fractions were evaluated for free radical scavenging ability. The most non-polar fraction (CDF1) was found to be more active than other fractions in scavenging DPPH, ABTS(-), nitric oxide and hydroxyl radicals in steady-state conditions. Stop-flow spectrometric studies showed 58.13% inhibition of 100 microM DPPH at a concentration of 150 microg/ml of CDF1 in 1000 s and 32.31% scavenging of 960 microM ABTS(-) at a concentration of 300 microg/ml of CDF1 in 100 s. The reaction of CDF1 with hydroxyl radicals produced by pulse radiolysis showed a transient spectrum with absorption peaks at 320, 390 and 400 nm, indicating the presence of flavonoids/related components. Competition kinetics with potassium thiocyanate against scavenging of hydroxyl radicals showed a reactivity of 0.1326 against thiocyanate. CDF1 also protected against Fenton reagent-induced calf thymus DNA damage at a concentration of 400 mg/ml indicating it to be the most potent fraction.     

Mycobacterium tuberculosis ClpP1 and ClpP2 Function Together in Protein Degradation and Are Required for Viability in vitro and During Infection

In most bacteria, Clp protease is a conserved, non-essential serine protease that regulates the response to various stresses. Mycobacteria, including Mycobacterium tuberculosis (Mtb) and Mycobacterium smegmatis, unlike most well studied prokaryotes, encode two ClpP homologs, ClpP1 and ClpP2, in a single operon. Here we demonstrate that the two proteins form a mixed complex (ClpP1P2) in mycobacteria. Using two different approaches, promoter replacement, and a novel system of inducible protein degradation, leading to inducible expression of clpP1 and clpP2, we demonstrate that both genes are essential for growth and that a marked depletion of either one results in rapid bacterial death. ClpP1P2 protease appears important in degrading missense and prematurely terminated peptides, as partial depletion of ClpP2 reduced growth specifically in the presence of antibiotics that increase errors in translation. We further show that the ClpP1P2 protease is required for the degradation of proteins tagged with the SsrA motif, a tag co-translationally added to incomplete protein products. Using active site mutants of ClpP1 and ClpP2, we show that the activity of each subunit is required for proteolysis, for normal growth of Mtb in vitro and during infection of mice. These observations suggest that the Clp protease plays an unusual and essential role in Mtb and may serve as an ideal target for antimycobacterial therapy.