Design enquiry: tacit knowledge and invention in science

For some years there has been discussion and speculation on the subject of "design enquiry" and a number of people, for example Richard Buchanan and Clive Dilnot , have looked for forms of enquiry appropriate to, or fruitful for, design as an academic and professional discipline. From a different perspective, Ranulph Glanville has suggested that the relationship between design and science might be redefined to acknowledge similarities of method that are disguised by forms of narrative employed by scientists. However most contributions in these debates deal with generalisations so I would like to propose some specific ways in which designers can explore and develop the concepts and practices of design enquiry. In particular I would like to discuss a kind of enquiry where designers can play a role in forming and pursuing questions which arise in the natural sciences and I will suggest that this role might be extended into some other fields. In doing so I will make reference to the subject of tacit knowledge, a concept which was formalised by Michael Polanyi in his consideration of the philosophy of science 50 years ago and which has attracted continuing interest (his 1958 book, Personal Knowledge, was reprinted most recently in 1998 and 2002), but also some shallow interpretation since then. I believe that Polanyi has a great deal to offer the design community, perhaps more in some respects than the widely cited work of Donald Schon who dealt with general questions of practice relevant to many disciplines while Polanyi addressed the relationship between enquiry and creativity in a very direct way. </p

Information system support in construction industry with semantic web technologies and/or autonomous reasoning agents

Information technology support is hard to find for the early design phases of the architectural design process. Many of the existing issues in such design decision support tools appear to be caused by a mismatch between the ways in which designers think and the ways in which information systems aim to give support. We therefore started an investigation of existing theories of design thinking, compared to the way in which design decision support systems provide information to the designer. We identify two main strategies towards information system support in the early design phase: (1) applications for making design try-outs, and (2) applications as autonomous reasoning agents. We outline preview implementations for both approaches and indicate to what extent these strategies can be used to improve information system support for the architectural designer

Identification and characterization of genes involved in ABA perception and signal transduction in Coffea spp : S02P13

The Coffea genus represents a major agricultural commodity in world trade. Nowadays, drought and elevated temperatures are the major climatic limitations for coffee production. These variations also influence biochemical composition of beans, affecting directly the final cup quality. There is genetic variability within the Coffea genus that could be used to increase drought tolerance and generate coffee varieties better adapted to climatic variations. Abscisic acid (ABA) is a vital plant hormone acting as central regulator that protects plants against abiotic stresses such as drought. Recently, novel intracellular ABA receptors (PYL/RCARs) involved in ABA sensing and signaling have been identified in several species. A mechanism of ABA transduction has been proposed, involving PYR/PYL/RCARs receptors interacting with PP2Cs phosphatases and SnRK2 protein kinases. The goal of this study was to identify and characterize ortholog genes of this tripartite system in Coffea sp. For this purpose, protein sequences from Arabidopsis, citrus, rice, grape, and tomato were chosen as query to search ortholog genes in the coffee-sequence database. Using 51 PYR/PYL/RCAR sequences from those plant species, it was possible to identify 9 sequences for ABA receptors in coffee. Likewise, the 40 and 29 sequences query resulted in 6 and 9 similar sequences of PP2Cs and SnRK2 specific to ABA in Coffea sp. The 24 genes isolated, that belong to the tripartite system of the coffee's ABA pathway, showed in silico differential expression in tissues as leaves, seeds, roots and floral organs. Polymorphisms were found among the orthologs and homeologs genes. All analyses allowed the identification in C. arabica genome of sequences variations between the two ancestral diploid sub-genomes, C. canephora (CaCc) and C. eugenioides (CaCe). Further analyses will predict the functional effect of these polymorphisms in protein structure in different coffee species. All these evidences will also help us to identify the genetic determinism of drought tolerance essential to obtain molecular markers that could be used in coffeebreeding programs. Work supported by CAPES-COFECUB, Consórcio Pesquisa Café and INCT-Café (CNPq/FAPEMIG). (Texte intégral

Analysis of CcDREB1D promoter region from drought-tolerant and susceptible clones of Coffea canephora by homologous genetic transformation of Coffea arabica

In several plant species, the DREB genes play a key role in responses to abiotic stress. Since the development of molecular markers is one of the major goals for accelerating breeding programs, a study was done to evaluate the sequence variability of the DREBID gene in several Coffee genotypes. The promoter and coding regions of DREBID gene were cloned and sequenced from 16 coffee plants (10 from C. arabica and 4 from C. canephora), most of them characterized by different phenotypes (tolerance vs. susceptibility) regarding to drought. This showed a high conservation of DREB1 D proteins among the homologous sequences due to the low level of diversity and the high number of synonymous mutations and neutral changes which represents the majority of sequence variations. However, several nucleic polymorphisms ("single nucleotide polymorphism" and insertion/deletion [InDels]) were found in the coffee DREBID promoters. A comparison of predicted cis-acting elements for all the promoter sequences signaled the loss of some regulatory DNA elements. The sequence variation and the loss of some regulatory DNA elements could explain the differences of DREBID gene expression previously observed in leaves of drought tolerant (clone 14) and susceptible (clone 22) clones of C. canephora. In fact, both clones 14 and 22, have one same CcDREBID allelic sequence (hp15), and diverge at a second allele. Thus, the CcDREBID allele in the tolerant 14 (hp16) was considered to be the favorable/tolerant allele and the allele in 22 (hp17) was inferior/sensitive. The capacity of CcDREBID promoter to control the expression of the uidA reporter gene is under evaluation in transgenic plants of Coffee arabica cv. caturra stably transformed by Agrobacterium tumefaciens mediated gene transfer procedure. Caturra transgenic embryos were placed on a clean bench and subjected to dehydration tests. Preliminary results of bioassays checking GUS (/3-glucuronidase) activities indicate that the observed sequence variations have a direct role in the regulation of CcDREBID expression. The proximal promoter of CcDREBID for the three alleles tested (hp15, hp16 and hp17) equally induced the uidA gene expression, however, expression of uidA under control of the complete CcDREBID promoter was significantly induced in the tolerant allele (hp16) in response to the osmotic stress, whereas, it was not significantly upregulated for the common (hp15) and sensitive alleles (hp17). These results also evidence that the sequence variation present at the first -700 by of CcDREBID promoter do not interfere the regulation activity of the promoter, probably due to the non-overlapping of SNPs and cis-regulatory elements. Though, the higher sequence variation and co-occurrence of SNPs and cis-regulatory elements observed between -700 and -1500 by seems to affect the regulation of CcDREBID promoter in response to drought stress.Support: CAPES COFECUB, INCT-Café, CNPq and ConsOrcio Pesquisa Café. (Texte intégral

Analysis of CcDREB1D promoter region from drought-tolerant and susceptible clones of Coffea canephora by homologous genetic transformation of Coffea arabica

In several plant species, the DREB genes play a key role in responses to abiotic stress. Since the development of molecular markers is one of the major goals for accelerating breeding programs, a study was done to evaluate the sequence variability of the DREBID gene in several Coffee genotypes. The promoter and coding regions of DREBID gene were cloned and sequenced from 16 coffee plants (10 from C. arabica and 4 from C. canephora), most of them characterized by different phenotypes (tolerance vs. susceptibility) regarding to drought. This showed a high conservation of DREB1 D proteins among the homologous sequences due to the low level of diversity and the high number of synonymous mutations and neutral changes which represents the majority of sequence variations. However, several nucleic polymorphisms ("single nucleotide polymorphism" and insertion/deletion [InDels]) were found in the coffee DREBID promoters. A comparison of predicted cis-acting elements for all the promoter sequences signaled the loss of some regulatory DNA elements. The sequence variation and the loss of some regulatory DNA elements could explain the differences of DREBID gene expression previously observed in leaves of drought tolerant (clone 14) and susceptible (clone 22) clones of C. canephora. In fact, both clones 14 and 22, have one same CcDREBID allelic sequence (hp15), and diverge at a second allele. Thus, the CcDREBID allele in the tolerant 14 (hp16) was considered to be the favorable/tolerant allele and the allele in 22 (hp17) was inferior/sensitive. The capacity of CcDREBID promoter to control the expression of the uidA reporter gene is under evaluation in transgenic plants of Coffee arabica cv. caturra stably transformed by Agrobacterium tumefaciens mediated gene transfer procedure. Caturra transgenic embryos were placed on a clean bench and subjected to dehydration tests. Preliminary results of bioassays checking GUS (/3-glucuronidase) activities indicate that the observed sequence variations have a direct role in the regulation of CcDREBID expression. The proximal promoter of CcDREBID for the three alleles tested (hp15, hp16 and hp17) equally induced the uidA gene expression, however, expression of uidA under control of the complete CcDREBID promoter was significantly induced in the tolerant allele (hp16) in response to the osmotic stress, whereas, it was not significantly upregulated for the common (hp15) and sensitive alleles (hp17). These results also evidence that the sequence variation present at the first -700 by of CcDREBID promoter do not interfere the regulation activity of the promoter, probably due to the non-overlapping of SNPs and cis-regulatory elements. Though, the higher sequence variation and co-occurrence of SNPs and cis-regulatory elements observed between -700 and -1500 by seems to affect the regulation of CcDREBID promoter in response to drought stress.Support: CAPES COFECUB, INCT-Café, CNPq and ConsOrcio Pesquisa Café. (Texte intégral

From "Periodical Observations” to "Anthochronology” and "Phenology” - the scientific debate between Adolphe Quetelet and Charles Morren on the origin of the word "Phenology”

Mankind has observed and documented life cycle stages of plants and animals for a long time. However, it was comparatively recently that the newly emerging science was given its name. The name of Charles Morren and the year 1853 are being cited, although not frequently. Exact information is hardly known among present-day phenologists, yet new evidence shows that the term "phenology” was already in use in 1849. In the early 1840s, physicist and astronomer Adolphe Quetelet set up an observational network named "Observations of periodical Phenomena of the Animal and Vegetable Kingdom” and issued instructions for it. Even though biologist Charles Morren welcomed Quetelet's initiative, differences between Morren and Quentlet regarding the instructions for the observations and the potential results soon arose and a debate started, which lasted for nearly 10years. In the wake of these disagreements, Morren was compelled to create a new term to denote his ideas on "periodical phenomena”. At first, he temporally used the word anthochronology, but in the end he coined the word phenology. The term was first used in a public lecture at the Académie royale des Sciences, des Lettres et des Beaux-Arts de Belgique' in Brussels on 16 December 1849, and simultaneously in the December 1849 issue of volume V of the Annales de la Société royale d'Agriculture et de Botanique de Gand. One had to wait until 1853 before the new name appeared in the title of one of Morren's publications. Based on evidence from archives and original publications, we trace the 10-year-long scientific debate between Morren and Quetelet. Morren states his biologist's view on the subject and extends the more climate-related definition of Quetelet of "periodical phenomena

Analysis of DREB1D gene sequence in different Coffea genotypes : S03P07

In several plant species, the DREB genes play a key role in responses to abiotic stress. Since the development of molecular markers is one of the major goals for accelerating breeding programs, a study was done to evaluate the sequence variability of the DREB1D gene in several Coffea genotypes. The promoter and coding regions of this gene were cloned and sequenced from 16 coffee plants (including 10 from C. arabica and 4 from C. canephora), most of them characterized by different phenotypes (tolerance vs. susceptibility) regarding to drought. This showed that the DREB1D-coding sequence was highly conserved within coffee plants. However, several nucleic polymorphisms ("single nucleotide polymorphism" [SNP] and insertion/deletion [INDELs]) were found in the coffee DREB1D promoter regions. These polymorphisms could explained the differences of DREB1D gene expression levels previously observed in leaves of drought tolerant and susceptible clones of C. canephora. These polymorphisms also allowed the identification of different haplotypes like orthologous sequence variants (OSVs) of C. canephora and C. eugenioides as well as homologous single-nucleotide variants (HSVs) for C. arabica subgenomes (C. canephora and C. eugenioides) that could be used to develop allele and homoeologous specific markers for this locus. Work is now under way to evaluate the capacity of DREB1D promoter regions to control the expression of the uidA reporter gene in transgenic coffee plants. Work supported by CAPES-COFECUB, Consórcio Pesquisa Café and INCT-Café (CNPq/FAPEMIG). (Texte intégral

www.eia.gov

The Energy Information Administration (EIA) produces projections of energy supply and demand each year in the Annual Energy Outlook (AEO). The projections in the AEO are not statements of what will happen but of what might happen, given the assumptions and methodologies. The Reference case projection assumes trends that are consistent with historical and current market behavior, technological and demographic changes, and current laws and regulations. The potential impacts of pending or proposed legislation, regulations, and standards—or of sections of legislation that have been enacted but that require implementing regulations or appropriation of funds that are not provided or specified in the legislation itself—are not reflected in the projections [1]. Thus, the AEO Reference case provides an impartial baseline that can be used to analyze potential new policies or legislative initiatives. Th

The early steps of drought response mediated by ABA: evolutionary and molecular mechanism of Coffea canephora PYR/PYL/RCAR receptors

The abscisic acid (ABA) is a vital phytohormone synthesized in roots and leaves, acting as central regulator involved in plant responses against abiotic stress, such as drought. It mediates stress-responsive gene expression by controlling stomatal closure, root growth modulation and seed dormancy, for example. Water deficit affects coffee plant development and production and consequently the biochemical composition of beans. It is also well known that genetic variability exists in the Coffea species for drought tolerance. Recently, novel intracellular ABA receptors (PYL/RCARs) involved in ABA sensing and signaling were identified. A mechanism of ABA transduction was proposed, involving PYR/PYL/RCARs ABA receptors interacting with PP2Cs phosphatases and SnRK2 protein kinases. The goal of this study was to identify and characterize orthologous genes of PYR/PYL/RCAR family in C. canephora. For this purpose, protein sequences from Arabidopsis, citrus, rice, grape and tomato species were chosen as query to search orthologous genes in coffee genome. This approach allowed the identification and characterization of 9 candidate genes for PYR/PYL/RCAR family in C. canephora genome. The protein domains identified in the predict coffee sequences enabled to characterize these genes as family's members of receptors of ABA response pathway. Phylogenetic analysis allowed classifying coffee polypeptides sequences in three subfamilies expected. These genes were functionally annotated in the Coffee Genome Hub (http://coffee-genome.org/). In silico analyses also revealed differential expression profiles of coffee PYR/PYL/RCAR genes in tissues such as leaves, seeds, and floral organs, although, the highest expression profiles were identified in roots. Regarding drought stress, in silico analyses from RNAseq data obtained from roots of tolerant (Cc14, Cc73, Cc120) and susceptible (Cc22) clones of C. canephora grown with (I) or without (NI) irrigation also confirmed differential expression profiles of PYR/PYL/RCAR genes, suggesting the existence of multiple biological mechanisms for drought tolerance in coffee. Among the 9 coffee candidate genes, only the PYR1, PYL6, PYL8-2, PYL8- 8, PYL9 appeared expressed in roots. By qPCR analyses, we showed that the two copies of PYL8 gene present in C. canephora genome are co-expressed in root. Even members of the same subfamily, an in depth analysis of the coffee genome sequence revealed that these two genes were located in different chromosomes. As previously reported for several specific coffee gene families, such gene expansion could evidence a sequential tandem duplication followed by functional diversification. In order to understand the genetic determinism of drought tolerance in coffee, analyses are currently on going to identify the nucleic polymorphisms in promoter regions and coding sequences of PYR/PYL gene family. (Résumé d'auteur

The Coffee Genome Hub : [W185]

The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently obtained and portends to be published and released in the coming months. In the context of the C.canephora genome sequence project and to support post-genomics efforts, we developed the Coffee Genome Hub, an integrative genome information system accessible through the South Green Bioinformatics Platform, providing centralized access to coffee community to genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied research in coffee. Available data are the complete genome sequence of C.canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics (ESTs, RNA-Seq), syntenic blocs, genetic markers and genetic maps. The hub provides also generic softwares (e.g. GMOD tools) for easy querying, visualizing and downloading research data. Notably, the Coffee Genome Hub includes a Genome Browser for the C.canephora genome sequence, enhanced by a Community Annotation System (CAS) enabling the improvement of automatic gene annotation through an annotation editor and facilitating the study of gene families, and a chromosome viewer displaying the distribution of genomics feature along the chromosomes. In addition, the hub aims at developing interoperability between other existing South Green tools managing Coffee data (phylogenomics resources, SNPs) and/or allowing data analyses (workflow manager). The Coffee Genome Hub can be accessed at http://coffee-genome.org/. (Texte intégral