Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region

BACKGROUND: The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification. RESULTS: We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2. CONCLUSION: The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network

Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni

<p>Abstract</p> <p>Background</p> <p>The parasitic trematode <it>Schistosoma mansoni </it>is one of the major causative agents of Schistosomiasis, a disease that affects approximately 200 million people, mostly in developing countries. Since much of the pathology is associated with eggs laid by the female worm, understanding the mechanisms involved in oogenesis and sexual maturation is an important step towards the discovery of new targets for effective drug therapy. It is known that the adult female worm only develops fully in the presence of a male worm and that the rates of oviposition and maturation of eggs are significantly increased by mating. In order to study gene transcripts associated with sexual maturation and oviposition, we compared the gene expression profiles of sexually mature and immature parasites using DNA microarrays.</p> <p>Results</p> <p>For each experiment, three amplified RNA microarray hybridizations and their dye swaps were analyzed. Our results show that 265 transcripts are differentially expressed in adult females and 53 in adult males when mature and immature worms are compared. Of the genes differentially expressed, 55% are expressed at higher levels in paired females while the remaining 45% are more expressed in unpaired ones and 56.6% are expressed at higher levels in paired male worms while the remaining 43.4% are more expressed in immature parasites. Real-time RT-PCR analysis validated the microarray results. Several new maturation associated transcripts were identified. Genes that were up-regulated in single-sex females were mostly related to energy generation (i.e. carbohydrate and protein metabolism, generation of precursor metabolites and energy, cellular catabolism, and organelle organization and biogenesis) while genes that were down-regulated related to RNA metabolism, reactive oxygen species metabolism, electron transport, organelle organization and biogenesis and protein biosynthesis.</p> <p>Conclusion</p> <p>Our results confirm previous observations related to gene expression induced by sexual maturation in female schistosome worms. They also increase the list of <it>S. mansoni </it>maturation associated transcripts considerably, therefore opening new and exciting avenues for the study of the conjugal biology and development of new drugs against schistosomes.</p

Magnetically Driven Outflows in a Starburst Environment

We here investigate the possibility that the observed collimated outflows in luminous infrared galaxies (LIGs) and some Seyfert galaxies can be produced in a starburst (SB) environment. A nuclear disk can be quickly produced by gas infall during star formation in a rotating, stellar cluster. We find that massive nuclear SBs with core disk masses M_d \sim 10^8 - 10^9 M_{\odot}, and supernova rates \nu_{SN} \simeq 5 \times 10^{-3} - 2 yr^{-1} (which are consistent with the \nu_{SN} values inferred from the observed non-thermal radio power in source candidates) may inject kinetic energies which are high enough to blow out directed flows from the accreting disk surface, within the SB lifetimes. In our models, the acceleration and collimation of the nuclear outflow are provided by magnetic fields anchored into the rotating SB-disk. The emerging outflow carries a kinetic power that is only a small fraction (a few percent) of the supernovae energy rate produced in the SB. Based on conditions determined from observed outflows and disks, we find that moderate disk magnetic fields (\gtrsim 8 \times 10^{-4} G) are able to accelerate the outflows up to the observed terminal velocities (\lesssim few 100 km s^{-1} in the case of the Seyfert galaxies, and \sim 400 - 950 km s^{-1} in the case of the LIGs). The outflow is produced within a wind zone in the disk of radius \lesssim 100 pc in the LIGs, and \lesssim 10 pc in the Seyferts, with wind mass loss to disk accretion rate ratios \dot M_w /\dot M_d \gtrsim 0.1 (where \dot M_d \sim 100 M_{\odot} yr^{-1}). The observation of rotating nuclear disks of gas within few 100 pc scales in source candidates like the LIG Arp 220, and magnetized outflows provide observational support for the picture drawn here.Comment: 31 pages, Latex file, 1 Figure, accepted for publication in the Astrophys. Journa

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans

Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, Loa loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4 Mb genome of Loa loa, and the genome of the related filarial parasite Wuchereria bancrofti, and predict 14,907 Loa loa genes based on microfilarial RNA sequencing. By comparing these genomes to that of another filarial parasite, Brugia malayi, and to several other nematode genomes, we demonstrate synteny among filariae but not with non-parasitic nematodes. The Loa loa genome encodes many immunologically relevant genes, as well as protein kinases targeted by drugs currently approved for humans. Despite lacking Wolbachia, Loa loa shows no new metabolic synthesis or transport capabilities compared to other filariae. These results suggest that the role played by Wolbachia in filarial biology is more subtle than previously thought and reveal marked differences between parasitic and non-parasitic nematodes

The Genome of Anopheles darlingi, the main neotropical Malaria vector

Anopheles darlingi is the principal neotropical malaria vector, responsible for more than a million cases of malaria per year on the American continent. Anopheles darlingi diverged from the African and Asian malaria vectors ∼100 million years ago (mya) and successfully adapted to the New World environment. Here we present an annotated reference A. darlingi genome, sequenced from a wild population of males and females collected in the Brazilian Amazon. A total of 10 481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species. In spite of a long period of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae. More than 10 million single nucleotide polymorphisms and short indels with potential use as genetic markers were identified. Transposable elements correspond to 2.3% of the A. darlingi genome. Genes associated with hematophagy, immunity and insecticide resistance, directly involved in vector–human and vector–parasite interactions, were identified and discussed. This study represents the first effort to sequence the genome of a neotropical malaria vector, and opens a new window through which we can contemplate the evolutionary history of anopheline mosquitoes. It also provides valuable information that may lead to novel strategies to reduce malaria transmission on the South American continent. The A. darlingi genome is accessible a

Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi

A novel large multigene family was recently identified in the human pathogen Trypanosoma cruzi, causative agent of Chagas disease, and corresponds to ∼6% of the parasite diploid genome. The predicted gene products, mucin-associated surface proteins (MASPs), are characterized by highly conserved N- and C-terminal domains and a strikingly variable and repetitive central region. We report here an analysis of the genomic organization and expression profile of masp genes. Masps are not randomly distributed throughout the genome but instead are clustered with genes encoding mucin and other surface protein families. Masp transcripts vary in size, are preferentially expressed during the trypomastigote stage and contain highly conserved 5′ and 3′ untranslated regions. A sequence analysis of a trypomastigote cDNA library reveals the expression of multiple masp variants with a bias towards a particular masp subgroup. Immunofluorescence assays using antibodies generated against a MASP peptide reveals that the expression of particular MASPs at the cell membrane is limited to subsets of the parasite population. Western blots of phosphatidylinositol-specific phospholipase C (PI-PLC)-treated parasites suggest that MASP may be GPI-anchored and shed into the medium culture, thus contributing to the large repertoire of parasite polypeptides that are exposed to the host immune system

New resources for functional analysis of omics data for the genus Aspergillus

<p>Abstract</p> <p>Background</p> <p>Detailed and comprehensive genome annotation can be considered a prerequisite for effective analysis and interpretation of omics data. As such, Gene Ontology (GO) annotation has become a well accepted framework for functional annotation. The genus <it>Aspergillus </it>comprises fungal species that are important model organisms, plant and human pathogens as well as industrial workhorses. However, GO annotation based on both computational predictions and extended manual curation has so far only been available for one of its species, namely <it>A. nidulans</it>.</p> <p>Results</p> <p>Based on protein homology, we mapped 97% of the 3,498 GO annotated <it>A. nidulans </it>genes to at least one of seven other <it>Aspergillus </it>species: <it>A. niger</it>, <it>A. fumigatus</it>, <it>A. flavus</it>, <it>A. clavatus</it>, <it>A. terreus</it>, <it>A. oryzae </it>and <it>Neosartorya fischeri</it>. GO annotation files compatible with diverse publicly available tools have been generated and deposited online. To further improve their accessibility, we developed a web application for GO enrichment analysis named FetGOat and integrated GO annotations for all <it>Aspergillus </it>species with public genome sequences. Both the annotation files and the web application FetGOat are accessible via the Broad Institute's website (<url>http://www.broadinstitute.org/fetgoat/index.html</url>). To demonstrate the value of those new resources for functional analysis of omics data for the genus <it>Aspergillus</it>, we performed two case studies analyzing microarray data recently published for <it>A. nidulans</it>, <it>A. niger </it>and <it>A. oryzae</it>.</p> <p>Conclusions</p> <p>We mapped <it>A. nidulans </it>GO annotation to seven other <it>Aspergilli</it>. By depositing the newly mapped GO annotation online as well as integrating it into the web tool FetGOat, we provide new, valuable and easily accessible resources for omics data analysis and interpretation for the genus <it>Aspergillus</it>. Furthermore, we have given a general example of how a well annotated genome can help improving GO annotation of related species to subsequently facilitate the interpretation of omics data.</p

Transcript Expression Analysis of Putative Trypanosoma brucei GPI-Anchored Surface Proteins during Development in the Tsetse and Mammalian Hosts

Human African Trypanosomiasis is a devastating disease caused by the parasite Trypanosoma brucei. Trypanosomes live extracellularly in both the tsetse fly and the mammal. Trypanosome surface proteins can directly interact with the host environment, allowing parasites to effectively establish and maintain infections. Glycosylphosphatidylinositol (GPI) anchoring is a common posttranslational modification associated with eukaryotic surface proteins. In T. brucei, three GPI-anchored major surface proteins have been identified: variant surface glycoproteins (VSGs), procyclic acidic repetitive protein (PARP or procyclins), and brucei alanine rich proteins (BARP). The objective of this study was to select genes encoding predicted GPI-anchored proteins with unknown function(s) from the T. brucei genome and characterize the expression profile of a subset during cyclical development in the tsetse and mammalian hosts. An initial in silico screen of putative T. brucei proteins by Big PI algorithm identified 163 predicted GPI-anchored proteins, 106 of which had no known functions. Application of a second GPI-anchor prediction algorithm (FragAnchor), signal peptide and trans-membrane domain prediction software resulted in the identification of 25 putative hypothetical proteins. Eighty-one gene products with hypothetical functions were analyzed for stage-regulated expression using semi-quantitative RT-PCR. The expression of most of these genes were found to be upregulated in trypanosomes infecting tsetse salivary gland and proventriculus tissues, and 38% were specifically expressed only by parasites infecting salivary gland tissues. Transcripts for all of the genes specifically expressed in salivary glands were also detected in mammalian infective metacyclic trypomastigotes, suggesting a possible role for these putative proteins in invasion and/or establishment processes in the mammalian host. These results represent the first large-scale report of the differential expression of unknown genes encoding predicted T. brucei surface proteins during the complete developmental cycle. This knowledge may form the foundation for the development of future novel transmission blocking strategies against metacyclic parasites

EM TEMPOS GLOBAIS, UM “NOVO” LOCAL: a Ford na Bahia

O artigo analisa a dinâmica da Região Metropolitana de Salvador (RMS) a partir da implantação da Ford, discutindo a perspectiva do ‘lugar’ (a periferia metropolitana), dentro de uma relação assimétrica com os negócios globais na era da flexibilidade. O texto caracteriza o complexo Ford de Camaçari a partir da reestruturação produtiva e das mudanças na organização e funcionamento dos territórios e, na segunda parte, seus impactos sobre a periferia metropolitana de Salvador. Na conclusão demonstra que as mesmas circunstâncias que permitiram a vinda da montadora para Camaçari constrangem as ambições originais de melhor equacionamento entre crescimento econômico e progresso social: a flexibilidade dos novos arranjos, que tornam os espaços periféricos estratégicos, compromete o “enraizamento” do investimento; a “produção enxuta”, exígua de emprego e diligente na sua precarização, inibe os benefícios sociais. PALAVRAS CHAVE: reestruturação produtiva, mercado de trabalho, indústria automobilística, periferia metropolitana, segregação socioespacial. IN GLOBAL TIMES, A “NEW” PLACE: Ford in Bahia Ângela Franco This paper makes an analysis of the dynamics of the Metropolitan Area of Salvador (in Portuguese, RMS) starting from the implantation of Ford, discussing the perspective of the ‘local’ (the metropolitan periphery), inside of an asymmetrical relationship with global businesses in the age of flexibility. The Ford Automotive Compound is caracterized in the first part of the paper from its productive reestructuring and changes in the organization and work of territories, and, in the second part, from its impact on the the metropolitan periphery from Salvador. In its conclusion it demonstrates that the same circumstances that allowed the arrival of the automotive maker in Camaçari constrain the original ambitions of better ratio between economical growth and social progress: the flexibility of the new automotive production methods, making peripheric spaces strategic, compromises on the permanence of the investments; and the “streamlined production”, easy on job production and hard on job flexibilization inhibit social benefits. KEYWORDS: productive restructuring, job market, automobile industry, metropolitan periphery, socioespatial segregation. EN PERIODE DE MONDIALISATION, UN “NOUVEAU” LOCAL: Ford à Bahia Ângela Franco Cet article traite de l’analyse de la dynamique de la Région Métropolitaine de Salvador (RMS), à partir de l’implantation de l’usine Ford. On y discute de la perspective du “lieu” (la périphérie métropolitaine), dans une relation asymétrique avec les affaires globales à une époque de flexibilité. On y caractérise le complexe Ford de Camaçari à partir de la restructuration productive et des changements dans l’organisation et le fonctionnement des territoires. Ses impacts sur la périphérie métropolitaine de Salvador sont présentés dans la deuxième partie. En conclusion, on y démontre que ce sont les mêmes circonstances qui ont permis l’arrivée de l’usine de montage à Camaçari qui représentent une contrainte pour les ambitions qui, à l’origine, voulaient atteindre une meilleure équation entre la croissance économique et le progrès social. La flexibilité de ces nouveaux arrangements, qui rendent les espaces périphériques stratégiques, compromet “l’enracinement” des investissements, la “production exiguë”, l’exiguïté des emplois et la diligence dans leur précarisation, elle inhibe les avantages sociaux. MOTS-CLÉS: restructuration productive, marché du travail, industrie automobile, périphérie métropolitaine, ségrégation sociale et spatiale. Publicação Online do Caderno CRH: http://www.cadernocrh.ufba.b