A computational approach to characterization of bovine sperm chromatin alterations

We describe here a computational morphology-based approach to the investigation of possible causes of chromatin alterations in sperm. A comprehensive set of state-of-the-art and geometric measures are computationally extracted from toluidine blue stained images and analyzed to infer the possible processes leading to normal and abnormal chromatin formation while seeking a possible taxonomy of chromatin alterations and their influence on sperm head morphology. Using this methodology, we have identified higher chromatin fragility at some specific points of the sperm head. Despite the lack of correlation between morphologies of sperm head and chromatin structure, four main morphological types of chromatin alterations in bull spermatozoa have been identified and their possible causes discussed.     

A novel harmony search-K means hybrid algorithm for clustering gene expression data

Recent progress in bioinformatics research has led to the accumulation of huge quantities of biological data at various data sources. The DNA microarray technology makes it possible to simultaneously analyze large number of genes across different samples. Clustering of microarray data can reveal the hidden gene expression patterns from large quantities of expression data that in turn offers tremendous possibilities in functional genomics, comparative genomics, disease diagnosis and drug development. The k- ¬means clustering algorithm is widely used for many practical applications. But the original k-¬means algorithm has several drawbacks. It is computationally expensive and generates locally optimal solutions based on the random choice of the initial centroids. Several methods have been proposed in the literature for improving the performance of the k-¬means algorithm. A meta-heuristic optimization algorithm named harmony search helps find out near-global optimal solutions by searching the entire solution space. Low clustering accuracy of the existing algorithms limits their use in many crucial applications of life sciences. In this paper we propose a novel Harmony Search-K means Hybrid (HSKH) algorithm for clustering the gene expression data. Experimental results show that the proposed algorithm produces clusters with better accuracy in comparison with the existing algorithms.     

Physiological acclimation of <Emphasis Type="Italic">Lessonia spicata</Emphasis> to diurnal changing PAR and UV radiation: differential regulation among down-regulation of photochemistry,ROS scavenging activity and phlorotannins as major photoprotective mechanisms

Intertidal macroalgae are constantly subjected to high variations in the quality and quantity of incident irradiance that can eventually generate detrimental effect on the photosynthetic apparatus. The success of these organisms to colonize the stressful coastal habitat is mainly associated with the complexity of their morphological structures and the efficiency of the anti-stress mechanisms to minimize the physiological stress. Lessonia spicata (Phaeophyceae), a brown macroalga, that inhabits the intertidal zone in central–southern Chile was studied in regard to their physiological (quantum yield, electron transport rate, pigments) and biochemical (phlorotannins content, antioxidant metabolism, oxidative stress) responses during a daily light cycle under natural solar radiation. Major findings were that F _v/F _m, photosynthetic parameters (ETR_max, alpha, E _k) and pigments in L. spicata showed an inverse relationship to the diurnal changes in solar radiation. Phlorotannins levels and antioxidant activity showed their highest values in treatment that included UV radiation. There was an increase in SOD and APX in relation at light stress, with a peak in activity between 5.2 and 10.1 W m^?2 of biologically effective dose. The increase in peroxidative damage was proportional to light dose. These results indicated that different light doses can trigger a series of complementary mechanisms of acclimation in L. spicata based on: (i) down-regulation of photochemistry activity and decrease in concentration of photosynthetic pigments; (ii) induction of phenolic compounds with specific UV-screening functions; and (iii) reactive oxygen species (ROS) scavenging activity via complementary repair of the oxidative damage through increased activity of antioxidant enzymes and potentially increased amounts of phenolic compounds.     

Evidence suggesting that chlorophyllin (CHLN) may act as an inhibitor or a promoter of genetic damage induced by chromium(VI) oxide (CrO3) in somatic cells of Drosophila

In Drosophila, 48h-old larvae were pretreated for 24h with chlorophyllin (CHLN) or sucrose and then treated with chromium(VI) oxide (CrO(3)) immediately following completion of the pretreatment period (0-day delay) or delayed 1, 2 or 3 days. The effects were scored in the wing spot test. After delays of 0 and 1 day, clear evidence of a protective effect of CHLN was found. Contrarily, after delays of 2 and 3 days, the results showed a reversal, i.e. CHLN-related events appeared more frequently than those in the sucrose control suggesting a promoting effect. It would appear prudent that CHLN be tested in a variety of situations in any given organism before decisions are reached regarding its inhibitor/promoter effects.     

Plasma levels of osteopontin identify patients at risk for organ damage in systemic lupus erythematosus

Introduction

Osteopontin (OPN) has been implicated as a mediator of Th17 regulation via type I interferon (IFN) receptor signaling and in macrophage activity at sites of tissue repair. This study assessed whether increased circulating plasma OPN (cOPN) precedes development of organ damage in pediatric systemic lupus erythematosus (pSLE) and compared it to circulating plasma neutrophil gelatinase-associated lipocalin (cNGAL), a predictor of increased SLE disease activity.

Methods

cOPN and cNGAL were measured in prospectively followed pSLE (n = 42) and adult SLE (aSLE; n = 23) patients and age-matched controls. Time-adjusted cumulative disease activity and disease damage were respectively assessed using adjusted-mean SLE disease activity index (SLEDAI) (AMS) and SLICC/ACR damage index (SDI).

Results

Compared to controls, elevated cOPN and cNGAL were observed in pSLE and aSLE. cNGAL preceded worsening SLEDAI by 3-6 months (P = 0.04), but was not associated with increased 6-month AMS. High baseline cOPN, which was associated with high IFNalpha activity and expression of autoantibodies to nucleic acids, positively correlated with 6-month AMS (r = 0.51 and 0.52, P = 0.001 and 0.01 in pSLE and aSLE, respectively) and was associated with SDI increase at 12 months in pSLE (P = 0.001). Risk factors for change in SDI in pSLE were cOPN (OR 7.5, 95% CI [2.9-20], P = 0.03), but not cNGAL, cumulative prednisone, disease duration, immunosuppression use, gender or ancestry using univariate and multivariate logistic regression. The area under the curve (AUC) when generating the receiver-operating characteristic (ROC) of baseline cOPN sensitivity and specificity for the indication of SLE patients with an increase of SDI over a 12 month period is 0.543 (95% CI 0.347-0.738; positive predictive value 95% and negative predictive value 38%).

Conclusion

High circulating OPN levels preceded increased cumulative disease activity and organ damage in SLE patients, especially in pSLE, and its value as a predictor of poor outcome should be further validated in large longitudinal cohorts.     

Plant pathogens convergently evolved to counteract redundant nodes of an NLR immune receptor network

In plants, nucleotide-binding domain and leucine-rich repeat (NLR)-containing proteins can form receptor networks to confer hypersensitive cell death and innate immunity. One class of NLRs, known as NLR required for cell death (NRCs), are central nodes in a complex network that protects against multiple pathogens and comprises up to half of the NLRome of solanaceous plants. Given the prevalence of this NLR network, we hypothesised that pathogens convergently evolved to secrete effectors that target NRC activities. To test this, we screened a library of 165 bacterial, oomycete, nematode, and aphid effectors for their capacity to suppress the cell death response triggered by the NRC-dependent disease resistance proteins Prf and Rpi-blb2. Among 5 of the identified suppressors, 1 cyst nematode protein and 1 oomycete protein suppress the activity of autoimmune mutants of NRC2 and NRC3, but not NRC4, indicating that they specifically counteract a subset of NRC proteins independently of their sensor NLR partners. Whereas the cyst nematode effector SPRYSEC15 binds the nucleotide-binding domain of NRC2 and NRC3, the oomycete effector AVRcap1b suppresses the response of these NRCs via the membrane trafficking-associated protein NbTOL9a (Target of Myb 1-like protein 9a). We conclude that plant pathogens have evolved to counteract central nodes of the NRC immune receptor network through different mechanisms. Coevolution with pathogen effectors may have driven NRC diversification into functionally redundant nodes in a massively expanded NLR network.

Plant pathogens have evolved to counteract their hosts’ immune systems. A screen for pathogen effectors that suppress sensor NLR-mediated cell death in tobacco identifies effectors from a cyst nematode and an oomycete that suppress the NRC branch of the immune network to inhibit the immune-related cell death response.     

Immunological relationships between Artemia RNA polymerases and between RNA polymerases II from different eukaryotic organisms

Summary Rabbit antibodies against Artemia RNA polymerase II have been raised and utilized to study the immunological relationships between the subunits from RNA polymerases I, II and III from this organism and RNA polymerase II from other eukaryotes. We describe here for the first time the subunit structure of Artemia RNA polymerases I and III. These enzymes have 9 and 13 subunits respectively. The anti-RNA polymerase II antibodies recognize two subunits of 19.4 and 18 kDa common to the three enzymes, and another subunit of 25.6 kDa common to RNA polymerases II and III. The antibodies against Artemia RNA polymerase II also react with the subunits of high molecular weight and with subunits of around 25 and 33 kDa of RNA polymerase II from other eukaryotes (Drosophila melanogaster, Chironomus thummi, triticum (wheat) and Rattus (rat)). This interspecies relatedness is a common feature of eukaryotic RNA polymerases.Abbreviations RNAp RNA polymerase - DPT diazophenylthioether - SDS sodium dodecylsulfate     

Acylation of sucrose with vinyl esters using immobilized hydrolases: demonstration that chemical catalysis may interfere with enzymatic catalysis

The acylation of sucrose with vinyl laurate in dimethylsulfoxide was catalyzed by Celite (28% conversion in 24 h at 40 °C, 150 mg catalyst ml^–1), Eupergit C (11% conversion in 24 h at 60 °C, 150 mg catalyst/ml), and even the simple Na₂HPO₄ (17% conversion in 24 h at 40 °C, 20 mg catalyst ml^–1). These chemical acylations must therefore be taken into account in acylations of hydroxyl-containing compounds with enol esters in polar solvents using immobilized enzymes.