Practical implications of using non-relational databases to store large genomic data files and novel phenotypes

The objective of our study was to provide practical directions on the storage of genomic information and novel phenotypes (treated here as unstructured data) using a non-relational database. The MongoDB technology was assessed for this purpose, enabling frequent data transactions involving numerous individuals under genetic evaluation. Our study investigated different genomic (Illumina Final Report, PLINK, 0125, FASTQ, and VCF formats) and phenotypic (including media files) information, using both real and simulated datasets. Advantages of our centralized database concept include the sublinear running time for queries after increasing the number of samples/markers exponentially, in addition to the comprehensive management of distinct data formats while searching for specific genomic regions. A comparison of our non-relational and generic solution, with an existing relational approach (developed for tabular data types using 2 bits to store genotypes), showed reduced importing time to handle 50M SNPs (PLINK format) achieved by the relational schema. Our experimental results also reinforce that data conversion is a costly step required to manage genomic data into both relational and non-relational database systems, and therefore, must be carefully treated for large applications.     

Identification of ISSR markers linked to flowering traits in a representative sample of <Emphasis Type="Italic">Eucalyptus cladocalyx</Emphasis>

Early flowering and flower abundance have long been considered desirable traits in eucalypt breeding programs. In particular, flowers of Eucalyptus cladocalyx provide a nectar source for the production of honey in arid ecosystems. To identify inter-simple sequence repeat (ISSR) markers that are associated with early flowering and flower abundance in the southern Atacama Desert, we used a sample of 47 trees, representing five Australian provenances of E. cladocalyx. A unified mixed linear model (which considered the effect of genetic structure and the kinship relationship among trees) revealed that three loci were significantly associated with early flowering, which accounted for 10–16 % of the phenotypic variation, while two loci accounted for 11–13 % in flowering intensity. Locus ISO_{1–500 bp} was associated with both flowering traits. This result is consistent with our previous findings indicating that marker-assisted selection on early flowering should have significant and positive impact on flowering intensity. The application of marker-assisted selection to identify trees that flower early and intensively may increase honey production, a resource that generates additional income for the local farmers of the southern Atacama Desert.     

Reactions between Cr(VI) and wood and its model compounds

Hexavalent chromium solutions at two pH levels (about 1.3 and 7.8) were reacted with wood, gum ghatti, lignin, cellulose and simple model compounds representing wood chemical structures (guaiacol, vanillin, vanillyl alcohol, homovanillyl alcohol, methyl-(β-D-glucoside, and methyl-β-cellobioside). Reaction products were isolated and characterised by elemental analysis, magnetic susceptibility, and Fourier-transform infrared spectroscopy (FTIR). Data suggest that all the chromium present in the reaction products is in its trivalent oxidation state. After reduction reactions, wood and macromolecular substances generally fixed a relatively low level of chromium, which contrasts with the high level in the products isolated from the reaction with the model compounds. It appears that the reaction of the simple model compounds with Cr(VI) did not produce complex adducts of Cr(III) but inorganic substances, of the hydrated chromium oxide type. Therefore, under the experimental conditions applied, simple model compounds do not seem to behave chemically as wood or as the macromolecular substances investigated. Hence, their significance as model compounds must be object of further assessment. An exception is the product from the reaction of vanillyl alcohol and K₂CrO₄ aq. This contains a relatively small amount of chromium and its FTIR spectrum presents rather well defined bands indicating reaction of the phenolic hydroxyl and secondary alcohol groups. This system must be worthy of further investigation as a model for lignin.     

Electrospray ionization mass spectrometry fingerprinting of Brazilian artisan cachaça aged in different wood casks

We have investigated the capability of direct infusion electrospray ionization mass spectrometry in the negative ion mode, ESI(-)-MS, to differentiate representative samples of artisan cacha?a, a Brazilian sugar cane distillate of large production, aged in four different types of wood casks: amburana (Amburana cearensis), jequitibA (Cariniana estrellensis), balm (Myroxylon peruiferum), and oak (Quercus rubra). The ESI(-)-MS were found to be very characteristic, showing sets of diagnostic ions for each of the four types of samples: amburana (m/z 271, 313, 377), jequitibA (m/z 143, 171, 255), balm (m/z 137, 269, 283, 297), and oak (m/z 197, 301, 307). Furthermore, principal component (PCA) and hierarchical cluster analysis (HCA), applied to the ESI(-)-MS data, divided these samples into four definite categories. The influence of the aging time on the ESI(-)-MS fingerprints of the cacha?a samples stored in oak casks was also established. An inversion in the relative intensity of the diagnostic ions of m/z 307 and 301 is detected in the ESI(-)-MS as the aging time increased from 1 to 2 years. The chemical structures of the major cacha?a components were proposed on the basis of the following: (a) the comparison of the ESI(-)-MS/MS of the diagnostic anions with those of the authentic anions or (b) the interpretation of the fragmentation patterns of the previously unknown diagnostic anions. Hence, direct infusion ESI(-)-MS allows not only a rapid, simple, and accurate way to distinguish among cacha?a samples stored in different wood casks but also monitoring changes in their chemical composition according to the aging time.     

Nitrogen fractions and mineral content in different lupin species (Lupinus albus, Lupinus angustifolius, and Lupinus luteus). Changes induced by the alpha-galactoside extraction process

The protein and mineral composition of different varieties of three different lupin species (Lupinus albus, Lupinus angustifolius, and Lupinus luteus) and the effect of alpha-galactoside removal by means of a hydroalcoholic extraction process on such composition were studied in relationship to nutrient distribution among the different anatomical parts of the seed (embryo, cotyledon, and seed coat). The extent of processing-derived protein insolubilization was assessed by both chemical and electrophoretic techniques and related to the amount of nitrogen soluble in H(2)O, NaCl, ethanol, NaOH, and sodium dodecyl sulfate/beta-mercaptoethanol (SDS/BME). The alpha-galactoside extraction process caused a significant increase in the amount of total and insoluble nitrogen and decreased the amount of soluble protein nitrogen, without affecting the content of soluble nonprotein nitrogen. alpha-Galactoside extraction was not effective at decreasing the levels of Mn present in lupins, and processing caused an increase in the content of this mineral in all of the species studied with the exception of L. albus var. multolupa. In general, the effect of processing on mineral content varied with the different lupin species, and mineral losses were lower in L. luteus.     

Identification and quantification of xanthophyll esters, carotenes, and tocopherols in the fruit of seven Mexican mango cultivars by liquid chromatography-atmospheric pressure chemical ionization-time-of-flight mass spectrometry [LC-(APcI(+))-MS

A liquid chromatography-mass spectrometry (LC-MS) method was developed to simultaneously identify and quantify carotenoids and tocopherols in the fruit of seven mango cultivars grown in Mexico. Fruit maturity was characterized objectively, and carotenoids and tocopherols were isolated by solvent extraction and analyzed by HPLC coupled to a C30 stationary phase and diode array, fluorescence, and mass (time-of-flight) detectors. All cultivars had a similar carotenoid pattern, in which all-trans-beta-carotene and dibutyrates of all-trans-violaxanthin and 9-cis-violaxanthin were the most abundant. The content of all-trans-beta-carotene ranged between 0.4 and 2.8 mg/100 g, and 'Haden' and 'Ataulfo' mangoes had the highest amount. The amounts of all-trans-violaxanthin and 9-cis-violaxanthin (as dibutyrates) ranged between 0.5 and 2.8 mg/100g and between 0.4 and 2.0 mg/100 g, respectively. The content of alpha-tocopherol was low (200-500 microg/100 g). The results of this study indicate that all-trans-beta-carotene, all-trans-violaxanthin, and 9-cis-violaxanthin are the most abundant carotenoids in mango grown in Mexico.     

Parasite density and impaired biochemical/hematological status are associated with severe clinical aspects of canine visceral leishmaniasis

We have performed a detailed investigation in 40 dogs naturally infected with Leishmania infantum (syn. chagasi), subdivided into three groups: asymptomatic (AD = 12), oligosymptomatic (OD = 12) and symptomatic (SD = 16), based on their clinical features. Twenty non-infected dogs (CD) were included as control group. Serological analysis, performed by IFAT and ELISA, demonstrated higher antibodies titers in SD in comparison to the AD. A positive correlation was found between parasite density in the spleen and skin smears as well as the bone marrow parasitism with clinical status of the infection. We observed that the progression of the disease from asymptomatic to symptomatic clinical form was accompanied by intense parasitism in the bone marrow. It is likely that this led to the impaired biochemical/hematological status observed. Finally, we believe that the follow-up of these parameters could be a relevant approach to be used as markers during therapeutic and vaccine evaluations.     

Differential diagnosis of dog hookworms based on PCR-RFLP from the ITS region of their rDNA

Species of Ancylostoma infecting dogs and sometimes humans are sympatric in many parts of the world. The establishment of a specific molecular diagnostic tool is important, not only to refine information for epidemiological studies, but also to evaluate the efficacy of vaccine programmes and assist in the development of specific drug treatments. The ITS region from 20 specimens of A. braziliense, collected from three separate geographical areas of Brazil, and from 10 specimens of A. caninum, collected from the same area in Brazil were sequenced and analyzed. Alignment of sequences showed that this gene is highly conserved. The intraspecific polymorphism for both species was less then 1%, whereas the interspecific polymorphism was 6.2, 7.3 and 9.4% between A. ceylanicum and A. braziliense; A. caninum and A. ceylanicum and A. ceylanicum and A. braziliense, respectively. Among the three species it was 12.3%. This revealed the ITS region as highly conserved and consequently a good molecular marker for diagnostic studies. In this work, four restriction enzymes were used in a PCR-RFLP using the ITS region of rDNA, to establish a differential diagnosis which discriminates between three Ancylostoma species, A. braziliense, A. caninum and A. ceylanicum. The best pattern was given by the HinfI enzyme, which produced different fragment sizes for each of the three species. Furthermore, the diagnostic tool differentiates DNA extracted directly from faeces of Ancylostoma-infected dogs.     

Sperm chromatin condensation as an in vivo fertility biomarker in bulls:a flow cytometry approach

Background:Genetic selection in cattle has been directed to increase milk production.This,coupled to the fact that the vast majority of bovine artificial inseminations(AI)are performed using cryopreserved sperm,have led to a reduction of fertility rates over the years.Thus,seeking sensitive and specific sperm biomarkers able to predict fertility rates is of vital importance to improve cattle reproductive efficiency.In humans,sperm chromatin condensation evaluated through chromomycin A3(CMA3)has recently been purported to be a powerful biomarker for sperm functional status and male infertility.The objectives of the present study were:a)to set up a flow cytometry method for simultaneously evaluating chromatin condensation and sperm viability,and b)to test whether this parameter could be used as a predictor of in vivo fertility in bulls.The study included pools of three independent cryopreserved ejaculates per bull from 25 Holstein males.Reproductive outcomes of each sire were determined by non-return rates,which were used to classify bulls into two groups(highly fertile and subfertile).Results:Chromatin condensation status of bovine sperm was evaluated through the combination of CMA3 and Yo-Pro-1 staining and flow cytometry.Sperm quality parameters(morphology,viability,total and progressive motility)were also assessed.Pearson correlation coefficients and ROC curves were calculated to assess their capacity to predict in vivo fertility.Sperm morphology,viability and total motility presented an area under the ROC curve(AUC)of 0.54,0.64 and 0.68,respectively(P>0.05),and thus were not able to discriminate between fertile and subfertile individuals.Alternatively,while the percentage of progressively motile sperm showed a significant predictive value,with an AUC of 0.73(P=0.05),CMA3/Yo-Pro-1 staining even depicted superior results for the prediction of in vivo fertility in bulls.Specifically,the percentage of viable sperm with poor chromatin condensation showed better accuracy and precision to predict in vivo fertility,with an AUC of 0.78(P=0.02).Conclusions:Chromatin condensation evaluated through CMA3/Yo-Pro-1 and flow cytometry is defined here as a more powerful tool than conventional sperm parameters to predict bull in vivo fertility,with a potential ability to maximising the efficiency of dairy breeding industry.     

Gastric Torsion from an Intestinal Hernia Through a Rent in the Gastrosplenic Ligament in a Horse

The present report describes an 8-year-old gelding presenting with signs of severe abdominal pain. After performing a thorough physical examination, including rectal palpation and additional diagnostic tests, an exploratory laparotomy was recommended. The jejunum was found herniated through the gastrosplenic ligament, and the stomach was severely distended with gas. Given a poor prognosis, the horse was euthanized on the table. At necropsy, the stomach appeared dilated, with an 180° horizontal gastric torsion, from left (lateral) to right (medial), dividing the organ into dorsal and ventral compartments. We believe that the chronic traction exerted by an incarcerated and distended loop of jejunum, in the dorsal aspect of the gastrosplenic ligament, associated with trauma during episodes of intense rolling, enlarged the rent until it ruptured. Because of this rupture, the lateral dorsal aspect of the stomach became unattached, predisposing it to the torsion.