Finding a needle in a haystack: DNA Haemoproteus columbae enrichment using percoll density gradient and flow cytometry.

Isolation of genomic DNA of blood parasites in birds, reptiles, amphibians, and fishes is a challenging task, given that their red blood cells are nucleated; for that reason, parasite genomic DNA is only a fraction of the total extracted DNA, and it is challenging to obtain concentrated high-quality genetic material. Percoll Density Gradient (PDG) and flow cytometry are tools for separating and analyzing cell populations or even a single cell, and both represent potent approaches for isolating avian haemosporidians parasites. Our experimental design included several steps seeking to concentrate the parasite´s DNA. We used blood samples from a Rock pigeon infected with Haemoproteus columbae. After inducing parasite exflagellation and gametogenesis in vitro, we subjected the samples to a Percoll Density Gradient to separate the parasites from the rest of the blood cells. Following centrifugation, the layer containing extracellular parasites underwent a flow cytometry and cell sorting process, during which we selected two different subpopulations of cells for analysis. Based on qPCR analyses, we demonstrate parasite DNA enrichment in Percoll Density Gradient and flow cytometry samples; simultaneously, these samples showed the lowest concentration of Columba livia DNA. However, the concentration of parasite DNA was higher in the PDG than in the cell sorting sample. This study reports the concentration of the Haemoproteus parasite by flow cytometry without DNA-intercalating dyes, and this methodology can serve as a technique for DNA enrichment of blood parasites infecting nucleated red blood cells to improve techniques that allow obtaining complete genomes.

Is Haemoproteus gabaldoni a valid species? An approach from morphology and molecular tools applied to parasites of Anseriformes.

Currently, there are three recognized species of haemoproteids infecting Anseriformes: Haemoproteus nettionis, H. macrovacuolatus, and H. greineri. Unfortunately, genetic information associated with a morphotype is available only for H. macrovacuolatus. We recently found a parasite morphologically compatible with Haemoproteus gabaldoni, a species Bennet (1993) described in a Cairina moschata (Muscovy duck) from Venezuela. This species was synonymized to H. nettionis by Valkiunas (2005), arguing not enough morphological differentiation between them; it was said that H. greineri could be as well a synonym of H. nettionis. In this study, we aimed to provide evidence to determine if Haemoproteus gabaldoni is a different species of H. nettionis and help to clarify other species status. We first performed morphological and morphometrical analyses and compared this information against the parahapantotypes of H. greineri, H. gabaldoni and material diagnosed as H. nettionis provided by the International Reference center for Avian Haematozoa (IRCAH), and H. macrovacuolatus from the Host-Parasite Relationship Study Group (GERPH, in Spanish Grupo de Estudio Relación Parásito Hospedero) biological collection. We used Principal Component Analysis (PCA) of dimensionless standard morphometrical variables from gametocytes. Furthermore, we amplified a small fragment of cytochrome b (cyt b) to compare the sequence with information in GenBank and Malavi through phylogenetic analyses and haplotype networks. PCA analyses revealed the presence of three distinct groups in the samples studied, supported in the morphological traits of each parasite species analyzed; phylogenetic analyses grouped parasite lineages separately according to the host and continent of provenance. Such results indicate that, H. gabaldoni, is a different species from H. nettionis. One more time, it is demonstrated the importance of linking barcode surveys to morphological studies. Finally, it is highlighted the importance of biological collections as repositories of worldwide biodiversity.

The genetic and morphological diversity of Haemogregarina infecting turtles in Colombia: Are mitochondrial markers useful as barcodes for these parasites?

Adeleorinid parasites commonly infect turtles and tortoises in nature. Currently, our knowledge about such parasites is extremely poor. Their characterization is based on morphological and molecular approaches using the 18S rDNA molecular marker. However, there is a limitation with the 18S rDNA due to its slow rate of evolution. For that reason, the goals of this study were to 1) design primers for new molecular mitochondrial markers to improve the phylogenetic reconstructions of adeleorinid parasites and 2) to determine the morphological and genetic diversity of Haemogregarina infecting turtles and tortoises in Colombia. Turtles from 16 species representing six families were examined for the presence of haemoparasites. We analyzed 457 samples using PCR, and 203 of them were also analyzed by microscopy. Using a mitochondrial genome of Haemogregarina sequenced in this study, we designed primers to amplify fragments of the cytochrome oxidase I (coxI), cytochrome oxidase III (coxIII), and cytochrome b (cytb) mitochondrial markers in adeleorinid parasites. Lineages obtained from nuclear and mitochondrial molecular markers clustered according to the turtle lineages from which they were isolated. It is noteworthy that we found different evolutionary lineages within the same morphotype, which may indicate heteroplasmy and/or cryptic diversity in Haemogregarina. Due to this situation, we could not make a species delimitation, even when integrating the different lines of evidence we had in this study. However, the primers presented here are useful for diagnosis and, moreover, according to the available information, all three genes retain phylogenetic signals; thereby fragments amplified can be used in reconstructing evolutionary relationships. This effort contributes to the knowledge of the diversity of these parasites infecting continental turtles from Colombia.

Molecular and morphological description of the first Hepatozoon (Apicomplexa: Hepatozoidae) species infecting a neotropical turtle, with an approach to its phylogenetic relationships.

Haemogregarines (Adeleorina) have a high prevalence in turtles. Nevertheless, there is only one Hepatozoon species described that infects Testudines so far; it is Hepatozoon fitzsimonsi which infects the African tortoise Kinixys belliana. Colombia harbours a great diversity of chelonians; however, most of them are threatened. It is important to identify and characterize chelonian haemoparasite infections to improve the clinical assessments, treatments and the conservation and reintroduction programs of these animals. To evaluate such infections for the Colombian wood turtle Rhinoclemmys melanosterna, we analysed blood from 70 individuals. By using the morphological characteristics of blood stages as well as molecular information (18S rRNA sequences), here we report a new Hepatozoon species that represents the first report of a hepatozoid species infecting a semi-aquatic continental turtle in the world. Although the isolated lineage clusters within the phylogenetic clades that have morphological species of parasites already determined, their low nodal support makes their position within each group inconclusive. It is important to identify new molecular markers to improve parasite species identification. In-depth research on blood parasites infecting turtles is essential for increasing knowledge that could assess this potential unknown threat, to inform the conservation of turtles and for increasing the state of knowledge on parasites.

Accediendo al pasado: uso de especímenes de colección como fuentes de información genética para el género Bombus (Hymenoptera: Apidae)

Introducción: Recientemente ha tomado relevancia el uso de especímenes de museo como fuente de información genética para desarrollar estudios que resuelven preguntas taxonómicas, ecológicas, demográficas y evolutivas a diversas escalas temporales y geográficas. Sin embargo, material genético obtenido a partir de ejemplares depositados en colecciones biológicas es poco usado, debido al deterioro natural del ADN preservado en dichos ejemplares, de manera que la obtención de material genético de calidad es demandante en términos de tiempo y dinero. Objetivo: Usando material de museo, identificar una secuencia mini-barcode que pueda ser empleada en la determinación taxonómica, y que a su vez suministre información que permita la estimación de relaciones filogenéticas de especies del género Bombus. Métodos: Se estandarizó el protocolo de extracción de ADN a partir de la extremidad mesotoracica derecha y/o una muestra de músculo torácico de 96 especímenes depositados en la colección LABUN entre 7 y 38 años atrás. Las diferentes combinaciones de oligonucleótidos evaluadas permitieron amplificar fragmentos de 152 a 407 pares de bases (pb) del gen mitocondrial Cytochrome Oxidase I (COI). Usando como plantilla un grupo de 31 secuencias amplificadas a partir de especímenes recolectados recientemente, los fragmentos obtenidos de los especímenes del museo fueron ensamblados y analizados en un marco filogenético. Además, se realizó un análisis de red de haplotipos para evaluar en detalle las relaciones entre los haplotipos mitocondriales resultantes. Resultados: Se determinó un mayor éxito de extracción de ADN a partir de muestras de extremidad depositadas a partir del año 1982.Entretanto, la amplificación exitosa de fragmentos de más de 300 pares de bases (pb) se logró principalmente en muestras depositadas en fechas posteriores a 1999, lo que indica una mayor integridad del material genético recuperado de individuos de 19 años de recolección en adelante. Aunque todos los fragmentos evaluados pueden ser empleados como mini-barcode, solo con uno se obtiene una topología similar a la observada con el fragmento completo. Se detectó una gran variacion genética, particularmente al interior de las especies Bombus atratus y B. funebris, en las que se reveló una clara estructura filogeográfica. Conclusiones: Se obtuvieron nuevas secuencias de códigos de barras mediante extracción de ADN y protocolo de amplificación de muestras de museos. Además, se generó nueva información sobre la variabilidad genética intraespecífica, detectando la presencia de haplotipos mitocondriales únicos que podrían constituir Unidades Significativas Evolutivas sujetas a conservación. Dicha información es de vital importancia para formular estrategias de conservación para estos polinizadores en Colombia.

Introduction: The use of museum specimens as a source of genetic information to develop studies that resolve taxonomic, ecological, demographic, and evolutionary questions at various temporal and geographic scales, has recently become relevant. However, genetic material obtained from specimens deposited in biological collections is not used frequently due to the natural deterioration of the DNA preserved in these specimens. Getting quality genetic material is demanding in terms of time and money. Objective: By using museum material,to identify a mini-barcode sequence that can be used in the taxonomic determination and provides information that allows the estimation of phylogenetic relationships of species of the genus Bombus. Methods: The DNA extraction protocol for museum samples was standardized using the mesothoracic right leg and / or a sample of thoracic muscle of 96 specimens deposited in the LABUN collection between 7 and 38 years ago. Different combinations of oligonucleotides allowed to amplify fragments from 152 to 407 base pairs (bp) of the mitochondrial gene Cytochrome Oxidase I (COI). Using as a template a group of 31 sequences amplified from recently collected specimens, the fragments obtained from the museum specimens were assembled and analyzed in a phylogenetic framework. Additionally, a haplotype network analysis was performed in order to evaluate in detail the relationships between the resulting mitochondrial haplotypes. Results: The greatest success of DNA extraction was achieved from limb samples deposited since the year 1982 on. Meanwhile, successful amplification of fragments longer than 300 base pairs (bp) was achieved mostly in samples deposited on dates after 1999, which indicates greater integrity of the genetic material recovered from individuals of 19 years of collection and onwards. Although all the fragments evaluated can be used as mini-barcode, only with one primer pair, it was possible to obtain a topology similar to that observed with the complete fragment. A large genetic variation was detected, particularly within the Bombus atratus and B. funebris species, in which a clear phylogeographic structure was revealed. Conclusions: New barcode sequences were obtained through DNA extraction and amplification protocol from museum samples. Furthermore, new information on intraspecific genetic variability was generated, detecting the presence of unique mitochondrial haplotypes that could constitute management units subject of conservation. Such information is of vital importance to formulate conservation strategies for these pollinators in Colombia.

Medicina de precisión en sepsis: utilidad de los en sepsis: utilidad de los biomarcadores en pacientes críticamente enfermos / Precision medicine in sepsis: usefulness of biomarkers In critically ill patientsbiomarkers In critically ill patients

Durante años la evolución del cuidado intensivo ha intentado ofrecer una atención basada en protocolos y paquetes de manejo agrupados por patologías y cuadro sindromáticos. Aunque se logró disminuir la mortalidad en diferentes patologías (sepsis y síndromes coronario agudo y de distrés respiratorio agudo), no se han resuelto por completo los problemas clínicos, en especial el diagnóstico y el manejo. Una nueva opción ha surgido en el horizonte denominada "medicina de precisión", entendida como estrategia de prevención y tratamiento que tiene en cuenta la variabilidad individual. La sepsis es un síndrome con múltiples aristas en cuanto al fenotipo y genotipo, cuyo diagnóstico temprano es relevante para los desenlaces clínicos. Hasta el momento el enfoque principal ha sido la identificación de un germen etiológico para diferenciarla del síndrome de respuesta inflamatoria sistémica (SIRS). En los últimos años el paradigma en enfermedades infecciosas ha cambiado debido a estudios que demuestran como la respuesta inmunitaria del paciente séptico tiene un papel clave en el desarrollo de la enfermedad, con implicaciones en el diagnóstico, pronóstico y tratamiento, que podrían ayudar a cambiar el abordaje en los próximos años gracias a una estrategia basada en medicina de precisión. Hoy los aislamientos microbiológicos y los cultivos siguen siendo el estándar de referencia con varias desventajas como el tiempo para obtener resultados, sobre todo en infecciones por gérmenes resistentes u hongos, que pueden retrasar el inicio de la terapia antimicrobiana. Como alternativa se ha planteado el uso de biomarcadores en sepsis que, siendo productos de la respuesta inflamatoria del individuo ante la infección, son útiles para el diagnóstico y pronóstico primordialmente en los críticamente enfermos. Decidimos realizar esta revisión narrativa acerca de la utilidad de los biomarcadores en pacientes con sepsis críticamente enfermos, para enfocarlos en un modelo de medicina personalizada.

For many years, critical care practice has been based on protocols and management guidelines categorized by pathologies or syndromes. Although mortality caused by various diseases such as sepsis, acute coronary syndrome and acute respiratory distress has decreased, clinical problems, particularly diagnosis and management, have not been completely resolved. A new option known as "precision medicine" is on the horizon, a prevention and treatment strategy based on individual variability. Sepsis is a syndrome encompassing multiple clinical phenotypes and genotypes coding and a prompt diagnosis is relevant to obtain better outcomes. To this moment the main approach has been the identification of microorganisms causing sepsis to distinguish sepsis from systemic inflammatory response (SIRS). Infectious diseases paradigm has changed during recent years due to studies demonstrating how septic patient immune response plays a key role in the development of the disease, with implications on diagnosis, prognosis and treatment, which may help change the approach in the next years thanks to a strategy based on precision medicine. Today microbiological identification and cultures continue to be the reference standard with several disadvantages such as turnaround time for test results predominantly in infections caused by resistant bacteria or fungi that may delay commencement of antibiotic therapy. The use of sepsis biomarkers determined by the individual ́s inflammatory response to infection have been proposed as a useful alternative for establishing diagnosis and prognosis mainly in critically ill patients. We decided to conduct this narrative review on the usefulness of biomarkers in critically ill septic patients using a personalized medicine model.

Experimental characterization of the complete life cycle of Haemoproteus columbae, with a description of a natural host-parasite system used to study this infection.

Characterization of complete life cycles of haemoparasites requires the maintenance of suitable susceptible vertebrate hosts and vectors for long periods in captivity, in order to follow the complete parasitic cycle in definitive and intermediate hosts. Currently, there are few host-parasite models established in avian haemosporidian research, and those have been developed mainly for species of Passeriformes and their parasites. This study aimed to develop an experimental methodology to access the complete life cycle of Haemoproteus columbae (cytb lineage HAECOL1), which parasitizes the Rock Pigeon (Columba livia) and louse fly (Pseudolynchia canariensis). A colony of louse flies, which are the natural vectors of this parasite, was established. Thirty newly emerged insects were exposed to H. columbae infection and used to infect naïve Rock Pigeons. The peak of parasitaemia (acute stage) was seen between 27 and 32 days p.i. when up to 70.8% of red blood cells were infected. The crisis occurred approximately 1 week after the peak, and the long-lasting chronic parasitaemia stage followed. Exo-erythrocytic meronts were seen mainly in the lungs where extensive tissue damage was reported, but also in the kidneys and spleen. In the vector, the sporogonic cycle of H. columbae was completed between 13 and 16 days p.i., at an average temperature ranging between 12 and 15 °C. This host-parasite model is tractable for maintenance in captivity. It is recommended for use in studies aiming for detailed characterization of host-parasite relationships in areas such as physiology, pathology, immunobiology, genetics, as well as for evaluative treatments and to follow the infection in any stage of parasite development both in the vertebrate or invertebrate host.

Indicaciones de estudio genético invasivo en una población seleccionada: Agosto de 2005 a diciembre de 2007 / Indications for invasive genetic studies in a population-based sample: August 2005 to december 2007

Antecedentes: la mayor utilización de ecografía prenatal y procedimientos diagnósticos invasivos ha permitido mejorar la identificación de malformaciones fetales al nacimiento. El dilema conlleva un riesgo relacionado con el procedimiento, por lo que los médicos siguen lidiando con la manera de identificar las pacientes con riesgo elevado para no someter a las de bajo riesgo a procedimientos diagnósticos innecesarios. En el presente estudio nos hemos planteado describir las diferentes indicaciones para el diagnóstico genético invasivo de alteraciones cromosómicas en una población seleccionada de Bogotá D.C. Pacientes y métodos: se realizó un estudio descriptivo de corte transversal entre el 1 de agosto de 2005 y el 31 de diciembre de 2007. Se revisaron las historias clínicas de embarazadas remitidas con indicación de estudio genético invasivo por anomalías cromosómicas. Resultados: se analizaron 374 embarazos, de los cuales el 98,9% (n=370) eran simples y el 1,1% (n=4) correspondían a gemelares, para un total de 378 análisis del cariotipo fetal. La edad materna promedio fue de 35 años y la gestacional promedio de 17,4 semanas. Se realizaron 366 amniocentesis (96,8%) y 12 biopsias de vellosidades coriónicas (3,2%). El estudio citogenético más solicitado fue el cariotipo 64,8% (n=245) y en 33,6% (n=127) de los casos se hizo análisis por FISH y cariotipo. Entre las indicaciones para solicitar estudio genético invasivo se destacan la edad materna con 35,7% (n=135), seguida de malformaciones menores ecográficas 14,8% (n=56), tamizaje segundo trimestre 9,3% (n=35), sonolucencia nucal aumentada 6,9% (n=26) y malformaciones mayores ecográficas 6,3% (n=24). Se reportaron 54 estudios citogenéticos alterados (14,3%); de ellos, 36 correspondieron a aneuploidías (66,67%) y dieciocho a variaciones estructurales (33,33%). Cuando la edad materna fue la única indicación de un procedimiento invasivo, sólo se detectó el 6,66% de cariotipos alterados, mientras que en el grupo...

Antecedents: increased use of prenatal ultrasound and invasive diagnostic procedures has improved the detection of congenital fetal defects. The dilemma entails a procedure-related risk for which physicians continue to put up with a way to identify highrisk patients to avoid unnecessary diagnostic procedures in low-risk patients. This population-based study, conducted in Bogotá D.C., describes the various indications for an invasive genetic study to identify chromosomal abnormalities. Patients and methods: this is a descriptive cross-sectional study performed between August 1st 2005 and December 31st 2007. The clinicalrecords of pregnant women referred with an indication for invasive prenatal testing due to chromosomal abnormalities were reviewed. Results: 374 pregnancies were assessed, where 98.9% (n=370) were single pregnancies and 1.1% (n=4) twin pregnancies, thus, 378 fetal karyotype analyses were conducted. The mean age was 35 years and the mean gestational age was 17.4 weeks. We performed 366 amniocentesis (96.8%) and 12 choryonic villus sampling (3.2%). Karyotype analysis was the most frequently requested cytogenetic study accounting for 64.8% (n=245) of cases and FISH and karyotype analyses wereperformed in 33.6% (n=127). Advanced maternal age in 35.7% (n=135) was the main indication for invasive genetic studies request, followed by minor malformations detected by ultrasound 14.8% (n=56), second-trimester screening 9.3% (n=35), enhanced nuchal translucency 6.9% (n=26) and major defects detected by ultrasound 6.3% (n=24). Fifty-four (54) cytogenetic studies were reported as abnormal (14.3%); 36 corresponding to aneuploidy (66.67%) and 18 to structural variations (33.33%). Only 6.66% abnormal karyotypes were determined when maternal age was the only indication for an invasive procedure, while aneuploidy was diagnosed in the minor or major defect or nuchal translucency groups in 25%, 29% and 26% respectively...