Fatty acid-specific alterations in leptin, PPARα, and CPT-1 gene expression in the rainbow trout

It is known that fatty acids (FA) regulate lipid metabolism by modulating the expression of numerous genes. In order to gain a better understanding of the effect of individual FA on lipid metabolism related genes in rainbow trout (Oncorhynchus mykiss), an in vitro time-course study was implemented where twelve individual FA (butyric 4:0; caprylic 8:0; palmitic (PAM) 16:0; stearic (STA) 18:0; palmitoleic16:1n-7; oleic 18:1n-9; 11-cis-eicosenoic 20:1n-9; linoleic (LNA) 18:2n-6; α-linolenic (ALA) 18:3n-3; eicosapentenoic (EPA) 20:5n-3; docosahexaenoic (DHA) 22:6n-3; arachidonic (ARA) 20:4n-6) were incubated in rainbow trout liver slices. The effect of FA administration over time was evaluated on the expression of leptin, PPARα and CPT-1 (lipid oxidative related genes). Leptin mRNA expression was down regulated by saturated fatty acids (SFA) and LNA, and was up regulated by monounsaturated fatty acids (MUFA) and long chain PUFA, whilst STA and ALA had no effect. PPARα and CPT-1mRNA expression were up regulated by SFA, MUFA, ALA, ARA and DHA; and down regulated by LNA and EPA. These results suggest that there are individual and specific FA induced modifications of leptin, PPARα and CPT-1 gene expression in rainbow trout, and it is envisaged that such results may provide highly valuable information for future practical applications in fish nutrition.

Maternal overnutrition programs changes in the expression of skeletal muscle genes that are associated with insulin resistance and defects of oxidative phosphorylation in adult male rat offspring.

Children of obese mothers have increased risk of metabolic syndrome as adults. Here we report the effects of a high-fat diet in the absence of maternal obesity at conception on skeletal muscle metabolic and transcriptional profiles of adult male offspring. Female Sprague Dawley rats were fed a diet rich in saturated fat and sucrose [high-fat diet (HFD): 23.5% total fat, 9.83% saturated fat, 20% sucrose wt:wt] or a normal control diet [(CD) 7% total fat, 0.5% saturated fat, 10% sucrose wt:wt] for the 3 wk prior to mating and throughout pregnancy and lactation. Maternal weights were not different at conception; however, HFD-fed dams were 22% heavier than controls during pregnancy. On a normal diet, the male offspring of HFD-fed dams were not heavier than controls but demonstrated features of insulin resistance, including elevated plasma insulin concentration [40.1 ± 2.5 (CD) vs 56.2 ± 6.1 (HFD) mU/L; P = 0.023]. Next-generation mRNA sequencing was used to identify differentially expressed genes in the offspring soleus muscle, and gene set enrichment analysis (GSEA) was used to detect coordinated changes that are characteristic of a biological function. GSEA identified 15 upregulated pathways, including cytokine signaling (P < 0.005), starch and sucrose metabolism (P < 0.017), inflammatory response (P < 0.024), and cytokine-cytokine receptor interaction (P < 0.037). A further 8 pathways were downregulated, including oxidative phosphorylation (P < 0.004), mitochondrial matrix (P < 0.006), and electron transport/uncoupling (P < 0.022). Phosphorylation of the insulin signaling protein kinase B was reduced [2.86 ± 0.63 (CD) vs 1.02 ± 0.27 (HFD); P = 0.027] and mitochondrial complexes I, II, and V protein were downregulated by 50-68% (P < 0.005). On a normal diet, the male offspring of HFD-fed dams did not become obese adults but developed insulin resistance, with transcriptional evidence of muscle cytokine activation, inflammation, and mitochondrial dysfunction. These data indicate that maternal overnutrition, even in the absence of prepregnancy obesity, can promote metabolic dysregulation and predispose offspring to type 2 diabetes.

An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture

Here we present an improved implementation of the TIGER2 Replica Exchange Molecular Dynamics (REMD) method, using the replica exchange Application Programming Interface (API) found in contemporary versions of the NAMD Molecular Dynamics Package. The implementation takes the form of a TCL script which is used in conjunction with the standard configuration file. This implementation is validated against a previous TIGER2 implementation, as well as data reported for the original TIGER2 simulations. Our implementation is compatible with a range of architectures; crucially it enables the use of this wrapper with the BlueGene/Q architecture, in addition to the x86 architecture. Program summary: Program title: TIGER2-NAMD. Catalogue identifier: AEWC_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 34151. No. of bytes in distributed program, including test data, etc.: 424217. Distribution format: tar.gz. Programming language: Tcl 8.5. Computer: x86 Clusters, BlueGene/Q, Workstations. Operating system: Linux, IBM Compute Node Kernel. Has the code been vectorised or parallelised?: Yes. MPI Parallelism. Classification: 3. External routines: NAMD 2.9 (http://www.ks.uiuc.edu/Research/namd/). Nature of problem: Replica Exchange Molecular Dynamics. Solution method: Each replica runs through multiple cycles of heating and cooling with exchanges between them being attempted. Running time: Typically 30 mins, up to an hour.

A glycosyl hydrolase family 16 gene is responsible for the endogenous production of β-1,3-glucanases within decapod crustaceans

To identify the gene responsible for the production of a β-1,3-glucanase (laminarinase) within crustacea, a glycosyl hydrolase family 16 (GHF16) gene was sequenced from the midgut glands of the gecarcinid land crab, Gecarcoidea natalis and the freshwater crayfish, Cherax destructor. An open reading frame of 1098bp for G. natalis and 1095bp for C. destructor was sequenced from cDNA. For G. natalis and C. destructor respectively, this encoded putative proteins of 365 and 364 amino acids with molecular masses of 41.4 and 41.5kDa. mRNA for an identical GHF16 protein was also expressed in the haemolymph of C. destructor. These putative proteins contained binding and catalytic domains that are characteristic of a β-1,3-glucanase from glycosyl hydrolase family 16. The amino acid sequences of two short 8-9 amino acid residue peptides from a previously purified β-1,3-glucanase from G. natalis matched exactly that of the putative protein sequence. This plus the molecular masses of the putative proteins matching that of the purified proteins strongly suggests that the sequences obtained encode for a catalytically active β-1,3-glucanase. A glycosyl hydrolase family 16 cDNA was also partially sequenced from the midgut glands of other amphibious (Mictyrisplatycheles and Paragrapsus laevis) and terrestrial decapod species (Coenobita rugosus, Coenobita perlatus, Coenobita brevimanus and Birgus latro) to confirm that the gene is widely expressed within this group. There are three possible hypothesised functions and thus evolutionary routes for the β-1,3-glucanase: 1) a digestive enzyme which hydrolyses β-1,3-glucans, 2) an enzyme which cleaves β-1,3-glycosidic bonds within cell walls to release cell contents or 3) an immune protein which can hydrolyse the cell walls of potentially pathogenic micro-organisms.

9 Incarnations

First exhibited as part of a curated exhibition by Laura Lantiera at Arc One Gallery in ‘Mind Shadows’ alongside international and nationally recognised artists Pat Brassington, Robert Owen, Justine Khamarra and Julie Wrap, this work has recently been exhibited in the exhibition ‘Inside the Matrix: a tango with light’ with an accompanying essay written by Sean Redmond in a catalogue with an ISBN # 978-1-944242-57-2. The light box work is another iteration of images exhibited and written about in the solo exhibition ‘Fly Rhythm’ 2013 at Arc One Gallery. The work has been referred to in the journal article ‘Technology as Collaborator in Somatic Photographic Practice.’ Intellect Books and at the conference ‘Photography in the 21st Century’ 2015

A matrix factorization framework for jointly analyzing multiple nonnegative data sources

Nonnegative matrix factorization based methods provide one of the simplest and most effective approaches to text mining. However, their applicability is mainly limited to analyzing a single data source. In this chapter, we propose a novel joint matrix factorization framework which can jointly analyze multiple data sources by exploiting their shared and individual structures. The proposed framework is flexible to handle any arbitrary sharing configurations encountered in real world data. We derive an efficient algorithm for learning the factorization and show that its convergence is theoretically guaranteed. We demonstrate the utility and effectiveness of the proposed framework in two real-world applications—improving social media retrieval using auxiliary sources and cross-social media retrieval. Representing each social media source using their textual tags, for both applications, we show that retrieval performance exceeds the existing state-of-the-art techniques. The proposed solution provides a generic framework and can be applicable to a wider context in data mining wherever one needs to exploit mutual and individual knowledge present across multiple data sources.

Efeitos da radiação ultravioleta b na expressão imunoistoquímica das metaloproteinases –2 e –9 em nevos melanocíticos

Introdução: a incidência dos melanomas permanece em ascensão em diversos países. Os nevos melanocíticos podem ser seus precursores ou marcadores de risco. A radiação ultravioleta é o principal fator de risco ambiental para o seu desenvolvimento. Estudos com nevos irradiados mostram que a radiação ultravioleta B (UVB) pode causar alterações morfológicas e bioquímicas semelhantes às de um melanoma in situ. As metaloproteinases da matriz (MMP) são enzimas proteolíticas e, particularmente, as MMP-2 e –9 (gelatinases A e B) parecem estar associadas à invasão tumoral, à formação de metástases e de neoangiogênese em melanomas. O objetivo do presente estudo é avaliar os efeitos da UVB nas expressões imunoistoquímicas de MMP-2 e –9 nas diferentes linhagens celulares de nevos melanocíticos. Métodos: quarenta e dois nevos melanocíticos tiveram suas metades irradiadas com dose de 2 DEM (dose eritematosa mínima) de UVB e foram excisados uma semana após. As expressões imunoistoquímicas das MMP-2 e -9 foram comparadas, quanto à sua intensidade, por três avaliadores diferentes entre os lados irradiados e não irradiados em queratinócitos, melanócitos de epiderme e derme superior, células endoteliais e fibroblastos. Os dados foram analisados pelo teste t pareado para as diferenças de expressão e pelo ICC para avaliação da homogeneidade entre as respostas dos observadores. Resultados: com relação à expressão imunoistoquímica de MMP-2, todas as linhagens celulares mostraram aumento no lado irradiado, especialmente os melanócitos epidérmicos. Quanto à MMP-9, somente nos queratinócitos, não se observou aumento de expressão do lado irradiado, ficando essa evidente nas demais linhagens celulares avaliadas. Conclusões: A UVB na dose de 2 DEM aumenta a expressão imunoistoquímica das MMP-2 e –9 em quase todas as linhagens celulares dos nevos melanocíticos avaliados até uma semana após a irradiação, com exceção feita queratinócitos, com a MMP-9.

Biologia do gene pheA de Mycobacterium tuberculosis : clonagem, seqüenciamento e superexpressão do seu produto - a proteína prefenato desidratase

A Tuberculose (TB) é a principal causa de óbitos entre as doenças infecciosas causadas por um único agente. De acordo com a Organização Mundial da Saúde (OMS) o agente etiológico da TB no homem, o complexo Mycobacterium (M. tuberculosis, M. africanum, M. bovis) é responsável por cerca de 8 milhões de novas infecções e 3 milhões de mortes a cada ano no mundo. No começo da década de 80, a reemergência da TB em países em desenvolvimento deve-se à crescente incidência do Vírus da Imunodeficiência Humana (HIV), à falta de recursos para o tratamento desta doença e à proliferação de cepas resistentes a múltiplas drogas (MDR-TB). Esta situação criou a necessidade da busca por novos agentes antimicobacterianos capazes de reduzir o tempo de tratamento, melhorar a adesão dos pacientes ao mesmo e ser efetiva contra cepas MDR-TB. A via do chiquimato leva à biossíntese do corismato, o precursor de aminoácidos aromáticos, tirosina, triptofano e fenilalanina. A primeira reação na biossíntese de fenilalanina envolve a conversão de corismato a prefenato, catalisada pela corismato mutase. A segunda reação na biossíntese de fenilalanina é a descarboxilação e desidratação de prefenato a fenilpiruvato, catalisada pela prefenato desidratase. Embora ausente em mamíferos, esta via está presente em bactérias, algas, fungos, plantas e parasitos do Phyllum Apicomplexa. Esta rota é essencial em M. tuberculosis e, portanto, suas enzimas representam alvos potenciais para o desenvolvimento de novas drogas antimicobacterianas. O objetivo deste trabalho foi estudar o gene pheA da linhagem de M. tuberculosis H37Rv e seu produto, a enzima prefenato desidratase Para isso, DNA genômico de M. tuberculosis H37RV foi extraído e o gene pheA foi amplificado pela técnica de PCR, clonado no vetor de expressão pET-23a(+), seqüenciado e superexpresso em células de Escherichia coli BL21(DE3). Os resultados obtidos confirmaram a região predita para o gene pheA, que foi amplificado com sucesso, mostrando 963 pb, sendo que a presença de 10% dimetil sulfoxido (DMSO) mostrou ser essencial para permitir a desnaturação do DNA rico em bases G-C. Análise da seqüência nucleotídica pelo método de Sanger confirmou a identidade do gene clonado e demonstrou que nenhuma mutação foi introduzida pelos passos de PCR e clonagem. A enzima prefenato desidratase foi superexpressa em células de E. coli BL21(DE3) eletroporadas com pET-23a(+)::pheA. Análise por SDS-PAGE mostrou expressão significativa de uma proteína com aproximadamente 33kDa, estando de acordo com a massa molecular esperada para a prefenato desidratase. A proteína recombinante foi superexpressa sem a adição de IPTG, e a presença da proteína pôde ser detectada em todos os intervalos de tempo testados (6, 9 e 24 horas depois da OD600nm alcançar o valor de 0,5). Foi realizado ensaio enzimático com a prefenato desidratase de acordo com Gething et al. (1976) utilizando prefenato de bário como substrato e coeficiente de extinção molar de 17.500 a 320 nm para calcular a concentração de fenilpiruvato. Houve um aumento de 1766 vezes na atividade específica da prefenato desidratase no extrato bruto da proteína recombinante em relação ao controle, no qual o vetor pET23a(+) sem o gene pheA foi introduzido em células de E. coli BL21(DE3).

Coptotermes gestroi (Isoptera: Rhinotermitidae) in Brazil: possible origins inferred by mitochondrial cytochrome oxidase II gene sequences

The Asian subterranean termite, Coptotermes gestroi, originally from northeast India through Burma, Thailand, Malaysia, and the Indonesian archipelago, is a major termite pest introduced in several countries around the world, including Brazil. We sequenced the mitochondrial COII gene from individuals representing 23 populations. Phylogenetic analysis of COII gene sequences from this and other studies resulted in two main groups: (1) populations of Cleveland (USA) and four populations of Malaysia and (2) populations of Brazil, four populations of Malaysia, and one population from each of Thailand, Puerto Rico, and Key West (USA). Three new localities are reported here, considerably enlarging the distribution of C. gestroi in Brazil: Campo Grande (state of Mato Grosso do Sul), Itajai (state of Santa Catarina), and Porto Alegre (state of Rio Grande do Sul).

Imunorreatividade da p53 associada à ausência de mutações no gene TP53 em linfomas caninos

Sabendo-se da influência das mutações no gene TP53 no desenvolvimento das neoplasias e da discrepância entre os resultados obtidos pelas técnicas de sequenciamento e imunoistoquímica, esta pesquisa teve como objetivo relacionar a sequência do TP53 com a imunorreatividade da p53. Foram obtidas amostras de linfoma de 12 cães. O diagnóstico histopatológico foi determinado pela classificação de Kiel. O imunofenótipo e a imunomarcação da p53 foram determinados por imunoistoquímica. Para reação com a p53, utilizou-se anticorpo policlonal anti-p53 (CM1) na diluição de 1:500. A região do gene TP53 compreendida entre os exons quatro e nove foi amplificada por PCR e submetida ao sequenciamento. Apesar dos resultados obtidos pela imunoistoquímica, nenhuma mutação foi encontrada nas sequências analisadas. Conclui-se que a imunorreatividade da p53 pela imunoistoquímica não pode ser atribuída à presença de mutações no domínio central do gene TP53.

Restriction fragment length polymorphism (RFLP) in Exon 2 of the BoLA-DRB3 gene in South American cattle

The Bola-DRB3 gene participates in the development of the immune response and is highly polymorphic. For these reasons, it has been a candidate gene in studies of the genetic basis of disease resistance and in population genetic analysis. South American native cattle breeds have been widely replaced by improved exotic breeds leading to a loss of genetic resources. In particular South American native breeds have high levels of fertility and disease resistance. This work describes genetic variability in the BoLA-DRB3 gene in native (Caracu, Pantaneiro, Argentinean Creole) and exotic (Holstein, Jersey, Nelore, Gir) cattle breeds in Brazil and Argentina. PCR-RFLP alleles were identified by combining the restriction patterns for the BoLA-DRB3.2 locus obtained with RsaI, BstY, and HaeIII restriction enzymes. Allelic frequencies and deviations from the Hardy-Weinberg equilibrium were also calculated. Analysis of the 24 BoLA-DRB3 PCR-RFLP alleles identified showed differences in the allele distributions among breeds.

Proteoliposomes Harboring Alkaline Phosphatase and Nucleotide Pyrophosphatase as Matrix Vesicle Biomimetics

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Associations of FASN gene polymorphisms with economical traits in Nellore cattle (Bos primigenius indicus)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evaluation of TFAM and FABP4 gene polymorphisms in three lines of Nellore cattle selected for growth

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)