Potentials and limits to basin stability estimation

Stability assessment methods for dynamical systems have recently been complemented by basin stability and derived measures, i.e. probabilistic statements whether systems remain in a basin of attraction given a distribution of perturbations. Their application requires numerical estimation via Monte Carlo sampling and integration of differential equations. Here, we analyse the applicability of basin stability to systems with basin geometries that are challenging for this numerical method, having fractal basin boundaries and riddled or intermingled basins of attraction. We find that numerical basin stability estimation is still meaningful for fractal boundaries but reaches its limits for riddled basins with holes

An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus

DNA polymerases of the Y-family, such as Escherichia coli UmuC and DinB, are specialized enzymes induced by the SOS response, which bypass lesions allowing the continuation of DNA replication. umuDC orthologs are absent in Caulobacter crescentus and other bacteria, raising the question about the existence of SOS mutagenesis in these organisms. Here, we report that the C.crescentus dinB ortholog is not involved in damage-induced mutagenesis. However, an operon composed of two hypothetical genes and dnaE2, encoding a second copy of the catalytic subunit of Pol III, is damage inducible in a recA-dependent manner, and is responsible for most ultraviolet (UV) and mitomycin C-induced mutations in C.crescentus. The results demonstrate that the three genes are required for the error-prone processing of DNA lesions. The two hypothetical genes were named imuA and imuB, after inducible mutagenesis. ImuB is similar to proteins of the Y-family of polymerases, and possibly cooperates with DnaE2 in lesion bypass. The mutations arising as a consequence of the activity of the imuAB dnaE2 operon are rather unusual for UV irradiation, including G:C to C:G transversions

Both XPA and DNA polymerase eta are necessary for the repair of doxorubicin-induced DNA lesions

Doxorubicin (DOX) is an important tumor chemotherapeutic agent, acting mainly by genotoxic action. This work focus on cell processes that help cell survival, after DOX-induced DNA damage. in fact, cells deficient for XPA or DNA polymerase eta (pol eta, XPV) proteins (involved in distinct DNA repair pathways) are highly DOX-sensitive. Moreover, LY294002, an inhibitor of PIKK kinases, showed a synergistic killing effect in cells deficient in these proteins, with a strong induction of G2/M cell cycle arrest. Taken together, these results indicate that XPA and pol eta proteins participate in cell resistance to DOX-treatment, and kinase inhibitors can selectively enhance its killing effects, probably reducing the cell ability to recover from breaks induced in DNA. (C) 2011 Elsevier Ireland Ltd. All rights reserved.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)USP-COFECUB (São Paulo, Brazil)Univ São Paulo, Dept Microbiol, Inst Biomed Sci, São Paulo, BrazilUniv Paris Sud, Inst Gustave Roussy, Ctr Natl Rech Sci, UMR8200, Villejuif, FranceFed Univ São Paulo UNIFESP, Dept Biol Sci, Diadema, SP, BrazilUniv Fed Rio Grande do Sul, Ctr Biotechnol, Dept Biophys, Porto Alegre, RS, BrazilFed Univ Hlth Sci Porto Alegre UFCSPA, Dept Basic Hlth Sci, Porto Alegre, RS, BrazilFed Univ São Paulo UNIFESP, Dept Biol Sci, Diadema, SP, BrazilWeb of Scienc

A quantitative view of the transcriptome of Schistosoma mansoni adult-worms using SAGE

<p>Abstract</p> <p>Background</p> <p>Five species of the genus Schistosoma, a parasitic trematode flatworm, are causative agents of Schistosomiasis, a disease that is endemic in a large number of developing countries, affecting millions of patients around the world. By using SAGE (Serial Analysis of Gene Expression) we describe here the first large-scale quantitative analysis of the Schistosoma mansoni transcriptome, one of the most epidemiologically relevant species of this genus.</p> <p>Results</p> <p>After extracting mRNA from pooled male and female adult-worms, a SAGE library was constructed and sequenced, generating 68,238 tags that covered more than 6,000 genes expressed in this developmental stage. An analysis of the ordered tag-list shows the genes of F10 eggshell protein, pol-polyprotein, HSP86, 14-3-3 and a transcript yet to be identified to be the five top most abundant genes in pooled adult worms. Whereas only 8% of the 100 most abundant tags found in adult worms of S. mansoni could not be assigned to transcripts of this parasite, 46.9% of the total ditags could not be mapped, demonstrating that the 3 sequence of most of the rarest transcripts are still to be identified. Mapping of our SAGE tags to S. mansoni genes suggested the occurrence of alternative-polyadenylation in at least 13 gene transcripts. Most of these events seem to shorten the 3 UTR of the mRNAs, which may have consequences over their stability and regulation.</p> <p>Conclusion</p> <p>SAGE revealed the frequency of expression of the majority of the S. mansoni genes. Transcriptome data suggests that alternative polyadenylation is likely to be used in the control of mRNA stability in this organism. When transcriptome was compared with the proteomic data available, we observed a correlation of about 50%, suggesting that both transcriptional and post-transcriptional regulation are important for determining protein abundance in S. mansoni. The generation of SAGE tags from other life-cycle stages should contribute to reveal the dynamics of gene expression in this important parasite.</p

El extracto acuoso de Cymbopogon citratus protege al ADN plasmídico del daño inducido por radiación UVC

Aim: to evaluate the photoprotective effect of aqueous extract of Cymbopogon citratus (DC) Stapf against UVC-induced damage to ADN. Material and methods: In the experimental procedure, samples of plasmid pBluescript SK II solutions were exposed to C. citratus aqueous extract in 0.01-4.0 mg/mL concentrations during 30, 60 and 90 min. In order to evaluate the photoprotective effect, the vegetal extract was applied before, during and after UVC radiation at 200 J/m2 doses. DNA repair enzymes T4 endonuclease V was employed in order to discriminate CPDs damage. Then, supercoiled and relaxed forms of DNA were separated after electrophoretic migration in agarose gels. Also aqueous extract transmittance was measure at 254 nm OD. Results: None of the concentrations tested were genotoxic in 30 min of exposition. Concentrations ≥ 2 mg/mL induced strand breaks at 90 min of incubation. The C. citratus extract at concentrations ≥ 0.5 mg/mL protect DNA in front of UVC radiation. Conclusions: In our experimental conditions, C. citratus extract protects DNA from the genotoxicity induced by light UVC, preventing the CPDs generation, but is not able to eliminate DNA damage once formed.Objetivo: Evaluar el efecto protector del extracto acuoso de Cymbopogon citratus (DC) Stapf, ante el daño inducido por las radiaciones UVC. Material y Métodos: Para evaluar si el extracto acuoso de C. citratus era capaz de inducir roturas de cadenas en el ADN, moléculas de plásmido pBluescript SK II fueron tratadas con diferentes concentraciones del extracto (0,01 - 4,0 mg/mL), en los tiempos de exposición: 30, 60 y 90 min. El efecto fotoprotector fue evaluado aplicando el extracto vegetal antes, durante, y después de la irradiación del ADN plasmídico con 200 J/m2 de UVC. La actividad enzimática de T4 endonucleasa V fue empleada para detectar formación de CPDs. Las formas superenrollada y relajada de las moléculas de plásmido fueron separadas electroforéticamente en gel de agarosa. Adicionalmente, se midió la transmitancia del extracto acuoso a la DO de 254 nm. Resultados: Ninguna de las concentraciones evaluadas resultó genotóxica con 30 min de tratamiento. Las concentraciones ≥ 2 mg/mL indujeron roturas de cadenas a los 90 min de incubación. El extracto de C. citratus a concentraciones ≥ 0,5 mg/mL protegió al ADN frente a las radiaciones UVC. Conclusiones: En nuestras condiciones experimentales, el extracto acuoso de C. citratus protege al ADN frente a la genotoxicidad inducida por la luz UVC, previniendo la generación de CPDs, pero no es capaz de eliminarlas una vez formadas

Cymbopogon citratus aqueous extract protects plasmid DNA from UVC-induced damage

Esta investigación fue financiada por un proyecto de colaboración bilateral entre Brasil y Cuba, CAPES/MES.Objetivo: Evaluar el efecto protector del extracto acuoso de Cymbopogon citratus (DC) Stapf, ante el daño inducido por las radiaciones UVC. Material y Métodos: Para evaluar si el extracto acuoso de C. citratus era capaz de inducir roturas de cadenas en el ADN, moléculas de plásmido pBluescript SK II fueron tratadas con diferentes concentraciones del extracto (0,01 - 4,0 mg/mL), en los tiempos de exposición: 30, 60 y 90 min. El efecto fotoprotector fue evaluado aplicando el extracto vegetal antes, durante, y después de la irradiación del ADN plasmídico con 200 J/m2 de UVC. La actividad enzimática de T4 endonucleasa V fue empleada para detectar formación de CPDs. Las formas superenrollada y relajada de las moléculas de plásmido fueron separadas electroforéticamente en gel de agarosa. Adicionalmente, se midió la transmitancia del extracto acuoso a la DO de 254 nm. Resultados: Ninguna de las concentraciones evaluadas resultó genotóxica con 30 min de tratamiento. Las concentraciones ≥ 2 mg/mL indujeron roturas de cadenas a los 90 min de incubación. El extracto de C. citratus a concentraciones ≥ 0,5 mg/mL protegió al ADN frente a las radiaciones UVC. Conclusiones: En nuestras condiciones experimentales, el extracto acuoso de C. citratus protege al ADN frente a la genotoxicidad inducida por la luz UVC, previniendo la generación de CPDs, pero no es capaz de eliminarlas una vez formadas.Aim: to evaluate the photoprotective effect of aqueous extract of Cymbopogon citratus (DC) Stapf against UVC-induced damage to ADN. Material and methods: In the experimental procedure, samples of plasmid pBluescript SK II solutions were exposed to C. citratus aqueous extract in 0.01-4.0 mg/mL concentrations during 30, 60 and 90 min. In order to evaluate the photoprotective effect, the vegetal extract was applied before, during and after UVC radiation at 200 J/m2 doses. DNA repair enzymes T4 endonuclease V was employed in order to discriminate CPDs damage. Then, supercoiled and relaxed forms of DNA were separated after electrophoretic migration in agarose gels. Also aqueous extract transmittance was measure at 254 nm OD. Results: None of the concentrations tested were genotoxic in 30 min of exposition. Concentrations ≥ 2 mg/mL induced strand breaks at 90 min of incubation. The C. citratus extract at concentrations ≥ 0.5 mg/ mL protect DNA in front of UVC radiation. Conclusions: In our experimental conditions, C. citratus extract protects DNA from the genotoxicity induced by light UVC, preventing the CPDs generation, but is not able to eliminate DNA damage once formed.Este trabajo fue realizado por el proyecto de colaboración internacional CAPES (Brasil)- MES (Cuba). El financiamiento y soporte fue brindado por CAPES (São Paulo, Brazil)

Interferon β-1a in relapsing multiple sclerosis: four-year extension of the European IFNβ-1a Dose-C omparison Study

Background: Multiple sclerosis (MS) is a chronic disease requiring long-term monitoring of treatment. Objective: To assess the four-year clinical efficacy of intramuscular (IM) IFNb-1a in patients with relapsing MS from the European IFNb-1a Dose-C omparison Study. Methods: Patients who completed 36 months of treatment (Part 1) of the European IFNb-1a Dose-C omparison Study were given the option to continue double-blind treatment with IFNb-1a 30 mcg or 60 mcg IM once weekly (Part 2). Analyses of 48-month data were performed on sustained disability progression, relapses, and neutralizing antibody (NA b) formation. Results: O f 608/802 subjects who completed 36 months of treatment, 493 subjects continued treatment and 446 completed 48 months of treatment and follow-up. IFNb-1a 30 mcg and 60 mcg IM once weekly were equally effective for up to 48 months. There were no significant differences between doses over 48 months on any of the clinical endpoints, including rate of disability progression, cumulative percentage of patients who progressed (48 and 43, respectively), and annual relapse rates; relapses tended to decrease over 48 months. The incidence of patients who were positive for NAbs at any time during the study was low in both treatment groups. Conclusion: C ompared with 60-mcg IM IFNb-1a once weekly, a dose of 30 mcg IM IFNb-1a once weekly maintains the same clinical efficacy over four years

Overexpression of KLC2 due to a homozygous deletion in the non-coding region causes SPOAN syndrome

SPOAN syndrome is a neurodegenerative disorder mainly characterized by spastic paraplegia, optic atrophy and neuropathy (SPOAN). Affected patients are wheelchair bound after 15 years old, with progressive joint contractures and spine deformities. SPOAN patients also have sub normal vision secondary to apparently non-progressive congenital optic atrophy. A potential causative gene was mapped at 11q13 ten years ago. Here we performed next-generation sequencing in SPOAN-derived samples. While whole-exome sequencing failed to identify the causative mutation, whole-genome sequencing allowed to detect a homozygous 216-bp deletion (chr11.hg19:g.66,024,557_66,024,773del) located at the non-coding upstream region of the KLC2 gene. Expression assays performed with patient’s fibroblasts and motor neurons derived from SPOAN patients showed KLC2 overexpression. Luciferase assay in constructs with 216-bp deletion confirmed the overexpression of gene reporter, varying from 48 to 74%, as compared with wild-type. Knockdown and overexpression of klc2 in Danio rerio revealed mild to severe curly-tail phenotype, which is suggestive of a neuromuscular disorder. Overexpression of a gene caused by a small deletion in the non-coding region is a novel mechanism, which to the best of our knowledge, was never reported before in a recessive condition. Although the molecular mechanism of KLC2 up-regulation still remains to be uncovered, such example adds to the importance of non-coding regions in human pathologyFil: Melo, Uira S.. Universidade de Sao Paulo; BrasilFil: Macedo Souza, Lucia I.. Universidade de Sao Paulo; BrasilFil: Figueiredo, Thalita. Federal University of Paraiba; Brasil. Paraiba State University; BrasilFil: Muotri, Alysson R. University of California at San Diego; Estados UnidosFil: Gleeson, Joseph G.. The Rockefeller University; Estados UnidosFil: Coux, Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Armas, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Calcaterra, Nora Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Kitajima, João P.. Mendelics Genomic Analysis; BrasilFil: Amorim, Simone. Universidade de Sao Paulo; BrasilFil: Olávio, Thiago R.. Universidade de Sao Paulo; BrasilFil: Griesi Oliveira, Karina. Universidade de Sao Paulo; BrasilFil: Coatti, Giuliana C.. Universidade de Sao Paulo; BrasilFil: Rocha, Clarissa R.R. Universidade de Sao Paulo; BrasilFil: Martins Pinheiro, Marinalva. Universidade de Sao Paulo; BrasilFil: Menck, Carlos F.M.. Universidade de Sao Paulo; BrasilFil: Zaki, Maha S.. National Research Center. EL Cairo; EgiptoFil: Kok, Fernando. Universidade de Sao Paulo; BrasilFil: Zatz, Mayana. Universidade de Sao Paulo; BrasilFil: Santos, Silvana. Federal University of Paraiba; Brasil. Paraiba State University; Brasi

Biological Sensors for Solar Ultraviolet Radiation

Solar ultraviolet (UV) radiation is widely known as a genotoxic environmental agent that affects Earth ecosystems and the human population. As a primary consequence of the stratospheric ozone layer depletion observed over the last decades, the increasing UV incidence levels have heightened the concern regarding deleterious consequences affecting both the biosphere and humans, thereby leading to an increase in scientific efforts to understand the role of sunlight in the induction of DNA damage, mutagenesis, and cell death. In fact, the various UV-wavelengths evoke characteristic biological impacts that greatly depend on light absorption of biomolecules, especially DNA, in living organisms, thereby justifying the increasing importance of developing biological sensors for monitoring the harmful impact of solar UV radiation under various environmental conditions. In this review, several types of biosensors proposed for laboratory and field application, that measure the biological effects of the UV component of sunlight, are described. Basically, the applicability of sensors based on DNA, bacteria or even mammalian cells are presented and compared. Data are also presented showing that on using DNA-based sensors, the various types of damage produced differ when this molecule is exposed in either an aqueous buffer or a dry solution. Apart from the data thus generated, the development of novel biosensors could help in evaluating the biological effects of sunlight on the environment. They also emerge as alternative tools for using live animals in the search for protective sunscreen products