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.     

Within and between-tree variation in the biometry of wood rays and fibres in cork oak (Quercus suber_L.)

The variability of fibre and ray dimensions was studied at three radial positions (10, 50 and 90% of radius) in 5 cork oaks (Quercus suber L.) approximately 40 years old. Uniseriate ray height and cell number as well as multiseriate ray height and width were measured in tangential sections. Fibre length, width and wall thickness were measured after maceration. The most striking features of cork oak wood were the large multiseriate rays and the frequent homocellular uniseriate rays. On average multiseriate rays were 5.16 mm high and 0.48 mm wide, and uniseriate rays contained 11 cells and were 227 μm high. Neighbour rays presented large dimensional differences but there was no radial variation and there were very small between-tree differences. The radial maintenance of high and wide rays was discussed as a means to improve water shortage in response to water stress. Fibre dimensions increased radially but differed little between trees: on average, 960–1,220 μm length, 18.40–21.49 μm width and 6.66–8.07 μm wall thickness. The ray pattern showed enough variation for visual appreciation while ensuring within and between-tree uniformity. The presence of rays has to be taken into consideration for designing wood drying programs.     

Triterpenic and other lipophilic components from industrial cork byproducts

The detailed chemical composition of the lipophilic extractives of cork and cork byproducts generated throughout industrial processing has been investigated by gas chromatography-mass spectrometry. Triterpenes (cerine, friedeline, and betulinic acid) were the major components detected. Betulinic acid is the main triterpene (11.7 g/kg) identified in industrial cork powder, whereas in black condensates friedeline (95.3 g/kg), betuline (13.1 g/kg), and betulinic acid (12.1 g/kg) are the main triperpenes. Significant fractions of alpha-hydroxy fatty acids (115.1 g/kg) and alpha,omega-dicarboxylic acids (21.2 g/kg) were also detected in black condensate after alkaline hydrolysis. The results demonstrate that these two industrial byproducts can be considered as promising sources of bioactive chemicals or chemical intermediates for the synthesis of polymeric materials.     

Genotype-environment interaction in Cordia trichotoma (Vell.)Arráb.Ex Steud.progenies in two different soil conditions

Investment in silvicultural techniques is notice-ably lacking,especially in breeding programs for non-con-ventional wood species.Studying genotype × environment interaction (G × E) is essential to the development of breed-ing programs.Thus,this study aimed to estimate genetic diversity of and the effects of G × E interaction on two prog-eny tests of Cordia trichotoma,including the estimation of genetic gain and genetic diversity after selection.For the experiment,30 progenies of C.trichotoma were tested at two sites with differing soil textures.Diameter at breast height (1.30 m above soil surface,dbh-cm),total height,diameter at 30 cm from the soil,first branch height,and survival were all monitored for four years.Statistical devi-ance,best linear unbiased estimator,and harmonic mean of relative performance of genetic values (MHPRVG) were all calculated to predict breeding values,estimate genetic parameters,and analyze deviance.All quantified traits varied significantly among progenies by soil type,with greatest variation recorded for genetic variability.Heritability of the progenies led to predictions of genetic gain,ranging from 7.73 to 15.45％,for dbh at four years of age.The calculated decrease in genetic diversity after selection showed that this parameter should be monitored in subsequent breed-ing cycles.G × E was low for all tests.The best-performing progenies proved most stable and best adapted to the differ-ent environmental conditions tested.     

Comparative study of hematological parameters of Colossoma macropomum anesthetized with benzocaine and eugenol by using different anticoagulants

Aquaculture International - The objective of the present study was to evaluate the action of benzocaine and eugenol over anesthesia stages and the use of three anticoagulants (ethylenediamine...     

Anomalous Pregnancies during Late Embryonic/Early Foetal Period in High Producing Dairy Cows

This study analyses anomalous cases of gestation ending in pregnancy loss during the early foetal period and their effect on progesterone and plasma pregnancy-associated glycoprotein-1 (PAG-1) concentrations. Data derived from a large-scale ultrasound pregnancy diagnosis programme in high producing dairy cows. Over a 3-year period (2004–2007), a very low incidence (0.5%: 15 of 3094) of anomalous pregnancies was recorded. The results revealed that the following anomalies were detected on days 35–41 of gestation in cows carrying singletons with one single corpus luteum: embryo death in eight cows (0.3%); and embryo in the uterine horn contralateral to the corpus luteum in seven cows (0.2%). All these animals suffered pregnancy loss during the early foetal period. In cows carrying dead embryos, no signs of conceptus degeneration were observed on pregnancy diagnosis. Amnion size (approximately 25 mm diameter) and uterine horn fluid contents were estimated to be similar to those of the normal pregnant cows in this period. In the contralateral gestations, live embryos were observed in all ultrasound checks before pregnancy loss. Uterine fluid contents increased in the two cows in which gestation continued for more than a week. In the cases of embryo death but not in those of contralateral gestation, a drop in PAG-1 levels was noted prior to pregnancy loss. Two cows carrying dead embryos increased with time allantoic fluid contents. The PAG-1 values increased with time in one cow bearing a dead embryo (from 2.31 to 6.79 ng/ml) and in two of the contralateral gestations (from 1.66 to 2.33 ng/ml and from 0.39 to 6.79 ng/ml, respectively). Results of this study indicate that the foetal membranes continue to undergo some activity following embryo death, and that contralateral pregnancy may determine failure of the gestation process.     

Correlation of five radioimmunoassay systems for measurement of bovine plasma pregnancy-associated glycoprotein concentrations at early pregnancy period

The measurement of serum or plasma PAG concentrations is currently used as a specific method for pregnancy diagnosis in cattle. In this study, the correlation between five radioimmunoassay systems (RIA-497, RIA-706, RIA-780, RIA-809 and RIA–Pool) developed for measurement of PAG concentrations in ruminant species was investigated in plasma from pregnant Friesian Holstein females. Plasma PAG concentrations (ng/mL) measured by different RIA systems were significantly correlated between them ( 0.81; P < 0.001). PAG concentrations increased significantly from Day 21 (n = 27) to 30 (n = 37) after AI by use of all PAG–RIA systems. From Day 30 to 80 after AI, lower PAG concentrations were observed when using the homologous system RIA-497. The addition of several proteinase inhibitors changed neither the non specific binding nor the B₀ binding to the tracer. Our results suggest that all tested PAG–RIA (RIA-497, RIA-706, RIA-780, RIA-809 and RIA–Pool) are highly correlated and can be useful to follow PAG concentrations in samples collected during the first trimester of gestation.     

Effects of inflammation-associated acute-phase response on hepatic and renal indices in the horse

Objectives To determine the effect of an acute soft tissue inflammatory response on biochemical and haematological indices of hepatic and renal function in the Thoroughbred horse.
Procedure Soft tissue inflammation was induced in four Thoroughbred horses by intramuscular injections of Freunds complete adjuvant. The horses were clinically examined and blood and urine samples were collected before and after the adjuvant injections. Biochemical and haematological indices were measured in samples collected and used to determine the onset of the acute-phase response and to assess hepatic and renal function at this time.
Results After adjuvant injection, significant increases (P< 0.01) in total white (13.1 ± 1.4 times 10⁹/L) and neutrophil (10.2 ± 1.2 times109/L) cell counts, rectal temperature (39.7 ± 0.5A°C) and various plasma protein concentrations, including fibrinogen (6.6 ± 1.2 g/L), haptoglobin (1.3 ± 0.1 g/L) and total protein (88.1 ± 2.7 g/L), indicated the induction of an acute-phase response. This corresponded with significant reductions (P< 0.01) in the plasma elimination half-lives (t½β) sodium bromo-sulphthalein (3.13 ± 0.05 to 2.82 ± 0.07 min) and sodium sulphanilate (38.29 ± 4.04 to 19.60 ± 5.68 min) and reductions in the plasma activities of aspartate aminotransferase, gluta-mate dehydrogenase, creatine kinase, alkaline phosphatase, gamma glutamyl transferase; the urinary creatinine clearance ratios of sodium, chloride and potassium; and the urinary gamma glutamyl transferase-to-creatinine clearance ratios. (All values mean ± SD.)
Conclusions The effects of the acute-phase response on indices of hepatic and renal function in the horse suggest that the disposition of pharmacological agents administered at this time may be altered and that indices of acute inflammation should be interpreted cautiously.     

Pharmacokinetics of tramadol and o-desmethyltramadol in goats after intravenous and oral administration

The aim of this trial was to implement a method to obtain a tool for analyses of tramadol and the main metabolite, o-desmethyltramadol (M1), in goat's plasma, and to evaluate the pharmacokinetics of these substances following intravenous (i.v.) and oral (p.o.) administration in female goats. The pharmacokinetics of tramadol and M1 were examined following i.v. or p.o. tramadol administration to six female goats (2 mg/kg). Average retention time was 5.13 min for tramadol and 2.42 min for M1. The calculated parameters for half-life, volume of distribution and total body clearance were 0.94+/-0.34 h, 2.48+/-0.58 L/kg and 2.18+/-0.23 L/kg/h following 2 mg/kg tramadol HCl administered intravenously. The systemic availability was 36.9+/-9.1% and half-life 2.67+/-0.54 h following tramadol 2 mg/kg p.o. M1 had a half-life of 2.89+/-0.43 h following i.v. administration of tramadol. Following p.o., M1 was not detectable.