Cocrystallisation involving the thioamide, amide and imide functional groups

The work presented in this dissertation focused on the development and characterisation of novel cocrystals that incorporated the thioamide, amide and imide functional groups. A particular emphasis was placed on the characterisation of these cocrystals by single crystal X-ray diffraction methods. In Chapter One a summary of the intermolecular interactions utilised in this work and a short review of the solid state and multicomponent systems is provided. A brief introduction to the ways in which different multicomponent systems can be distinguished, crystal engineering strategies and a number of cocrystal applications highlights the importance the understanding of intermolecular interactions can have on the physical and chemical properties of crystalline materials. Chapter Two is the first Results and Discussion chapter and includes an introduction that is specific to the chapter. The main body of this work focuses on the primary aromatic thioamide functional group and its propensity to cocrystallise with a number of sulfoxides. Unlike the amide functional group, thioamides are not commonly employed in cocrystallisation studies. This chapter presents the first direct comparison between the cocrystallisation abilities of these two functional groups and the intermolecular hydrogen bonding interactions present in the cocrystal structures are examined. Chapter Three describes the crystal landscape of a short series of secondary aromatic amides and their analogous thioamides. Building on the results obtained in Chapter Two, a cocrystal screen of the secondary thioamides with the sulfoxide functional group was carried out in order to determine the effect removing a hydrogen bond had on the supramolecular synthons observed in the cocrystals. These secondary thioamides are also utilised in Chapter Four, which examines their halogen bonding capabilities with two organoiodine coformers: 1,2- and 1,4-diiodotetrafluorobenzene. Chapter Five explores the cocrystallisation abilities of three related cyclic imides as coformers for cocrystallisation with a range of commonly used coformers. Chapter Six is an overall conclusions chapter that highlights the findings of the results presented in Chapters Two to Five. Chapter Seven details the instrument and experimental data for the compounds and cocrystals discussed in the Results and Discussion Chapters. The accompanying CD contains all of the crystallographic data in .cif format for the novel single crystal structures characterised in this work.

Seawater carbonate chemistry and calcification during a tropical lagoon study at SW lagoon, New Caledonia, 1991

A selective chemical photosynthesis inhibitor, DCMU (Dichorophenyl-dimethylurea), dissolved in DMSO (Dimethyl sulfoxide) was substituted for the dark incubation method commonly used to measure the oxygen consumption in metabolic and primary production studies. We compared oxygen fluxes during light incubations with DCMU and dark incubations procedure, on soft bottom benthos. For this purpose, we studied the effects of different DCMU concentrations. A concentration of 5 · 10-5 mol l-1 inside a clear incubation enclosure completely inhibits photosynthesis without affecting the metabolism of soft bottom benthos.

Bulk and amino acid parameters of core SO188-342KL from the Northern Bay of Bengal for the last 18 ka

The Northern Bay of Bengal (NBoB) is a globally important region for deep-sea organic matter (OM) deposition due to massive fluvial discharge from the Ganges-Brahmaputra-Meghna (G-B-M) rivers and moderate to high surface productivity. Previous studies have focused on carbon burial in turbiditic sediments of the Bengal Fan. However, little is known about the storage of carbon in pelagic and hemipelagic sediments of the Bay of Bengal over millennial time scales. This study presents a comprehensive history of OM origin and fate as well as a quantification of carbon sediment storage in the Eastern Bengal Slope (EBS) during the last 18 ka. Bulk organic proxies (TOC, TIC, TN, d13CTOC, d15NTN) and content and composition of total hydrolysable amino acids (THAA) in a sediment core (SO188-342KL) from the EBS were analyzed. Three periods of high OM accumulation were identified: the Late Glacial (LG), the Bölling/Alleröd (B/A), and the Early Holocene Climatic Optimum (EHCO). Lower eustatic sea level before 15 ka BP allowed a closer connection between the EBS and the fluvial debouch, favoring high terrestrial OM input to the core site. This connection was progressively lost between 15 and 7 ka BP as sea level rose to its present height and terrestrial OM input decreased considerably. Export and preservation of marine OM was stimulated during periods of summer monsoon intensification (B/A and EHCO) as a consequence of higher surface productivity enhanced by cyclonic-eddy nutrient pumping and fluvial nutrient delivery into the photic zone. Changes in the THAA composition indicate that the marine plankton community structure shifted from calcareous-dominated before 13 ka BP to siliceous-dominated afterwards. They also indicate that the relative proportion of marine versus terrestrial OM deposited at site 342KL was primarily driven by relative sea level and enlarged during the Holocene. The ballasting effect of lithogenic particles during periods of high coastal proximity and/or enhanced fluvial discharge promoted the export and preservation of OM. The high organic carbon accumulation rates in the EBS during the LG (18-17 ka BP) were 5-fold higher than at present and comparable to those of glacial upwelling areas. Despite the differences in sediment and OM transport and storage among the Western and Eastern sectors of the NBoB, this region remains important for global carbon sequestration during sea level low-stands. In addition, the summer monsoon was a key promotor of terrestrial and marine OM export to the deep-ocean, highlighting its relevance as regulator of the global carbon budget.

Seawater carbonate chemistry, Mg/Ca, Sr/Ca, oxygen production and calcification rate during experiments with coral Pocillopora damicornis, 2011

The Sr/Ca of aragonitic coral skeletons is a commonly used palaeothermometer. However skeletal Sr/Ca is typically dominated by weekly-monthly oscillations which do not reflect temperature or seawater composition and the origins of which are currently unknown. To test the impact of transcellular Ca2+ transport processes on skeletal Sr/Ca, colonies of the branching coral, Pocillopora damicornis, were cultured in the presence of inhibitors of Ca-ATPase (ruthenium red) and Ca channels (verapamil hydrochloride). The photosynthesis, respiration and calcification rates of the colonies were monitored throughout the experiment. The skeleton deposited in the presence of the inhibitors was identified (by 42Ca spike) and analysed for Sr/Ca and Mg/Ca by secondary ion mass spectrometry. The Sr/Ca of the aragonite deposited in the presence of either of the inhibitors was not significantly different from that of the solvent (dimethyl sulfoxide) control, although the coral calcification rate was reduced by up to 66% and 73% in the ruthenium red and verapamil treatments, respectively. The typical precision (95% confidence limits) of mean Sr/Ca determinations within any treatment was <±1% and differences in skeletal Sr/Ca between treatments were correspondingly small. Either Ca-ATPase and Ca channels transport Sr2+ and Ca2+ in virtually the same ratio in which they are present in seawater or transcellular processes contribute little Ca2+ to the skeleton and most Ca is derived from seawater transported directly to the calcification site. Variations in the activities of Ca-ATPase and Ca-channels are not responsible for the weekly-monthly Sr/Ca oscillations observed in skeletal chronologies, assuming that the specificities of Ca transcellular transport processes are similar between coral genera.

Evidence for methane production by the marine algae Emiliania huxleyi

Methane (CH4), an important greenhouse gas that affects radiation balance and consequently the earth's climate, still has uncertainties in its sinks and sources. The world's oceans are considered to be a source of CH4 to the atmosphere, although the biogeochemical processes involved in its formation are not fully understood. Several recent studies provided strong evidence of CH4 production in oxic marine and freshwaters, but its source is still a topic of debate. Studies of CH4 dynamics in surface waters of oceans and large lakes have concluded that pelagic CH4 supersaturation cannot be sustained either by lateral inputs from littoral or benthic inputs alone. However, regional and temporal oversaturation of surface waters occurs frequently. This comprises the observation of a CH4 oversaturating state within the surface mixed layer, sometimes also termed the "oceanic methane paradox". In this study we considered marine algae as a possible direct source of CH4. Therefore, the coccolithophore Emiliania huxleyi was grown under controlled laboratory conditions and supplemented with two 13C-labeled carbon substrates, namely bicarbonate and a position-specific 13C-labeled methionine (R-S-13CH3). The CH4 production was 0.7 µg particular organic carbon (POC) g−1 d−1, or 30 ng g−1 POC h−1. After supplementation of the cultures with the 13C-labeled substrate, the isotope label was observed in headspace CH4. Moreover, the absence of methanogenic archaea within the algal culture and the oxic conditions during CH4 formation suggest that the widespread marine algae Emiliania huxleyi might contribute to the observed spatially and temporally restricted CH4 oversaturation in ocean surface waters.

Evidence for methane production by the marine algae Emiliania huxleyi

Methane (CH4), an important greenhouse gas that affects radiation balance and consequently the earth's climate, still has uncertainties in its sinks and sources. The world's oceans are considered to be a source of CH4 to the atmosphere, although the biogeochemical processes involved in its formation are not fully understood. Several recent studies provided strong evidence of CH4 production in oxic marine and freshwaters, but its source is still a topic of debate. Studies of CH4 dynamics in surface waters of oceans and large lakes have concluded that pelagic CH4 supersaturation cannot be sustained either by lateral inputs from littoral or benthic inputs alone. However, regional and temporal oversaturation of surface waters occurs frequently. This comprises the observation of a CH4 oversaturating state within the surface mixed layer, sometimes also termed the "oceanic methane paradox". In this study we considered marine algae as a possible direct source of CH4. Therefore, the coccolithophore Emiliania huxleyi was grown under controlled laboratory conditions and supplemented with two 13C-labeled carbon substrates, namely bicarbonate and a position-specific 13C-labeled methionine (R-S-13CH3). The CH4 production was 0.7 µg particular organic carbon (POC) g−1 d−1, or 30 ng g−1 POC h−1. After supplementation of the cultures with the 13C-labeled substrate, the isotope label was observed in headspace CH4. Moreover, the absence of methanogenic archaea within the algal culture and the oxic conditions during CH4 formation suggest that the widespread marine algae Emiliania huxleyi might contribute to the observed spatially and temporally restricted CH4 oversaturation in ocean surface waters.

Insight into the mechanism of galactokinase: role of a critical glutamate residue and helix/coil transitions

Galactokinase, the enzyme which catalyses the first committed step in the Leloir pathway, has attracted interest due to its potential as a biocatalyst and as a possible drug target in the treatment of type I galactosemia. The mechanism of the enzyme is not fully elucidated. Molecular dynamics (MD) simulations of galactokinase with the active site residues Arg-37 and Asp-186 altered predicted that two regions (residues 174-179 and 231-240) had different dynamics as a consequence. Interestingly, the same two regions were also affected by alterations in Arg-105, Glu-174 and Arg- 228. These three residues were identified as important in catalysis in previous computational studies on human galactokinase. Alteration of Arg-105 to methionine resulted in a modest reduction in activity with little change in stability. When Arg-228 was changed to methionine, the enzyme’s interaction with both ATP and galactose was affected. This variant was significantly less stable than the wild-type protein. Changing Glu-174 to glutamine (but not to aspartate) resulted in no detectable activity and a less stable enzyme. Overall, these combined in silico and in vitro studies demonstrate the importance of a negative charge at position 174 and highlight the critical role of the dynamics in to key regions of the protein. We postulate that these regions may be critical for mediating the enzyme’s structure and function. 

Development and application of sensitive genome-wide platforms to study the genetic and epigenetic (DNA methylation) makeup of gametes and early bovine embryos

Pour ce projet, nous avons développé une plateforme pour l’analyse pangénomique de la méthylation de l’ADN chez le bovin qui est compatible avec des échantillons de petites tailles. Cet outil est utilisé pour étudier les caractéristiques génétiques et épigénétiques (méthylation de l’ADN) des gamètes soumis aux procédures de procréation médicalement assisitée et des embryons précoces. Dans un premier temps, une plateforme d’analyse de biopuces spécifiques pour l’étude de la méthylation de l’ADN chez l’espèce bovine a été développée. Cette plateforme a ensuite été optimisée pour produire des analyses pangénomiques de méthylation de l’ADN fiables et reproductibles à partir d’échantillons de très petites tailles telle que les embryons précoces (≥ 10 ng d’ADN a été utilisé, ce qui correspond à 10 blastocystes en expansion). En outre, cet outil a permis d’évaluer de façon simultanée la méthylation de l’ADN et le transcriptome dans le même échantillon, fournissant ainsi une image complète des profils génétiques et épigénétiques (méthylation de l’ADN). Comme preuve de concept, les profils comparatifs de méthylation de l’ADN spermatique et de blastocystes bovins ont été analysés au niveau de l’ensemble du génome. Dans un deuxième temps, grâce à cette plateforme, les profils globaux de méthylation de l’ADN de taureaux jumeaux monozygotes (MZ) ont été analysés. Malgré qu’ils sont génétiquement identiques, les taureaux jumeaux MZ ont des descendants avec des performances différentes. Par conséquent, l’hypothèse que le profil de méthylation de l’ADN spermatique de taureaux jumeaux MZ est différent a été émise. Dans notre étude, des différences significatives entre les jumeaux MZ au niveau des caractéristiques de la semence ainsi que de la méthylation de l’ADN ont été trouvées, chacune pouvant contribuer à l’obtention de performances divergentes incongrues des filles engendrées par ces jumeaux MZ. Dans la troisième partie de ce projet, la même plateforme a été utilisée pour découvrir les impacts d’une supplémentation à forte concentration en donneur de méthyle universel sur les embryons précoces bovins. La supplémentation avec de grandes quantités d’acide folique (AF) a été largement utilisée et recommandée chez les femmes enceintes pour sa capacité bien établie à prévenir les malformations du tube neural chez les enfants. Cependant, plus récemment, plusieurs études ont rapporté des effets indésirables de l’AF utilisé à des concentrations élevées, non seulement sur le développement de l’embryon, mais aussi chez les adultes. Au niveau cellulaire, l’AF entre dans le métabolisme monocarboné, la seule voie de production de S-adénosyl méthionine (SAM), un donneur universel de groupements méthyles pour une grande variété de biomolécules, y compris l’ADN. Par conséquent, pour résoudre cette controverse, une forte dose de SAM a été utilisée pour traiter des embryons produits in vitro chez le bovin. Ceci a non seulement permis d’influencer le phénotype des embryons précoces, mais aussi d’avoir un impact sur le transcriptome et le méthylome de l’ADN. En somme, le projet en cours a permis le développement d’une plateforme d’analyse de la méthylation de l’ADN à l’échelle du génome entier chez le bovin à coût raisonnable et facile à utiliser qui est compatible avec les embryons précoces. De plus, puisque c’est l’une des premières études de ce genre en biologie de la reproduction bovine, ce projet avait trois objectifs qui a donné plusieurs nouveaux résultats, incluant les profils comparatifs de méthylation de l’ADN au niveau : i) blastocystes versus spermatozoïdes ; ii) semence de taureaux jumeaux MZ et iii) embryons précoces traités à de fortes doses de SAM versus des embryons précoces non traités.

Drying kinetics, biochemical and functional properties of products in convective drying of anchovy (Engraulis Anchoita) fillets

The aim of this work was to study the convective drying of anchovy (Engraulis anchoita) fillets and to evaluate the final product characteristics through its biochemical and functional properties. The drying temperatures were of 50, 60 and 70°C, and the fillet samples were dried with the skins down (with air flow one or the two sides) and skins up (with air flow one side). The drying experimental data were analyzed by Henderson–Pabis model, which showed a good fit (R2 > 0.99 and REQM < 0.05). The moisture effective diffusivity values ranged from 4.1 10–10 to 8.6 10–10 m2 s−1 with the skin down and 2.2 10–10 to 5.5 10–10 m2 s−1 with the skin up, and the activation energy values were 32.2 and 38.4 kJ mol−1, respectively. The product characteristics were significantly affected (p < 0.05) by drying operation conditions. The lower change was in drying at 60°C with air flow for two sides of the samples and skin up. In this condition, the product showed solubility 22.3%; in vitro digestibility 87.4%; contents of available lysine and methionine 7.21 and 2.64 g 100 g−1, respectively; TBA value 1.16 mgMDA kg−1; specific antioxidant activity was 1.91 mMDPPH g−1 min−1, and variation total color was 10.72.

Obtenção de concentrado proteico do farelo de arroz e avaliação das propriedades químicas e funcionais

Esta dissertação é composta por 5 artigos.

Dinâmica de nitrogênio em cultivo heterotrófico a partir de cianobactéria sob o escopo de biorrefinarias agroindustriais

O trabalho teve por objetivo avaliar a dinâmica de nitrogênio, em cultivo heterotrófico, a partir da cianobactéria Aphanothece microscopica Nägeli, sob o escopo de uma biorrefinaria. Neste sentido, foi avaliada a contribuição dos compostos nitrogenados não proteicos, na dinâmica de distribuição do nitrogênio, na biomassa gerada pelo micro-organismo em estudo, quando cultivado em sistema autotrófico e heterotrófico. Para o cultivo em condições autotróficas, foi utilizado o meio padrão BG-11, enquanto que, para o cultivo em condições heterotróficas, foi empregado o efluente da indústria de laticínios. Inicialmente, foi avaliada a contribuição dos pigmentos na fração nitrogenada não proteica tendo como base dois experimentos. No primeiro experimento foi selecionada a melhor condição para a produção de pigmentos, expressos pela clorofila-a em sistema heterotrófico, tendo como base os parâmetros C/N (20, 40 e 60), N/P (5, 10 e 15) e concentração de inóculo (100, 200 e 300 mg.L-1), mediante um planejamento fatorial 23 . Os experimentos foram conduzidos em biorreator heterotrófico a 20°C, pH 7,6 e aeração contínua de 1VVM. A melhor condição de produção de pigmento foi indicada como sendo a 200 mg.L-1 de concentração celular, razões C/N 20 e N/P 10. Com base nestes resultados, um segundo experimento foi delineado, visando avaliar a contribuição de pigmentos na fração de nitrogênio não proteico, bem como avaliar a produção de clorofila-a e ficobiliproteínas (ficocianina, aloficocianina e ficoeritrina), sob influência da luz e do meio de cultivo. Foi possível destacar teores superiores de ficobiliproteínas na biomassa gerada no cultivo heterotrófico. No entanto, com notada diferença (p≤0,05) nos teores de clorofila-a, quando são comparadas as concentrações na biomassa de meios autotróficos (10,7 mg.g-1) e heterotróficos (1,0 mg.g-1). Fato este compensado pelo menor tempo de cultivo registrado para atingir o final do experimento, quando o micro-organismo é cultivado em condições heterotróficas. Fica demonstrado assim, ainda, a importante contribuição dos pigmentos na fração de nitrogênio não proteico. Na sequência, um terceiro e quarto experimentos foram delineados, visando avaliar a influência do nitrogênio inorgânico intracelular na fração não proteica e na produção de proteína, assim como a caracterização da fração proteica quanto ao seu perfil aminoacídico. O estudo da dinâmica do nitrogênio intracelular demonstrou que o N-NH4 + foi a forma nitrogenada predominante, perfazendo importante fração de N-NP, sendo, portanto, os teores de N-NP significativamente dependente dos teores de pigmentos e nitrogênio intracelular. Os aminogramas das biomassas geradas pelos cultivos autotróficos e heterotróficos indicaram como aminoácidos majoritários o ácido glutâmico e aspártico, seguidos por valina, leucina e isoleucina, e como minoritários, lisina, glicina e metionina. O perfil aminoacídico caracterizou-se por apresentar aminoácidos essenciais como isoleucina, metionina + cisteína, fenilalanina + tirosina, valina e treonina em concentrações superiores ao preconizado pela FAO/WHO. A caracterização da fração proteica quanto ao perfil aminoacídico qualificou esta biomassa como fonte potencial de proteína. Os resultados obtidos neste trabalho demonstram a influência e dinâmica de distribuição dos compostos nitrogenados em Aphanothece microscopica Nägeli. Fica demonstrado, ainda, que a implementação do conceito de biorrefino, no tipo de agroindústria estudado, poderá representar importantes possibilidades de aproveitamento sustentável do efluente gerado.

A study of fish ice cream formulation by use of silver carp proteins instead of milk proteins

Fish is a valuable nutritional source witch use of it in daily meal has a beneficial role on nutritional needs supply and also causes mental and physical health especially in people who have protein and food deficiencies. Unfortunately, per capita consumption of sea foods in Iran is 5.5Kg witch is very lower than world standards. So, study on fish ice cream formulation, by use of fish protein concentrate (FPC) instead of milk protein, had done to make variation in sea foods products and also increase per capita consumption of these kinds of foods. FPC has very high protein concentration and a lot of necessary Also it's protein is very digestible amino acids like lysine and methionine with highly biological value and it's PER in compare with casein PER is high. At first fish protein concentrate type A produced from silver carp in three steps by the extraction with isopropyl alcohol solvent and heat. Microbiological and physicochemical specifications of produced FPC by rules of FDA and FAO were accepted. Finally according to panel test results, substitution of 30 percent of milk with FPC is acceptable. Also microbiological and physicochemical specifications of product were tested and results in compare with national standards of Iran were accepted.

Odour flux from litter of broiler chickens fed diets differing in protein levels and additives

The effect of dietary crude protein (CP) and additives on odour flux from broiler litter was investigated using 180 day-old Ross 308 male chicks randomly allocated to five dietary treatments with three replications of 12 birds each. A 5×3 factorial arrangement of treatments was employed. Factors were: diet (low CP, high CP, high CP+antibiotic, high CP+probiotic, high CP+saponin) and age (15, 29, 35 days). Low CP (LCP) and high CP (HCP) diets differed in CP levels by 4.5-5%. The low CP diets were supplemented with L-valine, L-isoleucine, L-arginine, L-lysine, D,L-methionine and L-threonine. The antibiotic used was Zn Bacitracin, the probiotic was a blend of three Bacillus subtilis strains and the saponin came from a blend of Yucca and Quillaja. Odorants were measured from litter headspace using a flux hood and selective ion flow tube mass spectrometry (SIFT-MS). Results were log tranformed and analysed by two-way ANOVA with repeated measures using JMP statistical software v.8, and means were separated by Tukey's HSD test at P<0.05.The results showed that LCP group produced lower flux of dimethyl amine, trimethyl amine, H2S, NH3 and phenol in litter compared to HCP group (P<0.05). Similarly, HCP+probiotic group produced lower flux of H2S (P<0.05) and HCP+saponin group produced lower flux of trimethylamine and phenol in litter compared to HCP group (P<0.05). The dietary treatments tended (P=0.065) to have higher flux of methanethiol in HCP group compared to others. There was a diet x age interaction for litter flux of diacetyl, acetoin, 3-methyl-1-butanol, 3-methylbutanal, ethanethiol, propionic acid and hexane (P<0.05). Concentrations of diacetyl, acetoin, propionic acid and hexane in litter were higher from LCP group compared to all other treatments on d 35 (P<0.05) but not on days 15 and 29. Thus, the low CP diet, Bacillus subtilis based probiotic and Yucca/Quillaja based saponin were effective in reducing the emissions of some key odorants from broiler litter.

Catalytic dehydration of glycerol to acrolein: catalysts and processes

The valorization of glycerol has been widely studied notably due to the oversupply of the latter from biodiesel production. Among the different upgrading reactions, dehydration to acrolein is of high interest due to the importance of acrolein as an intermediate for polymer industry (via acrylic acid) and for feed additive (synthon for DL-methionine). It is known that acrolein can be obtained by glycerol catalytic dehydration over acid catalysts. Zeolites and heteropolyacid catalysts are initially highly active, but deactivate rapidly with time on stream by coking, whilst mixed metal oxides are more stable catalytic systems but less selective and in addition they require an activation period. In this talk, the strategy we followed is described. It consisted in a parallel approach in which we developed supported heteropolyacid-based catalysts with increased stability and acrolein selectivity by using a ZrO2-grafted SBA-15 playing the role of the support for silico-tungstic acid active phase, as well as a new concept based on a two zones fluidized bed reactor (TZFBR) to tackle the unavoidable deactivation issue of the HPA catalysts. This type of reactor comprises – in one single capacity – reaction and regeneration zones. In the second part of the lecture the REALCAT platform was introduced. REALCAT (French acronym standing for ‘Advanced High-Throughput Technologies Platform for Biorefineries Catalysts Design’) is an highly integrated platform devoted to the acceleration of innovation in all the fields of industrial catalysis with an emphasis on emergent biorefinery catalytic processes. In this extremely competitive field, REALCAT consists in a versatile High-Throughput Technologies (HTT) platform devoted to innovation in heterogeneous, homogeneous or biocatalysts AND their combinations under the ultra-efficient very novel concept of hybrid catalysis.