Genetically engineered crops: from idea to product.

Genetically engineered crops were first commercialized in 1994 and since then have been rapidly adopted, enabling growers to more effectively manage pests and increase crop productivity while ensuring food, feed, and environmental safety. The development of these crops is complex and based on rigorous science that must be well coordinated to create a plant with desired beneficial phenotypes. This article describes the general process by which a genetically engineered crop is developed from an initial concept to a commercialized product.

Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes.

The Brucella abortus strain S19, a spontaneously attenuated strain, has been used as a vaccine strain in vaccination of cattle against brucellosis for six decades. Despite many studies, the physiological and molecular mechanisms causing the attenuation are not known. We have applied pyrosequencing technology together with conventional sequencing to rapidly and comprehensively determine the complete genome sequence of the attenuated Brucella abortus vaccine strain S19. The main goal of this study is to identify candidate virulence genes by systematic comparative analysis of the attenuated strain with the published genome sequences of two virulent and closely related strains of B. abortus, 9-941 and 2308. The two S19 chromosomes are 2,122,487 and 1,161,449 bp in length. A total of 3062 genes were identified and annotated. Pairwise and reciprocal genome comparisons resulted in a total of 263 genes that were non-identical between the S19 genome and any of the two virulent strains. Amongst these, 45 genes were consistently different between the attenuated strain and the two virulent strains but were identical amongst the virulent strains, which included only two of the 236 genes that have been implicated as virulence factors in literature. The functional analyses of the differences have revealed a total of 24 genes that may be associated with the loss of virulence in S19. Of particular relevance are four genes with more than 60 bp consistent difference in S19 compared to both the virulent strains, which, in the virulent strains, encode an outer membrane protein and three proteins involved in erythritol uptake or metabolism.

Application of current allergy assessment guidelines to next-generation biotechnology-derived crops.

In any single day, our immune systems are exposed to thousands of different proteins from the environment and the food we eat. In a portion of the human population, some of those proteins will stimulate the immune systems to synthesize immunoglobulin E in an allergenic response. The discrepancy between the vast numbers of proteins we encounter and the limited number of proteins that actually become allergens have led scientists on a quest to discover what unique features exist that make proteins destined to be allergens. The information gained from these studies has led to an allergy assessment strategy that characterizes the potential allergenicity of biotechnology products prior to their commercialization. This testing strategy appears to be effective as shown by the fact that there have been no clinically documented food allergic reactions to any of the biotechnology proteins introduced into food crops, to date. The next generation of biotechnology products will most likely contain more complex traits, including nutritionally enhanced food crops, and the question arises as to whether the current allergy assessment strategy will be sufficient to protect the health of the consuming public. In this paper, we discuss general allergen characteristics in order to better understand how proteins become allergens, summarize the current allergy assessment process, evaluate the different aspects of this process for their adequacy in determining the allergenic potential of engineered functional foods, and, finally, we assess the possibility of new technologies having a positive impact on the allergy assessment of nutritionally enhanced crops.

Gene expression profiling of nonhuman primates exposed to aerosolized Venezuelan equine encephalitis virus.

Host responses to Venezuelan equine encephalitis viruses (VEEV) were studied in cynomolgus macaques after aerosol exposure to the epizootic virus. Changes in global gene expression were assessed for the brain, lungs, and spleen. In the brain, major histocompatibility complex (MHC) class I transcripts were induced, while the expression of S100b, a factor associated with brain injury, was inhibited, as was expression of the encephalitogenic gene MOG. Cytokine-mediated signals were affected by infection, including those involving IFN-mediated antiviral activity (IRF-7, OAS, and Mx transcripts), and the increased transcription of caspases. Induction of a few immunologically relevant genes (e.g. IFITM1 and STAT1) was common to all tested tissues. Herein, both tissue-specific and nontissue specific transcriptional changes in response to VEEV are described, including induction of IFN-regulated transcripts and cytokine-induced apoptotic factors, in addition to cellular factors in the brain that may be descriptive of the health status of the brain during the infectious process. Altogether, this work provides novel information on common and tissue-specific host responses against VEEV in a nonhuman primate model of aerosol exposure.

Comparison of sampling techniques for parallel analysis of transcript and metabolite levels in Saccharomyces cerevisiae.

Mathematical modelling of cellular processes is crucial for the understanding of the cell or organism as a whole. Genome-wide observations, at the levels of the transcriptome, proteome and metabolome, provide a high coverage of the molecular constituents of the system in study. Time-course experiments are important for gaining insight into a system's dynamics and are needed for mathematical modelling. In time-course experiments it is crucial to use efficient and fast sampling techniques. We evaluated several techniques to sample and process yeast cultures for parallel analysis of the transcriptome and metabolome. The evaluation was made by measuring the quality of the RNA obtained with UV-spectroscopy, capillary electrophoresis and microarray hybridization. The protocol developed involves rapid collection by spraying the sample into -40 degrees C tricine-buffered methanol (as previously described for yeast metabolome analysis), followed by the separation of cells from the culture medium in low-temperature rapid centrifugation. Removal of the residual methanol is carried out by freeze-drying the pellet at -35 degrees C. RNA and metabolites can then be extracted from the same freeze-dried sample obtained with this procedure.

Impact of intestinal colonization and invasion on the Entamoeba histolytica transcriptome.

A genome-wide transcriptional analysis of Entamoeba histolytica was performed on trophozoites isolated from the colon of six infected mice and from in vitro culture. An Affymetrix platform gene expression array was designed for this analysis that included probe sets for 9435 open reading frames (ORFs) and 9066 5' and 3' flanking regions. Transcripts were detected for > 80% of all ORFs. A total of 523 transcripts (5.2% of all E. histolytica genes) were significantly changed in amebae isolated from the intestine on Days 1 and 29 after infection: 326 and 109 solely on Days 1 and 29, and 88 on both days. Quantitative real-time reverse transcriptase PCR confirmed these changes in 11/12 genes tested using mRNA isolated from an additional six mice. Adaptation to the intestinal environment was accompanied by increases in a subset of cell signaling genes including transmembrane kinases, ras and rho family GTPases, and calcium binding proteins. Significant decreases in mRNA abundance for genes involved in glycolysis and concomitant increases in lipases were consistent with a change in energy metabolism. Defense against bacteria present in the intestine (but lacking from in vitro culture) was suggested by alterations in mRNA levels of genes similar to the AIG1 plant antibacterial proteins. Decreases in oxygen detoxification pathways were observed as expected in the anaerobic colonic lumen. Of the known virulence factors the most remarkable changes were a 20-35-fold increase in a cysteine proteinase four-like gene, and a 2-3-fold decrease in two members of the Gal/GalNAc lectin light subunit family. Control of the observed changes in mRNA abundance in the intestine might potentially rest with four related proteins with DNA binding domains that were down-regulated 6-16-fold in the intestinal environment. In conclusion, the first genome-wide analysis of the transcriptome of E. histolytica demonstrated that the vast majority of genes are transcribed in trophozoites, and that in the host intestine trophozoites altered the expression of mRNAs for genes implicated in metabolism, oxygen defense, cell signaling, virulence, antibacterial activity, and DNA binding.

Activation of PPAR gamma and delta by conjugated linoleic acid mediates protection from experimental inflammatory bowel disease.

BACKGROUND & AIMS: The molecular targets for the protective actions of conjugated linoleic acid (CLA) on experimental inflammatory bowel disease (IBD) are unknown. We used a loss-of-function approach to investigate whether CLA ameliorated colitis through a peroxisome proliferator-activated receptor gamma (PPAR gamma)-dependent mechanism. METHODS: The expression of PPAR gamma, delta, and their target genes in the colon of mice fed control or CLA-supplemented diets was assayed after a 7-day dextran sodium sulfate (DSS) challenge by quantitative real-time polymerase chain reaction (PCR). Additionally, nuclear factor-kappa B (NF-kappaB) p65 activation was quantified in the colon. To determine the involvement of PPAR gamma in the mechanism of action of CLA directly, specific deletions of PPAR gamma in the colon were performed in mice by using the Cre-lox recombination system. Colonic PPAR gamma null mice and wild-type littermates were fed either a CLA-supplemented or a control diet for 42 days and challenged with 2.5% DSS. The therapeutic efficacy of CLA also was examined by using the CD4 + CD45RB hi transfer colitis model. RESULTS: CLA induced PPAR gamma and delta, transcriptionally modulated PPAR gamma and delta-responsive gene clusters involved in lipid metabolism (uncoupling protein [UCP]1, UCP3, PPAR gamma coactivator 1alpha [PGC-1alpha], and CD36) and epithelial cell maturation (Gob-4 and Keratin 20). Additionally, CLA repressed tumor necrosis factor alpha (TNF-alpha) expression and NF-kappaB activation while inducing the immunoregulatory cytokine transforming growth factor beta 1 (TGF-beta 1 ). Clinically, CLA ameliorated DSS- and CD4 + -induced colitis. Loss of the PPAR gamma gene in the colon abrogated the beneficial effects of CLA in DSS colitis. CONCLUSIONS: Our studies provide molecular evidence in vivo, suggesting that CLA ameliorates colitis through a PPAR gamma-dependent mechanism.