Activités tertiaires et hiérarchies urbaines : une évaluation de six méthodes d’analyse

Urban and regional economists are often asked to construct central place models which will properly describe the urban hierarchy (in terms of the service sector) of the region which they are studying. In all such studies, the chief analytical problem is basically one of correctly defining (and measuring) tertiary activity and of correctly weighting the various functions which make up the service sector.In this paper, the authors review six alternative methods for measuring and weighting tertiary functions. The mathematical and conceptual properties of each approach are discussed and evaluated. In the second part of the article, the authors compare the actual results obtained by these alternative methods, using data on the Quebec urban system to test their results. They conclude that no one method is entirely satisfactory, each approach measuring a part of reality. But some methods do nevertheless seem to perform better than others: in this respect, the use of localization coefficient type approach seems generally to give the least biased results

Activités tertiaires et hiérarchies urbaines : une évaluation de six méthodes d’analyse

Urban and regional economists are often asked to construct central place models which will properly describe the urban hierarchy (in terms of the service sector) of the region which they are studying. In all such studies, the chief analytical problem is basically one of correctly defining (and measuring) tertiary activity and of correctly weighting the various functions which make up the service sector.

Analyse fonctionnelle d'homologues végétaux de Bax Inhibitor-1 et développement d'un modèle de mort cellulaire programmée induite par Bax chez des cultures cellulaires de Nicotiana tabacum

La mort cellulaire programmée est un phénomène essentiel retrouvé chez pratiquement toutes les formes de vie. Chez les mammifères, l'apoptose est une forme de mort importante et très étudiée qui a beaucoup influencé l'étude de la mort cellulaire programmée chez les végétaux. Si la plupart des régulateurs et des effecteurs de l'apoptose animale ne sont pas retrouvés chez les plantes, la similarité de certaines caractéristiques morphologiques et biochimiques laisse croire que certains sentiers de régulation sont évolutivement conservés entre ces deux règnes. Dans ce travail, nous démontrons que les homologues végétaux de BI-1, l'un des rares régulateurs de l'apoptose retrouvé chez les plantes, sont très bien conservés structurellement; certaines caractéristiques déduites des BI-1 végétaux permettent de supposer un mode d'action dans la régulation de la mort. Aussi, nous montrons que les homologues végétaux de BI-1 inhibent l'apoptose induite par la surexpression de Bax chez les cellules humaines 293. Le développement et la caractérisation d'un modèle de mort cellulaire induite par Bax chez les végétaux ont aussi été entrepris. Dans un premier temps, l'expression transitoire de Bax murin par infiltration d'Agrobacterium dans des feuilles de tabac n'a pas causé de phénotype de mort. Par contre, des lignées stables de cellules de tabac BY-2 exprimant constitutivement Bax, seul ou en fusion avec les rapporteurs GFP ou GUS, présentent une mort cellulaire prématurée. La mort de ces cellules est accompagnée d'un changement de l'aspect des cultures, de la fragmentation de l'ADN génomique et de modifications morphologiques caractéristiques des cellules végétales en PCD. Ces lignées ont aussi une sensibilité accrue à la mort causée par un milieu de culture sans sucrose. L'ensemble de ces données, remis dans un contexte plus large, renforce l'idée de l'existence une forme de mort évolutivement ancienne à l'origine de toutes les formes de PCD retrouvées aujourd'hui

Utilizing a highly responsive gene, yhjX, in E. coli based production of 1,4-butanediol

AbstractThe role of yhjX, a predicted major facilitator superfamily protein, was examined in context of E. coli response to 1,4-butanediol (1,4-BDO). E. coli DH1 and MG1655, two commonly used metabolic engineering hosts, were both sensitive to the presence of 1,4-BDO in the growth medium, but to different extents. The strains also showed differences in the transcriptional response of the yhjX gene that was highly induced in response to 1,4-BDO. yhjX deletion improved growth of the E. coli strains in the control defined medium but did not significantly impact 1,4-BDO sensitivity. Overexpression of yhjX using a plasmid-borne copy and lactose-inducible promoter also did not result in an improvement in 1,4-BDO tolerance. However, the large differential expression of yhjX in response to this diol provided the foundation to develop a biosensor for the detection of 1,4-BDO using a fluorescent gene under the control of the yhjX promoter. A basic PyhjX:GFP biosensor in E. coli DH1 allows the detection of 4–7% 1,4-BDO in the extracellular medium and provides a tool for high throughput engineering for improving 1,4-BDO production strains

A rapid and inexpensive labeling method for microarray gene expression analysis

BACKGROUND: Global gene expression profiling by DNA microarrays is an invaluable tool in biological research. However, existing labeling methods are time consuming and costly and therefore often limit the scale of microarray experiments and sample throughput. Here we introduce a new, fast, inexpensive method for direct random-primed fluorescent labeling of eukaryotic cDNA for gene expression analysis and compare the results obtained on the NimbleGen microarray platform with two other widely-used labeling methods, namely the NimbleGen-recommended double-stranded cDNA protocol and the indirect (aminoallyl) method. RESULTS: Two total RNA samples were labeled with each method and hybridized to NimbleGen expression arrays. Although all methods tested here provided similar global results and biological conclusions, the new direct random-primed cDNA labeling method provided slightly better correlation between replicates compared to the other methods and thus increased ability to find statistically significant differentially expressed genes. CONCLUSION: The new direct random-primed cDNA labeling method introduced here is suitable for gene expression microarrays and provides a rapid, inexpensive alternative to existing methods. Using NimbleGen microarrays, the method produced excellent results comparable to those obtained with other methods. However, the simplicity and cost-effectiveness of the new method allows for increased sample throughput in microarray experiments and makes the process amenable to automation with a relatively simple liquid handling system

Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol

<p>Abstract</p> <p>Background</p> <p>Increasing energy costs and environmental concerns have motivated engineering microbes for the production of "second generation" biofuels that have better properties than ethanol.</p> <p>Results and conclusion</p> <p><it>Saccharomyces cerevisiae </it>was engineered with an n-butanol biosynthetic pathway, in which isozymes from a number of different organisms (<it>S. cerevisiae</it>, <it>Escherichia coli</it>, <it>Clostridium beijerinckii</it>, and <it>Ralstonia eutropha</it>) were substituted for the Clostridial enzymes and their effect on n-butanol production was compared. By choosing the appropriate isozymes, we were able to improve production of n-butanol ten-fold to 2.5 mg/L. The most productive strains harbored the <it>C. beijerinckii </it>3-hydroxybutyryl-CoA dehydrogenase, which uses NADH as a co-factor, rather than the <it>R. eutropha </it>isozyme, which uses NADPH, and the acetoacetyl-CoA transferase from <it>S. cerevisiae </it>or <it>E. coli </it>rather than that from <it>R. eutropha</it>. Surprisingly, expression of the genes encoding the butyryl-CoA dehydrogenase from <it>C. beijerinckii </it>(<it>bcd </it>and <it>etfAB</it>) did not improve butanol production significantly as previously reported in <it>E. coli</it>. Using metabolite analysis, we were able to determine which steps in the n-butanol biosynthetic pathway were the most problematic and ripe for future improvement.</p

Induction of multiple pleiotropic drug resistance genes in yeast engineered to produce an increased level of anti-malarial drug precursor, artemisinic acid

<p>Abstract</p> <p>Background</p> <p>Due to the global occurrence of multi-drug-resistant malarial parasites (<it>Plasmodium falciparum</it>), the anti-malarial drug most effective against malaria is artemisinin, a natural product (sesquiterpene lactone endoperoxide) extracted from sweet wormwood (<it>Artemisia annua</it>). However, artemisinin is in short supply and unaffordable to most malaria patients. Artemisinin can be semi-synthesized from its precursor artemisinic acid, which can be synthesized from simple sugars using microorganisms genetically engineered with genes from <it>A. annua</it>. In order to develop an industrially competent yeast strain, detailed analyses of microbial physiology and development of gene expression strategies are required.</p> <p>Results</p> <p>Three plant genes coding for amorphadiene synthase, amorphadiene oxidase (<it>AMO </it>or <it>CYP71AV1</it>), and cytochrome P450 reductase, which in concert divert carbon flux from farnesyl diphosphate to artemisinic acid, were expressed from a single plasmid. The artemisinic acid production in the engineered yeast reached 250 μg mL^-1in shake-flask cultures and 1 g L^-1in bio-reactors with the use of <it>Leu2d </it>selection marker and appropriate medium formulation. When plasmid stability was measured, the yeast strain synthesizing amorphadiene alone maintained the plasmid in 84% of the cells, whereas the yeast strain synthesizing artemisinic acid showed poor plasmid stability. Inactivation of AMO by a point-mutation restored the high plasmid stability, indicating that the low plasmid stability is not caused by production of the AMO protein but by artemisinic acid synthesis or accumulation. Semi-quantitative reverse-transcriptase (RT)-PCR and quantitative real time-PCR consistently showed that pleiotropic drug resistance (<it>PDR</it>) genes, belonging to the family of ATP-Binding Cassette (ABC) transporter, were massively induced in the yeast strain producing artemisinic acid, relative to the yeast strain producing the hydrocarbon amorphadiene alone. Global transcriptional analysis by yeast microarray further demonstrated that the induction of drug-resistant genes such as ABC transporters and major facilitator superfamily (MSF) genes is the primary cellular stress-response; in addition, oxidative and osmotic stress responses were observed in the engineered yeast.</p> <p>Conclusion</p> <p>The data presented here suggest that the engineered yeast producing artemisinic acid suffers oxidative and drug-associated stresses. The use of plant-derived transporters and optimizing AMO activity may improve the yield of artemisinic acid production in the engineered yeast.</p

Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees

BACKGROUND: Class III Homeodomain Leucine Zipper (HD-Zip III) proteins have been implicated in the regulation of cambium identity, as well as primary and secondary vascular differentiation and patterning in herbaceous plants. They have been proposed to regulate wood formation but relatively little evidence is available to validate such a role. We characterised and compared HD-Zip III gene family in an angiosperm tree, Populus spp. (poplar), and the gymnosperm Picea glauca (white spruce), representing two highly evolutionarily divergent groups. RESULTS: Full-length cDNA sequences were isolated from poplar and white spruce. Phylogenetic reconstruction indicated that some of the gymnosperm sequences were derived from lineages that diverged earlier than angiosperm sequences, and seem to have been lost in angiosperm lineages. Transcript accumulation profiles were assessed by RT-qPCR on tissue panels from both species and in poplar trees in response to an inhibitor of polar auxin transport. The overall transcript profiles HD-Zip III complexes in white spruce and poplar exhibited substantial differences, reflecting their evolutionary history. Furthermore, two poplar sequences homologous to HD-Zip III genes involved in xylem development in Arabidopsis and Zinnia were over-expressed in poplar plants. PtaHB1 over-expression produced noticeable effects on petiole and primary shoot fibre development, suggesting that PtaHB1 is involved in primary xylem development. We also obtained evidence indicating that expression of PtaHB1 affected the transcriptome by altering the accumulation of 48 distinct transcripts, many of which are predicted to be involved in growth and cell wall synthesis. Most of them were down-regulated, as was the case for several of the poplar HD-Zip III sequences. No visible physiological effect of over-expression was observed on PtaHB7 transgenic trees, suggesting that PtaHB1 and PtaHB7 likely have distinct roles in tree development, which is in agreement with the functions that have been assigned to close homologs in herbaceous plants. CONCLUSIONS: This study provides an overview of HD-zip III genes related to woody plant development and identifies sequences putatively involved in secondary vascular growth in angiosperms and in gymnosperms. These gene sequences are candidate regulators of wood formation and could be a source of molecular markers for tree breeding related to wood properties

Wheat EST resources for functional genomics of abiotic stress

BACKGROUND: Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project. RESULTS: We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology. CONCLUSION: We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals