In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences

Avian pathogenic Escherichia coli (APEC) infections are responsible for significant losses in the poultry industry worldwide. A zoonotic risk has been attributed to APEC strains because they present similarities to extraintestinal pathogenic E. coli (ExPEC) associated with illness in humans, mainly urinary tract infections and neonatal meningitis. Here, we present in silico analyses with pathogenic E. coli genome sequences, including recently available APEC genomes. The phylogenetic tree, based on multi-locus sequence typing (MLST) of seven housekeeping genes, revealed high diversity in the allelic composition. Nevertheless, despite this diversity, the phylogenetic tree was able to cluster the different pathotypes together. An in silico virulence gene profile was also determined for each of these strains, through the presence or absence of 83 well-known virulence genes/traits described in pathogenic E. coli strains. The MLST phylogeny and the virulence gene profiles demonstrated a certain genetic similarity between Brazilian APEC strains, APEC isolated in the United States, UPEC (uropathogenic E. coli) and diarrheagenic strains isolated from humans. This correlation corroborates and reinforces the zoonotic potential hypothesis proposed to APEC.

The influence of the human genome on chronic viral hepatitis outcome

The mechanisms that determine viral clearance or viral persistence in chronic viral hepatitis have yet to be identified. Recent advances in molecular genetics have permitted the detection of variations in immune response, often associated with polymorphism in the human genome. Differences in host susceptibility to infectious disease and disease severity cannot be attributed solely to the virulence of microbial agents. Several recent advances concerning the influence of human genes in chronic viral hepatitis B and C are discussed in this article: a) the associations between human leukocyte antigen polymorphism and viral hepatic disease susceptibility or resistance; b) protective alleles influencing hepatitis B virus (HBV) and hepatitis C virus (HCV) evolution; c) prejudicial alleles influencing HBV and HCV; d) candidate genes associated with HBV and HCV evolution; d) other genetic factors that may contribute to chronic hepatitis C evolution (genes influencing hepatic stellate cells, TGF-beta1 and TNF-alpha production, hepatic iron deposits and angiotensin II production, among others). Recent discoveries regarding genetic associations with chronic viral hepatitis may provide clues to understanding the development of end-stage complications such as cirrhosis or hepatocellular carcinoma. In the near future, analysis of the human genome will allow the elucidation of both the natural course of viral hepatitis and its response to therapy.

Restriction enzyme analysis of the human cytomegalovirus genome in specimens collected from immunodeficient patients in Belém, State of Pará, Brazil

INTRODUCTION: Human cytomegalovirus is an opportunistic betaherpesvirus that causes persistent and serious infections in immunodeficient patients. Recurrent infections occur due to the presence of the virus in a latent state in some cell types. It is possible to examine the virus using molecular methods to aid in the immunological diagnosis and to generate a molecular viral profile in immunodeficient patients. The objective of this study was to characterize cytomegalovirus genotypes and to generate the epidemiological and molecular viral profile in immunodeficient patients. METHODS: A total of 105 samples were collected from immunodeficient patients from the City of Belém, including newborns, hemodialysis patients, transplant recipients and HIV+ patients. An IgG and IgM antibody study was completed using ELISA, and enzymatic analysis by restriction fragment length polymorphism (RFLP) was performed to characterize viral genotypes. RESULTS: It was observed that 100% of the patients had IgG antibodies, 87% of which were IgG+/IgM-, consistent with a prior infection profile, 13% were IgG+/IgM+, suggestive of recent infection. The newborn group had the highest frequency (27%) of the IgG+/IgM+ profile. By RFLP analysis, only one genotype was observed, gB2, which corresponded to the standard AD169 strain. CONCLUSIONS: The presence of IgM antibodies in new borns indicates that HCMV continues to be an important cause of congenital infection. The low observed genotypic diversity could be attributed to the small sample size because newborns were excluded from the RFLP analysis. This study will be continued including samples from newborns to extend the knowledge of the general and molecular epidemiology of HCMV in immunodeficient patients.

Shifts in composition of avian communities related to temperate-grassland afforestation in southeastern South America

Afforestation of temperate grasslands with fast-growing trees for industrial pulpwood production is spreading in South America. Despite high afforestation rates resulting from governmental policies that stimulate pulpwood production in grasslands of southern Brazil and Uruguay, the impact of this activity on biodiversity remains to be properly assessed. We used an Impact-Reference study design to evaluate how grassland afforestation affects the composition of grassland bird assemblages. We sampled eucalyptus plantations and neighboring natural grasslands in southern Brazil from 2006-2009, and relied on nested sampling and analysis to separate the effects of afforestation from the natural variability of grasslands. We recorded a significant difference in composition between assemblages from grasslands and tree plantations. Species adapted to open, treeless areas tended to be negatively affected in relation to edge or forest birds in eucalyptus plantations. Afforestation is systematically replacing the bird assemblage of hilltop grasslands by a collection of common edge and forest species that occur in nearby riverine and hillside forests. Although most grassland birds negatively affected by tree plantations are common and widespread, observed and predicted afforestation rates in southeastern South America may result in regional population reductions in the near future.

Prevalence of avian haematozoa in São Paulo state, Brazil

The blood parasites of 15,574 birds representing 266 species of 43 families from primarily three areas in São Paulo State, Brazil were examined for haematozoa. Only 1240 (8.0% of 121 species fo 32 families were infected with blood parasites. This prevalence was similar to that reported in a previous study. Species of Haemoproteus were the most commonly encountered haematozoans (38.9%), followed by microfilaria (30.7%), Trypanosoma (13.7%), Plasmodium (7.5%) and Leucocytozoon (0.8%). Prevalence of parasitism was significantly different between the three major areas sampled. It was shown that this was due in part to differences in the avifaunas at both the familial and species levels. Prevalence varied markedly in only one of the 10 years of the study. Monthly fluctuations in prevalence were largely due to changes in relative proportions of highlytion of both. Prevalences of both microfilaria and Trypanosoma were higher than reported for any other similar survey in the world.

Toxoplasma gondii: a rapid method for the isolation of pure tachyzoites: preliminary characterization of its genome

A rapid and simple technique for the purification of Toxoplasma gondii tachyzoites was developed. Highly purified parasites were obtained from the peritoneal exudates of infected mice by means of two consecutive discontinous sucrose gradients run at low speed (10,000xg, 30 min). Parasites obtained by this method conserved its biological activity. Hybridizations tudies with DNA from healthy mice and from purified tachyzoites preparations demonstrated that Toxoplasma gondii tachyzoites DNA could be obtained with better than 90 per cents purity. Preliminary studies with DNA endonucleases showed the presence in the tachyzoites genome of highly repetitives sequences.

Re-description of Trypanosoma corvi Stephens and Christophers,1908 Emend. Baker, 1976 and remarks on the Trypanosomes of the Avian Family Corvidae

The trypomastigote, epimastigote and amastigote stages of Trypanosoma corvi Stephens and Christophers, 1908 emend. Baker, 1976 from the peripheral blood, heart and bone marrow are described herein. Other trypanosomes described from the Corvidae are compared to T. corvi and their status is discussed.

Observations on some Avian Coccidia (Apicomplexa: Eimeriidae) in Amazonian Brazil

Oocysts of Eimeria porphyrulae n. sp. are described in faeces of Porphyrula martinica (Aves: Gruiformes: Rallidae). They are ellipsoidal to oval, 22.4 x 17.7 (20.0-23.7 x 16.2-18.7) µm, shape-index (length/width) 1.3. Oocyst wall about 1.25 µm thick, colourless, with two layers: inner one prominently striated. Micropyle and sub-micropylar granule present: no oocyst residuum. Sporocysts 17.5 x 9.0 (17.0-19.0 x 8.0-10.0) µm, shape-index 1.9, with inconspicuous Stieda/sub-Stieda bodies. Sporocyst residuum of scattered granules, sometimes a compact mass: sporozoites with two refractile bodies. Eimeria crypturelli n. sp. is described in faeces of Crypturellus soiu (Tinamiformes: Tinamidae). Oocysts ellipsoidal-oval, 20.75 x 14.5 (17.5-25.0 x 11.25-21.25) µm, shape-index 1.4. Oocysts wall about 1.25 µm thick and bi-layered: inner layer faintly striated. Micropyle present, with oocyst residuum immediately below: single polar body rarely present. Sporocysts 13.0 x 7.5 (12.5-13.75 x 7,5-8.1) µm, shape-index 1.7, with a Stieda body but seemingly no sub-Stieda. Sporocyst residuum compact: sporozoites with two refractile bodies. Isospora cacici n. sp. is recorded from faeces of Cacicus cela cela (Passeriformes: Icteridae). Oocysts subspherical-spherical, 26.5 x 23.7 (22.5-27.5 x 20.0-26.2) µm, shape-index 1.1. Wall a single, colourless layer about 1.5 µm thick. No micropyle or oocyst residuum: 1-2 polar bodies. Sporocysts ellipsoidal, 17.7 x 12.5 (17.5-18.75 x 11.25-13.75) µm, shape-index 1.4, with pronounced Stieda/sub-Stieda bodies: residuum compact and sporozoites with two refractile bodies. Isospora thraupis n. sp. is described from faeces of Thraupis palmarum melanoptera (Passeriformes: Thraupidae). Oocysts subspherial-spherical, 19.9 x 19.0 (18.7-21.2 x 18.75-20.0) µm, shape-index 1.0. Wall about 0.6 µm thick, smooth, colourless and a single layer: no micropyle, oocyst residuum or polar bodies. Sporocysts 14.2 x 9.2 (13.7-16.2 x 8.7-10.0) µm, shape-index 1.5: Stied/sub-Stieda bodies inconspicuous. Residuum compact: sporozoites with two refractile bodies.

TcruziDB, an Integrated Database, and the WWW Information Server for the Trypanosoma cruzi Genome Project

Data analysis, presentation and distribution is of utmost importance to a genome project. A public domain software, ACeDB, has been chosen as the common basis for parasite genome databases, and a first release of TcruziDB, the Trypanosoma cruzi genome database, is available by ftp from ftp://iris.dbbm.fiocruz.br/pub/genomedb/TcruziDB as well as versions of the software for different operating systems (ftp://iris.dbbm.fiocruz.br/pub/unixsoft/). Moreover, data originated from the project are available from the WWW server at http://www.dbbm.fiocruz.br. It contains biological and parasitological data on CL Brener, its karyotype, all available T. cruzi sequences from Genbank, data on the EST-sequencing project and on available libraries, a T. cruzi codon table and a listing of activities and participating groups in the genome project, as well as meeting reports. T. cruzi discussion lists (tcruzi-l@iris.dbbm.fiocruz.br and tcgenics@iris.dbbm.fiocruz.br) are being maintained for communication and to promote collaboration in the genome project

Biological Parameters and Molecular Markers of Clone CL Brener - The Reference Organism of the Trypanosoma cruzi Genome Project

Clone CL Brener is the reference organism used in the Trypanosoma cruzi Genome Project. Some biological parameters of CL Brener were determined: (a) the doubling time of epimastigote forms cultured in liver infusion-tryptose (LIT) medium at 28oC is 58±13 hr; (b) differentiation of epimastigotes to metacyclic trypomastigotes is obtained by incubation in LIT-20% Grace´s medium; (c) trypomastigotes infect mammalian cultured cells and perform the complete intracellular cycle at 33 and 37oC; (d) blood forms are highly infective to mice; (e) blood forms are susceptible to nifurtimox and benznidazole. The molecular typing of CL Brener has been determined: (a) isoenzymatic profiles are characteristic of zymodeme ZB; (b) PCR amplification of a 24Sa ribosomal RNA sequence indicates it belongs to T. cruzi lineage 1; (c) schizodeme, randomly amplified polymorphic DNA (RAPD) and DNA fingerprinting analyses were performed

The Trypanosoma cruzi Genome Project: Nuclear Karyotype and Gene Mapping of Clone CL Brener

By using improved pulsed field gel electrophoresis conditions, the molecular karyotype of the reference clone CL Brener selected for Trypanosoma cruzi genome project was established. A total of 20 uniform chromosomal bands ranging in size from 0.45 to 3.5 Megabase pairs (Mbp) were resolved in a single run. The weighted sum of the chromosomal bands was approximately 87 Mbp. Chromoblots were hybridized with 39 different homologous probes, 13 of which identified single chromosomes. Several markers showed linkage and four different linkage groups were identified, each comprising two markers. Densitometric analysis suggests that most of the chromosomal bands contain two or more chromosomes representing either homologous chromosomes and/or heterologous chromosomes with similar sizes

Proceedings of the Schistosome Genome Project

"The host-parasite relationship" is a vast and diverse research field which, despite huge human and financial input over many years, remains largely shrouded in mystery. Clearly, the adaptation of parasites to their different host species, and to the different environmental stresses that they represent, depends on interactions with, and responses to, various molecules of host and/or parasite origin. The schistosome genome project is a primary strategy to reach the goal; this systematic research project has successfully developed novel technologies for qualitative and quantitative characterization of schistosome genes and genome organization by extensive international collaboration between top quality laboratories. Schistosomes are a family of parasitic blood flukes (Phylum Platyhelminthes), which have seven pairs of autosomal chromosomes and one pair of sex chromosomes (ZZ for a male worm and ZW for a female), of a haploid genome size of 2.7x108 base pairs (Simpson et al. 1982). Schistosomes are ideal model organisms for the development of genome mapping strategies since they have a small genome size comparable to that of well-characterized model organisms such as Caenorhabditis elegans (100 Mb) and Drosophila (165 Mb), and contain functional genes with a high level of homology to the host mammalian genes. Here we summarize the current progress in the schistosome genome project, the information of 3,047 transcribed genes (Expressed Sequence Tags; EST), complete sets of cDNA and genomic DNA libraries (including YAC and cosmid libraries) with a mapping technique to the well defined schistosome chromosomes. The schistosome genome project will further identify and characterize the key molecules that are responsible for host-parasite adaptation, i.e., successful growth, development, maturation and reproduction of the parasite within its host in the near future