Fishes of the perciform suborder Notothenioidei are found in Antarctic and sub-Antarctic waters that are separated by the Antarctic Polar Front (APF), with some species being distributed on both sides of this front. In this wide latitudinal range, these fishes are exposed to different temperatures ranging from -2 °C in the High Antarctic regions to 12 °C in the sub-Antarctic regions. To survive in icy Antarctic waters, the Antarctic notothenioid species have evolved antifreeze glycoproteins (AFGPs) that prevent their body fluids from freezing. The findings of past research on the AFGP attributes of several notothenioid species inhabiting ice-free sub-Antarctic environments have presented a complex picture. Furthermore, previous taxonomic studies split widely distributed notothenioids into different species and/or subspecies, with other studies disagreeing with these splits. To understand the response of the sub-Antarctic notothenioids to warmer, ice-free environments, it is necessary to have a good understanding of their antifreeze biology and systematics. Therefore, this study aimed to determine the association, if any, between the antifreeze attributes of sub-Antarctic notothenioid fishes and their taxonomic status. And more...

One of the most crucial steps towards nanopore-based nucleic acid analysis is extending the dwell time of DNA molecules within the sensing region of the nanopore. I address this issue by interfacing solid-state nanopores with gel media, which sterically hinders translocating DNA molecules, increasing dwell times. Specifically, my experimental results focus on two reptation regimes: when the DNA molecule is flexible on the length scale of the gel pore, and when the DNA molecule is inflexible on the length scale of the gel pore. The first regime is achieved through the use of agarose gel and 5 kbp dsDNA fragments, and produces a wide distribution of translocation times, spanning roughly three orders of magnitude. The second regime is achieved through the use of polyacrylamide gel and 100 bp dsDNA fragments, and displays a shift in translocation times by an order of magnitude while maintaining a tight distribution.

No description available.

Mitochondria are double membraned organelles responsible for the majority of ATP production in eukaryotic cells. The mitochondrial inner membrane is folded into cristae structures and is the site of the electron transport chain which terminates in ATP generation. ATP is produced by ATP synthase, a protein complex that has also been shown to have a role in the maintenance of cristae folding. This activity is dependent on Tim11p, a subunit required for the dimerization of ATP synthase super-complexes. Additional proteins located within the inner membrane that are important to mitochondrial morphology include Pcp1p, a serine protease, and its substrate, Mgm1p. Mgm1p is required for mitochondrial fusion and cells deleted for MGM1 do not contain detectable Tim11p. Using biochemical assays and transmission electron microscopy, this study characterized pcp1 mutants in order to analyze the link between Pcp1p functionality, ATP synthase super-complex assembly, and mitochondrial morphology.

No description available.

: L’une des méthodes qui consiste à optimiser la production d’hydrocarbure est basée sur l’injection d’eau, viscosifiée par addition de polymères de type polyacrylamides, afin d’améliorer l’extraction de pétrole (RAH). Or, les propriétés viscosifiantes des polymères dépendent de leurs masses molaires. L’enjeu de ce travail de thèse a donc été de mettre en place de nouvelles méthodes pour la détermination de larges distributions en masses molaires et de grande dispersité, caractéristiques propres aux échantillons d’intérêt industriel dans le domaine pétrolier. La stratégie d’analyse retenue repose sur la chromatographie d’exclusion stérique (CES) et le fractionnement par couplage flux force (A4F) couplés à la diffusion de lumière et à la réfractométrie. Des polymères modèles ont été synthétisés par un procédé de polymérisation par transfert de chaîne réversible par addition fragmentation (RAFT/MADIX). Cela a permis d’obtenir des polymères dans une gamme de masses molaires comprises entre 103 et 107 g/mol et avec une dispersité inférieure à 1,4. Via l’utilisation de ces polymères, les performances et limites des deux méthodes séparatives investies ont été évaluées. Les conditions opératoires en A4F ont été déterminées et cette méthode s’est avérée être adaptée à l’analyse de polymères industriels distribués sur 3 décades de masses molaires. Au delà de l’analyse dimensionnelle, le couplage avec l’A4F a également permis une analyse conformationnelle. / One method for optimizing the production of hydrocarbon is based on the injection of water, viscosified by the addition of polymers such as polyacrylamides, in order to enhance the oil extraction (EOR). The viscosifying properties of polymers depend on their molecular masses. The aim of this thesis was therefore to develop new methods for determining wide molecular mass distributions and high dispersity, which are specific characteristics of samples of industrial interest in the oil sector. The analytical strategy used is based on size exclusion chromatography (SEC) and flow field flow fractionation (A4F), coupled to light scattering and refractometer. Model polymers were synthesized by a polymerization process by reversible addition fragmentation chain transfer (RAFT/MADIX). This allowed to obtain polymers in a range of molar masses between 103 and 107 g / mol and with a dispersity lower than 1.4. Through the use of these polymers, the capabilities and limitations of the two separation methods invested were evaluated. The A4F operating conditions were determined and this method has proved to be adapted to the analysis of industrial polymers distributed over 3 decades of molecular masses. Beyond the dimensional analysis, A4F-based coupling also allowed conformational analysis.

Assignment (MMed)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: Lipoprotein X (LpX) is an abnormal cholesterol-containing particle that may be present in the serum of subjects with cholestasis, lecithin:cholesterol acyltransferase (LCAT) deficiency and parenteral nutrition. The biochemistry, metabolism, clinical significance and laboratory analysis of LpX is discussed in this study. This laboratory-based project investigated icteric samples received at the Chemical Pathology laboratory, Tygerberg Hospital, for serum predictors of LpX and the use of a modified non-denaturing polyacrylamide gradient gel electrophoresis system in the detection of LpX. The study showed that the non-denaturing polyacrylamide gradient gel electrophoresis system (2-8%) is a useful test in demonstrating LpX in icteric plasma and has potential for a screening test in LCAT deficiency. Serum concentration of conjugated bilirubin, alkaline phosphatase, gamma glutamyltransferase, free cholesterol, phospholipid, free cholesterol: total cholesterol ratio and conjugated bilirubin: total bilirubin ratio are all good predictors of LpX. The ratio of free cholesterol to total cholesterol (FC/TC > 0.6) was the best predictor of LpX. In the setting of obstructive liver disease LpX is seen in 66% of patients if total cholesterol is > 7.5 mmol/L. / AFRIKAANSE OPSOMMING: Lipoproteien X (LpX) is ‘n abnormale cholesterol-bevattende partikel wat teenwoordig mag wees in die serum van persone met cholestase, lesitien:cholesterol asieltransferase (LCAT) gebrek en parenterale voeding. Die biochemie, metabolisme, kliniese belang en laboratorium analise van LpX word bespreek in hierdie werkstuk. Hierdie laboratorium-gebaseerde projek het geelsugtige monsters ondersoek wat ontvang is by die Chemiese Patologie laboratorium, Tygerberg Hospitaal, vir serum voorspellers van LpX en die gebruik van ‘n gemodifiseerde nie-denaturerende polie-akrielamied gradiënt gel elektroforese sisteem in die demonstrasie van LpX. Die bevindinge was dat die nie-denaturerende polie-akrielamied gradient gel elektroforese sisteem (2-8%) is ‘n nuttige toets om LpX te demonstreer in geelsugtige plasma en het potensiaal as ‘n siftingstoets in LCAT gebrek. Serum konsentrasie van gekonjugeerde bilirubien, alkaliese fosfatase, gamma glutamieltransferase, vry cholesterol, fosfolipied, vry cholesterol:totale cholesterol verhouding en gekonjugeerde bilirubien:totale bilirubien verhouding is alles goeie voorspellers van LpX. Die verhouding van vry cholesterol tot totale cholesterol (VC/TC > 0.6) was die beste voorspeller van LpX. In gevalle van obstruktiewe lewersiekte word LpX gesien in 66% van pasiente as die totale cholesterol meer as 7.5 mmol/l is.

Στην παρούσα εργασία αξιολογήθηκε η χρήση των μικροδορυφορικών δεικτών για τη μελέτη της γενετικής δομής και των φυλογενετικών σχέσεων των φυσικών πληθυσμών της Atherina boyeri που προέρχονταν τόσο από θαλάσσιες όσο και λιμναίες/λιμνοθαλάσσιες περιοχές της Ελλάδας. Προηγούμενες μελέτες βασιζόμενες κυρίως σε μιτοχονδριακούς και RAPD δείκτες έχουν υποδείξει την πιθανή παρουσία τριών ομάδων πληθυσμών στην Atherina boyeri με τόσο υψηλές γενετικές αποστάσεις μεταξύ τους που θα μπορούσαν να τις καθιστούν ακόμα και διαφορετικά είδη. Οι ομάδες αυτές είναι: οι θαλάσσιοι πληθυσμοί τύπου Ι (μη εστιγμένοι),οι θαλάσσιοι πληθυσμοί τύπου ΙΙ (εστιγμένοι) και οι λιμναίοι/λιμνοθαλάσσιοι πληθυσμοί. Η ανάλυση στην παρούσα εργασία πραγματοποιήθηκε με χρήση 11 μικροδορυφορικών δεικτών που σχεδιάστηκαν από τους Milana et al. (2009). Οι μικροδορυφορικοί δείκτες θεωρούνται εξαιρετικό εργαλείο μελέτης των φυλογενετικών σχέσεων μεταξύ πρόσφατα διαχωρισμένων ειδών δεδομένου ότι είναι άφθονοι, πυρηνικοί, διάσπαρτοι στο γονιδίωμα, υψηλά πολυμορφικοί και ταχέως εξελισσόμενοι. Τα αποτελέσματα έδειξαν πολύ υψηλό βαθμό πολυμορφισμού στους υπό ανάλυση πληθυσμούς και μεγάλη γενετική διαφοροποίηση μεταξύ των ελληνικών πληθυσμών του είδους όπως αυτή εκφράζεται από τις διαφορές στις συχνότητες των αλληλομόρφων των μικροδορυφορικών δεικτών. Φαίνεται επίσης να επιβεβαιώνεται η διάκριση μεταξύ των δυο θαλάσσιων τύπων της Atherina boyeri, ωστόσο οι λιμναίοι/λιμνοθαλάσσιοι πληθυσμοί παρουσιάζουν τόσο διαφορετικό γενετικό πρότυπο που θεωρείται εξαιρετικά δύσκολο να συνιστούν μια ενιαία ομάδα πληθυσμών. Οι δείκτες αυτοί δεν ήταν δυνατό να χρησιμοποιηθούν στην ανάλυση όλων των διαθέσιμων πληθυσμών, κυρίως λόγω της παρουσίας μη ενισχυόμενων (null) αλληλομόρφων, καθώς επίσης και πολλαπλών ή/και ασθενών ζωνών, γεγονός που επίσης υποδεικνύει την ύπαρξη μεγάλων γενετικών διαφοροποιήσεων, που πιθανώς ξεπερνούν τα όρια του είδους. Προκείμενου να ξεπεραστούν τα ανωτέρω προβλήματα απαιτείται η βελτιστοποίησή τους ανά ομάδα πληθυσμών, μέσω α) αλλαγών στις συνθήκες των PCR αντιδράσεων και β) κλωνοποίησης και αλληλούχισης των δεικτών αυτών από άτομα των πληθυσμών στα οποία ήταν λειτουργικοί, ώστε να επιτευχθεί ο σχεδιασμός νέων ζευγών εκκινητών, ειδικών για επιμέρους ομάδες πληθυσμών. / The present study aims at the measure of the genetic differentiation and the resolution of the phylogenetic relationships among A.boyeri populations originating from lakes/lagoons and marine sites of Greece. Previously studies based on RAPD and mitochondrial markers suggest the existence of three forms of populations of A.boyeri which could represent three different species. These three types are: marine type I, which includes almost all marine populations (non-punctuated), excluding specimens collected from Preveza, Evoia and Kos, which form the marine type II (punctuated) and the “lagoon” type which consists of all the lagoon/lake populations. In the present study, eleven microsatellite markers designed by Milana et al. (2009), were used. Microsatellite markers are supposed to be great tools in phylogenetic studies among recently separated species because they are abundant, nuclear, dispersed around the genome, highly polymorphic and rapidly evolving. Our results showed very high degree of polymorphism in the analyzed populations and extended genetic differentiation among Greek populations of the species as expressed by differences in allele frequencies of the microsatellite markers. They also seems to confirm the distinction between the two marine types of A.boyeri, but the lagoon/lake populations present different allele paterns, pointing to the possible existence of differentiated groups among them. Some of the markers could not be used in the analysis of all the available populations. This is mainly attributed to the presence of null alleles for some of the populations and to scoring difficulties raising from the presence of multiple and/or weak amplicons. This also indicates the existence of great genetic variations, which possibly exceed species limit. To overcome the above difficulties, optimization per marker is required, including a) optimization of PCR conditions and b) cloning and sequencing of these markers from individuals of the population that were functional to achieve the design of new prime pairs, specific for each group of populations .

The purpose of this work was to study polymer degradation mechanisms as well as ways to mitigate it. In the area of chemical stability, defined as divalent cation tolerance of acrylic polymers as hydrolysis increases, use of the n-vinyl pyrrolidone (NVP) monomer helps to preserve viscosity and tolerate higher calcium concentrations over those polymers without NVP. Also, ethylenediaminetetraacetate tetrasodium salt (EDTA-Na+4) is shown to sequester calcium ions at alkaline conditions (pH>10) and, in the case of lab-aged post-hydrolyzed poly(AM-co-AMPS), helps to retain full viscosity at all calcium concentrations when EDTA is present at a stoichiometric equivalence of calcium. Many discrepancies exist in the literature concerning the presence or absence of degradation under various field or laboratory conditions. Carbonate and bicarbonate, which are typically present in natural waters but often neglected in lab-prepared brines, prove to be a hidden variable in resolving why Shupe (1981) saw no loss in viscosity when sodium dithionite was added to polymer in the presence of oxygen (with bicarbonates) but others (Knight, 1973 and Levitt and Pope, 2008) observed severe degradation under similar conditions (but without bicarbonates). A commercial HPAM polymer (Flopaam 3630S) has been shown to be stable in the presence of ferrous iron in the absence of oxygen, clarifying an apparent discrepancy in the literature between the results of Yang and Treiber (1985) and Kheradmand (1987). Dissolved oxygen (DO) levels, and not redox potential (ORP) measurements, are often reported in polymer stability research on oxidative degradation. ORP is shown to be a better measure of the onset of degradation because oxygen is initially being consumed and may not appear until substantial degradation has occurred. Although generally believed to be a detriment to polymer stability in the field, aeration of iron-laden source water prior to hydration of polymer may be beneficial in certain cases where exposure to air in unavoidable. Also, a novel process of safely producing sodium dithionite in the field proves to perform better in terms of long-term polymer stability in anaerobic conditions than the traditional method of using a solution made from powder dithionite. Finally, a pre-sheared 5 million Dalton HPAM is successfully injected into a 3 mD carbonate reservoir core plug. Remarkably, permeability reduction factors remain at values close to unity. However, pressure data from ASP tertiary corefloods suggest that polymer is not feasible for field injections. / text

No description available.