Microbiota of De-Novo Pediatric IBD: Increased Faecalibacterium Prausnitzii and Reduced Bacterial Diversity in Crohn's But Not in Ulcerative Colitis

OBJECTIVES: The gastrointestinal microbiota is considered important in inflammatory bowel disease (IBD) pathogenesis. Discoveries from established disease cohorts report reduced bacterial diversity, changes in bacterial composition, and a protective role for Faecalibacterium prausnitzii in Crohn's disease (CD). The majority of studies to date are however potentially confounded by the effect of treatment and a reliance on established rather than de-novo disease.

METHODS: Microbial changes at diagnosis were examined by biopsying the colonic mucosa of 37 children: 25 with newly presenting, untreated IBD with active colitis (13 CD and 12 ulcerative colitis (UC)), and 12 pediatric controls with a macroscopically and microscopically normal colon. We utilized a dual-methodology approach with pyrosequencing (threshold >10,000 reads) and confirmatory real-time PCR (RT-PCR).

RESULTS: Threshold pyrosequencing output was obtained on 34 subjects (11 CD, 11 UC, 12 controls). No significant changes were noted at phylum level among the Bacteroidetes, Firmicutes, or Proteobacteria. A significant reduction in bacterial alpha-diversity was noted in CD vs. controls by three methods (Shannon, Simpson, and phylogenetic diversity) but not in UC vs. controls. An increase in Faecalibacterium was observed in CD compared with controls by pyrosequencing (mean 16.7% vs. 9.1% of reads, P = 0.02) and replicated by specific F. prausnitzii RT-PCR (36.0% vs. 19.0% of total bacteria, P = 0.02). No disease-specific clustering was evident on principal components analysis.

CONCLUSIONS: Our results offer a comprehensive examination of the IBD mucosal microbiota at diagnosis, unaffected by therapeutic confounders or changes over time. Our results challenge the current model of a protective role for F. prausnitzii in CD, suggesting a more dynamic role for this organism than previously described.

Trait directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass Holcus lanatus

The aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate toler- ance in wild grass Holcus lanatus genotypes screened from the same habitat.

De novo transcriptome sequencing, RNAseq (RNA sequencing) and single nucleotide poly- morphism (SNP) calling were conducted on RNA extracted from H.lanatus. Roche 454 sequencing data were assembled into c. 22 000 isotigs, and paired-end Illumina reads for phosphorus-starved (P) and phosphorus-treated (P+) genovars of tolerant (T) and nontoler- ant (N) phenotypes were mapped to this reference transcriptome.

Heatmaps of the gene expression data showed strong clustering of each P+/P treated genovar, as well as clustering by N/T phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between N and T phenotypes and 258 between P+ and P treated plants. SNPs and transcript expression that systematically differed between N and T phenotypes had regulatory function, namely proteases, kinases and ribonuclear RNA- binding protein and transposable elements.

A single gene for arsenate tolerance led to distinct phenotype transcriptomes and SNP pro- files, with large differences in upstream post-translational and post-transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism per se.

DNA methyltransferase expression in the mouse germ line during periods of de novo methylation

DNA methyltransferase (DNMT) 3A and DNMT3B are both active de novo DNA methyltransferases required for development, whereas DNMT3L, which has no demonstrable methyltransferase activity, is required for methylation of imprinted genes in the oocyte. We show here that different mechanisms are used to restrict access by these proteins to their targets during germ cell development. Transcriptional control of the Dnmt3l promoter guarantees that message is low or absent except during periods of de novo activity. Use of an alternative promoter at the Dnmt3a locus produces the shorter Dnmt3a2 transcript in the germ line and postimplantation embryo only, whereas alternative splicing of the Dnmt3b transcript ensures that Dnmt3b1 is absent in the male prospermatogonia. Control of subcellular protein localization is a common theme for DNMT3A and DNMT3B, as proteins were seen in the nucleus only when methylation was occurring. These mechanisms converge to ensure that the only time that functional products from each locus are present in the germ cell nuclei is around embryonic day 17.5 in males and after birth in the growing oocytes in females.

The fungal microbiota of de-novo paediatric inflammatory bowel disease

Inflammatory bowel disease (IBD) is characterised by an inappropriate chronic immune response against resident gut microbes. This may be on account of distinct changes in the gut microbiota termed as dysbiosis. The role of fungi in this altered luminal environment has been scarcely reported. We studied the fungal microbiome in de-novo paediatric IBD patients utilising next generation sequencing and compared with adult disease and normal controls. We report a distinct difference in fungal species with Ascomycota predominating in control subjects compared to Basidiomycota dominance in children with IBD, which could be as a result of altered tolerance in these patients. 

De novo sequencing of two novel peptides homologous to calcitonin-like peptides, from skin secretion of the Chinese Frog, Odorrana schmackeri

An MS/MS based analytical strategy was followed to solve the complete sequence of two new peptides from frog (Odorrana schmackeri) skin secretion. This involved reduction and alkylation with two different alkylating agents followed by high resolution tandem mass spectrometry. De novo sequencing was achieved by complementary CID and ETD fragmentations of full-length peptides and of selected tryptic fragments. Heavy and light isotope dimethyl labeling assisted with annotation of sequence ion series. The identified primary structures are GCD[I/L]STCATHN[I/L]VNE[I/L]NKFDKSKPSSGGVGPESP-NH2 and SCNLSTCATHNLVNELNKFDKSKPSSGGVGPESF-NH2, i.e. two carboxyamidated 34 residue peptides with an aminoterminal intramolecular ring structure formed by a disulfide bridge between Cys2 and Cys7. Edman degradation analysis of the second peptide positively confirmed the exact sequence, resolving I/L discriminations. Both peptide sequences are novel and share homology with calcitonin, calcitonin gene related peptide (CGRP) and adrenomedullin from other vertebrates. Detailed sequence analysis as well as the 34 residue length of both O. schmackeri peptides, suggest they do not fully qualify as either calcitonins (32 residues) or CGRPs (37 amino acids) and may justify their classification in a novel peptide family within the calcitonin gene related peptide superfamily. Smooth muscle contractility assays with synthetic replicas of the S–S linked peptides on rat tail artery, uterus, bladder and ileum did not reveal myotropic activity.

Review of Pedro Ramos Brandão, A Igreja Católica e o “Estado Novo” em Moçambique, 1960/1974.

Book review of Pedro Ramos Brandão, A Igreja Católica e o “Estado Novo” em Moçambique, 1960/1974, Lisbonne, Editorial Notícias, 2004, 259p. ISBN: 972-46-1567-7, préface de José Capela, note scientifique de António Costa Pinto

A Internet como Novo Meio de Comunicação para os Destinos Turísticos: O caso da Ilha da Madeira

Com o aparecimento da Internet, assiste-se cada vez mais ao nascimento e desenvolvimento de novos destinos turísticos. O novo meio de comunicação faz com que os consumidores aumentem os seus patamares de exigências e de expectativas. Ao poder público e às empresas privadas cabe-lhes o papel de sensibilizar o imaginário dos turistas para visitarem as suas comunidades e regiões e não outras. O presente artigo pretende analisar a importância que o poder local e regional da Madeira atribui à Internet para a divulgação dos seus municípios como destinos turísticos a serem fruídos. A pesquisa foi baseada em entrevistas e análise dos sites municipais. O trabalho de campo realizou-se de Janeiro de 2004 a Junho de 2004. Este artigo centra-se essencialmente na análise das entrevistas e está estruturado nos seguintes tópicos: Introdução à problemática; fundamentação teórica sobre a temática; análise das entrevistas e conclusão.

Análise das implicações do novo RCCTE nos edifícios de habitação

O novo Regulamento das Características de Comportamento Térmico dos Edifícios (RCCTE) formula as exigências de forma que não evidencia as implicações sobre as soluções arquitectónicas e construtivas. A comunicação define um quadro de variáveis que caracterizam completamente o comportamento térmico dos edifícios e, com base nelas, constrói um modelo de cálculo que permite determinar as exigências de isolamento térmico da envolvente opaca e de protecção solar da envolvente não opaca. Considera depois gamas de valores típicos dessas variáveis e apresenta os resultados sob a forma de gráficos e de quadros. Apenas são contemplados edifícios de habitação.

O novo perfil do engenheiro civil: o profissional de síntese

O Homem tem modificado consideravelmente o meio natural e transformado profundamente as paisagens primitivas. As vias de comunicação e os aglomerados populacionais constituem referências evidentes da sua presença e denotam o percurso do homem no tempo. Neste processo de mudança contínua o papel dos engenheiros foi fundamental pois a sua prática remonta às civilizações anteriores à era Cristã da qual temos o testemunho de Arquimedes (287-212 a.C.) que foi um grande cientista e engenheiro da Antiguidade. O termo engenharia em termos semânticos tem a sua origem da palavra latina ingeniatorum significando “engenhoso na arte de projectar” (Duffell, 1990). De facto a engenharia tem sido definida como uma arte que permite que os principais recursos da natureza sejam transformados, adaptados e aplicados para o uso ou conveniência do homem (The New Caxton Encyclopedia, 1986).

Estruturas industriais urbanas: o emergir de um novo conceito criativo no projecto de arquitectura paisagista

Dissertação de mest., Arquitectura Paisagista, Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2011