A HMM Classifier with Contextual Observability: Application to Indoor People Tracking

Indoor tracking people activities with sensors networks is of high importance in number of domains, such as ambient assisted living. Home sensors have seen strong development over the last few years, especially due to the emergence of Internet of Things. A wide range of sensors are today available to be installed at home : video cameras, RGB-D Kinect, binary proximity sensors, thermometers, accelerometers, etc. An important issue in deploying sensors is to make them work in a common reference frame (extrinsic calibration issue), in order to jointly exploit the data they retrieve. Determining the perception areas that are covered by each sensor is also an issue that is not so easy to solve in practice. In this paper we address both calibration and coverage isssues within in a common framework, based on Hidden Mar-kov Models (HMMs) and clustering techniques. The proposed solution requires a map of the environment, as well as the ground truth of a tracked moving object/person, which are both provided by an external system (e.g. a robot that performs telemetric mapping). The objective of the paper is twofold. On one hand, we propose an extended framework of the classical HMM in order to (a) handle contextual observations and (b) solve general classification problems. In the other, we demonstrate the relevancy of the approach by tracking a person with 4 Kinects in an apartment. A sensing floor allows the implicit calibration and mapping during an initial learning phase

The isolation and mapping of a novel hydroxycinnamoyltransferase in the globe artichoke chlorogenic acid pathway

<p>Abstract</p> <p>Background</p> <p>The leaves of globe artichoke and cultivated cardoon (<it>Cynara cardunculus </it>L.) have significant pharmaceutical properties, which mainly result from their high content of polyphenolic compounds such as monocaffeoylquinic and dicaffeoylquinic acid (DCQ), and a range of flavonoid compounds.</p> <p>Results</p> <p>Hydroxycinnamoyl-CoA:quinate hydroxycinnamoyltransferase (HQT) encoding genes have been isolated from both globe artichoke and cultivated cardoon (GenBank accessions <ext-link ext-link-type="gen" ext-link-id="DQ915589">DQ915589</ext-link> and <ext-link ext-link-type="gen" ext-link-id="DQ915590">DQ915590</ext-link>, respectively) using CODEHOP and PCR-RACE. A phylogenetic analysis revealed that their sequences belong to one of the major acyltransferase groups (anthranilate N-hydroxycinnamoyl/benzoyltransferase). The heterologous expression of globe artichoke HQT in <it>E. coli </it>showed that this enzyme can catalyze the esterification of quinic acid with caffeoyl-CoA or <it>p</it>-coumaroyl-CoA to generate, respectively, chlorogenic acid (CGA) and <it>p</it>-coumaroyl quinate. Real time PCR experiments demonstrated an increase in the expression level of HQT in UV-C treated leaves, and established a correlation between the synthesis of phenolic acids and protection against damage due to abiotic stress. The HQT gene, together with a gene encoding hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase (HCT) previously isolated from globe artichoke, have been incorporated within the developing globe artichoke linkage maps.</p> <p>Conclusion</p> <p>A novel acyltransferase involved in the biosynthesis of CGA in globe artichoke has been isolated, characterized and mapped. This is a good basis for our effort to understand the genetic basis of phenylpropanoid (PP) biosynthesis in <it>C. cardunculus</it>.</p

Identification and characterisation of CYP75A31, a new flavonoid 3'5'-hydroxylase, isolated from Solanum lycopersicum

<p>Abstract</p> <p>Background</p> <p>Understanding the regulation of the flavonoid pathway is important for maximising the nutritional value of crop plants and possibly enhancing their resistance towards pathogens. The flavonoid 3'5'-hydroxylase (F3'5'H) enzyme functions at an important branch point between flavonol and anthocyanin synthesis, as is evident from studies in petunia (<it>Petunia hybrida</it>), and potato (<it>Solanum tuberosum</it>). The present work involves the identification and characterisation of a <it>F3'5'H </it>gene from tomato (<it>Solanum lycopersicum</it>), and the examination of its putative role in flavonoid metabolism.</p> <p>Results</p> <p>The cloned and sequenced tomato <it>F3'5'H </it>gene was named <it>CYP75A31</it>. The gene was inserted into the <it>pYeDP60 </it>expression vector and the corresponding protein produced in yeast for functional characterisation. Several putative substrates for F3'5'H were tested <it>in vitro </it>using enzyme assays on microsome preparations. The results showed that two hydroxylation steps occurred. Expression of the <it>CYP75A31 </it>gene was also tested <it>in vivo</it>, in various parts of the vegetative tomato plant, along with other key genes of the flavonoid pathway using real-time PCR. A clear response to nitrogen depletion was shown for <it>CYP75A31 </it>and all other genes tested. The content of rutin and kaempferol-3-rutinoside was found to increase as a response to nitrogen depletion in most parts of the plant, however the growth conditions used in this study did not lead to accumulation of anthocyanins.</p> <p>Conclusions</p> <p><it>CYP75A31 </it>(NCBI accession number GQ904194), encodes a flavonoid 3'5'-hydroxylase, which accepts flavones, flavanones, dihydroflavonols and flavonols as substrates. The expression of the <it>CYP75A31 </it>gene was found to increase in response to nitrogen deprivation, in accordance with other genes in the phenylpropanoid pathway, as expected for a gene involved in flavonoid metabolism.</p

Isolation and functional characterization of a cDNA coding a hydroxycinnamoyltransferase involved in phenylpropanoid biosynthesis in Cynara cardunculus L

BACKGROUND: Cynara cardunculus L. is an edible plant of pharmaceutical interest, in particular with respect to the polyphenolic content of its leaves. It includes three taxa: globe artichoke, cultivated cardoon, and wild cardoon. The dominating phenolics are the di-caffeoylquinic acids (such as cynarin), which are largely restricted to Cynara species, along with their precursor, chlorogenic acid (CGA). The scope of this study is to better understand CGA synthesis in this plant. RESULTS: A gene sequence encoding a hydroxycinnamoyltransferase (HCT) involved in the synthesis of CGA, was identified. Isolation of the gene sequence was achieved by using a PCR strategy with degenerated primers targeted to conserved regions of orthologous HCT sequences available. We have isolated a 717 bp cDNA which shares 84% aminoacid identity and 92% similarity with a tobacco gene responsible for the biosynthesis of CGA from p-coumaroyl-CoA and quinic acid. In silico studies revealed the globe artichoke HCT sequence clustering with one of the main acyltransferase groups (i.e. anthranilate N-hydroxycinnamoyl/benzoyltransferase). Heterologous expression of the full length HCT (GenBank accession DQ104740) cDNA in E. coli demonstrated that the recombinant enzyme efficiently synthesizes both chlorogenic acid and p-coumaroyl quinate from quinic acid and caffeoyl-CoA or p-coumaroyl-CoA, respectively, confirming its identity as a hydroxycinnamoyl-CoA: quinate HCT. Variable levels of HCT expression were shown among wild and cultivated forms of C. cardunculus subspecies. The level of expression was correlated with CGA content. CONCLUSION: The data support the predicted involvement of the Cynara cardunculus HCT in the biosynthesis of CGA before and/or after the hydroxylation step of hydroxycinnamoyl esters

Evolution of substrate recognition sites (SRSs) in cytochromes P450 from Apiaceae exemplified by the CYP71AJ subfamily

Background Large proliferations of cytochrome P450 encoding genes resulting from gene duplications can be termed as ‘blooms’, providing genetic material for the genesis and evolution of biosynthetic pathways. Furanocoumarins are allelochemicals produced by many of the species in Apiaceaous plants belonging to the Apioideae subfamily of Apiaceae and have been described as being involved in the defence reaction against phytophageous insects.[br/] Results A bloom in the cytochromes P450 CYP71AJ subfamily has been identified, showing at least 2 clades and 6 subclades within the CYP71AJ subfamily. Two of the subclades were functionally assigned to the biosynthesis of furanocoumarins. Six substrate recognition sites (SRS1-6) important for the enzymatic conversion were investigated in the described cytochromes P450 and display significant variability within the CYP71AJ subfamily. Homology models underline a significant modification of the accession to the iron atom, which might explain the difference of the substrate specificity between the cytochromes P450 restricted to furanocoumarins as substrates and the orphan CYP71AJ.[br/] Conclusion Two subclades functionally assigned to the biosynthesis of furanocoumarins and four other subclades were identified and shown to be part of two distinct clades within the CYP71AJ subfamily. The subclades show significant variability within their substrate recognition sites between the clades, suggesting different biochemical functions and providing insights into the evolution of cytochrome P450 ‘blooms’ in response to environmental pressures

Optimization of the Culture Medium Composition to Improve the Production of Hyoscyamine in Elicited Datura stramonium L. Hairy Roots Using the Response Surface Methodology (RSM)

Traditionally, optimization in biological analyses has been carried out by monitoring the influence of one factor at a time; this technique is called one-variable-at-a-time. The disadvantage of this technique is that it does not include any interactive effects among the variables studied and requires a large number of experiments. Therefore, in recent years, the Response Surface Methodology (RSM) has become the most popular optimization method. It is an effective mathematical and statistical technique which has been widely used in optimization studies with minimal experimental trials where interactive factors may be involved. This present study follows on from our previous work, where RSM was used to optimize the B5 medium composition in [NO3−], [Ca2+] and sucrose to attain the best production of hyoscyamine (HS) from the hairy roots (HRs) of Datura stramonium elicited by Jasmonic Acid (JA). The present paper focuses on the use of the RSM in biological studies, such as plant material, to establish a predictive model with the planning of experiments, analysis of the model, diagnostics and adjustment for the accuracy of the model. With the RSM, only 20 experiments were necessary to determine optimal concentrations. The model could be employed to carry out interpolations and predict the response to elicitation. Applying this model, the optimization of the HS level was 212.7% for the elicited HRs of Datura stramonium, cultured in B5-OP medium (optimized), in comparison with elicited HRs cultured in B5 medium (control). The optimal concentrations, under experimental conditions, were determined to be: 79.1 mM [NO3−], 11.4 mM [Ca2+] and 42.9 mg/L of sucrose

Molecular cloning and functional characterization of psoralen synthase, the first committed monooxygenase of furanocoumarin biosynthesis

Ammi majus L. accumulates linear furanocoumarins by cytochrome P450 (CYP)-dependent conversion of 6-prenylumbelliferone via (؉)-marmesin to psoralen. Relevant activities, i.e. psoralen synthase, are induced rapidly from negligible background levels upon elicitation of A. majus cultures with transient maxima at 9 -10 h and were recovered in labile microsomes. Expressed sequence tags were cloned from elicited Ammi cells by a nested DD-RT-PCR strategy with CYP-specific primers, and full-size cDNAs were generated from those fragments correlated in abundance with the induction profile of furanocoumarin-specific activities. One of these cDNAs representing a transcript of maximal abundance at 4 h of elicitation was assigned CYP71AJ1. Functional expression in Escherichia coli or yeast cells initially failed but was accomplished eventually in yeast cells after swapping the N-terminal membrane anchor domain with that of CYP73A1. The recombinant enzyme was identified as psoralen synthase with narrow substrate specificity for (؉)-marmesin. Psoralen synthase catalyzes a unique carbon-chain cleavage reaction concomitantly releasing acetone by syn-elimination. Related plants, i.e. Heracleum mantegazzianum, are known to produce both linear and angular furanocoumarins by analogous conversion of 8-prenylumbelliferone via (؉)-columbianetin to angelicin, and it was suggested that angelicin synthase has evolved from psoralen synthase. However, (؉)-columbianetin failed as substrate but competitively inhibited psoralen synthase activity. Analogy modeling and docked solutions defined the conditions for high affinity substrate binding and predicted the minimal requirements to accommodate (؉)-columbianetin in the active site cavity. The studies suggested that several point mutations are necessary to pave the road toward angelicin synthase evolution. Furanocoumarins are produced by many plants, mostly of the Apiaceae, Rutaceae, Moraceae, or the Coronilla and Psoralea genera of the Fabaceae (1-3). Multiple pharmacological effects have been ascribed to several of these metabolites (4 -6), which were included in clinical screenings but received attention also for their inhibitory effect on monooxygenases involved in drug metabolism (7-9) and potential toxicity (10). The (dihydro)furan-substituted 2H-1-benzopyran-2-one forms the characteristic core structure, and the annulation type distinguishes the linear furanocoumarins or psoralens from the angular furanocoumarin

Impact of Temporary Nitrogen Deprivation on Tomato Leaf Phenolics

Reducing the use of pesticides represents a major challenge of modern agriculture. Plants synthesize secondary metabolites such as polyphenols that participate in the resistance to parasites. The aim of this study was to test: (1) the impact of nitrogen deficiency on tomato (Solanum lycopersicum) leaf composition and more particularly on two phenolic molecules (chlorogenic acid and rutin) as well as on the general plant biomass; and (2) whether this effect continued after a return to normal nitrogen nutrition. Our results showed that plants deprived of nitrogen for 10 or 19 days contained higher levels of chlorogenic acid and rutin than control plants. In addition, this difference persisted when the plants were once again cultivated on a nitrogen-rich medium. These findings offer interesting perspectives on the use of a short period of deprivation to modulate the levels of compounds of interest in a plant

Caffeoylquinic Acids Biosynthesis and Accumulation in Cynara cardunculus: State of the Art

Plant secondary metabolites are highly evolved compounds performing different functions, and have been widely exploited from food to medicine. A constant supply of phenols, a class of secondary metabolites, provides preventive and defensive mechanisms to reduce the risk of chronic diseases in human beings; among them mono- and di-caffeoylquinic acids (monoCQAs, diCQAs) have attracted a growing academic and industrial interest in recent years. In Cynara cardunculus L. the biosynthetic pathway of chlorogenic acid (CGA, 5-O-caffeoylquinic acid) has been the subject of our several recent studies. Here, we report the state of the art on the isolation and in vitro functional characterization of the genes involved in the biosynthetic pathway of the CGA: HCT (hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl-transferase), HQT (hydroxycinnamoyl-CoA quinate hydroxyl-cinnamoyl-transferase), two HQT-like genes, we named Acyltransf_1 and Acyltransf_2, and C3’H (p-coumaroyl ester 3’-hydroxylase). Plant phenolics are known to be involved in the plant stress response and we found out that in globe artichoke the exposure to UV-C induces the production of diCQAs. In UV-C treated globe artichoke leaves, the expression level of C3´H, HCT, HQT, Acyltransf_1, Acyltransf_2 genes was strongly increased, thus confirming their involvement in the synthesis of chlorogenic acid. The development of DNA-based markers for the isolated genes made it possible to locate them within the previously developed genetic maps of the species

The CYP71AZ P450 Subfamily: A Driving Factor for the Diversification of Coumarin Biosynthesis in Apiaceous Plants

International audienceThe production of coumarins and furanocoumarins (FCs) in higher plants is widely considered a model illustration of the adaptation of plants to their environment. In this report, we show that the multiplication of cytochrome P450 variants within the CYP71AZ subfamily has contributed to the diversification of these molecules. Multiple copies of genes encoding this enzyme family are found in Apiaceae, and their phylogenetic analysis suggests that they have different functions within these plants. CYP71AZ1 from Ammi majus and CYP71AZ3, 4, and 6 from Pastinaca sativa were functionally characterized. While CYP71AZ3 merely hydroxylated esculetin, the other enzymes accepted both simple coumarins and FCs. Superimposing in silico models of these enzymes led to the identification of different conformations of three regions in the enzyme active site. These sequences were subsequently utilized to mutate CYP71AZ4 to resemble CYP71AZ3. The swapping of these regions lead to significantly modified substrate specificity. Simultaneous mutations of all three regions shifted the specificity of CYP71AZ4 to that of CYP71AZ3, exclusively accepting esculetin. This approach may explain the evolution of this cytochrome P450 family regarding the appearance of FCs in parsnip and possibly in the Apiaceae