The 245 kb amplified chromosome of Leishmania (V.) braziliensis contains a biopterin transporter gene

Leishmania (V.) braziliensis M2903 presents a small linear and stable 245 kb chromosome originating from a genomic amplification. Similar amplifications present in other species of Leishmania contain a gene coding for a biopterin transporter. Since Leishmania is auxotrophic for this metabolite, this amplification could result from the need to better capture biotpterin from growth media under specific circumstances. In this paper we show that this gene is also present in L. (V.) braziliensis small chromosome, which shares sequences with other genomic amplifications already described.

A sensitized RNA interference screen identifies a novel role for the PI3K p110γ isoform in medulloblastoma cell proliferation and chemoresistance.

Medulloblastoma is the most common malignant brain tumor in children and is associated with a poor outcome. We were interested in gaining further insight into the potential of targeting the human kinome as a novel approach to sensitize medulloblastoma to chemotherapeutic agents. A library of small interfering RNA (siRNA) was used to downregulate the known human protein and lipid kinases in medulloblastoma cell lines. The analysis of cell proliferation, in the presence or absence of a low dose of cisplatin after siRNA transfection, identified new protein and lipid kinases involved in medulloblastoma chemoresistance. PLK1 (polo-like kinase 1) was identified as a kinase involved in proliferation in medulloblastoma cell lines. Moreover, a set of 6 genes comprising ATR, LYK5, MPP2, PIK3CG, PIK4CA, and WNK4 were identified as contributing to both cell proliferation and resistance to cisplatin treatment in medulloblastoma cells. An analysis of the expression of the 6 target genes in primary medulloblastoma tumor samples and cell lines revealed overexpression of LYK5 and PIK3CG. The results of the siRNA screen were validated by target inhibition with specific pharmacological inhibitors. A pharmacological inhibitor of p110γ (encoded by PIK3CG) impaired cell proliferation in medulloblastoma cell lines and sensitized the cells to cisplatin treatment. Together, our data show that the p110γ phosphoinositide 3-kinase isoform is a novel target for combinatorial therapies in medulloblastoma.

Utilização da medida do clorofilômetro no manejo da adubação nitrogenada em plantas de pimentão

O adequado manejo da adubação nitrogenada ao longo do ciclo da cultura do pimentão é complicado pela falta de um índice do N disponível no solo e por ser a análise química de folhas um método de diagnose demorado. Foi realizado um experimento em vasos, em um túnel de plástico pertencente ao Departamento de Recursos Naturais/Ciência do Solo, da FCA/UNESP, Botucatu (SP), com o objetivo de avaliar o índice de suficiência de nitrogênio (ISN), calculado com base nas medidas do clorofilômetro, como ferramenta auxiliar no manejo da adubação nitrogenada em plantas de pimentão. O experimento foi composto de doses de N (4,9; 9,8; 14,7; 19,6; e 24,5 g de N 50 kg-1 de solo - uma planta) aplicadas de modo convencional ou pela fertirrigação e um tratamento em que as plantas não receberam apenas a adubação nitrogenada, com sete repetições. As medidas do clorofilômetro foram realizadas a cada 15 dias em cinco folhas recém-maduras por planta. O ISN foi calculado pela relação entre a média das medidas do clorofilômetro nas plantas dos tratamentos (MCT) e a média das medidas do clorofilômetro nas plantas que receberam a maior dose (MCR), na área de referência (ISN = MCT/MCR x 100). O ISN pode ser um bom indicador do momento de aplicação do adubo nitrogenado e auxiliar no ajuste da dose de N de acordo com a exigência das plantas de pimentão, com a finalidade de aumentar a eficiência de utilização do N aplicado.

Integrated Analysis of High-Resolution Gene Expression and Copy Number Profiling Identified Biallelic Deletion of CDKN2A/2B Tumor Suppressor Locus As the Most Frequent and Unique Genomic Abnormality in Diffuse Large B-Cell Lymphoma (DLBCL) with Strong Prognostic Value in Both GCB and ABC Subtypes and Not Overcome by a Dose-Intensive Immunochemotherapy Regimen Plus Rituximab. Results of a Prospective GELA Clinical Trial Program

Background and aim of the study: Genomic gains and losses play a crucial role in the development and progression of DLBCL and are closely related to gene expression profiles (GEP), including the germinal center B-cell like (GCB) and activated B-cell like (ABC) cell of origin (COO) molecular signatures. To identify new oncogenes or tumor suppressor genes (TSG) involved in DLBCL pathogenesis and to determine their prognostic values, an integrated analysis of high-resolution gene expression and copy number profiling was performed. Patients and methods: Two hundred and eight adult patients with de novo CD20+ DLBCL enrolled in the prospective multicentric randomized LNH-03 GELA trials (LNH03-1B, -2B, -3B, 39B, -5B, -6B, -7B) with available frozen tumour samples, centralized reviewing and adequate DNA/RNA quality were selected. 116 patients were treated by Rituximab(R)-CHOP/R-miniCHOP and 92 patients were treated by the high dose (R)-ACVBP regimen dedicated to patients younger than 60 years (y) in frontline. Tumour samples were simultaneously analysed by high resolution comparative genomic hybridization (CGH, Agilent, 144K) and gene expression arrays (Affymetrix, U133+2). Minimal common regions (MCR), as defined by segments that affect the same chromosomal region in different cases, were delineated. Gene expression and MCR data sets were merged using Gene expression and dosage integrator algorithm (GEDI, Lenz et al. PNAS 2008) to identify new potential driver genes. Results: A total of 1363 recurrent (defined by a penetrance > 5%) MCRs within the DLBCL data set, ranging in size from 386 bp, affecting a single gene, to more than 24 Mb were identified by CGH. Of these MCRs, 756 (55%) showed a significant association with gene expression: 396 (59%) gains, 354 (52%) single-copy deletions, and 6 (67%) homozygous deletions. By this integrated approach, in addition to previously reported genes (CDKN2A/2B, PTEN, DLEU2, TNFAIP3, B2M, CD58, TNFRSF14, FOXP1, REL...), several genes targeted by gene copy abnormalities with a dosage effect and potential physiopathological impact were identified, including genes with TSG activity involved in cell cycle (HACE1, CDKN2C) immune response (CD68, CD177, CD70, TNFSF9, IRAK2), DNA integrity (XRCC2, BRCA1, NCOR1, NF1, FHIT) or oncogenic functions (CD79b, PTPRT, MALT1, AUTS2, MCL1, PTTG1...) with distinct distribution according to COO signature. The CDKN2A/2B tumor suppressor locus (9p21) was deleted homozygously in 27% of cases and hemizygously in 9% of cases. Biallelic loss was observed in 49% of ABC DLBCL and in 10% of GCB DLBCL. This deletion was strongly correlated to age and associated to a limited number of additional genetic abnormalities including trisomy 3, 18 and short gains/losses of Chr. 1, 2, 19 regions (FDR < 0.01), allowing to identify genes that may have synergistic effects with CDKN2A/2B inactivation. With a median follow-up of 42.9 months, only CDKN2A/2B biallelic deletion strongly correlates (FDR p.value < 0.01) to a poor outcome in the entire cohort (4y PFS = 44% [32-61] respectively vs. 74% [66-82] for patients in germline configuration; 4y OS = 53% [39-72] vs 83% [76-90]). In a Cox proportional hazard prediction of the PFS, CDKN2A/2B deletion remains predictive (HR = 1.9 [1.1-3.2], p = 0.02) when combined with IPI (HR = 2.4 [1.4-4.1], p = 0.001) and GCB status (HR = 1.3 [0.8-2.3], p = 0.31). This difference remains predictive in the subgroup of patients treated by R-CHOP (4y PFS = 43% [29-63] vs. 66% [55-78], p=0.02), in patients treated by R-ACVBP (4y PFS = 49% [28-84] vs. 83% [74-92], p=0.003), and in GCB (4y PFS = 50% [27-93] vs. 81% [73-90], p=0.02), or ABC/unclassified (5y PFS = 42% [28-61] vs. 67% [55-82] p = 0.009) molecular subtypes (Figure 1). Conclusion: We report for the first time an integrated genetic analysis of a large cohort of DLBCL patients included in a prospective multicentric clinical trial program allowing identifying new potential driver genes with pathogenic impact. However CDKN2A/2B deletion constitutes the strongest and unique prognostic factor of chemoresistance to R-CHOP, regardless the COO signature, which is not overcome by a more intensified immunochemotherapy. Patients displaying this frequent genomic abnormality warrant new and dedicated therapeutic approaches.

BIRO1, a cell-permeable BH3 peptide, promotes mitochondrial fragmentation and death of retinoblastoma cells.

Retinoblastoma is the most common pediatric intraocular neoplasm. While retinoblastoma development requires the inactivation of both alleles of the retinoblastoma tumor suppressor gene (RB1) in the developing retina, additional genomic changes are involved in tumor progression, which progressively lead to resistance of tumor cells to death. Therapeutics acting at very downstream levels of death signaling pathways should therefore be interesting in killing retinoblastoma cells. The BH3-only proteins promote apoptosis by modulating the interaction between the pro- and antiapoptotic members of the BCL2 protein family, and this effect can be recapitulated by the BH3 domains. This report analyzes the effect of various BH3 peptides, corresponding to different BH3-only proteins, on two retinoblastoma cell lines, Y79 and WERI-Rb, as well as on the photoreceptor cell line 661W. The BH3 peptide BIRO1, derived from the BCL2L11 death domain, was very effective in promoting Y79 and WERI-Rb cell death without affecting the 661W photoreceptor cells. This cell death was efficient even in absence of BAX and was shown to be caspase independent. While ROS production or AIF release was not detected from mitochondria of treated cells, BIRO1 initiated mitochondria fragmentation in a short period of time following treatment. IMPLICATIONS: The BIRO1 peptide is highly effective at killing retinoblastoma cells and has potential as a peptidomimetic.

Deficiency of glucose-dependent insulinotropic polypeptide receptor prevents ovariectomy-induced obesity in mice.

Menopause and premature gonadal steroid deficiency are associated with increases in fat mass and body weight. Ovariectomized (OVX) mice also show reduced locomotor activity. Glucose-dependent-insulinotropic-polypeptide (GIP) is known to play an important role both in fat metabolism and locomotor activity. Therefore, we hypothesized that the effects of estrogen on the regulation of body weight, fat mass, and spontaneous physical activity could be mediated in part by GIP signaling. To test this hypothesis, C57BL/6 mice and GIP-receptor knockout mice (Gipr(-/-)) were exposed to OVX or sham operation (n = 10 per group). The effects on body composition, markers of insulin resistance, energy expenditure, locomotor activity, and expression of hypothalamic anorexigenic and orexigenic factors were investigated over 26 wk in all four groups of mice. OVX wild-type mice developed obesity, increased fat mass, and elevated markers of insulin resistance as expected. This was completely prevented in OVX Gipr(-/-) animals, even though their energy expenditure and spontaneous locomotor activity levels did not significantly differ from those of OVX wild-type mice. Cumulative food intake in OVX Gipr(-/-) animals was significantly reduced and associated with significantly lower hypothalamic mRNA expression of the orexigenic neuropeptide Y (NPY) but not of cocaine-amphetamine-related transcript (CART), melanocortin receptors (MCR-3 and MCR-4), or thyrotropin-releasing hormone (TRH). GIP receptors thus interact with estrogens in the hypothalamic regulation of food intake in mice, and their blockade may carry promising potential for the prevention of obesity in gonadal steroid deficiency.

Arsenic trioxide-based therapy of relapsed acute promyelocytic leukemia: registry results from the European LeukemiaNet.

In 2008, a European registry of relapsed acute promyelocytic leukemia was established by the European LeukemiaNet. Outcome data were available for 155 patients treated with arsenic trioxide in first relapse. In hematological relapse (n=104), 91% of the patients entered complete hematological remission (CR), 7% had induction death and 2% resistance, 27% developed differentiation syndrome and 39% leukocytosis, whereas no death or side effects occurred in patients treated in molecular relapse (n=40). The rate of molecular (m)CR was 74% in hematological and 62% in molecular relapse (P=0.3). All patients with extramedullary relapse (n=11) entered clinical and mCR. After 3.2 years median follow-up, the 3-year overall survival (OS) and cumulative incidence of second relapse were 68% and 41% in hematological relapse, 66% and 48% in molecular relapse and 90 and 11% in extramedullary relapse, respectively. After allogeneic or autologous transplantation in second CR (n=93), the 3-year OS was 80% compared with 59% without transplantation (n=55) (P=0.03). Multivariable analysis demonstrated the favorable prognostic impact of first remission duration ⩾1.5 years, achievement of mCR and allogeneic or autologous transplantation on OS of patients alive after induction (P=0.03, P=0.01, P=0.01) and on leukemia-free survival (P=0.006, P<0.0001, P=0.003), respectively.

Oxidação de glicerol sobre nanopartículas de ouro suportadas em carvão ativado: monitoramento quimiométrico da reação por ESI-MS e MIR

A study on the monitoring of glycerol oxidation catalyzed by gold nanoparticles supported on activated carbon under mild conditions by chemometric methods is presented. The reaction was monitored by mass spectrometry-electrospray ionization (ESI-MS) and comparatively by mid infrared spectroscopy (MIR). Concentration profiles of reagent and products were determined by chemometric tools such as Principal Component Analysis (PCA), Evolving Factor Analysis (EFA) and Multivariate Curve Resolution (MCR). The gold nanoparticle catalyst was relatively active in glycerol oxidation, favoring formation of high added value products. It was found that the reaction stabilization was reached at four hours, with approximately 70% glycerol conversion and high selectivity for glycerate.

Resolução multivariada de curvas com mínimos quadrados alternantes: descrição, funcionamento e aplicações

Multivariate Curve Resolution with Alternating Least Squares (MCR-ALS) is a resolution method that has been efficiently applied in many different fields, such as process analysis, environmental data and, more recently, hyperspectral image analysis. When applied to second order data (or to three-way data) arrays, recovery of the underlying basis vectors in both measurement orders (i.e. signal and concentration orders) from the data matrix can be achieved without ambiguities if the trilinear model constraint is considered during the ALS optimization. This work summarizes different protocols of MCR-ALS application, presenting a case study: near-infrared image spectroscopy.

Qualidade de vida de estudantes de medicina medida pelo WHOQOL-bref - UERJ, 2010

O WHOQOL-bref foi utilizado em estudo transversal para avaliar a influência do sexo, da forma de ingresso, do ano de graduação, da classe econômica e da presença de morbidade crônica referida (MCR), na qualidade de vida (QV) de 394 estudantes de medicina da UERJ (72% dos 545 matriculados em 2010, erro 6,5%). A análise estatística foi feita no SPSS v17 e utilizados testes qui-quadrado, ANOVA/ pós Hoc de Bonferroni (p valor = 5%) e razão dos produtos cruzados ("Odds Ratio" - OR) com respectivos intervalos de confiança (IC 95%). A idade média foi de 23 anos, sendo 61% mulheres, 43% cotistas (dos quais 64% mulheres) e 20% referiu morbidade crônica. De 0-100, a média da QV referida foi 66 e da satisfação com saúde 62. Os menores escores de QV foram observados nos estudantes do sexo feminino, com morbidade crônica referida (MCR), que ingressaram por reserva de vagas, da classe C e do terceiro e sexto ano. Os resultados apontam para a necessidade de estudos qualitativos para aprofundar as informações sobre a QV dos estudantes da UERJ.

Deglaciation of the Caucasus Mountains, Russia/Georgia, in the 21st century observed with ASTER satellite imagery and aerial photograpy

Changes in the map area of 498 glaciers located on the Main Caucasus ridge (MCR) and on Mt. Elbrus in the Greater Caucasus Mountains (Russia and Georgia) were assessed using multispectral ASTER and panchromatic Landsat imagery with 15 m spatial resolution in 1999/2001 and 2010/2012. Changes in recession rates of glacier snouts between 1987–2001 and 2001–2010 were investigated using aerial photography and ASTER imagery for a sub-sample of 44 glaciers. In total, glacier area decreased by 4.7 ± 2.1% or 19.2 ± 8.7 km2 from 407.3 ± 5.4 km2 to 388.1 ± 5.2 km2. Glaciers located in the central and western MCR lost 13.4 ± 7.3 km2 (4.7 ± 2.5%) in total or 8.5 km2 (5.0 ± 2.4%) and 4.9 km2 (4.1 ± 2.7%) respectively. Glaciers on Mt. Elbrus, although located at higher elevations, lost 5.8 ± 1.4 km2 (4.9 ± 1.2%) of their total area. The recession rates of valley glacier termini increased between 1987–2000/01 and 2000/01–2010 (2000 for the western MCR and 2001 for the central MCR and Mt.~Elbrus) from 3.8 ± 0.8, 3.2 ± 0.9 and 8.3 ± 0.8 m yr−1 to 11.9 ± 1.1, 8.7 ± 1.1 and 14.1 ± 1.1 m yr−1 in the central and western MCR and on Mt. Elbrus respectively. The highest rate of increase in glacier termini retreat was registered on the southern slope of the central MCR where it has tripled. A positive trend in summer temperatures forced glacier recession, and strong positive temperature anomalies in 1998, 2006, and 2010 contributed to the enhanced loss of ice. An increase in accumulation season precipitation observed in the northern MCR since the mid-1980s has not compensated for the effects of summer warming while the negative precipitation anomalies, observed on the southern slope of the central MCR in the 1990s, resulted in stronger glacier wastage.

p53 Mutant Human Glioma Cells Are Sensitive to UV-C-Induced Apoptosis Due to Impaired Cyclobutane Pyrimidine Dimer Removal

The p53 protein is a key regulator of cell responses to DNA damage, and it has been shown that It sensitizes glioma cells to the alkylating agent temozolomide by up-regulating the extrinsic apoptotic pathway, whereas it increases the resistance to chloroethylating agents, such as ACNU and BCNU, probably by enhancing the efficiency of DNA repair. However, because these agents induce a wide variety of distinct DNA lesions, the direct Importance of DNA repair is hard to access. Here, it is shown that the Induction of photoproducts by UV light (UV-C) significantly Induces apoptosis In a p53-mutated glioma background. This Is caused by a reduced level of photoproduct repair, resulting In the persistence of DNA lesions in p53-mutated glioma cells. UV-C-Induced apoptosis in p53 mutant glioma cells Is preceded by strong transcription and replication inhibition due to blockage by unrepaired photolesions. Moreover, the results Indicate that UV-C-induced apoptosis of p53 mutant glioma cells Is executed through the intrinsic apoptotic pathway, with Bcl-2 degradation and sustained Bax and Bak up-regulation. Collectively, the data Indicate that unrepaired DNA lesions Induce apoptosis In p53 mutant gliomas despite the resistance of these gliomas to temozolomide, suggesting that efficiency of treatment of p53 mutant gliomas might be higher with agents that Induce the formation of DNA lesions whose global genomic repair is dependent on p53. (Mol Cancer Res 2009;7(2):237-46)

Utilização da medida do clorofilômetro no manejo da adubação nitrogenada em plantas de pimentão

O adequado manejo da adubação nitrogenada ao longo do ciclo da cultura do pimentão é complicado pela falta de um índice do N disponível no solo e por ser a análise química de folhas um método de diagnose demorado. Foi realizado um experimento em vasos, em um túnel de plástico pertencente ao Departamento de Recursos Naturais/Ciência do Solo, da FCA/UNESP, Botucatu (SP), com o objetivo de avaliar o índice de suficiência de nitrogênio (ISN), calculado com base nas medidas do clorofilômetro, como ferramenta auxiliar no manejo da adubação nitrogenada em plantas de pimentão. O experimento foi composto de doses de N (4,9; 9,8; 14,7; 19,6; e 24,5 g de N 50 kg-1 de solo - uma planta) aplicadas de modo convencional ou pela fertirrigação e um tratamento em que as plantas não receberam apenas a adubação nitrogenada, com sete repetições. As medidas do clorofilômetro foram realizadas a cada 15 dias em cinco folhas recém-maduras por planta. O ISN foi calculado pela relação entre a média das medidas do clorofilômetro nas plantas dos tratamentos (MCT) e a média das medidas do clorofilômetro nas plantas que receberam a maior dose (MCR), na área de referência (ISN = MCT/MCR x 100). O ISN pode ser um bom indicador do momento de aplicação do adubo nitrogenado e auxiliar no ajuste da dose de N de acordo com a exigência das plantas de pimentão, com a finalidade de aumentar a eficiência de utilização do N aplicado.

The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome

open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning.

Estudo das propriedades críticas do processo de contato por par para diferentes atualizações

We study the critical behavior of the one-dimensional pair contact process (PCP), using the Monte Carlo method for several lattice sizes and three different updating: random, sequential and parallel. We also added a small modification to the model, called Monte Carlo com Ressucitamento" (MCR), which consists of resuscitating one particle when the order parameter goes to zero. This was done because it is difficult to accurately determine the critical point of the model, since the order parameter(particle pair density) rapidly goes to zero using the traditional approach. With the MCR, the order parameter becomes null in a softer way, allowing us to use finite-size scaling to determine the critical point and the critical exponents β, ν and z. Our results are consistent with the ones already found in literature for this model, showing that not only the process of resuscitating one particle does not change the critical behavior of the system, it also makes it easier to determine the critical point and critical exponents of the model. This extension to the Monte Carlo method has already been used in other contact process models, leading us to believe its usefulness to study several others non-equilibrium models