Establishment of a Developmental Compartment Requires Interactions between Three Synergistic Cis-regulatory Modules.

The subdivision of cell populations in compartments is a key event during animal development. In Drosophila, the gene apterous (ap) divides the wing imaginal disc in dorsal vs ventral cell lineages and is required for wing formation. ap function as a dorsal selector gene has been extensively studied. However, the regulation of its expression during wing development is poorly understood. In this study, we analyzed ap transcriptional regulation at the endogenous locus and identified three cis-regulatory modules (CRMs) essential for wing development. Only when the three CRMs are combined, robust ap expression is obtained. In addition, we genetically and molecularly analyzed the trans-factors that regulate these CRMs. Our results propose a three-step mechanism for the cell lineage compartment expression of ap that includes initial activation, positive autoregulation and Trithorax-mediated maintenance through separable CRMs.

"Role of long non-coing RNAs in the stressed heart". Wisper : a novel cardiac fibroblast-enriched IncRNA that modulate fibrosis in the failing heart

LncRNAs are transcripts greater than 200 nucleotides in length with no apparent coding potential. They exert important regulatory functions in the genome. Their role in cardiac fibrosis is however unexplored. To identify IncRNAs that could modulate cardiac fibrosis, we profiled the long non-coding transcriptome in the infarcted mouse heart, and identified 1500 novel IncRNAs. These IncRNAs have unique characteristics such as high tissue and cell type specificity. Their expression is highly correlated with parameters of cardiac dimensions and function. The majority of these novel IncRNAs are conserved in human. Importantly, human IncRNAs appear to be differentially expressed in heart disease. Using a computational pipeline, we identified a super-enhancer-associated IncRNA, which is dynamically expressed after myocardial infarction. We named this particular transcript Wisper for «Wisp2 super-enhancer- derived IncRNA ». Interestingly, Wisper expression is overexpressed in cardiac fibroblasts as compared to cardiomyocytes or to fibroblasts isolated from other organs than the heart. The importance of Wisper in the biology of fibroblasts was demonstrated in knockdown experiments. Differentiation of cardiac fibroblast into myofibroblasts in vitro is significantly impaired upon Wisper knockdown. Wisper downregulation in cardiac fibroblasts results in a dramatic reduction of fibrotic gene expression, a diminished cell proliferation and an increase in apoptotic cell death. In vivo, depletion of Wisper during the acute phase of the response to infarction is detrimental via increasing the risk of cardiac rupture. On the other hand, Wisper knockdown following infarction in a prevention study reduces fibrosis and preserves cardiac function. Since WISPER is detectable in the human heart, where it is associated with severe cardiac fibrosis, these data suggest that Wisper could represent a novel therapeutic target for limiting the extent of the fibrotic response in the heart. -- Les long ARN non-codants (IncRNAs) sont des ARN de plus de 200 nucléotides qui ne codent pas pour des protéines. Ils exercent d'importantes fonctions dans le génome. Par contre, leur importance dans le développement de la fibrose cardiaque n'a pas été étudiée. Pour identifier des IncRNAs jouant un rôle dans ce processus, le transcriptome non-codant a été étudié dans le coeur de'souris après un infarctus du myocarde. Nous avons découverts 1500 nouveaux IncRNAs. Ces transcrits ont d'uniques caractéristiques. En particulier ils sont extrêmement spécifiques de sous-populations de cellules cardiaques. Par ailleurs, leur expression est remarquablement corrélée avec les paramètres définissant les dimensions du coeur et la fonction cardiaque. La majorité de ces IncRNAs sont conservés chez l'humain. Certains sont modulés dans des pathologies cardiaques. En utilisant une approche bioinformatique, nous avons identifié un IncRNA qui est associé à des séquences amplificatrices et qui est particulièrement enrichi dans les fibroblastes cardiaques. Ce transcrit a été nommé Wisper pour «Wisp2 super-enhancer-derived IncRNA ». L'importance de Wisper dans la biologie des fibroblastes cardiaques est démontrée dans des expériences de déplétion. En l'absence de Wisper, l'expression de protéines impliquées dans le développement de la fibrose est dramatiquement réduite dans les fibroblastes cardiaques. Ceux-ci montrent une prolifération réduite. Le niveau d'apoptose est largement augmenté. In vivo, la déplétion de Wisper pendant la phase aiguë de l'infarctus rehausse le risque de rupture cardiaque. Au contraire, la réduction de l'expression de Wisper pendant la phase chronique diminue la fibrose cardiaque et améliore la fonction du coeur. Puisque Wisper est exprimé dans le coeur humain, ce transcrit représente une nouvelle cible thérapeutique pour limiter la réponse fibrotique dans le coeur.

Fundamentals of beer and hop chemistry

Beer brewing is an intricate process encompassing mixing and further elaboration of four essential raw materials, including barley malt, brewing water, hops and yeast. Particularly hops determine to a great extent typical beer qualities such as bitter taste, hoppy flavour, and foam stability. Conversely, hop-derived bitter acids account for an offending lightstruck flavour, which is formed on exposure of beer to light. These various processes are presented in detail, while due emphasis is placed on state-of-the-art hop technology, which provides brewers with efficient means to control bitterness, foam, and light-stability thereby allowing for the production of beers with consistent quality.

Queijos: aspectos químicos, bioquímicos e microbiológicos

This article presents a brief historical outline of cheese manufacture. Chemical, biochemical and microbiological aspects are presented: the main constituents of curd, the reactions involved in the development of flavour, and the role of micro-organisms and enzymes in the fermentation and maturation processes. A brief description of the characteristics of some cheeses is also given.

Ralstonia solanacearum, a widespread bacterial plant pathogen in the post-genomic era

Ralstonia solanacearum is a soil-borne bacterium causing the widespread disease known as bacterial wilt. Ralstonia solanacearum is also the causal agent of Moko disease of banana and brown rot of potato. Since the last R. solanacearum pathogen profile was published 10 years ago, studies concerning this plant pathogen have taken a genomic and post-genomic direction. This was pioneered by the first sequenced and annotated genome for a major plant bacterial pathogen and followed by many more genomes in subsequent years. All molecular features studied now have a genomic flavour. In the future, this will help in connecting the classical field of pathology and diversity studies with the gene content of specific strains. In this review, we summarize the recent research on this bacterial pathogen, including strain classification, host range, pathogenicity determinants, regulation of virulence genes, type III effector repertoire, effector-triggered immunity, plant signalling in response to R. solanacearum, as well as a review of different new pathosystems.

Synchronous scanning phosphorimetry for the selective determination of chrysene: a metrological study

Room-temperature phosphorimetry was used to quantify trace levels of chrysene in sugar-cane spirits and in fish bile. A selective phosphorescence enhancer (AgNO3) and synchronous scanning allowed the detection of ng amounts of chrysene. Accuracy (113 ± 17%) and selectivity was evaluated using the CRM-NIST-1647d - Priority Pollutant Polycyclic Aromatic Hydrocarbons in acetonitrile. Analysis of sugar-cane spirit samples enabled recovery of 108 ± 18% which agreed with the one achieved using HPLC. Method's uncertainty was equivalent to 3.4 ng of the analyte, however, the analyte pre-concentration (SPE) improved sensibility and minimized the relative uncertainty. Characterization and homogeneity studies in fish bile were also performed.

Uso de perfis cromatográficos de voláteis de cafés arábicas torrados para a diferenciação das amostras segundo o sabor, o aroma e a qualidade global da bebida

In this work, the volatile chromatographic profiles of roasted Arabica coffees, previously analyzed for their sensorial attributes, were explored by principal component analysis. The volatile extraction technique used was the solid phase microextraction. The correlation optimized warping algorithm was used to align the gas chromatographic profiles. Fifty four compounds were found to be related to the sensorial attributes investigated. The volatiles pyrrole, 1-methyl-pyrrole, cyclopentanone, dihydro-2-methyl-3-furanone, furfural, 2-ethyl-5-methyl-pyrazine, 2-etenyl-n-methyl-pyrazine, 5-methyl-2-propionyl-furan compounds were important for the differentiation of coffee beverage according to the flavour, cleanliness and overall quality. Two figures of merit, sensitivity and specificity (or selectivity), were used to interpret the sensory attributes studied.

Sensory and Non-sensory Factors Behind the Liking and Choice of Healthy Food Products

A healthy and balanced diet can reduce health problems, such as overweight and metabolic syndrome. In general, people have a considerably good knowledge of what constitutes a healthy diet and how they could achieve it with their food choices. Besides, people argue that health is among their top five food choice motives. Nevertheless, the prevalence of overweight is increasing and other food choice motives, such as taste, seem to conflict with the health. Liking for food does not necessarily determine acceptance alone, thus several non-sensory factors, such as brand, country of origin and nutrition claim, can also influence. Moreover, consumers are individuals in how they prioritize sensory and nonsensory factors of foods, but e.g. increasing age, female gender and health concern have been connected to a more health-oriented dietary behaviour. To sum up, identifying different factors that can increase the liking and consumption of healthy food is essential in order to develop more attractive healthful food products. Adding vitamins, minerals, fibre or other ingredients to a food product can be used to enrich the nutritional quality of the products. However, this may be difficult in practice as regards the sensory quality and pleasantness of the foods. Generally, consumers are not willing to compromise on taste in food. On the other hand, consumers are very heterogeneous in their likings, and their personal values and attitudes may interact with preferences for specific sensory characteristics. The aims of this study were to investigate the effects of intrinsic product characteristics on sensory properties and hedonic responses; to determine the impact of few non-sensory factors; and to examine the interaction between sensory and non-sensory factors with consumers’ demographics, values and attitudes in liking of healthy model foods. The results showed that product composition influenced sensory quality and had an effect on hedonic responses. Adding flaxseed to bakery products showed a significant improvement in the nutritional quality without negative effects on sensory properties. On the other hand, the fortification of wellness beverages with vitamins and minerals may impart off-flavours. In general, sweetness of yoghurts, freshness of wellness beverages and low intensity of rye bread flavour appealed to consumers. Information about the domestic origin of yoghurts and claiming a specific function for wellness beverages enhanced liking. However, consumers who were more concerned about their health and considered natural content as an important food choice motive, rated sourer and less sweet yoghurts and wellness beverages as more pleasant. In addition, interest in health increased the consumption of rye breads and other whole grain breads among adolescents. The results showed that the optimal product quality in terms of intrinsic and extrinsic factors differs between individual consumers, and personal values and food choice motives can be connected to preferences for specific sensory characteristics of foods. This indicates that each food product needs to be considered in relation to its specific market niche, and to which segment of consumer will respond most positively to its characteristics.

Cromatografia gasosa quiral na resolução de enantiômeros envolvidos em flavours de frutas

This work addresses the use of chiral gas chromatography in resolving optically active stereoisomers and racemates found in fruit flavours. It presents the types of chiral selectors applied to terpene-derived metal coordination compounds, polysiloxane-linked α-amino acid and mixed chiral stationary phases, and focuses on derivatized cyclodextrins, the most popular chiral stationary phases presently used in chromatographic analysis. Knowledge about the techniques involved in chiral recognition and enantiomer identification in the fruit flavour field is given along with examples from the latest studies.

Astringent Food Compounds and Their Interactions with Taste Properties

Astringency is traditionally thought to be induced by plant tannins in foods. Because of this current research concerning the mechanism of astringency is focused on tannin‐protein interactions and thus on precipitation, which may be perceived by mechanoreceptors. However, astringency is elicited by a wide range of different phenolic compounds, as well as, some non‐phenolic compounds in various foods. Many ellagitannins or smaller compounds that contribute to astringent properties do not interact with salivary proteins and may be directly perceived through some receptors. Generally, the higher degree of polymerization of proanthocyanidins can be associated with more intense astringency. However, the astringent properties of smaller phenolic compounds may not be directly predicted from the structure of a compound, although glycosylation has a significant role. The astringency of organic acids may be directly linked to the perception of sourness, and this increases along with decreasing pH. Astringency can be divided into different sub‐qualities, including even other qualities than traditional mouth‐drying, puckering or roughing sensations. Astringency is often accompanied by bitter or sour or both taste properties. The different sub‐qualities can be influenced by different astringent compounds. In general, the glycolysation of the phenolic compound results in more velvety and smooth mouthdrying astringency. Flavonol glycosides and other flavonoid compounds and ellagitannins contribute to this velvety mouthdrying astringency. Additionally, they often lack the bitter properties. Proanthocyanidins and phenolic acids elicit more puckering and roughing astringency with some additional bitter properties. Quercetin 3‐O‐rutinoside, along with other quercetin glycosides, is among the key astringent compounds in black tea and red currants. In foods, there are always various other additional attributes that are perceived at the same with astringency. Astringent compounds themselves may have other sensory characteristics, such as bitter or sour properties, or they may enhance or suppress other sensory properties. Components contributing to these other properties, such as sugars, may also have similar effects on astringent sensations. Food components eliciting sweetness or fattiness or some polymeric polysaccharides can be used to mask astringent subqualities. Astringency can generally be referred to as a negative contributor to the liking of various foods. On the other hand, perceptions of astringent properties can vary among individuals. Many genetic factors that influence perceptions of taste properties, such as variations in perceiving a bitter taste or variations in saliva, may also effect the perception of astringency. Individuals who are more sensitive to different sensations may notice the differences between astringent properties more clearly. This may not have effects on the overall perception of astringency. However, in many cases, the liking of astringent foods may need to be learned by repetitive exposure. Astringency is often among the key sensory properties forming the unique overall flavour of certain foods, and therefore it also influences whether or not a food is liked. In many cases, astringency may be an important sub‐property suppressed by other more abundant sensory properties, but it may still have a significant contribution to the overall flavour and thus consumer preferences. The results of the practical work of this thesis show that the astringent phenolic compounds are mostly located in the skin fractions of black currants, crowberries and bilberries (publications I–III). The skin fractions themselves are rather tasteless. However, the astringent phenolic compounds can be efficiently removed from these skin fractions by consecutive ethanol extractions. Berries contain a wide range of different flavonol glycosides, hydroxycinnamic acid derivatives and anthocyanins and some of them strongly contribute to the different astringent and bitterness properties. Sweetness and sourness are located in the juice fractions along with the majority of sugars and fruit acids. The sweet and sour properties of the juice may be used to mask the astringent and bitterness properties of the extracts. Enzymatic treatments increase the astringent properties and fermented flavour of the black currant juice and decrease sweetness and freshness due to the effects on chemical compositions (IV). Sourness and sweetness are positive contributors to the liking of crowberry and bilberry fractions, whereas bitterness is more negative (V). Some astringent properties in berries are clearly negative factors, whereas some may be more positive. The liking of berries is strongly influenced by various consumer background factors, such as motives and health concerns. The liking of berries and berry fractions may also be affected by genetic factors, such as variations in the gene hTAS2R38, which codes bitter taste receptors (V).

Vibration analysis for Bearing outer race condition diagnostics

This paper investigates defect detection methodologies for rolling element bearings through vibration analysis. Specifically, the utility of a new signal processing scheme combining the High Frequency Resonance Technique (HFRT) and Adaptive Line Enhancer (ALE) is investigated. The accelerometer is used to acquire data for this analysis, and experimental results have been obtained for outer race defects. Results show the potential effectiveness of the signal processing technique to determine both the severity and location of a defect. The HFRT utilizes the fact that much of the energy resulting from a defect impact manifests itself in the higher resonant frequencies of a system. Demodulation of these frequency bands through use of the envelope technique is then employed to gain further insight into the nature of the defect while further increasing the signal to noise ratio. If periodic, the defect frequency is then present in the spectra of the enveloped signal. The ALE is used to enhance the envelope spectrum by reducing the broadband noise. It provides an enhanced envelope spectrum with clear peaks at the harmonics of a characteristic defect frequency. It is implemented by using a delayed version of the signal and the signal itself to decorrelate the wideband noise. This noise is then rejected by the adaptive filter that is based upon the periodic information in the signal. Results have been obtained for outer race defects. They show the effectiveness of the methodology to determine both the severity and location of a defect. In two instances, a linear relationship between signal characteristics and defect size is indicated.

Transcriptional and Epigenetic Regulation of Human CD4+ T Helper Lineage Specification

Activated T helper (Th) cells have ability to differentiate into functionally distinct Th1, Th2 and Th17 subsets through a series of overlapping networks that include signaling and transcriptional control and the epigenetic mechanisms to direct immune responses. However, inappropriate execution in the differentiation process and abnormal function of these Th cells can lead to the development of several immune mediated diseases. Therefore, the thesis aimed at identifying genes and gene regulatory mechanisms responsible for Th17 differentiation and to study epigenetic changes associated with early stage of Th1/Th2 cell differentiation. Genome wide transcriptional profiling during early stages of human Th17 cell differentiation demonstrated differential regulation of several novel and currently known genes associated with Th17 differentiation. Selected candidate genes were further validated at protein level and their specificity for Th17 as compared to other T helper subsets was analyzed. Moreover, combination of RNA interference-mediated downregulation of gene expression, genome-wide transcriptome profiling and chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq), combined with computational data integration lead to the identification of direct and indirect target genes of STAT3, which is a pivotal upstream transcription factor for Th17 cell polarization. Results indicated that STAT3 directly regulates the expression of several genes that are known to play a role in activation, differentiation, proliferation, and survival of Th17 cells. These results provide a basis for constructing a network regulating gene expression during early human Th17 differentiation. Th1 and Th2 lineage specific enhancers were identified from genome-wide maps of histone modifications generated from the cells differentiating towards Th1 and Th2 lineages at 72h. Further analysis of lineage-specific enhancers revealed known and novel transcription factors that potentially control lineage-specific gene expression. Finally, we found an overlap of a subset of enhancers with SNPs associated with autoimmune diseases through GWASs suggesting a potential role for enhancer elements in the disease development. In conclusion, the results obtained have extended our knowledge of Th differentiation and provided new mechanistic insights into dysregulation of Th cell differentiation in human immune mediated diseases.

Polyphenolic cells and their interrelation with cotyledon cells in seven species of Theobroma (Sterculiaceae)

The amount of cotyledon polyphenolic cells varies extensively within the Theobroma species. The polyphenolic compounds of these cells play a protective role and furthermore have an important function in the development of chocolate flavour. The morphology of the polyphenolic cells of the mesophyll is described and the development of these idioblasts in Theobroma cacao L., T. subincanum Mart., T. obovatum Klotzsch ex Bernoulli, T. grandiflorum (Willd. ex Spreng.) K. Schum., T. microcarpum Mart., T. bicolor Bonpl. and T. speciosum Willd. ex Spreng analysed. The total polyphenolic content in the seeds as determined by spectrophotometry showed a variation of about forty times. The alive, transparent polyphenolic cells are scattered throughout the cotiledonary mesophyll. However the polyphenolic cells of T. cacao and T. grandiflorum are also aligned perpendicularly with respect to the mesophyll borders and, in addition, both species display polyphenolic cells with a natural translucent purple colour. All the species analysed contained polyphenolic cells scattered throughout the parenchymal cells and also in a lengthwise association with vascular bundles. In T. bicolor and T. speciosum, the species with the lowest polyphenolic contents, these cells were mostly located around the vascular bundles. Using Scanning Electron Microscopy, the polyphenolic cells demonstrated a complex cytoarchitecture, and after fixing with glutaraldhyde, the polyphenolic secretion was shown to remain as a single unit or was organized into round droplets. Transmission Electron Microscopy displayed immature plastids from young mesophyll cells containing eletron-dense deposits similar to phenolic substances, suggesting that Theobroma plastids are involved in the synthesis of phenolics.

Association of hepatic nuclear factor-4 in the apolipoprotein B promoter: a preliminary report

Previous studies have examined the arrangement of regulatory elements along the apolipoprotein B (apoB) promoter region (-3067 to +940) and a promoter fragment extending from nucleotides -150 to +124 has been demonstrated to be essential for transcriptional activation of the apoB gene in hepatic and intestinal cells. It has also been shown that transcriptional activation of apoB requires a synergistic interaction between hepatic nuclear factor-4 (HNF-4) and CCAAT/enhancer-binding protein a (C/EBPa) transcription factors. Here, we have examined the hypothesis that HNF-4 factor binding to DNA may induce a DNA helix bend, thus facilitating the communication with a C/EBPa factor located one helix turn from this HNF-4 factor in the apoB promoter. A gel electrophoretic mobility shift assay using wild type double-stranded oligonucleotides or modified wild type duplex oligonucleotides with 10 nucleotides inserted between HNF-4 and C/EBPa factor motifs showed similar retarded complexes, indicating that HNF-4 and C/EBPa factors interact independently of the distance between binding sites. However, when only one base, a thymidine, was inserted at the -71 position of the apoB promoter, the complex shift was completely abolished. In conclusion, these results regarding the study of the mechanisms involving the interaction between HNF-4 and C/EBPa factors in the apoB promoter suggest that the perfect 5'-CCCTTTGGA-3' motif is needed in order to facilitate the interaction between the two factors.

Main features of DNA-based immunization vectors

DNA-based immunization has initiated a new era of vaccine research. One of the main goals of gene vaccine development is the control of the levels of expression in vivo for efficient immunization. Modifying the vector to modulate expression or immunogenicity is of critical importance for the improvement of DNA vaccines. The most frequently used vectors for genetic immunization are plasmids. In this article, we review some of the main elements relevant to their design such as strong promoter/enhancer region, introns, genes encoding antigens of interest from the pathogen (how to choose and modify them), polyadenylation termination sequence, origin of replication for plasmid production in Escherichia coli, antibiotic resistance gene as selectable marker, convenient cloning sites, and the presence of immunostimulatory sequences (ISS) that can be added to the plasmid to enhance adjuvanticity and to activate the immune system. In this review, the specific modifications that can increase overall expression as well as the potential of DNA-based vaccination are also discussed.