De Novo Next Generation Sequencing of Plant Genomes

The genome sequencing of all major food and bioenergy crops is of critical importance in the race to improve crop production to meet the future food and energy security needs of the world. Next generation sequencing technologies have brought about great improvements in sequencing throughput and cost, but do not yet allow for de novo sequencing of large repetitive genomes as found in most crop plants. We present a strategy that combines cutting edge next generation sequencing with “old school” genomics resources and allows rapid cost-effective sequencing of plant genomes.     

Assessment of pesticide residues in honey samples from portugal and Spain

Fifty samples of honey collected from local markets of Portugal and Spain during year 2002 were analyzed for 42 organochlorine, carbamate, and organophosphorus pesticide residues. An analytical procedure based on solid-phase extraction with octadecyl sorbent followed by gas chromatography-mass spectrometry (GC-MS), for organochlorines, and by liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry (LC-APCI-MS), for organophosphorus and carbamates, has been developed. Recoveries of spiked samples ranged from 73 to 98%, except for dimethoate (40%), with relative standard deviations from 3 to16% in terms of repeatability, and from 6 to 19% in terms of reproducibility. Limits of quantification were from 0.003 to 0.1 mg kg(-)(1). Most of the pesticides found in honey were organochlorines. Among them, gamma-HCH was the most frequently detected in 50% of the samples, followed by HCB in 32% of the samples and the other isomers of HCH (alpha-HCH and beta-HCH) in 28 and 26% of the samples, respectively. Residues of DDT and their metabolites were detected in 20% of the samples. Of the studied carbamates, both methiocarb and carbofuran were detected in 10% of the samples, pirimicarb in 4% and carbaryl in 2%. The only organophosphorus pesticides found were heptenophos in 16%, methidathion in 4%, and parathion methyl in 2% of honey samples. Results indicate that Portuguese honeys were more contaminated than Spanish ones. However, honey consumers of both countries should not be concerned about the amounts of pesticide residues found in honeys available on the market.     

Repertoire of Escherichia coli agonists sensed by innate immunity receptors of the bovine udder and mammary epithelial cells

ABSTRACT: Escherichia coli is a frequent cause of clinical mastitis in dairy cows. It has been shown that a prompt response of the mammary gland after E. coli entry into the lumen of the gland is required to control the infection, which means that the early detection of bacteria is of prime importance. Yet, apart from lipopolysaccharide (LPS), little is known of the bacterial components which are detected by the mammary innate immune system. We investigated the repertoire of potential bacterial agonists sensed by the udder and bovine mammary epithelial cells (bMEC) during E. coli mastitis by using purified or synthetic molecular surrogates of bacterial agonists of identified pattern-recognition receptors (PRRs). The production of CXCL8 and the influx of leucocytes in milk were the readouts of reactivity of stimulated cultured bMEC and challenged udders, respectively. Quantitative PCR revealed that bMEC in culture expressed the nucleotide oligomerization domain receptors NOD1 and NOD2, along with the Toll-like receptors TLR1, TLR2, TLR4, and TLR6, but hardly TLR5. In line with expression data, bMEC proved to react to the cognate agonists C12-iE-DAP (NOD1), Pam3CSK4 (TLR1/2), Pam2CSK4 (TLR2/6), pure LPS (TLR4), but not to flagellin (TLR5). As the udder reactivity to NOD1 and TLR5 agonists has never been reported, we tested whether the mammary gland reacted to intramammary infusion of C12-iE-DAP or flagellin. The udder reacted to C12-iE-DAP, but not to flagellin, in line with the reactivity of bMEC. These results extend our knowledge of the reactivity of the bovine mammary gland to bacterial agonists of the innate immune system, and suggest that E. coli can be recognized by several PRRs including NOD1, but unexpectedly not by TLR5. The way the mammary gland senses E. coli is likely to shape the innate immune response and finally the outcome of E. coli mastitis.     

Ochratoxin A in feed of food-producing animals: an undesirable mycotoxin with health and performance effects

Mycotoxins are secondary fungal metabolites, whose presence in feed- and foodstuffs is unavoidable. Ochratoxin A (OTA) is one of the known mycotoxins with greatest public health and agro-economic significance. Several toxic effects have been ascribed following exposure, namely nephrotoxicity, as well negative impacts in the performance of farm animals, resulting in major economic implications. Of no less importance for the route of human exposure that can also embody the carry-over of OTA from feed into animal-derived products is also a concern. For all these reasons the present article updates the worldwide occurrence of OTA in different raw ingredients and finished feed destined to food-producing animals. After that a brief characterization of specie susceptibility and the major rationales is made. An historical overview of field outbreaks linked to OTA exposure in farm animals, concerning the implicated feeds, contamination levels and major clinical and productivity effects is presented. Finally a review of the major animal health and performance potential impacts of animals being reared on contaminated feed is made allied to a perspective regarding its co-occurrence with other mycotoxins, and simultaneous parasitic and bacterial infections. Ultimately, this article aims to be instructive and draw attention to a mycotoxin so often neglected and elapsed from the list of differential diagnosis in farm practice. For the unpredictability and unavoidability of occurrence, OTA will definitely be an enduring problem in animal production.     

Bisphosphonates: Pharmacology and Clinical Approach to Their Use in Equine Osteoarticular Diseases

Bisphosphonates (BPs) are drugs widely used in various bone diseases, mainly for their skeletal antiresorptive effect. Nowadays, they are also used to treat degenerative pathologies such as arthritis because of their particular anti-inflammatory and analgesic properties. Since the sixties, BPs with different characteristics and biological activity profiles have been studied, although most of the pharmacologic and clinical trials have been carried out in humans. By 2002, however, tiludronate was granted a marketing license in France for use in horses. The objective of this article is to review the literature available on BPs and apply this knowledge, either experimentally or clinically, to equine osteoarticular disease therapy.     

Intestinal bacterial flora of Mediterranean gilthead sea bream (Sparus aurata Linnaeus) as a novel source of natural surface active compounds

Microbial communities play different functions in the digestive tract of fish and represent a source of bioactive compounds. This study was aimed to detect the presence of biosurfactant (BS)‐producing bacteria in the intestine of gilthead sea bream (Sparus aurata L.) to select strains candidate for biotechnological applications in aquaculture. A total of 100 bacterial strains were isolated from the guts of three groups of fish and analysed by different qualitative screening tests and the tensiometric analysis. BSs were extracted, characterized by thin‐layer chromatography (TLC) and their antibacterial activity against bacterial pathogens of interest in aquaculture was determined. A total of 17 out of 100 strains, affiliated to the genera Pseudomonas (11 isolates), Acinetobacter (1 isolate), Sphingomonas (4 isolates) and Aeromonas (1 isolate), displayed a stable emulsion production with the E₂₄ index from 0% to 44%, a surface tension reduction from 8.3 to 30 mN/m and 11 of them exhibited antibacterial activity against fish pathogens. The TLC analysis indicated that the intestinal BSs consisted of compounds ascribed to the class of glycolipids–rhamnolipids. This is the first study reporting on the isolation and selection of BS‐producing bacteria from fish gut, a natural novel source of surface active compounds with potential biotechnological applications in aquaculture.     

Selective cutting of woody species in a Mexican tropical dry forest: Incompatibility between use and conservation

A major challenge of forest management is to maintain the biodiversity and integrity of the forests while at the same time satisfying human needs through productive activities. While selective extraction of natural resources has less severe consequences on biodiversity and ecosystem function than complete removal of vegetation, such consequences need to be evaluated in detail. “Varas” or stems cut from small trees of tropical dry forests (TDF) in the Pacific Coast of Mexico have been used as plant support stakes in horticultural fields (mainly tomato crops) since the middle of the last century. In this study, we evaluated the effects of selective cutting of plant support stakes on the diversity of woody vegetation of a TDF in northwestern Mexico. Stakes were cut by local harvesters before our assessment of cutting effects. In each of three cutting treatments (T₀ = uncut, T₁ = one cut event, and T₂ = two cut events), we established three sampling plots each consisting of ten 50 m × 2 m parallel transects. All woody plants (stems ≥1.0 cm diameter at 1.3 m height, DBH) were identified and measured on each transect. Species richness (S) decreased as the number of cuts increased (T₀ = 65 species, T₁ = 50 species, and T₂ = 38 species). The Simpson (C) and the Shannon (H′) diversity indices, as well as the rarefaction curves and non-parametric estimates of diversity (Chao1 and ACE) confirmed this tendency of change. Comparison of dominance–diversity curves showed that the woody plant community loses equitability with every additional stake cutting event. The total number of stake providing species did not vary notably across treatments (T₀ = 8 species, T₁ = 9 species, and T₂ = 7 species), but four species reduced their dominance considerably in T₂, while Croton septemnervius, the most used species, increased its abundance and relative basal area with each additional stake harvest, reaching a representation of more than 59% of total number of stems in T₂. The reduction in species diversity, changes in patterns of dominance, and the proliferation of species associated to disturbed sites suggest that current practices of selective cutting require adjustments to make this forest management application more consistent with local conservation of woody plant species diversity and community structure.     

Molecular identification of tick-borne pathogens in Nigerian ticks

A molecular epidemiology investigation was undertaken in two Nigerian states (Plateau and Nassarawa) to determine the prevalence of pathogens of veterinary and public health importance associated with ticks collected from cattle and dogs using PCR, cloning and sequencing or reverse line blot techniques. A total of 218 tick samples, Amblyomma variegatum (N=153), Rhipicephalus (Boophilus) decoloratus (N=45), and Rhipicephalus sanguineus (N=20) were sampled. Pathogens identified in ticks included piroplasmids (Babesia spp., Babesia bigemina and Babesia divergens), Anaplasma marginale and Rickettsia africae. Piroplasmids were identified in A. variegatum, A. marginale was found in R. decoloratus, while R. africae was detected in all tick species examined. Ehrlichia spp. and Theileria spp. were not identified in any of the ticks examined. Of the 218 ticks examined, 33 (15.1%) contained pathogen DNA, with the presence of B. divergens and R. africae that are zoonotic pathogens of public health and veterinary importance. The variety of tick-borne pathogens identified in this study suggests a risk for the emergence of tick-borne diseases in domestic animals and humans, especially amongst the Fulani pastoralists in Plateau and Nassarawa states of Nigeria.