Transgenic cereals: current status and future prospects

This review summarises the history of transgenic (GM) cereals, principally maize, and then focuses on the scientific literature published in the last two years. It describes the production of GM cereals with modified traits, divided into input traits and output traits. The first category includes herbicide tolerance and insect resistance, and resistance to abiotic and biotic stresses; the second includes altered grains for starch, protein or nutrient quality, the use of cereals for the production of high value medical or other products, and the generation of plants with improved efficiency of biofuel production. Using data from field trial and patent databases the review considers the diversity of GM lines being tested for possible future development. It also summarises the dichotomy of response to GM products in various countries, describes the basis for the varied public acceptability of such products, and assesses the development of novel breeding techniques in the light of current GM regulatory procedures.

Accounting information systems as institutional carriers: a case study of regulatory compliance in UK asset management houses

Previously, governments have responded to the impacts of economic failures and consequently have developed more regulations to protect employees, customers, shareholders and the economic wellbeing of the state. Our research addresses how Accounting Information Systems (AIS) may act as carriers for institutionalised practices associated with maintaining regulatory compliance within the context of UK Asset Management Houses. The AIS was found to be a strong conduit for institutionalized compliance related practices, utilising symbolic systems, relational systems, routines and artefacts to carry approaches relating to regulative, normative and cultural-cognitive strands of institutionalism. Thus, AIS are integral to the development and dissipation of best practice for the management of regulatory compliance. As institutional elements are clearly present we argue that AIS and regulatory compliance provide a rich context to further institutionalism. Since AIS may act as conduits for regulatory approaches, both systems adopters and clients may benefit from actively seeking to codify and abstract best practices into AIS. However, the application of generic institutionalized approaches, which may be applied across similar organizations, must be tempered with each firm���s business environment and associated regulatory exposure. A balance should be sought between approaches specific enough to be useful but generic enough to be universally applied.

Economic evidence in regulatory disputes: revisiting the court-regulatory agency relationship in the US and the UK

This article examines the issue of the appropriate scope of review of economic evidence enshrined in the discretionary assessments of utility regulators in the US and the UK. It advances a balance of institutional competencies approach to the question of the degree of deference owed to the regulatory agency���s economic assessments. In doing so, it revisits the doctrinal positions advanced in the US and UK for the substantive review of administrative discretion, so as to become attuned to the challenges posed by economic evidence. Drawing on insights from political science and economics, the suggested approach illuminates the institutional disadvantages of the courts that may warrant a high degree of deference. At the same time, however, it remains sensitive to the polycentric elements of regulatory disputes as well as to a number of institutional realties that may attenuate the weight of such comparative institutional disadvantages.

Cadmium availability and accumulation by lettuce and rice

Among the toxic elements, Cd has received considerable attention in view of its association with a number of human health problems. The objectives of this study were to evaluate the Cd availability and accumulation in soil, transfer rate and toxicity in lettuce and rice plants grown in a Cd-contaminated Typic Hapludox. Two simultaneous greenhouse experiments with lettuce and rice test plants were conducted in a randomized complete block design with four replications. The treatments consisted of four Cd rates (CdCl2), 0.0; 1.3; 3.0 and 6.0 mg kg(-1), based on the guidelines recommended by the Environmental Agency of the State of S��o Paulo, Brazil (Cetesb). Higher Cd rates increased extractable Cd (using Mehlich-3, Mehlich-1 and DTPA chemical extractants) and decreased lettuce and rice dry matter yields. However, no visual toxicity symptoms were observed in plants. Mehlich-1, Mehlich-3 and DTPA extractants were effective in predicting soil Cd availability as well as the Cd concentration and accumulation in plant parts. Cadmium concentration in rice remained below the threshold for human consumption established by Brazilian legislation. on the other hand, lettuce Cd concentration in edible parts exceeded the acceptable limit.

Muscle-specific growth hormone receptor (GHR) overexpression induces hyperplasia but not hypertrophy in transgenic zebrafish

Conselho Nacional de Desenvolvimento Cient��fico e Tecnol��gico (CNPq)

Evaluation of Rice Bran Extract as a Nitrogen Source for Improved Hemicellulosic Ethanol Production from Sugarcane Bagasse by New Xylose-Fermenting Yeast Strains Isolated from Brazilian Forests

Xylose is the main sugar in hemicellulosic hydrolysates and its fermentation into ethanol by microorganisms is influenced by nutritional factors, such as nitrogen source, vitamins and other elements. Rice bran extract (RBE) is an inexpensive nitrogen source primarily consisting of high amount of protein. This study evaluates the potential of RBE as a nitrogen source for the hemicellulosic ethanol production from sugarcane bagasse dilute acid hydrolysate by novel yeast strains Scheffersomyces shehatae (syn. Candida shehatae) CG8-8BY and Spathaspora arborariae UFMG-HM19.1A, isolated from Brazilian forests. Two different media formulations were used for inoculum preparation and production medium, using yeast extract and RBE as nitrogen sources. S. shehatae CG8-8BY showed ethanol production of 17.0��g/l with the ethanol yield (0.33��g/g) and fermentation efficiency (64��%) from medium supplemented with RBE. On the other hand, S. arborariae presented 5.4��g/l of ethanol production with ethanol yield (0.14��g/g) and fermentation efficiency (21��%) in a fermentation medium supplemented with RBE. Appropriate media formulation is an important parameter to increase the productivity of bioconversion process and RBE proved to be an efficient and inexpensive nitrogen source to supplement sugarcane bagasse hemicellulosic hydrolysate for second generation ethanol production. �� 2013 Society for Sugar Research & Promotion.

Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes

Background: Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes. Results: Physical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6. Conclusion: Our data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins. �� 2013 Schneider et al.; licensee BioMed Central Ltd.

Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

Funda����o de Amparo �� Pesquisa do Estado de S��o Paulo (FAPESP)

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

Background: Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Results: Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Conclusions: Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.

Preimplantation development regulatory pathway construction through a text-mining approach

Background: The integration of sequencing and gene interaction data and subsequent generation of pathways and networks contained in databases such as KEGG Pathway is essential for the comprehension of complex biological processes. We noticed the absence of a chart or pathway describing the well-studied preimplantation development stages; furthermore, not all genes involved in the process have entries in KEGG Orthology, important information for knowledge application with relation to other organisms. Results: In this work we sought to develop the regulatory pathway for the preimplantation development stage using text-mining tools such as Medline Ranker and PESCADOR to reveal biointeractions among the genes involved in this process. The genes present in the resulting pathway were also used as seeds for software developed by our group called SeedServer to create clusters of homologous genes. These homologues allowed the determination of the last common ancestor for each gene and revealed that the preimplantation development pathway consists of a conserved ancient core of genes with the addition of modern elements. Conclusions: The generation of regulatory pathways through text-mining tools allows the integration of data generated by several studies for a more complete visualization of complex biological processes. Using the genes in this pathway as ���seeds��� for the generation of clusters of homologues, the pathway can be visualized for other organisms. The clustering of homologous genes together with determination of the ancestry leads to a better understanding of the evolution of such process.

Modularity and evolutionary constraints in a baculovirus gene regulatory network

Abstract Background The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape and behave. The Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is a large double-stranded DNA virus, whose genome may encode for 152 open reading frames (ORFs). Here we present the analysis of the ordered cascade of the AgMNPV gene expression. Results We observed an earlier onset of the expression than previously reported for other baculoviruses, especially for genes involved in DNA replication. Most ORFs were expressed at higher levels in a more permissive host cell line. Genes with more than one copy in the genome had distinct expression profiles, which could indicate the acquisition of new functionalities. The transcription gene regulatory network (GRN) for 149 ORFs had a modular topology comprising five communities of highly interconnected nodes that separated key genes that are functionally related on different communities, possibly maximizing redundancy and GRN robustness by compartmentalization of important functions. Core conserved functions showed expression synchronicity, distinct GRN features and significantly less genetic diversity, consistent with evolutionary constraints imposed in key elements of biological systems. This reduced genetic diversity also had a positive correlation with the importance of the gene in our estimated GRN, supporting a relationship between phylogenetic data of baculovirus genes and network features inferred from expression data. We also observed that gene arrangement in overlapping transcripts was conserved among related baculoviruses, suggesting a principle of genome organization. Conclusions Albeit with a reduced number of nodes (149), the AgMNPV GRN had a topology and key characteristics similar to those observed in complex cellular organisms, which indicates that modularity may be a general feature of biological gene regulatory networks.

Identification of Drosophila heart-specific Cis-Regulatory Modules under Hox control

Cardiac morphogenesis is a complex process governed by evolutionarily conserved transcription factors and signaling molecules. The Drosophila cardiac tube is linear, made of 52 pairs of cardiomyocytes (CMs), which express specific transcription factor genes that have human homologues implicated in Congenital Heart Diseases (CHDs) (NKX2-5, GATA4 and TBX5). The Drosophila cardiac tube is linear and composed of a rostral portion named aorta and a caudal one called heart, distinguished by morphological and functional differences controlled by Hox genes, key regulators of axial patterning. Overexpression and inactivation of the Hox gene abdominal-A (abd-A), which is expressed exclusively in the heart, revealed that abd-A controls heart identity. The aim of our work is to isolate the heart-specific cisregulatory sequences of abd-A direct target genes, the realizator genes granting heart identity. In each segment of the heart, four pairs of cardiomyocytes (CMs) express tinman (tin), homologous to NKX2-5, and acquire strong contractile and automatic rhythmic activities. By tyramide amplified FISH, we found that seven genes, encoding ion channels, pumps or transporters, are specifically expressed in the Tin-CMs of the heart. We initially used online available tools to identify their heart-specific cisregutatory modules by looking for Conserved Non-coding Sequences containing clusters of binding sites for various cardiac transcription factors, including Hox proteins. Based on these data we generated several reporter gene constructs and transgenic embryos, but none of them showed reporter gene expression in the heart. In order to identify additional abd-A target genes, we performed microarray experiments comparing the transcriptomes of aorta versus heart and identified 144 genes overexpressed in the heart. In order to find the heart-specific cis-regulatory regions of these target genes we developed a new bioinformatic approach where prediction is based on pattern matching and ordered statistics. We first retrieved Conserved Noncoding Sequences from the alignment between the D.melanogaster and D.pseudobscura genomes. We scored for combinations of conserved occurrences of ABD-A, ABD-B, TIN, PNR, dMEF2, MADS box, T-box and E-box sites and we ranked these results based on two independent strategies. On one hand we ranked the putative cis-regulatory sequences according to best scored ABD-A biding sites, on the other hand we scored according to conservation of binding sites. We integrated and ranked again the two lists obtained independently to produce a final rank. We generated nGFP reporter construct flies for in vivo validation. We identified three 1kblong heart-specific enhancers. By in vivo and in vitro experiments we are determining whether they are direct abd-A targets, demonstrating the role of a Hox gene in the realization of heart identity. The identified abd-A direct target genes may be targets also of the NKX2-5, GATA4 and/or TBX5 homologues tin, pannier and Doc genes, respectively. The identification of sequences coregulated by a Hox protein and the homologues of transcription factors causing CHDs, will provide a mean to test whether these factors function as Hox cofactors granting cardiac specificity to Hox proteins, increasing our knowledge on the molecular mechanisms underlying CHDs. Finally, it may be investigated whether these Hox targets are involved in CHDs.

A novel phase variation mechanism in the meningococcus driven by a ligand-responsive repressor and differential spacing of distal promoter elements

Phase variable expression, mediated by high frequency reversible changes in the length of simple sequence repeats, facilitates adaptation of bacterial populations to changing environments and is frequently important in bacterial virulence. Here we elucidate a novel phase variable mechanism for NadA expression, an adhesin and invasin of Neisseria meningitidis. The NadR repressor protein binds to operators flanking the phase variable tract of the nadA promoter gene and contributes to the differential expression levels of phase variant promoters with different numbers of repeats, likely due to different spacing between operators. It is shown that IHF binds between these operators, and may permit looping of the promoter, allowing interaction of NadR at operators located distally or overlapping the promoter. The 4-hydroxyphenylacetic acid, a metabolite of aromatic amino acid catabolism that is secreted in saliva, induces nadA expression by inhibiting the DNA binding activity of the NadR repressor. When induced, only minor differences are evident between NadR-independent transcription levels of promoter phase variants, which are likely due to differential RNA polymerase contacts leading to altered promoter activity. These results suggest that NadA expression is under both stochastic and tight environmental-sensing regulatory control, and both regulations are mediated by the NadR repressor that and may be induced during colonization of the oropharynx where it plays a major role in the successful adhesion and invasion of the mucosa. Hence, simple sequence repeats in promoter regions may be a strategy used by host-adapted bacterial pathogens to randomly switch between expression states that may nonetheless still be induced by appropriate niche-specific signals.

Transkriptionelle Regulation des humanen Interferon-gamma-Promotors in T-Lymphocyten

Interferon-gamma is mainly produced by activated T helper cells and cytotoxic T lymphocytes and sustains the immune-defense against viral and bacterial infections. For a better understanding of IFN-gamma promoter regulation in T cells, different DNA-binding motivs were examined. Hereby, a new motiv (-196 to -183) was identified, that binds to the transcription factor AP-1 in T helper cells and Jurkat T cells. This factor acts as an essential activator protein. Further investigation demonstrated that IL-12 and IL-18 induce different regulatory pathways. Both AP-1 and STAT-4 bindings at their cognate DNA elements (-196 to -183 and -224 to -215) are required for the IL-12 dependent activation whereas IL-18 causes direct activation via AP-1.Moreover, the TH2 cytokine IL-4 represses significantly the IFN-gamma promoter activity in CD4+ T cells. IL-4 induces GATA-3, that interacts with two DNA-motivs (-111 to -87) at the IFN-gamma promoter.Furthermore, transgenic mice were generated, yielding a human IFN-gamma promoter construct (410 bp) under the control of a luciferase reporter gene. The data demonstrated a specific IFN-gamma promoter activation by antiCD3 plus antiCD28 in CD4+ and CD8+ T cells. The luciferase activty in CD4+ T cells was reinforced by addition of IL-12 and IL-18 and repressed by IL-4.

Conditional and transgenic mouse models as tools to study the role of TGFbeta, BMP signaling in skeletal development

Die TGFbeta/BMP Signaltransduktionskaskade ist wichtig f��r viele Entwicklungsprozesse fast aller embryonaler sowie extraembryonaler Gewebe und sie ist ebenso essentiell bei der Aufrechterhaltung der Hom��ostase im adulten Organismus. In vielen Mausmodellen und Zellkulturversuchen wurde gezeigt, dass Liganden dieses Signalweges in verschiedene Stadien der Knorpel- und Knochenentwicklung involviert sind. BMPs sind beispielsweise ma��geblich an der fr��hen Kondensation und Bildung des Knorpels und sp��ter an Proliferation und Hypertrophie der Chondrozyten beteiligt. BMPs k��nnen ektopisch Knochenbildung ausl��sen und das Expressionsmuster der Liganden und spezifischen Rezeptoren in der Wachstumsfuge l��sst auf eine wichtige Rolle der BMPs in der Wachstumsfuge schlie��en. Der gezielte knock out der BMP-Rezeptoren Bmpr1a und Bmpr1b in proliferierenden Chondrozyten f��hrt zur Ausbildung einer generellen Chondrodysplasie. Smad1, Smad5 und Smad8 sind die Mediatoren der BMP-Signalkaskade. Im Rahmen der vorliegenden Arbeit sollte die Rolle und Funktion der Smad1- und Smad5-Proteine in der Wachstumsfuge untersucht werden. Hierzu wurden konditionale Smad1-knock out-M��use mit einer transgenen Mauslinie gekreuzt, die die Cre-Rekombinase spezifisch in proliferierenden Chondrozyten exprimiert. Diese M��use wurden mit und ohne heterozygotem Smad5-Hintergrund charakterisiert. Bei einem knock out von Smad1 allein konnte ein leichte Verk��rzung der Wachstumsfuge beobachtet werden, wobei pr��hypertrophe und hypertrophe Zone gleicherma��en betroffen waren. Dieser Ph��notyp war verst��rkt in M��usen mit zus��tzlichem heterozygotem Smad5-Hintergrund. Eine Verringerung der Proliferationsrate konnte zusammen mit einer verminderten Ihh-Expression nachgewiesen werden. Zus��tzlich konnte anhand von R��ntgenaufnahmen eine Dysorganisation der nasalen Region und ein fehlendes nasales Septum beobachtet werden. Produktion und Mineralisation der extrazellul��ren Matrix waren nicht beeintr��chtigt. Um die Rolle der BMP- und TGFbeta-Signalkaskaden w��hrend der endochondralen Ossifikation zu vergleichen, wurden transgene M��use generiert, in denen die TGFbeta-Signalkaskade spezifisch in proliferierenden Chondrozyten gest��rt war. Zwei Mauslinien, die ��hnliche Ph��notypen zeigten, wurden untersucht. Esl1 ist ein TGFbeta-bindendes Protein, von dem man annimmt, dass es die TGFbeta-Signalkaskade inhibieren kann. Esl1-knock out-M��use sind kleiner als Wildtypm��use und die ��berexpression von Esl1 in proliferierenden Chondrozyten f��hrt zu einer Verl��ngerung der Wachstumsfuge und einer verst��rkten Proliferationsrate. Knorpelmarker, wie Col2a1 und Sox9 sind in diesen M��usen herunterreguliert, w��hrend Col10a1 und Ihh als Marker f��r die hypertrophe und pr��hypertrophe Zone herunterreguliert waren. Dies f��hrt zu der Annahme, dass mehr Zellen in die terminale Differenzierung eintreten. Bei transgenen M��usen, in denen ein dominant-negativer (dn) TGFbeta-Rezeptor in proliferierenden Chondrozyten ��berexprimiert wurde, konnte eine verl��ngerte pr��hypertrophe Zone, eine erh��hte Ihh-Expression, sowie eine verst��rkte Proliferationsrate beobachtet werden. Zus��tzlich konnte in homozygoten Tieren ein craniofacialer Ph��notyp beschrieben werden, der zu Problemen bei der Nahrungsaufnahme und damit zu einer starken Wachstumsbeeintr��chtigung f��hrte. Die BMP- und TGFbeta-Signalkaskaden haben m��glicherweise antagonistische Effekte in der Wachstumsfuge. W��hrend der Ausfall von BMP in proliferierenden Chondrozyten aufgrund einer gesunkenen Proliferationsrate zu einer Verk��rzung der Wachstumsfuge f��hrte, kann man in M��usen mit einer St��rung der TGFbeta-Signalkaskade eine verst��rkte Proliferation in einer daher verl��ngerten Wachstumsfuge beobachten. Ein weiteres Ziel dieser Arbeit war die Generation einer transgenen Mauslinie, die die Cre-Rekombinase spezifisch in hypertrophen Chondrozyten exprimiert. Promoterstudien mit transgenen M��usen weisen darauf hin, dass ein putatives AP1-Element, etwa 4 kb vor dem ersten Exon des Col10a1 gelegen, wichtig f��r die spezifische Expression in hypertrophen Chondrozyten ist. Ein Konstrukt, dass vier Kopien dieses Elements und den basalen Promoter enth��lt, wurde benutzt, um die Cre-Rekombinase spezifisch zu exprimieren. Diese Mauslinie befindet sich in der Testphase und erste Daten deuten auf eine spezifische Expression der Cre-Rekombinase in hypertrophen Chondrozyten hin.