Diversity and host assemblage of avian haemosporidians in different terrestrial ecoregions of Peru.

Characterizing the diversity and structure of host-parasite communities is crucial to understanding their eco-evolutionary dynamics. Malaria and related haemosporidian parasites are responsible for fitness loss and mortality in bird species worldwide. However, despite exhibiting the greatest ornithological biodiversity, avian haemosporidians from Neotropical regions are quite unexplored. Here, we analyze the genetic diversity of bird haemosporidian parasites (Plasmodium and Haemoproteus) in 1,336 individuals belonging to 206 bird species to explore for differences in diversity of parasite lineages and bird species across 5 well-differentiated Peruvian ecoregions. We detected 70 different haemosporidian lineages infecting 74 bird species. We showed that 25 out of the 70 haplotypes had not been previously recorded. Moreover, we also identified 81 new host-parasite interactions representing new host records for these haemosporidian parasites. Our outcomes revealed that the effective diversity (as well as the richness, abundance, and Shannon-Weaver index) for both birds and parasite lineages was higher in Amazon basin ecoregions. Furthermore, we also showed that ecoregions with greater diversity of bird species also had high parasite richness, hence suggesting that host community is crucial in explaining parasite richness. Generalist parasites were found in ecoregions with lower bird diversity, implying that the abundance and richness of hosts may shape the exploitation strategy followed by haemosporidian parasites. These outcomes reveal that Neotropical region is a major reservoir of unidentified haemosporidian lineages. Further studies analyzing host distribution and specificity of these parasites in the tropics will provide important knowledge about phylogenetic relationships, phylogeography, and patterns of evolution and distribution of haemosporidian parasites.

Predicting complications of diabetes mellitus using advanced machine learning algorithms.

OBJECTIVE: We sought to predict if patients with type 2 diabetes mellitus (DM2) would develop 10 selected complications. Accurate prediction of complications could help with more targeted measures that would prevent or slow down their development. MATERIALS AND METHODS: Experiments were conducted on the Healthcare Cost and Utilization Project State Inpatient Databases of California for the period of 2003 to 2011. Recurrent neural network (RNN) long short-term memory (LSTM) and RNN gated recurrent unit (GRU) deep learning methods were designed and compared with random forest and multilayer perceptron traditional models. Prediction accuracy of selected complications were compared on 3 settings corresponding to minimum number of hospitalizations between diabetes diagnosis and the diagnosis of complications. RESULTS: The diagnosis domain was used for experiments. The best results were achieved with RNN GRU model, followed by RNN LSTM model. The prediction accuracy achieved with RNN GRU model was between 73% (myocardial infarction) and 83% (chronic ischemic heart disease), while accuracy of traditional models was between 66% - 76%. DISCUSSION: The number of hospitalizations was an important factor for the prediction accuracy. Experiments with 4 hospitalizations achieved significantly better accuracy than with 2 hospitalizations. To achieve improved accuracy deep learning models required training on at least 1000 patients and accuracy significantly dropped if training datasets contained 500 patients. The prediction accuracy of complications decreases over time period. Considering individual complications, the best accuracy was achieved on depressive disorder and chronic ischemic heart disease. CONCLUSIONS: The RNN GRU model was the best choice for electronic medical record type of data, based on the achieved results.

Seroprevalence and risk factor associated with respiratory viral pathogens in dual-purpose cattle of Aguachica, Rio de Oro, and La Gloria municipalities in Cesar department, Colombia.

AIM: The research was conducted to determine the seroprevalence and risk factor associated with respiratory viral pathogens in dual-purpose cattle of Aguachica, Rio de Oro and La Gloria municipalities in Cesar department, Colombia. MATERIALS AND METHODS: The seroprevalence study was done from the random sampling (n=1000) of blood collected from 29 dual-purpose herds, located in three municipalities (Aguachica, Rio de Oro, and La Gloria) of Cesar department. The presence of antibodies against bovine herpesvirus type 1 (BHV-1), bovine respiratory syncytial virus (BRSV), bovine viral diarrhea virus (BVDV), and bovine parainfluenza-3 virus (BPI-3V) in the samples was detected by indirect enzyme-linked immunosorbent assay. Epidemiological data were obtained using a questionnaire administered to the owner or manager of each herd. RESULTS: The overall highest seroprevalence was observed for BHV-1 (94.7%), followed by BRSV (98.6%), BVDV (35.2%), and BPI-3V (47.1%). Regarding the seroprevalence by municipalities, there was a statistical association (p<0.05) for BVDV; however, for BRSV, BHV-1, and BPI-3V, no statistical association was found (p>0.05) between seropositive values and the municipalities, indicating that animal was seropositive in similar proportions in the three municipalities. Female sex and older animals (>24 months) were a significant risk factor for BHV-1 and BPI-3V infection. Regarding the clinical signs, there was a statistical association (p<0.05) between the seropositive values of BVDV and most of clinical signs observed, except for abortion. CONCLUSION: This research confirms the high seroprevalence of the respiratory viral pathogens in nonvaccinated cattle within the study areas. Therefore, appropriate sanitary management practices and routine vaccination programs should be adopted to reduce the seroprevalence of these infectious agents.

Presence of IgG antibodies against reproductive infections in breeding bulls of Magdalena Medio, Colombia / Presencia de anticuerpos tipo IgG contra infecciones reproductivas en toros reproductores de la región del Magdalena Medio, Colombia / Presença de anticorpos IgG contra infecções reprodutivas de touros reprodutores do Magdalena Médio, Colômbia

Background: cattle farming is an important economic activity in several regions of Colombia. However, farmers are unaware of their cattle health status, and particularly of bacterial, parasitic, and viral diseases, which affect reproduction and profitability. Objective: to assess the presence of IgG antibodies against infectious bovine rhinotracheitis (IBR), bovine viral diarrhea (BVD), bovine leukosis, leptospirosis, brucellosis, and Neospora caninum in breeding bulls in the Magdalena Medio of Colombia, according to age, breed, and origin. Methods: a descriptive, cross-sectional study was conducted with 174 male breeding cattle from several subspecies. Animals were above 18 months of age and belonged to dual-purpose farms in the Magdalena Medio region. Presence of IgG anti-IBR, BVD, brucellosis, neosporosis, and leukosis antibodies were determined with an enzyme-linked immunosorbent assay (ELISA). A sample of 156 males was assessed for leptospirosis using a microscopic agglutination test (MAT) in a dark field. Results: IgG anti-IBR antibodies were found in 92.5% of the animals, anti-BVD in 62.6%, anti-Neospora caninum in 79.3%, anti-Brucella abortus in 4.02%, anti-Leptospira pomona in 8.33%, and anti-L. hardjo in 15.38%, with >1:100 titres. Besides, 64.94% prevalence was observed for bovine leukosis. Conclusions: a high prevalence of IgG anti-IBR, IgG anti-BVD, IgG anti- Neospora caninum, IgG anti-leukosis, and IgG anti-lepstospirosis antibodies were observed in Magdalena Medio bulls. With respect to B. abortus, confirmatory and competitive ELISA test should be performed and sanitary standards need to be established. Detection of IgG antibodies among bulls reveals poor sanitary conditions, absent of protective-vaccination antibodies and an urgent need for health control measurements.

Antecedentes: la ganadería bovina es una importante actividad económica desarrollada en varias regiones del país, sin embargo, los ganaderos desconocen el estado sanitario de los bovinos con respecto a enfermedades bacterianas, parasitarias y virales, lo que afecta la reproducción y la rentabilidad. Objetivo: evidenciar la presencia de anticuerpos tipo IgG anti-rinotraqueitis infecciosa bovina (IBR), diarrea viral bovina (BVD), leucosis bovina, leptospirosis, brucelosis y Neospora caninum en los toros reproductores del Magdalena Medio colombiano, en asociación con variables de edad, raza y procedencia. Métodos: se realizó un estudio descriptivo de corte transversal en un grupo poblacional de 174 machos reproductores bovinos de diferentes subespecies. Los animales eran mayores de 18 meses en fincas destinadas a ganadería doble propósito ubicadas en la región del Magdalena Medio. Mediante un ensayo de inmunoabsorción enzimática (ELISA) se determinó la presencia de anticuerpos tipo IgG anti-IBR, BVD, brucelosis, neosporosis y leucosis. Para el caso de la leptospirosis, a 156 de los machos se les realizó la prueba de microaglutinación en campo oscuro (MAT). Resultados: se hallaron anticuerpos tipo IgG anti-IBR en un 92,5%, anti-BVD en el 62,6%, anti-Neospora caninum 79,3%, anti-Brucella abortus 4,02%, anti-Leptospira pomona 8,33% y anti-L. hardjo 15,38%, con títulos >1:100. Además, para leucosis bovina se obtuvo una prevalencia del 64,94%. Conclusión: se observaron altos porcentajes de casos con presencia de anticuerpos IgG anti-IBR, BVD, N. caninum, leucosis y lepstospirosis en el ganado bovino del Magdalena Medio colombiano. Para B. abortus debe realizarse la prueba confirmativa ELISA competitiva y aplicar la norma sanitaria. La determinación de anticuerpos tipo IgG permitió conocer el delicado estado sanitario de los reproductores bovinos, teniendo en cuenta que no han recibido ningún esquema de vacunación y se hace necesario un adecuado control sanitario.

Antecedentes: a pecuária é uma atividade econômica importante em várias regiões do país, no entanto, os agricultores não têm conhecimento do estado de saúde do gado em relação adoenças bacterianas, parasitárias e virais. É por esta razão que as perdas econômicas aumentam e diminuem a qualidade de reprodução. Objetivo: demonstrar a presença de anticorpos IgG para rinotraqueíte-viral bovina (IBR), diarréia viral bovina (BVD), leucose bovina, leptospirose, brucelose e Neospora caninum. Nos machos reprodutores do Magdalena Medio tendo em conta as variáveis idade, raça e origens. Métodos: i foi realizada estudo descritivo transversal em duas populações de 174 machos reprodutores de diferentes subespécies de gado com mais de 18 meses de edad procedentes de fazendas utilizadas para a pecuária de duplo propósito, localizadas na região do Madalena Médio. Para detectar a presença de anticorpos IgG anti-IBR, BVD, brucelose, e enzoótica, neosporose foi determinada pela técnica de ensaio imunoenzimático (ELISA). Para o caso de leptospirose foi realizado teste de microaglutinação em campo escuro (MAT). Resultados: anticorpos IgG anti-IBR foram encontrados em 92,5%, anti-BVD num 62,6%, anti-Neospora caninum num 79,3%, anti-Brucella abortus 4,02%, anti-Leptospira pomona num 8,33% e anti-L. hardjo 15,38% com títulos > 1:100. Para leucose bovina, uma percentagem de 64,94%, foi obtido. Conclusão: foram observados altos percentagens de casos na presença de anticorpos IgG anti-IBR, BVD, N. caninum, lepstospirosis e leucose nos bovinos do Madalena Médio colombiano, o teste confirmatorio ELISA competitivo. Para a determinação de B. abortus deve ser realizado e dar cumplimento a normatividade sanitaria. A determinação de anticorpos IgG tem permitido conhecer o delicado estado sanitario dos reprodutores bovinos, considerando que eles não receberam qualquer vacinação é necessário um adequado controle de saúde.

pFiD188, the linear virulence plasmid of Rhodococcus fascians D188.

Rhodococcus fascians is currently the only phytopathogen of which the virulence genes occur on a linear plasmid. To get insight into the origin of this replicon and into the virulence strategy of this broad-spectrum phytopathogen, the sequence of the linear plasmid of strain D188, pFiD188, was determined. Analysis of the 198,917 bp revealed four syntenic regions with linear plasmids of R. erythropolis, R. jostii, and R. opacus, suggesting a common origin of these replicons. Mutational analysis of pFi_086 and pFi_102, similar to cutinases and type IV peptidases, respectively, showed that conserved region R2 was involved in plasmid dispersal and pointed toward a novel function for actinobacterial cutinases in conjugation. Additionally, pFiD188 had three regions that were unique for R. fascians. Functional analysis of the stk and nrp loci of regions U2 and U3, respectively, indicated that their role in symptom development was limited compared with that of the previously identified fas, att, and hyp virulence loci situated in region U1. Thus, pFiD188 is a typical rhodococcal linear plasmid with a composite structure that encodes core functions involved in plasmid maintenance and accessory functions, some possibly acquired through horizontal gene transfer, implicated in virulence and the interaction with the host.

An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences.

BACKGROUND: cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) is a commonly used technique for genome-wide expression analysis that does not require prior sequence knowledge. Typically, quantitative expression data and sequence information are obtained for a large number of differentially expressed gene tags. However, most of the gene tags do not correspond to full-length (FL) coding sequences, which is a prerequisite for subsequent functional analysis. METHODOLOGY: A medium-throughput screening strategy, based on integration of polymerase chain reaction (PCR) and colony hybridization, was developed that allows in parallel screening of a cDNA library for FL clones corresponding to incomplete cDNAs. The method was applied to screen for the FL open reading frames of a selection of 163 cDNA-AFLP tags from three different medicinal plants, leading to the identification of 109 (67%) FL clones. Furthermore, the protocol allows for the use of multiple probes in a single hybridization event, thus significantly increasing the throughput when screening for rare transcripts. CONCLUSIONS: The presented strategy offers an efficient method for the conversion of incomplete expressed sequence tags (ESTs), such as cDNA-AFLP tags, to FL-coding sequences.

Gene-to-metabolite networks for terpenoid indole alkaloid biosynthesis in Catharanthus roseus cells.

Rational engineering of complicated metabolic networks involved in the production of biologically active plant compounds has been greatly impeded by our poor understanding of the regulatory and metabolic pathways underlying the biosynthesis of these compounds. Whereas comprehensive genome-wide functional genomics approaches can be successfully applied to analyze a select number of model plants, these holistic approaches are not yet available for the study of nonmodel plants that include most, if not all, medicinal plants. We report here a comprehensive profiling analysis of the Madagascar periwinkle (Catharanthus roseus), a source of the anticancer drugs vinblastine and vincristine. Genome-wide transcript profiling by cDNA-amplified fragment-length polymorphism combined with metabolic profiling of elicited C. roseus cell cultures yielded a collection of known and previously undescribed transcript tags and metabolites associated with terpenoid indole alkaloids. Previously undescribed gene-to-gene and gene-to-metabolite networks were drawn up by searching for correlations between the expression profiles of 417 gene tags and the accumulation profiles of 178 metabolite peaks. These networks revealed that the different branches of terpenoid indole alkaloid biosynthesis and various other metabolic pathways are subject to differing hormonal regulation. These networks also served to identify a select number of genes and metabolites likely to be involved in the biosynthesis of terpenoid indole alkaloids. This study provides the basis for a better understanding of periwinkle secondary metabolism and increases the practical potential of metabolic engineering of this important medicinal plant.

Pruebas de agitación para determinar surfactante pulmonar en aspirado gástrico del recién nacido / Gastric aspirate shake test to determine pulmonary surfactant in newborns

Tipo de estudio: Prospectivo transversal, con una duración de seis meses, desde el 1 de febrero al 31 de agosto de 2003. Se realizó en 23 recién nacidos prematuros de <37 semanas de edad gestacional que ingresan al Servicio de Neonatología del Hospital Provincial General Docente Riobamba (H.P.G.D.R.); con el diagnóstico de Síndrome de Dificultad Respiratoria. Objetivo general: Determinar cualitativamente la presencia de surfactante pulmonar en contenido de aspirado gástrico, mediante la prueba de agitación, y relacionarlo con el diagnóstico de madurez pulmonar en recién nacidos prematuros que ingresan al servicio de neonatología del H.P.G.D.R. con diagnóstico de síndrome de dificultad respiratoria. Objetivos específicos: Predecir la gravedad del síndrome de dificultad respiratoria. Dar prioridad a los recién nacidos cuyas pruebas para determinar surfactante son negativas o levemente positivas. Proponer pautas para mejorar el tratamiento del síndrome de dificultad respiratoria. Metodología: En todos los niños estudiados se obtiene contenido gástrico 3cc antes de la hora de vida, previa colocación en estómago de sonda de polietileno Nº 6, se considera muestra insuficiente <1cc, se descarta cuando tiene sangre o meconio, luego se procede a realizar las diluciones. Estas pruebas fueron realizadas por médico residente o por el tratante del servicio, los datos y resultados obtenidos se recogen en el formulario de registro del estudio. Resultados: En nuestro estudio encontramos que prevaleció: pulmón en vías de maduración en 13 recién nacidos, 56%. Síndrome de dificultad respiratoria moderada en 14 niños, 61%. Llama la atención que no se administró corticoides antenatales en recién nacidos prematuros extremos y moderados en 12 casos, 67%, a pesar de ser una estrategia barata para producir madurez pulmonar y evitar el síndrome de dificultad respiratoria.

Type of study: A Transversal prospective study, between the months of February 1 – August 31, of 2003.. This study was done in 23 premature newborns with respiratory-distress syndrome of <37 weeks of age in the neonatology service of the Provincial General Docente Hospital in Riobamba (HP.GD.R.) Objective: The main objective was determine the presence of pulmonary surfactant in the gastric aspirate shake test and relate it with the diagnosis of pulmonary maturity.Methodology: We acquired Gastric liquid (3cc) by putting a 6 Fr polyethylene suction catheter before one hour of life. The sample is inadequate when it is <1cc and the presence of either blood or meconium in the fluid. The test was performed either by the resident physician or pediatrician.Results: In this study we found: lung in ways of maturity: 13 new borns (56%), modurate respiratory distress syndrome: 14 newborns (61%). In 12 of the cases 67% who were moderate and extremely premature babies did not receive prenatal corticoids being a cheap drug that avoids respiratory distress syndrome. Conclusions: The shake test in our study was useful and reliable; this allowed us to evaluate with efficiency the newborns with respiratory distress syndrome. The was a priority in newborns with immature lung or in ways of maturity.