More productive in vitro culture of Cryptosporidium parvum for better study of the intra- and extracellular phases

The great difficulties in treating people and animals suffering from cryptosporidiosis have prompted the development of in vitro experimental models. Due to the models of in vitro culture, new extracellular stages of Cryptosporidium have been demonstrated. The development of these extracellular phases depends on the technique of in vitro culture and on the species and genotype of Cryptosporidium used. Here, we undertake the molecular characterization by polymerase chain reaction-restriction fragment lenght polymorphism of different Cryptosporidium isolates from calves, concluding that all are C. parvum of cattle genotype, although differing in the nucleotide at positions 472 and 498. Using these parasites, modified the in vitro culture technique for HCT-8 cells achieving greater multiplication of parasites. The HCT-8 cell cultures, for which the culture had not been renewed in seven days, were infected with C. parvum sporozoites in RPMI-1640 medium with 10% IFBS, CaCl2 and MgCl2 1 mM at pH 7.2. Percentages of cell parasitism were increased with respect to control cultures (71% at 48 h vs 14.5%), even after two weeks (47% vs 1.9%). Also, the percentage of extracellular stages augmented (25.3% vs 1.1% at 96 h). This new model of in vitro culture of C. parvum will enable easier study of the developmental phases of C. parvum in performing new chemotherapeutic assays.

Population structure and diversity of the pathogenic fungus Aspergillus fumigatus isolated from different sources and geographic origins

Fifty-five clinical and environmental Aspergillus fumigatus isolates from Mexico, Argentina, France and Peru were analyzed to determine their genetic variability, reproductive system and level of differentiation using amplified fragment length polymorphism markers. The level of genetic variability was assessed by measuring the percentage of polymorphic loci, number of effective alleles, expected heterozygocity and by performing an association index test (I A). The degree of genetic differentiation and variation was determined using analysis of molecular variance at three levels. Using the paired genetic distances, a dendrogram was built to detect the genetic relationship among alleles. Finally, a network of haplotypes was constructed to determine the geographic relationship among them. The results indicate that the clinical isolates have greater genetic variability than the environmental isolates. The I A of the clinical and environmental isolates suggests a recombining population structure. The genetic differentiation among isolates and the dendrogram suggest that the groups of isolates are different. The network of haplotypes demonstrates that the majority of the isolates are grouped according to geographic origin.

An MLSA-based online scheme for the rapid identification of Stenotrophomonas isolates

An online scheme to assign Stenotrophomonas isolates to genomic groups was developed using the multilocus sequence analysis (MLSA), which is based on the DNA sequencing of selected fragments of the housekeeping genes ATP synthase alpha subunit (atpA), the recombination repair protein (recA), the RNA polymerase alpha subunit (rpoA) and the excision repair beta subunit (uvrB). This MLSA-based scheme was validated using eight of the 10 Stenotrophomonas species that have been previously described. The environmental and nosocomial Stenotrophomonas strains were characterised using MLSA, 16S rRNA sequencing and DNA-DNA hybridisation (DDH) analyses. Strains of the same species were found to have greater than 95% concatenated sequence similarity and specific strains formed cohesive readily recognisable phylogenetic groups. Therefore, MLSA appeared to be an effective alternative methodology to amplified fragment length polymorphism fingerprint and DDH techniques. Strains of Stenotrophomonas can be readily assigned through the open database resource that was developed in the current study (www.steno.lncc.br/).

Change in mutation patterns of Plasmodium vivax dihydrofolate reductase (Pvdhfr) and dihydropteroate synthase (Pvdhps) in P. vivax isolates from malaria endemic areas of Thailand

Malaria is the most important public health problem in several countries. In Thailand, co-infections of Plasmodium vivax and Plasmodium falciparum are common. We examined the prevalence and patterns of mutations in P. vivax dihydrofolate reductase (Pvdhfr) and P. vivax dihydropteroate synthase (Pvdhps) in 103 blood samples collected from patients with P. vivax infection who had attended the malaria clinic in Mae Sot, Tak Province during 2009 and 2010. Using nested polymerase chain reaction-restriction fragment length polymorfism, we examined single nucleotide polymorphisms-haplotypes at amino acid positions 13, 33, 57, 58, 61, 117 and 173 of Pvdhfr and 383 and 553 of Pvdhps. All parasite isolates carried mutant Pvdhfr alleles, of which the most common alleles were triple mutants (99%). Eight different types of Pvdhfr and combination alleles were found, as follows: 57I/58R/117T, 57I/58R/117T, 57I/58R/117T/N, 57L/58R/117T, 57L/58R/117T, 58R/61M/117N, 58R/61M/117N and 13L/57L/58R/117T. The most common Pvdhfr alleles were 57I/58R/117T (77.7%), 57I/58R/117T/N (1%), 57L/58R/117T (5.8%) and 58R/61M/117N (14.5%). The most common Pvdhfr alleles were 57I/58R/117T (77.7%), 57I/58R/117T/N (1%), 57L/58R/117T (5.8%) and 58R/61M/117N (14.5%). Additionally, we recovered one isolate of a carrying a quadruple mutant allele, 13L/57L/58R/117T. The most prevalent Pvdhps allele was a single mutation in amino acid 383 (82.5%), followed by the wild-type A383/A553 (17.5%) allele. Results suggest that all P. vivax isolates in Thailand carry some combination of mutations in Pvdhfr and Pvdhps. Our findings demonstrate that development of new antifolate drugs effective against sulfadoxine-pyrimethamine-resistant P. vivax is required.

Genetic divergence among tomato leafminer populations based on AFLP analysis

The objective of this work was to determine the genetic differences among eight Brazilian populations of the tomato leafminer Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae), from the states of Espírito Santo (Santa Tereza), Goiás (Goianápolis), Minas Gerais (Uberlândia and Viçosa), Pernambuco (Camocim de São Félix), Rio de Janeiro (São João da Barra) and São Paulo (Paulínia and Sumaré), using the amplified fragment length polymorphism (AFLP) technique. Fifteen combinations of EcoRI and MseI primers were used to assess divergence among populations. The data were analyzed using unweighted pair-group method, based on arithmetic averages (UPGMA) bootstrap analysis and principal coordinate analysis. Using a multilocus approach, these populations were divided in two groups, based on genetic fingerprints. Populations from Goianápolis, Santa Tereza, and Viçosa formed one group. Populations from Camocim de São Félix, Paulínia, São João da Barra, Sumaré, and Uberlândia fitted in the second group. These results were congruent with differences in susceptibility of this insect to insecticides, previously identified by other authors.

Citrus asymmetric somatic hybrids produced via fusion of gamma-irradiated and iodoacetamide-treated protoplasts

The objective of this study was to produce citrus somatic asymmetric hybrids by fusing gamma-irradiated protoplasts with iodoacetamide-treated protoplasts. Protoplasts were isolated from embryogenic suspension cells of grapefruit (Citrus paradisi Macfad.) cultivars Ruby Red and Flame, sweet oranges (C. sinensis Osbeck) 'Itaboraí', 'Natal', Valencia', and 'Succari', from 'Satsuma' (C. unshiu Marcow.) and 'Changsha' mandarin (C. reticulata Blanco) and 'Murcott' tangor (C. reticulata x C. sinensis). Donor protoplasts were exposed to gamma rays and receptor protoplasts were treated with 3 mmol L-1 iodoacetamide (IOA), and then they were fused for asymmetric hybridization. Asymmetric embryos were germinated, and the resulting shoots were either grafted onto sour orange, rough lemon or 'Swingle' (C. paradisi x Poncirus trifoliata) x 'Sunki' mandarin rootstock seedlings, or rooted after dipping their bases in indol-butyric acid (IBA) solution. The products were later acclimatized to greenhouse conditions. Ploidy was analyzed by flow cytometry, and hybridity was confirmed by amplified fragment length polymorphism (AFLP) analysis of plantlet DNAsamples. The best treatment was the donor-recipient fusion combination of 80 Gy-irradiated 'Ruby Red' protoplasts with 20 min IOA-treated 'Succari' protoplasts. Tetraploid and aneuploid plants were produced. Rooting recalcitrance was solved by dipping shoots' stems in 3,000 mg L-1 IBA solution for 10 min.

Genética molecular de caracteres cuantitativos en cruzamientos dialélicos de tomate

El objetivo de este trabajo fue evaluar marcadores moleculares y caracteres cuantitativos en un cruzamiento dialélico completo sin recíprocos, entre cinco líneas recombinantes de tomate y sus híbridos. Se obtuvieron perfiles de AFLP ("amplified fragment length polymorphism") y de polipéptidos del pericarpio en cuatro estados de madurez del fruto de 15 genotipos. Se evaluaron, entre otros: peso, acidez titulable, pH, vida poscosecha y firmeza. Se calculó el porcentaje de polimorfismo para los marcadores moleculares y el porcentaje de variabilidad genética para los caracteres cuantitativos en el grupo de líneas recombinantes, el de híbridos y el conjunto de genotipos. Se realizaron análisis de agrupamiento con cada nivel de variación genética. Para AFLP, el porcentaje de polimorfismo varió entre 34 y 54% y, para los perfiles polipeptídicos, entre 40 y 78%. Mayor polimorfismo fue observado en el grupo de híbridos. La variabilidad genética fue de 100% para acidez y 34% para firmeza, con los mayores valores en los parentales. La similitud genética varió entre los genotipos según el nivel de variación genética; pero la consistencia en el agrupamiento de algunas líneas recombinantes y sus híbridos fue conservada, lo que evidenció asociaciones entre los datos moleculares y fenotípicos.

Similaridade genética entre cultivares de marmeleiro avaliadas por marcadores AFLP

O objetivo deste trabalho foi determinar as relações genéticas de 21 cultivares de marmeleiro com base no marcador "amplified fragment length polymorphism" (AFLP), para melhoramento e conservação de recursos genéticos da espécie na região sul do Rio Grande do Sul. O DNA das cultivares foi extraído pelo método CTAB, e as reações de AFLP foram realizadas com os iniciadores EcoRI/MseI. Foram identificados dois grupos entre as 21 cultivares de marmeleiro, um com quatro e outro com sete cultivares geneticamente mais relacionadas. As cultivares de marmeleiro apresentam alta variabilidade genética, com máximo de 43% de similaridade.

Molecular characterization of papaya genotypes using AFLP markers

Due to the low genetic variability reported in the commercial plantations of papaya (Carica papaya L.), the objective of this study was analyze the genetic diversity of 32 genotypes including cultivars, landraces, inbred lines, and improved germplasm using the AFLP technique (Amplified Fragment Length Polymorphism). The genetic distance matrix was obtained using the Nei and Li genetic distance and clustering was performed using the unweighted pair-method with arithmetic mean (UPGMA). Using 11 combinations of EcoRI/MseI primers, 383 polymorphic bands were obtained. On average, 34.8 polymorphic bands were obtained per primer combination. Five clusters were formed. The traditional cultivar 'Sunrise' and the inbred line CMF-L30-08 were the closest genotypes, and the improved germplasm (CMF041) and landrace (CMF233) the most distant. The main papaya cultivars commercially grown in Brazil, as well as four inbred lines and three improved germplasm, were clustered together, however, were not grouped in the same branch. The genetic distance between the Sunrise and Golden cultivars was 0.329, and even arising from mutation and selection within the Sunrise variety, the Golden stores considerable genetic variability. Additional variability was observed in the inbred lines derived from papaya breeding program at Embrapa Cassava and Fruits.

AFLP markers differentiate isolates of Colletotrichum gossypii from C. gossypii var. cephalosporioides

Fungal diseases in cotton (Gossypium hirsutum), such as anthracnose caused by Colletotrichum gossypii and ramulose caused by C. gossypii var. cephalosporioides, are responsible for large yield losses. These pathogens are seed borne and morphologically similar although they induce different symptoms, which can lead to misdiagnosis using the blotter testing method. The present study was carried out to assess the viability of using Amplified Fragment Length Polymorphism (AFLP) markers to differentiate these pathogens. Five isolates, for each pathogen, were classified according to pathogenicity on cotton plants, and mycelial growth morphology. Conidial suspensions were sprayed on 30-day-old cotton plants and the symptoms assessed ten and 40 days after inoculation. For growth morphology 200 cottonseeds were inoculated with seven-day-old pure cultures, and the mycelial traits observed under a stereoscopic microscope seven days after inoculation. The DNA for AFLP analysis was obtained from seven-day-old fungal mycelia grown in liquid medium, using the Dneasy Qiagen protocol. Using the AFLP technique 318 polymorphic bands were selected to estimate similarities using Dice's Coefficient. The results clearly distinguished between ramulose and anthracnose isolates, which agreed with morphological and pathogenicity testing.

Caracterização molecular através da técnica fAFLP de isolados de Diaporthe citri

A citricultura é um mercado em expansão, principalmente no Estado de São Paulo, cuja importância na balança comercial já é reconhecida. Como em qualquer espécie cultivada, o crescimento das áreas de cultivo favorecem também o crescimento de problemas fitossanitários. Desta forma, as espécies de citros são afetadas por diversas doenças destacando-se entre elas a melanose, causada por Diaporthe citri (Wolf.), à qual a grande maioria das variedades comerciais são suscetíveis. O conhecimento da diversidade intra-específica é de grande importância, já que esta poderá auxiliar na seleção de variedades com resistência. O objetivo deste trabalho foi avaliar a variabilidade genética em isolados de Diaporthe citri, originários de diferentes locais, variedades e partes da planta, utilizando marcadores moleculares. Marcadores do tipo AFLP (Amplified Fragment Length Polymorphism) foram utilizados para caracterização de dez isolados do patógeno. Os DNAs genômicos extraídos da massa micelial foram utilizados nas reações de amplificação. A técnica fluorescent AFLP permitiu a distinção dos isolados estudados, tendo sido classificados em quatro grupos distintos. Contudo, estes grupos não foram formados em razão da região geográfica, parte da planta ou variedade.

Genetic diversity among proso millet (Panicum miliaceum) biotypes assessed by AFLP technique

The Amplified Fragment Length Polymorphism (AFLP) technique was used to access genetic diversity between three domestic and nine wild proso millet biotypes from the United States and Canada. Eight primer combinations detected 39 polymorphic DNA fragments, with the genetic distance estimates among biotypes ranging from 0.02 to 0.04. Colorado-Weld County black seeded and Wyoming-Platte County were the most distinct biotypes according to the dissimilarity level. A UPGMA cluster analysis revealed two distinct groups of proso millet without any geographic association. Six weed biotypes exhibiting some characters of cultivated plants were grouped together with domesticated biotypes of proso millet while the three typical wild phenotypes were clearly clustered into another group according to AFLP markers.

Restriction site heteroplasmy in the mitochondrial DNA of Brycon opalinus (Cuvier, 1819) (Characiformes, Characidae, Bryconiae)

Homoplasmy is a feature usually found in the mtDNA of higher animal taxa. On the other hand, the presence of two classes of mtDNA in the same cell or organism is rare and may appear in length or site variation. Data from mtDNA RFLP analysis of Brycon opalinus populations (Cuvier, 1819; Characiformes, Characidae, Bryconinae) revealed site heteroplasmy from endonuclease NheI digestion. Southern blotting hybridization was used to survey a total of 257 specimens with 24 restriction enzymes. Three different restriction fragment patterns of mtDNA were obtained from NheI digestion. Two individuals from hatchery broodstock were found to have two of them. NheI digests of heteroplasmic individuals yielded two fragments of approximately 1180 and 1260 bp. Despite the low frequency of this type of heteroplasmy in the whole B. opalinus population, the presence of site heteroplasmy in this species supports the evidence of this phenomenon in lower vertebrate groups.

Genetic diversity of Colombian sylvatic Trypanosoma cruzi isolates revealed by the ribosomal DNA

American trypanosomiasis is a common zoonosis in Colombia and Trypanosoma cruzi presents a wide distribution throughout the country. Although some studies based on enzyme electrophoresis profiles have described the population structure of the parasite, very few molecular analyses of genotipic markers have been conducted using Colombian strains. In this study, we amplified the non-transcribed spacer of the mini-gene by PCR, typing the isolates as T. cruzi I, T. cruzi zymodeme 3 or T. rangeli. In addition, the internal transcribed spacers of the ribosomal gene concomitant with the 5.8S rDNA were amplified and submitted to restriction fragment polymorphism analysis. The profiles were analyzed by a numerical methodology generating a phenetic dendrogram that shows heterogeneity among the T. cruzi isolates. This finding suggests a relationship between the complexity of the sylvatic transmission cycle in Colombia and the diversity of the sylvan parasites.

Optimization of the Sybr Green real time PCR for the detection of Human Herpes Virus type 6 (HHV-6)

HHV-6 is the etiological agent of Exanthem subitum which is considered the sixth most frequent disease in infancy. In immuno-compromised hosts, reactivation of latent HHV-6 infection may cause severe acute disease. We developed a Sybr Green Real Time PCR for HHV-6 and compared the results with nested conventional PCR. A 214 pb PCR derived fragment was cloned using pGEM-T easy from Promega system. Subsequently, serial dilutions were made in a pool of negative leucocytes from 10-6 ng/µL (equivalent to 2465.8 molecules/µL) to 10-9 (equivalent to 2.46 molecules/µL). Dilutions of the plasmid were amplified by Sybr Green Real Time PCR, using primers HHV3 (5' TTG TGC GGG TCC GTT CCC ATC ATA 3)'and HHV4 (5' TCG GGA TAG AAA AAC CTA ATC CCT 3') and by conventional nested PCR using primers HHV1 (outer): 5'CAA TGC TTT TCT AGC CGC CTC TTC 3'; HHV2 (outer): 5' ACA TCT ATA ATT TTA GAC GAT CCC 3'; HHV3 (inner) and HHV4 (inner) 3'. The detection threshold was determined by plasmid serial dilutions. Threshold for Sybr Green real time PCR was 24.6 molecules/µL and for the nested PCR was 2.46 molecules/µL. We chose the Real Time PCR for diagnosing and quantifying HHV-6 DNA from samples using the new Sybr Green chemistry due to its sensitivity and lower risk of contamination.