The distribution of word matches between Markovian sequences with periodic boundary conditions

Word match counts have traditionally been proposed as an alignment-free measure of similarity for biological sequences. The D2 statistic, which simply counts the number of exact word matches between two sequences, is a useful test bed for developing rigorous mathematical results, which can then be extended to more biologically useful measures. The distributional properties of the D2 statistic under the null hypothesis of identically and independently distributed letters have been studied extensively, but no comprehensive study of the D2 distribution for biologically more realistic higher-order Markovian sequences exists. Here we derive exact formulas for the mean and variance of the D2 statistic for Markovian sequences of any order, and demonstrate through Monte Carlo simulations that the entire distribution is accurately characterized by a Pólya-Aeppli distribution for sequence lengths of biological interest. The approach is novel in that Markovian dependency is defined for sequences with periodic boundary conditions, and this enables exact analytic formulas for the mean and variance to be derived. We also carry out a preliminary comparison between the approximate D2 distribution computed with the theoretical mean and variance under a Markovian hypothesis and an empirical D2 distribution from the human genome

Etude d'un nouveau procédé de fractionnement des co-produits de fabrication de jambon sec et des propriétés physico-chimiques et fonctionnelles des extraits et raffinats

Le coproduit de fabrication de jambon sec est issu de l'opération de désossage de la cuisse de porc parée, salée, séchée et affinée. Il est constitué à plus de 85 % d'os et de tissus associés (cartilages, ligaments, tendons). Le concassage au broyeur à marteau permet d'homogénéiser le coproduit en morceaux de taille inférieure à 8 cm (> 90 % compris entre 40 et 80 mm). La composition chimique de la matière sèche du mélange (77 ± 3 % de MS) est de 33 ± 5 % en protéines (89 % de collagène, 14 % de protéines hydrosolubles, 6 % d'acide aminés libres), 31 ± 3 % en lipides (triglycérides : 70 % ; diglycérides : 3,5 % ; acides gras libres : 11 % ; saturé/insaturé : 0,87 ; 24 % C16 :0 ; 13 % C18 :0 ; 2 % C16 :1 ; 38 % C18 :1 ; 4 % C18 :2) et 26 ± 4 % de matière minérale (phosphate de calcium 88 % ; NaCl 9 %). L'extraction aqueuse des lipides et des protéines du coproduit est étudiée en contacteur agité. Le raffinat solide est séparé par filtration à chaud sous forme de granulat et la matière grasse entraînée est séparée par décantation à froid. L'étude de l'influence des principaux facteurs de l'extraction liquide/solide (temps de contact : 30 à 90 min, température : 40 à 90°C ; ratio eau/coproduit : 4 à 10) grâce à la réalisation d'un plan d'expérience met en évidence les effets de la solubilisation et la coagulation des protéines sur l'entraînement des lipides et leur décantation sous forme de matière grasse. Mis en oeuvre à l'échelle pilote (64 kg de coproduit de jambon sec concassé, 207 kg d'eau, 30 min à 90°C en contacteur agité), le procédé de fractionnement aqueux conduit par filtration centrifuge et séchage à un granulat stable (rendement : 59 % ; matière minérale : 41 % ; protéines : 43 % ; lipides : 16 %), source de phosphate de calcium (95 % de la matière minérale) et de gélatine ou de colle d'os (88 % de protéines de nature collagénique). La fraction matière grasse décantée (rendement : 24 % ; lipides : 93 % ; triglycérides : 75 % ; diglycérides : 4 % ; acides gras libres : 7 % ; saturé/insaturé : 0,82 % ; 37 % C16 :0 ; 15 % C18 :0 ; 2 % C16 :1 ; 44 % C18 :1 ; 8 % C18 :2) présente les mêmes caractéristiques physicochimiques que le saindoux, avec une odeur proche de celle du jambon sec (19 COV aromatiques identifiés présents dans les arômes majoritaires de jambon). La fraction protéines solubilisées, obtenue sous forme de lyophilisat après concentration de la phase aqueuse (rendement : 8 % ; protéines : 52 % dont 29 % d'acides aminés libres ; matière minérale : 29 % dont 90 % NaCl, lipides : 3 %), contient aussi des glucosaminoglycanes sulfatés (GAGs : 3,4 %). Ces caractéristiques de composition, associées à ses propriétés épaississantes et gélifiantes, adhésives et stabilisantes d'émulsion, font de cette fraction minoritaire du procédé de fractionnement aqueux du coproduit de jambon sec, un extrait aux multiples applications à forte valeur ajoutée (source de peptones pour la culture de champignons et de levures, adhésif et liant naturel, ingrédient de formulation alimentaire nutracétique et cosmétique). ABSTRACT : The ham production by-product comes from the deboning of dressed, salted, dried and refined pork leg. It consists of more than 85% of bone and associated tissues (cartilage, ligaments, tendons). Hammer mill crushing allows homogenizing the by-product into pieces smaller than 8 cm (> 90% between 40 and 80 mm).Dry matter chemical composition of the blend; (77 ± 3% DM) is 33 ± 5% protein (89% collagen, 14% of watersoluble proteins, 6% free amino acid), 31 ± 3% lipids (triglycerides: 70% diglycerides: 3.5%; free fatty acids: 11%; saturated / unsaturated: 0.87; 24% C16: 0; 13% C18: 0; 2% C16: 1; 38% C18: 1; 4% C18: 2) and 26 ± 4% mineral matter (calcium phosphate 88%, 9% NaCl). Lipids and proteins aqueous extraction of the by-product is studied in an agitated contactor reactor. The solid raffinate was separated by hot filtration to an aggregate and the fat is separated by cold decantation.The study of the influence of main factors of the liquid / solid extraction (contact time: 30 to 90 min, temperature: 40 to 90 °C; ratio water / by-product: 4 to 10) through the implementation of an experimental design, highlights the effects of proteins dissolution and coagulation on lipid output and decantation as fat matter.By pilot scale implementation (64 kg of crushed by-product of dry-cured ham, 207 kg of water, 30 min at 90 ° C in agitated contactor), the aqueous fractionation process leads, by centrifugal filtration and drying, to a stable aggregate (yield: 59%; mineral matter: 41%; protein 43%; lipids: 16%), source of calcium phosphate (95% of the mineral) and gelatin or bone glue (88% collagenous protein).The decanted fat fraction (yield: 24%; lipids: 93%; triglycerides: 75%; diglycerides: 4% free fatty acids: 7%; saturated / unsaturated: 0.82%; 37% C16: 0; 15% C18: 0; 2% C16: 1; 44% C18: 1; 8% C18: 2) has the same physicochemical characteristics as lard, with an odor similar to that of dry-cured ham (19 identified aromatic VOC part of ham main flavors). The solubilized protein fraction, obtained as a lyophilized extract after concentration of the aqueous phase (yield: 8%; protein: 52% with 29% of free amino acids; mineral matter: 29%, with 90% NaCl, lipids: 3%), also contains sulfated glycosaminoglycans (GAGs: 3.4%). These composition characteristics, associated with its thickening and gelling properties, adhesive and stabilizing for emulsion, transforms this minor fraction of the aqueous fractionation process of the dry-cured ham byproduct, in an high added value multiple applications extract (source of peptones for culture for fungi and yeasts, a natural and binding adhesive, ingredient for food nutraceutic and cosmetic formulation)

MicroRNAs in Honey Bee Caste Determination

The cellular mechanisms employed by some organisms to produce contrasting morphological and reproductive phenotypes from the same genome remains one of the key unresolved issues in biology. Honeybees (Apis mellifera) use differential feeding and a haplodiploid sex determination system to generate three distinct organismal outcomes from the same genome. Here we investigate the honeybee female and male caste-specific microRNA and transcriptomic molecular signatures during a critical time of larval development. Both previously undetected and novel miRNAs have been discovered, expanding the inventory of these genomic regulators in invertebrates. We show significant differences in the microRNA and transcriptional profiles of diploid females relative to haploid drone males as well as between reproductively distinct females (queens and workers). Queens and drones show gene enrichment in physio-metabolic pathways, whereas workers show enrichment in processes associated with neuronal development, cell signalling and caste biased structural differences. Interestingly, predicted miRNA targets are primarily associated with non-physio-metabolic genes, especially neuronal targets, suggesting a mechanistic disjunction from DNA methylation that regulates physio-metabolic processes. Accordingly, miRNA targets are under-represented in methylated genes. Our data show how a common set of genetic elements are differentially harnessed by an organism, which may provide the remarkable level of developmental flexibility required

Light-inducible transcriptomic and epigenomic changes underlying brain plasticity in honeybees

Dissertação de Mestrado apresentada à Faculdade de Letras da Universidade de Coimbra.Pretendemos, com esta dissertação, fundamentar a categorização como ritual laico da Arte como Veículo, propósito da última fase do trabalho de Jerzy Grotowski, discutindo os modos particulares dessa categorização. No primeiro capítulo expomos, resumidamente, o percurso artístico de Grotowski e as principais influências que marcaram o seu pensamento. Explicamos os conceitos fundamentais que estruturam a sua prática artística e ensaiamos uma definição para a Arte como Veículo. Finalizamos o capítulo com uma discussão sobre a categorização como ritual das criações performativas produzidas segundo este modelo. No segundo capítulo abordamos o ritual como performance e discutimos a origem ritual dos géneros estéticos performativos. Apresentamos definições operativas de ritual e performance e abordamos os principais aspectos do ritual enquanto performance, recorrendo sobretudo à Antropologia da Performance de Victor Turner. No final do capítulo exploramos a categorização da Arte como Veiculo como ritual, à luz da Antropologia da Performance. No terceiro capítulo fazemos um estudo sumário de um ritual tradicional, o culto dos Theyyams do Norte Malabar, na Índia. Contextualizamos e descrevemos o ritual e algumas das suas particularidades. Relatamos as impressões recolhidas durante um estudo de campo na região, à luz da experiência da Arte como Veículo e dos aspectos realçados pela Antropologia da Performance. Concluímos com a enumeração de resultados obtidos e a confrontação entre o que se apurou na investigação sobre a Arte como Veículo e as impressões recolhidas no estudo do Theyyam, apontando-se desenvolvimentos que possam futuramente confirmar ou reforçar os resultados agora apresentados.With this dissertation I intend to justify the categorization as a secular ritual of the Art as Vehicle, the last phase of Jerzy Grotowski's work, discussing the particular ways of this categorization. In the first chapter I briefly expose the artistic course of Grotowski and the main influences that marked his thought. I explain the fundamental concepts that structure his artistic practice and I essay a definition for Art as Vehicle. I end the chapter with a discussion of the categorization as a ritual of performing works created according to this model. In the second chapter I address the ritual as performance and briefly discuss the ritual origin of performative aesthetic genres. I propose operative definitions for ritual and performance and I enumerate the main aspects of ritual as performance, calling upon, mostly, the Anthropology of Performance from Victor Turner. At the end of the chapter I explore the categorization as ritual of Art as Vehicle at the light of the Anthropology of Performance. In the third chapter I make a summary study of a traditional ritual, the worship of Theyyams in the North Malabar, India. I contextualize and describe the ritual and some of its special features. I report the impressions gathered during a field study in the region, at the light of the experience of Art as Vehicle and of the aspects highlighted by the Anthropology of Performance. I conclude with an enumeration of results and the confrontation between what was found in the research on Art as Vehicle and the impressions gathered in the study of Theyyam, pointing out future developments that may confirm or strengthen the results now presented

Epigenetic regulation of the honey bee transcriptome: unravelling the nature of methylated genes

Background: Epigenetic modification of DNA via methylation is one of the key inventions in eukaryotic evolution. It provides a source for the switching of gene activities, the maintenance of stable phenotypes and the integration of environmental and genomic signals. Although this process\ud is widespread among eukaryotes, both the patterns of methylation and their relevant biological roles not only vary noticeably in different lineages, but often are poorly understood. In addition, the evolutionary origins of DNA methylation in multicellular organisms remain enigmatic. Here we used a new 'epigenetic' model, the social honey bee Apis mellifera, to gain insights into the significance of methylated genes.\ud \ud Results: We combined microarray profiling of several tissues with genome-scale bioinformatics and bisulfite sequencing of selected genes to study the honey bee methylome. We find that around 35% of the annotated honey bee genes are expected to be methylated at the CpG dinucleotides by a highly conserved DNA methylation system. We show that one unifying feature of the methylated genes in this species is their broad pattern of expression and the associated 'housekeeping' roles. In contrast, genes involved in more stringently regulated spatial or temporal functions are predicted to be un-methylated.\ud \ud Conclusion: Our data suggest that honey bees use CpG methylation of intragenic regions as an epigenetic mechanism to control the levels of activity of the genes that are broadly expressed and might be needed for conserved core biological processes in virtually every type of cell. We discuss the implications of our findings for genome-scale regulatory network structures and the evolution\ud of the role(s) of DNA methylation in eukaryotes. Our findings are particularly important in the context of the emerging evidence that environmental factors can influence the epigenetic settings of some genes and lead to serious metabolic and behavioural disorders

Etude d'un nouveau procédé de fractionnement des co-produits de fabrication de jambon sec et des propriétés physico-chimiques et fonctionnelles des extraits et raffinats

Le coproduit de fabrication de jambon sec est issu de l'opération de désossage de la cuisse de porc parée, salée, séchée et affinée. Il est constitué à plus de 85 % d'os et de tissus associés (cartilages, ligaments, tendons). Le concassage au broyeur à marteau permet d'homogénéiser le coproduit en morceaux de taille inférieure à 8 cm (> 90 % compris entre 40 et 80 mm). La composition chimique de la matière sèche du mélange (77 +- 3 % de MS) est de 33 +- 5 % en protéines (89 % de collagène, 14 % de protéines hydrosolubles, 6 % d'acide aminés libres), 31 +- 3 % en lipides (triglycérides : 70 % ; diglycérides : 3,5 % ; acides gras libres : 11 % ; saturé/insaturé : 0,87 ; 24 % C16 :0 ; 13 % C18 :0 ; 2 % C16 :1 ; 38 % C18 :1 ; 4 % C18 :2) et 26 +- 4 % de matière minérale (phosphate de calcium 88 % ; NaCl 9 %). L'extraction aqueuse des lipides et des protéines du coproduit est étudiée en contacteur agité. Le raffinat solide est séparé par filtration à chaud sous forme de granulat et la matière grasse entraînée est séparée par décantation à froid. L'étude de l'influence des principaux facteurs de l'extraction liquide/solide (temps de contact : 30 à 90 min, température : 40 à 90C ; ratio eau/coproduit : 4 à 10) grâce à la réalisation d'un plan d'expérience met en évidence les effets de la solubilisation et la coagulation des protéines sur l'entraînement des lipides et leur décantation sous forme de matière grasse. Mis en oeuvre à l'échelle pilote (64 kg de coproduit de jambon sec concassé, 207 kg d'eau, 30 min à 90C en contacteur agité), le procédé de fractionnement aqueux conduit par filtration centrifuge et séchage à un granulat stable (rendement : 59 % ; matière minérale : 41 % ; protéines : 43 % ; lipides : 16 %), source de phosphate de calcium (95 % de la matière minérale) et de gélatine ou de colle d'os (88 % de protéines de nature collagénique). La fraction matière grasse décantée (rendement : 24 % ; lipides : 93 % ; triglycérides : 75 % ; diglycérides : 4 % ; acides gras libres : 7 % ; saturé/insaturé : 0,82 % ; 37 % C16 :0 ; 15 % C18 :0 ; 2 % C16 :1 ; 44 % C18 :1 ; 8 % C18 :2) présente les mêmes caractéristiques physicochimiques que le saindoux, avec une odeur proche de celle du jambon sec (19 COV aromatiques identifiés présents dans les arômes majoritaires de jambon). La fraction protéines solubilisées, obtenue sous forme de lyophilisat après concentration de la phase aqueuse (rendement : 8 % ; protéines : 52 % dont 29 % d'acides aminés libres ; matière minérale : 29 % dont 90 % NaCl, lipides : 3 %), contient aussi des glucosaminoglycanes sulfatés (GAGs : 3,4 %). Ces caractéristiques de composition, associées à ses propriétés épaississantes et gélifiantes, adhésives et stabilisantes d'émulsion, font de cette fraction minoritaire du procédé de fractionnement aqueux du coproduit de jambon sec, un extrait aux multiples applications à forte valeur ajoutée (source de peptones pour la culture de champignons et de levures, adhésif et liant naturel, ingrédient de formulation alimentaire nutracétique et cosmétique).The ham production by-product comes from the deboning of dressed, salted, dried and refined pork leg. It consists of more than 85% of bone and associated tissues (cartilage, ligaments, tendons). Hammer mill crushing allows homogenizing the by-product into pieces smaller than 8 cm (> 90% between 40 and 80 mm).Dry matter chemical composition of the blend; (77 +- 3% DM) is 33 +- 5% protein (89% collagen, 14% of watersoluble proteins, 6% free amino acid), 31 +- 3% lipids (triglycerides: 70% diglycerides: 3.5%; free fatty acids: 11%; saturated / unsaturated: 0.87; 24% C16: 0; 13% C18: 0; 2% C16: 1; 38% C18: 1; 4% C18: 2) and 26 +- 4% mineral matter (calcium phosphate 88%, 9% NaCl). Lipids and proteins aqueous extraction of the by-product is studied in an agitated contactor reactor. The solid raffinate was separated by hot filtration to an aggregate and the fat is separated by cold decantation.The study of the influence of main factors of the liquid / solid extraction (contact time: 30 to 90 min, temperature: 40 to 90 C; ratio water / by-product: 4 to 10) through the implementation of an experimental design, highlights the effects of proteins dissolution and coagulation on lipid output and decantation as fat matter.By pilot scale implementation (64 kg of crushed by-product of dry-cured ham, 207 kg of water, 30 min at 90 C in agitated contactor), the aqueous fractionation process leads, by centrifugal filtration and drying, to a stable aggregate (yield: 59%; mineral matter: 41%; protein 43%; lipids: 16%), source of calcium phosphate (95% of the mineral) and gelatin or bone glue (88% collagenous protein).The decanted fat fraction (yield: 24%; lipids: 93%; triglycerides: 75%; diglycerides: 4% free fatty acids: 7%; saturated / unsaturated: 0.82%; 37% C16: 0; 15% C18: 0; 2% C16: 1; 44% C18: 1; 8% C18: 2) has the same physicochemical characteristics as lard, with an odor similar to that of dry-cured ham (19 identified aromatic VOC part of ham main flavors). The solubilized protein fraction, obtained as a lyophilized extract after concentration of the aqueous phase (yield: 8%; protein: 52% with 29% of free amino acids; mineral matter: 29%, with 90% NaCl, lipids: 3%), also contains sulfated glycosaminoglycans (GAGs: 3.4%). These composition characteristics, associated with its thickening and gelling properties, adhesive and stabilizing for emulsion, transforms this minor fraction of the aqueous fractionation process of the dry-cured ham byproduct, in an high added value multiple applications extract (source of peptones for culture for fungi and yeasts, a natural and binding adhesive, ingredient for food nutraceutic and cosmetic formulation).TOULOUSE-ENSIACET (315552325) / SudocSudocFranceF

Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome

Context-dependent gene expression in eukaryotes is controlled by several mechanisms including cytosine methylation that primarily occurs in the CG dinucleotides (CpGs). However, less frequent non-CpG asymmetric methylation has been found in various cell types, such as mammalian neurons, and recent results suggest that these sites can repress transcription independently of CpG contexts. In addition, an emerging view is that CpG hemimethylation may arise not only from deregulation of cellular processes but also be a standard feature of the methylome. Here, we have applied a novel approach to examine whether asymmetric CpG methylation is present in a sparsely methylated genome of the honeybee, a social insect with a high level of epigenetically driven phenotypic plasticity. By combining strand-specific ultra-deep amplicon sequencing of illustrator genes with whole-genome methylomics and bioinformatics, we show that rare asymmetrically methylated CpGs can be unambiguously detected in the honeybee genome. Additionally, we confirm differential methylation between two phenotypically and reproductively distinct castes, queens and workers, and offer new insight into the heterogeneity of brain methylation patterns. In particular, we challenge the assumption that symmetrical methylation levels reflect symmetry in the underlying methylation patterns and conclude that hemimethylation may occur more frequently than indicated by methylation levels. Finally, we question the validity of a prior study in which most of cytosine methylation in this species was reported to be asymmetric