GRYFUN: A Web Application for GO Term Annotation Visualization and Analysis in Protein Sets

Functional context for biological sequence is provided in the form of annotations. However, within a group of similar sequences there can be annotation heterogeneity in terms of coverage and specificity. This in turn can introduce issues regarding the interpretation of actual functional similarity and overall functional coherence of such a group. One way to mitigate such issues is through the use of visualization and statistical techniques. Therefore, in order to help interpret this annotation heterogeneity we created a web application that generates Gene Ontology annotation graphs for protein sets and their associated statistics from simple frequencies to enrichment values and Information Content based metrics. The publicly accessible website http://xldb.di.fc.ul.pt/gryfun/ currently accepts lists of UniProt accession numbers in order to create user-defined protein sets for subsequent annotation visualization and statistical assessment. GRYFUN is a freely available web application that allows GO annotation visualization of protein sets and which can be used for annotation coherence and cohesiveness analysis and annotation extension assessments within under-annotated protein sets.     

Size and symmetry of sex combs were not related to male mating success in Drosophila melanogaster reared at different temperatures

Temperature is one of the most important climatic factors that may influence different traits (morphological, physiological or behavioral) in Drosophila. In this study, we examined the effects of two developmental temperatures (18°C and 25°C) on the size and the symmetry of sex combs (a male sexual trait) and their importance for male mating success in Drosophila melanogaster. However, the number of sex comb teeth (“size”) and its difference between right and left legs (“symmetry”) were relevant neither to male mating success nor to the growth temperatures.     

A novel neuroprotective agent with antioxidant and nitric oxide synthase inhibitory action

N^α-vanillyl-N^ω-nitroarginine (N ? 1) that combines the active functions of natural antioxidant and nitric oxide synthase inhibitor was developed for its neuroprotective properties. N ? 1 exhibited protective effects against hydrogen peroxide-induced cell damage and the inhibitory effect on nitric oxide ‘NO’ production induced by calcium ionophore in NG 108-15 cells. N ? 1 inhibited the constitutive NOS isolated from rat cerebellar in a greater extent than constitutive NOS from human endothelial cells. Low binding energy ( ? 10.2 kcal/mol) obtained from docking N ? 1 to nNOS supported the additional mode of action of N ? 1 as an nNOS inhibitor. The in vivo neuroprotective effect on kainic acid-induced nitric oxide production and neuronal cell death in rat brain was investigated via microdialysis. Rats were injected intra-peritonially with N ? 1 at 75 μmol/kg before kainic acid injection (10 mg/kg). The significant suppression effect on kainic acid-induced NO and significant increase in surviving cells were observed in the hippocampus at 40 min after the induction.     

Chronic intranasal treatment with an anti-Aβ(30-42) scFv antibody ameliorates amyloid pathology in a transgenic mouse model of Alzheimer's disease

Amyloid-beta peptide (Aβ)-directed active and passive immunization therapeutic strategies reduce brain levels of Aβ, decrease the severity of beta-amyloid plaque pathology and reverse cognitive deficits in mouse models of Alzheimer's disease (AD). As an alternative approach to passive immunization with full IgG molecules, single-chain variable fragment (scFv) antibodies can modulate or neutralize Aβ-related neurotoxicity and inhibit its aggregation in vitro. In this study, we characterized a scFv derived from a full IgG antibody raised against the C-terminus of Aβ, and studied its passage into the brains of APP transgenic mice, as well as its potential to reduce Aβ-related pathology. We found that the scFv entered the brain after intranasal application, and that it bound to beta-amyloid plaques in the cortex and hippocampus of APP transgenic mice. Moreover, the scFv inhibited Aβ fibril formation and Aβ-mediated neurotoxicity in vitro. In a preventative therapeutic approach chronic intranasal treatment with scFv reduced congophilic amyloid angiopathy (CAA) and beta-amyloid plaque numbers in the cortex of APPswe/PS1dE9 mice. This reduction of CAA and plaque pathology was associated with a redistribution of brain Aβ from the insoluble fraction to the soluble peptide pool. Due to their lack of the effector domain of full IgG, scFv may represent an alternative tool for the treatment of Aβ-related pathology without triggering Fc-mediated effector functions. Additionally, our observations support the possibility that Aβ-directed immunotherapy can reduce Aβ deposition in brain vessels in transgenic mice.     

Silicon mitigates the Cd toxicity in maize in relation to cadmium translocation, cell distribution, antioxidant enzymes stimulation and enhanced endodermal apoplasmic barrier development

The objective of this study was to assess the effect of different Cd and Si concentrations on the maize plants. The following Cd and/or Si treatments were used: 5 Cd; 10 Cd; 100 Cd; 5 Cd + 0.08 Si; 10 Cd + 0.08 Si; 100 Cd + 5 Si treatments (Cd concentration in μM, Si concentration in mM). The plant growth, photosynthetic pigments content, antioxidant enzymes activities (POX, SOD, CAT), Cd and Si accumulation, translocation and cell wall deposition of the maize plants was observed. Changes in the endodermal cell walls development and late metaxylem elements lignification due to Cd and/or Si treatment were also evaluated. The negative effect of Cd (5 and 10 μM) on the growth parameters was alleviated by Si at 0.08 mM. The positive effect of Si was not observed at higher Cd and Si concentrations. This indicates that the alleviating effect of Si on Cd toxicity depends on the Cd and Si concentrations. Plants responded to Cd toxicity by an increase of antioxidant enzyme activity. Silicon addition in Cd + Si treatment stimulated an increase in the activity of antioxidant enzymes in comparison with the Cd treatment. Chlorophyll and carotenoid content in the Cd treated plants was not significantly affected by Si. The young maize plants retained much more Cd in their roots as they translocated into the shoots. 5 Cd + 0.08 Si and 10 Cd + 0.08 Si treatments correlated with an increase in Cd concentration in the roots and shoots, and in the cell walls. Silicon caused a slight decrease of the Cd translocation into the shoots in 5 Cd + 0.08 Si and 10 Cd + 0.08 Si treatments. Negative correlation between the root Cd cell wall deposition and Cd translocation was observed. Cadmium and/or Si altered root anatomy. Cadmium enhanced suberin lamellae development and late metaxylem lignification; silicon in Cd + Si treatments accelerated suberin lamellae deposition and enhanced the tertiary endodermal cell walls formation in comparison with Cd treatments. Negative correlation between the endodermal cell walls development and Cd translocation was observed.     

Effects of experimentally planting non-crop flowers into cabbage fields on the abundance and diversity of predators

Flowery field margins and intersowing of crops with flowers are used as management practices to promote arthropod biodiversity as well as biocontrol agents. Positive effects of enhancement (in abundance and species richness) of hymenopteran parasitoids on control of Lepidoptera pests have previously been demonstrated. However, effects on predatory arthropods, which may also serve as pest control agents, remain unclear. In an experimental study in cabbage fields we tested how sown flower strips on field margins and intersowing with cornflower affected the species richness, abundance and community composition of ground beetles and spiders. Furthermore, we investigated whether effects of flower margins are dependent on the distance from the field margins. We found that field margins generally harboured higher species richness, whereas effects on abundance were weaker. Intersown cornflower had positive effects on spider and ground beetle abundance, but affected species richness only weakly. Our results do not provide evidence for effects of distance from the flowery field margins on predator richness or abundance. Species composition was strongly affected by the habitat management actions. We conclude that habitat management practices like flower strips on field margins and intersowing with flowers, which are primarily added to attract and enhance parasitoids for pest control, also benefit biodiversity conservation in spiders and ground beetles. They also positively affect the abundance of these primarily predatory taxa, which adds to the biocontrol potential of non-crop flowering plants.     

Pentadecapeptide BPC 157 and its effects on a NSAID toxicity model: diclofenac-induced gastrointestinal, liver, and encephalopathy lesions

AimsWe attempted to fully antagonize the extensive toxicity caused by NSAIDs (using diclofenac as a prototype).Main methodsHerein, we used the stable gastric pentadecapeptide BPC 157 (GEPPPGKPADDAGLV, MW 1419), an anti-ulcer peptide shown to be efficient in inflammatory bowel disease clinical trials (PL 14736) and various wound treatments with no toxicity reported. This peptide was given to antagonize combined gastrointestinal, liver, and brain toxicity induced by diclofenac (12.5 mg/kg intraperitoneally, once daily for 3 days) in rats.Key findingsAlready considered a drug that can reverse the toxic side effects of NSAIDs, BPC 157 (10 μg/kg, 10 ng/kg) was strongly effective throughout the entire experiment when given (i) intraperitoneally immediately after diclofenac or (ii) per-orally in drinking water (0.16 μg/mL, 0.16 ng/mL). Without BPC 157 treatment, at 3 h following the last diclofenac challenge, we encountered a complex deleterious circuit of diclofenac toxicity characterized by severe gastric, intestinal and liver lesions, increased bilirubin, aspartate transaminase (AST), alanine transaminase (ALT) serum values, increased liver weight, prolonged sedation/unconsciousness (after any diclofenac challenge) and finally hepatic encephalopathy (brain edema particularly located in the cerebral cortex and cerebellum, more in white than in gray matter, damaged red neurons, particularly in the cerebral cortex and cerebellar nuclei, Purkinje cells and less commonly in the hippocampal neurons).SignificanceThe very extensive antagonization of diclofenac toxicity achieved with BPC 157 (μg-/ng-regimen, intraperitoneally, per-orally) may encourage its further use as a therapy to counteract diclofenac- and other NSAID-induced toxicity.     

Chronic patients--persons with diabetes frequent attenders in Croatian family practice

Chronic diseases cause high frequency visits and generate the long-term frequent attenders (FAs). The connection between frequent attendance and specific morbidities in the health care systems in transitional Europe has been underestimated. We investigated whether frequent visits of chronic patients in primary care are related to characteristic of chronic disease (diabetes mellitus) and whether this is influenced by the family practice in the transitional health care. We analyzed the number of visits a day time work for 490 persons with diabetes in the period 1997 to 2000. As the cut-off points between frequent attenders and non frequent attenders (NFAs) we used the value of the third quartile (Q3) of visits determined for the sex and age groups in the parallel study in the whole population. The analysis was performed for 23 variables: demographic characteristics of patients, disease characteristic and variables of physician. Logistic regressions were employed to identify the predictors of FAs/NFAs. 56.9% (in 1997) to 62.4% (in 2000) persons with diabetes were FAs, compared to 22.4% to 24.3% FAs patients in the whole population. Logistic regression analysis significantly differentiated the two group of visits with 68% accuracy. 4 variables are significant predictors for FAs/NFAs: diabetes as the main disease (p = 0.0005), diet-only-treatment (p = 0.0062), treatment by secondary care (p = 0.0116), and if glycated hemoglobin test (HbA1c) is determined (p = 0.0272). Understanding the similarities and differences of FAs/NFAs persons with diabetes may be important in improving the care and management of chronic diseases in family medicine in transitional health care systems.     

A method for in-gel fluorescent visualization of proteins after native and sodium dodecyl sulfate polyacrylamide gel electrophoresis

We have developed a simple one-step 30-min method for fluorescent visualization of proteins in native and sodium dodecyl sulfate polyacrylamide gel electrophoresis (PAGE) gels. The method is based on formation of strong fluorophores via potassium ferricyanide-provoked oxidation of tryptophan (Trp). Following PAGE, gels are soaked in water solution of potassium ferricyanide (100 mM) and NaOH (1 M) and are kept in the dark for 30 min. Gels are then transferred to water and scanned. The sensitivity of the method was slightly lower compared with standard Coomassie Brilliant Blue (CBB) staining. The method can be useful when rapid acquisition of data is of the essence. After preview, gels can be post-stained using the CBB protocol for further analysis. The intensity of fluorescence is dependent on Trp number, so the protocol might find application in the quantification of Trp residues as illustrated here. Importantly, there is room for improvement of the method. Namely, according to excitation–emission matrix analysis of stained protein bands, maximal fluorescence intensity (at 345/460 nm) was 3.5-fold higher compared with the settings that were available on a commercial imager (395/525 nm). As a supplement, we present an upgrade of the previously described method for in-gel detection of non-heme iron-binding proteins that also employs potassium ferricyanide.     

Immune Protection against Virus Challenge in Aging Mice Is Not Affected by Latent Herpesviral Infections

Latent herpesvirus infections alter immune homeostasis. To understand if this results in aging-related loss of immune protection against emerging infections, we challenged old mice carrying latent mouse cytomegalovirus (CMV), herpes simplex virus 1 (HSV-1), and/or murine gammaherpesvirus 68 (MHV-68) with influenza virus, West Nile virus (WNV), or vesicular stomatitis virus (VSV). We observed no increase in mortality or weight loss compared to results seen with herpesvirus-negative counterparts and a relative but not absolute reduction in CD8 responses to acute infections. Therefore, the presence of herpesviruses does not appear to increase susceptibility to emerging infections in aging patients.