Meta-taxonomic analysis of prokaryotic and eukaryotic gut flora in stool samples from visceral leishmaniasis cases and endemic controls in Bihar State India.

Visceral leishmaniasis (VL) caused by Leishmania donovani remains of public health concern in rural India. Those at risk of VL are also at risk of other neglected tropical diseases (NTDs) including soil transmitted helminths. Intestinal helminths are potent regulators of host immune responses sometimes mediated through cross-talk with gut microbiota. We evaluate a meta-taxonomic approach to determine the composition of prokaryotic and eukaryotic gut microflora using amplicon-based sequencing of 16S ribosomal RNA (16S rRNA) and 18S rRNA gene regions. The most abundant bacterial taxa identified in faecal samples from Bihar State India were Prevotella (37.1%), Faecalibacterium (11.3%), Escherichia-Shigella (9.1%), Alloprevotella (4.5%), Bacteroides (4.1%), Ruminococcaceae UCG-002 (1.6%), and Bifidobacterium (1.5%). Eukaryotic taxa identified (excluding plant genera) included Blastocystis (57.9%; Order: Stramenopiles), Dientamoeba (12.1%; Family: Tritrichomonadea), Pentatrichomonas (10.1%; Family: Trichomonodea), Entamoeba (3.5%; Family: Entamoebida), Ascaridida (0.8%; Family: Chromodorea; concordant with Ascaris by microscopy), Rhabditida (0.8%; Family: Chromodorea; concordant with Strongyloides), and Cyclophyllidea (0.2%; Order: Eucestoda; concordant with Hymenolepis). Overall alpha (Shannon's, Faith's and Pielou's indices) and beta (Bray-Curtis dissimilarity statistic; weighted UniFrac distances) diversity of taxa did not differ significantly by age, sex, geographic subdistrict, or VL case (N = 23) versus endemic control (EC; N = 23) status. However, taxon-specific associations occurred: (i) Ruminococcaceae UCG- 014 and Gastranaerophilales_uncultured bacterium were enriched in EC compared to VL cases; (ii) Pentatrichomonas was more abundant in VL cases than in EC, whereas the reverse occurred for Entamoeba. Across the cohort, high Escherichia-Shigella was associated with reduced bacterial diversity, while high Blastocystis was associated with high bacterial diversity and low Escherichia-Shigella. Individuals with high Blastocystis had low Bacteroidaceae and high Clostridiales vadin BB60 whereas the reverse held true for low Blastocystis. This scoping study provides useful baseline data upon which to develop a broader analysis of pathogenic enteric microflora and their influence on gut microbial health and NTDs generally.

Mo-CBP3, an antifungal chitin-binding protein from Moringa oleifera seeds, is a member of the 2S albumin family.

Mo-CBP3 is a chitin-binding protein from M. oleifera seeds that inhibits the germination and mycelial growth of phytopathogenic fungi. This protein is highly thermostable and resistant to pH changes, and therefore may be useful in the development of new antifungal drugs. However, the relationship of MoCBP3 with the known families of carbohydrate-binding domains has not been established. In the present study, full-length cDNAs encoding 4 isoforms of Mo-CBP3 (Mo-CBP3-1, Mo-CBP3-2, Mo-CBP3-3 and Mo-CBP3-4) were cloned from developing seeds. The polypeptides encoded by the Mo-CBP3 cDNAs were predicted to contain 160 (Mo-CBP3-3) and 163 amino acid residues (Mo-CBP3-1, Mo-CBP3-2 and Mo-CBP3-4) with a signal peptide of 20-residues at the N-terminal region. A comparative analysis of the deduced amino acid sequences revealed that Mo-CBP3 is a typical member of the 2S albumin family, as shown by the presence of an eight-cysteine motif, which is a characteristic feature of the prolamin superfamily. Furthermore, mass spectrometry analysis demonstrated that Mo-CBP3 is a mixture of isoforms that correspond to different mRNA products. The identification of Mo-CBP3 as a genuine member of the 2S albumin family reinforces the hypothesis that these seed storage proteins are involved in plant defense. Moreover, the chitin-binding ability of Mo-CBP3 reveals a novel functionality for a typical 2S albumin.

In silico single strand melting curve: a new approach to identify nucleic acid polymorphisms in Totiviridae.

BACKGROUND: The PCR technique and its variations have been increasingly used in the clinical laboratory and recent advances in this field generated new higher resolution techniques based on nucleic acid denaturation dynamics. The principle of these new molecular tools is based on the comparison of melting profiles, after denaturation of a DNA double strand. Until now, the secondary structure of single-stranded nucleic acids has not been exploited to develop identification systems based on PCR. To test the potential of single-strand RNA denaturation as a new alternative to detect specific nucleic acid variations, sequences from viruses of the Totiviridae family were compared using a new in silico melting curve approach. This family comprises double-stranded RNA virus, with a genome constituted by two ORFs, ORF1 and ORF2, which encodes the capsid/RNA binding proteins and an RNA-dependent RNA polymerase (RdRp), respectively. RESULTS: A phylogenetic tree based on RdRp amino acid sequences was constructed, and eight monophyletic groups were defined. Alignments of RdRp RNA sequences from each group were screened to identify RNA regions with conserved secondary structure. One region in the second half of ORF2 was identified and individually modeled using the RNAfold tool. Afterwards, each DNA or RNA sequence was denatured in silico using the softwares MELTSIM and RNAheat that generate melting curves considering the denaturation of a double stranded DNA and single stranded RNA, respectively. The same groups identified in the RdRp phylogenetic tree were retrieved by a clustering analysis of the melting curves data obtained from RNAheat. Moreover, the same approach was used to successfully discriminate different variants of Trichomonas vaginalis virus, which was not possible by the visual comparison of the double stranded melting curves generated by MELTSIM. CONCLUSION: In silico analysis indicate that ssRNA melting curves are more informative than dsDNA melting curves. Furthermore, conserved RNA structures may be determined from analysis of individuals that are phylogenetically related, and these regions may be used to support the reconstitution of their phylogenetic groups. These findings are a robust basis for the development of in vitro systems to ssRNA melting curves detection.

Desfechos clínicos após investigação para Embolia Pulmonar utilizando TC de tórax/membros inferiores / Clinical outcomes after investigation for pulmonary embolism using CT angiography and venography

FUNDAMENTO: O diagnóstico de Embolia Pulmonar (EP) ainda requer longos períodos de trabalho e inúmeros testes. OBJETIVO: Nosso objetivo é avaliar os desfechos clínicos após uma investigação negativa usando um protocolo combinado de angio TC de tórax e venografia por TC (CTA/CTV) como único teste de diagnóstico em pacientes não selecionados com suspeita de EP. MÉTODOS: Estudo de coorte retrospectivo que incluiu pacientes consecutivos com suspeita de EP que foram investigados com um protocolo combinado de CTA/CTV. Os pacientes que apresentaram inicialmente uma investigação negativa e não receberam anticoagulantes foram acompanhados por seis meses para ocorrência de eventos tromboembólicos venosos recorrentes. RESULTADOS: De 425 pacientes com suspeita de EP, 62 (14,6%) tiveram diagnóstico de tromboembolismo venoso no CTA/CTV inicial. A média de idades foi de 56 ± 19 anos, e 61% da população se enquadravam na categoria de baixa probabilidade clínica. A trombose venosa profunda isolada representou 21% de todos os eventos tromboembólicos venosos, e quando se considerou toda a população, a CTV foi associada a um incremento no rendimento diagnóstico de 3,1%. Nosso grupo era composto de 320 pacientes com CTA/CTV inicialmente negativo e que não receberam anticoagulantes. Após seis meses de acompanhamento, apenas três pacientes apresentaram recorrência de eventos tromboembólicos (0,9%, IC 95% -0,1% - 2,0%) e nenhum foi fatal. Não houve mortes relacionadas com a EP. CONCLUSÕES: Nosso estudo sugere que uma estratégia de diagnóstico que utiliza CTA/CTV como único teste de diagnóstico pode descartar EP com segurança, em população com risco baixo a moderado, e está associada a resultados favoráveis, com um valor preditivo negativo de 99,1%. (Arq Bras Cardiol. 2012; [online].ahead print, PP.0-0).

BACKGROUND: The diagnosis of pulmonary embolism (PE) still requires long work-up periods and multiple tests. OBJECTIVE: We aim to assess clinical outcomes after a negative investigation using a combined protocol of CT pulmonary angiography and CT venography (CTA/CTV) as a sole diagnostic test in unselected patients with suspected PE. METHODS: This retrospective cohort study enrolled consecutive patients with suspected PE who were investigated with a combined CTA/CTV protocol. Patients who had an initially negative investigation and were not anticoagulated were followed for 6 months for the occurrence of recurrent venous thromboembolic events. RESULTS: Out of 425 patients with suspected PE, 62 (14.6%) had venous thromboembolism diagnosed on the initial CTA/CTV. The mean age was 56 ± 19 years and 61% of the population fell into the low clinical probability category. Isolated deep vein thrombosis represented 21% of all venous thromboembolic events, and when considering the whole population, CTV was associated with an increment in diagnostic yield of 3.1%. Our cohort was composed of 320 patients with initially negative CTA/CTVs and who were not anticoagulated. After 6 months of follow up, only three patients presented with recurrent thromboembolic events (0.9%; 95% CI -0.1% - 2.0%) and none was fatal. There were no PE-related deaths. CONCLUSION: Our study suggests that a diagnostic strategy that utilizes CTA/CTV as a sole diagnostic test can safely rule out PE in a low to moderate risk population and is associated with favorable outcomes with a negative predictive value of 99.1%. (Arq Bras Cardiol. 2012; [online].ahead print, PP.0-0).

Clinical outcomes after investigation for pulmonary embolism using CT angiography and venography.

BACKGROUND: The diagnosis of pulmonary embolism (PE) still requires long work-up periods and multiple tests. OBJECTIVE: We aim to assess clinical outcomes after a negative investigation using a combined protocol of CT pulmonary angiography and CT venography (CTA/CTV) as a sole diagnostic test in unselected patients with suspected PE. METHODS: This retrospective cohort study enrolled consecutive patients with suspected PE who were investigated with a combined CTA/CTV protocol. Patients who had an initially negative investigation and were not anticoagulated were followed for 6 months for the occurrence of recurrent venous thromboembolic events. RESULTS: Out of 425 patients with suspected PE, 62 (14.6%) had venous thromboembolism diagnosed on the initial CTA/CTV. The mean age was 56 ± 19 years and 61% of the population fell into the low clinical probability category. Isolated deep vein thrombosis represented 21% of all venous thromboembolic events, and when considering the whole population, CTV was associated with an increment in diagnostic yield of 3.1%. Our cohort was composed of 320 patients with initially negative CTA/CTVs and who were not anticoagulated. After 6 months of follow up, only three patients presented with recurrent thromboembolic events (0.9%; 95% CI -0.1% - 2.0%) and none was fatal. There were no PE-related deaths. CONCLUSION: Our study suggests that a diagnostic strategy that utilizes CTA/CTV as a sole diagnostic test can safely rule out PE in a low to moderate risk population and is associated with favorable outcomes with a negative predictive value of 99.1%.