We have examined phylogenetic relationships of suckers of tribe Moxostomatini (Cypriniformes, Catostomidae) using cytochrome-b and Growth Hormone gene intron sequences. Phylogenies were significantly different from recent estimates of relationships based primarily on morphology (Smith, 1992) and cytochrome-b sequences (Harris et al., 2002). Overall, there was little support for many basal nodes in the phylogeny, however it was clear that Scartomyzon and Moxostoma were not monophyletic, despite morphological evidence provided Robins and Raney (1956, 1957), Jenkins (1970), and Smith (1992). Growth Hormone sequences provided good support for a monophyletic Western Scartomyzon lineage and thus suggested a single ancestral invasion of Scartomyzon-like fishes into drainages of Texas and Mexico. Phylogenetic relationships of Western Scartomyzon are structured geographically and do not conform well to current taxonomy.

The greenside darter, Etheostoma blennioides (Teleostomi: Percidae), is a wide-ranging polytypic taxon that occurs throughout eastern North America. A previous morphological study recognized four subspecies (blennioides, newmanii, gutselli, and pholidotum), several morphological races, and three zones of morphological intergradation. We generated complete cytochrome b (1140 bp) sequence data for 51 individuals from across the range of the greenside darter inclusive of all of the currently recognized taxa to assess genetic variation and taxonomic boundaries. Both maximum parsimony and mixed model Bayesian analyses resulted in two strongly supported deeply divergent clades including (1) a Tennessee River drainage clade, and (2) an Ohio River and Great Lakes basins, Interior Highlands, and Atlantic slope clade. Etheostoma blennius, a closely related congener, nested within the Tennessee River clade of E. blennioides, rendering the complex paraphyletic. Test of alternative topologies failed to support the current taxonomic designations. The inclusion of nuclear sequence data from intron 1 of the S7 ribosomal protein (523 bp) from a subset of the populations was included to independently test whether the currently recognized taxa conform to distinct evolutionary lineages and also to clarify potential issues associated with ancestral hybridization. Although the nuclear data was less variable than the mitochondrial data, the monophyly of several of the subspecies could not be rejected.

Thesis (MSc) Stellenbosch University, 2014 / ENGLISH ABSTRACT: In this study, the effect of the amino acid residues at positions 40 and 407 on the catalytic activity of porcine CYP17A1 was investigated. Porcine cofactor CYB5 was cloned from porcine liver tissue and its effect on the catalytic activity of porcine CYP17A1 was determined. The influence of rat, human and angora CYB5 on the lyase activity of porcine CYP17A1 was subsequently determined and compared to the influence of porcine CYB5. Wt porcine CYP17A1, which has residues Val40 and His407, catalysed the conversion of prog efficiently with ~50% prog converted to 17OHprog (~40%) and A4 (~10%) after 3 hr. After 24 hr, negligible levels prog remained with ~71% 17OHprog and ~25% A4 being produced. Low levels of 16OHprog were formed (~9%). The Leu105Ala mutation reduced wt 17α-hydroxylase activity, with 70% prog remaining after 24 hr while 16OHprog (~10%) levels remained unchanged. Porcine CYP17A1 with residues Leu40 and His407, exhibited similar catalytic activity towards prog as did wt porcine CYP17A1 (Val40 and His407 residues), while porcine CYP17A1 with residues Leu40 and Leu407 increased the formation of A4 2-fold to 54% at 24 hr and porcine CYP17A1 with residues Val40 and Leu407 resulted in the highest formation of A4 (90%). Wt porcine CYP17A1, while having converted 95% of the prog substrate, produces only ~16% A4 after 24 hr. In the presence of porcine CYB5, however, the lyase activity was stimulated with 85% of prog being converted to A4 and only 13% 17OHprog remaining. The lyase activity was also stimulated by CYB5 from other species, resulting in an increase in A4 production of 60.6%, 24% and 11.6% by rat, angora and human CYB5, respectively. The degree of lyase stimulation correlated to the percentage identity of the CYB5 amino acid sequences to porcine CYB5. While the Val and Leu residues at position 40 do not appear to influence the lyase activity of porcine CYP17A1 as prominently as the residue at position 407, it is the charged residue at 407 that plays a significant role in the production of A4, decreasing A4 production irrespective of the Val and the Leu residues at position 40. It would, furthermore, appear that the stimulation of lyase activity of CYP17A1 is the greatest when assaying this activity in the presence of CYB5 of the same species as was detected when co-expressing porcine CYP17A1 and porcine CYB5. / AFRIKAANSE OPSOMMING: In hierdie studie is die invloed van die aminosuurresidue by posisies 40 en 407 op die katalitiese aktiwiteit van vark CYP17A1 ondersoek. Vark CYB5 is geklooneer vanuit vark lewer weefsel en die effek van hierdie kofaktor op die katalitiese aktiwiteit van vark CYP17A1 is bepaal. Die invloed van rot, mens en angora CYB5 op die liase aktiwiteit van vark CYP17A1 is daarna bepaal en vergelyk met die invloed van vark CYB5. Vark CYP17A1-VH, (kodeer Val40 en His407), kataliseer die omskakeling van prog doeltreffend met ~50 % prog wat omgeskakel word na 17OHprog (~40%) en A4 (~10%) na 3 uur. Na 24 uur, is feitlik alle prog omgeskakel, met ~71% 17OHprog en ~25% A4 geproduseer. Lae vlakke 16OHprog is ook gevorm (~9%). Die Leu105Ala mutasie verminder 17α- hidroksilase aktiwiteit, met 70% prog wat na 24 uur nie omgesit is nie, terwyl 16OHprog (~10%) vlakke onveranderd gebly het. Vark CYP17A1-LH (kodeer Leu40 en His407), en CYP17A1-VH het diselfde katalitiese aktiwiteit teenoor prog getoon, terwyl vark CYP17A1-LL (kodeer Leu40 en Leu407) die vorming van A4 2-voudig verhoog het tot 54% na 24 uur. Vark CYP17A1-VL (kodeer Val40 en Leu407) se katalitiese aktiwiteit het gelei tot die hoogste vorming van A4 (90%). Alhoewel CYP17A1-VH, 95% van die prog substraat omgeskakel het is slegs ~16% A4 geproduseer na 24 uur. In die teenwoordigheid van vark CYB5 is die liase aktiwiteit egter gestimuleer, en is 85% van die prog substraat omgeskakel na A4 met slegs 13% 17OHprog teenwoordig na 24 uur. Die liase aktiwiteit is ook gestimuleer deur CYB5 van ander spesies, wat lei tot 'n toename in A4 produksie van 60,6% , 24% en 11,6% deur rot, angora en menslike CYB5, onderskeidelik. Daar is gevind dat daar’n sterk korrelasie is tussen die stimulering van die liase aktiwitieit en die persentasie aminosuur volgorde identiteit van CYB5 afkomstig vanaf die verskillende spesies. Terwyl die Val en die Leu aminosuurresidu op posisie 40 wel die liase aktiwitiet tot ‘n mate beȉnvloed, blyk dit uit die data dat die potitief gelaaide residue by 407 'n belangrike rol speel in die produksie van A4, en A4 produksie verlaag ongeag van die Val en die Leu residu by posisie 40. Dit wil ook verdermeer voorkom asof die stimulering van die liase aktiwiteit van CYP17A1 die hoogste is wanneer die ensiem gekataliseerde reaksie deurgevoer word in die teenwoordigheid van CYB5 en CYP17A1 afkomstig vanaf dieselfde spesies.

In this study, I sequenced the mitochondrial cytochrome b gene to elucidate the extent and pattern of genetic variations among and within populations of Rhinichthys osculus (Santa Ana Speckled Dace) found in the different watersheds in Southern California, Central California Coast and Eastern California Desert. I described and analyzed the structural characteristics and pattern of base sequence substitutions in the cytochrome b gene to understand the molecular evolution of the gene. The Phylogenetic analyses showed that the Southern California Santa Ana Speckled dace is a distinct population from the Central California Coast dace population and Eastern California Desert dace population, and is more closely related to the Colorado River speckled dace population. There is a high degree of genetic variation among all populations including a significant genetic structure associated with watersheds, mountain ranges, and geographic grouping based on locations. The SWISS-Model automated protein structure homology elucidated the conserved and invariant residues within the cytochrome b gene where the amino acid substitutions are located in the trans-membrane of the protein sequence. The implication for conservation and management of the Southern California Santa Ana Speckled dace is high because of habitat lost for this distinct dace population. The data from this study will contribute to preserving the genetic variability of the Santa Ana Speckled Dace as a separate taxa and species, as well as to help maintain intact the population in the different Southern California creeks.

Des inhibiteurs du complexe bc1 de la chaîne respiratoire mitochondriale ont été développés comme agents antimicrobiens pour lutter contre des pathogènes de l'Homme et de plantes. Ces drogues ciblent les poches catalytiques Qo et Qi formées par le cytochrome b. La comparaison de séquences de cette protéine montre que les sites Qo et Qi sont bien conservés entre les organismes mais qu'il existe toutefois des variations qui pourraient expliquer leur différence de sensibilité aux drogues. A l'aide du modèle levure S. cerevisiae, nous avons étudié les déterminants de la résistance/sensibilité naturelle à deux antipaludiques se liant au site Qo de Plasmodium: l'atovaquone et RCQ06. Nous avons notamment montré que le résidu 275 joue un rôle clé dans ce phénomène. Une approche similaire est actuellement utilisée pour identifier les facteurs de la sensibilité différentielle à deux drogues ciblant le site Qi des oomycètes. Malheureusement, des cas de résistance acquise à ces antimicrobiens ont été rapportés et ont pour origine des mutations dans le cytochrome b. De ce fait, de nouvelles molécules sont requises pour court-circuiter ces résistances. Au cours de ma thèse, nous avons mis au point un test qui permet de cribler des molécules capables d'inhiber la fonction respiratoire. Nous avons ainsi pu identifier un nouvel inhibiteur du complexe bc1 : D12. Nous avons ensuite déterminé le mode de liaison de cette molécule ainsi que celui d'un composé capable d'inhiber la prolifération de Plasmodium, HDQ, grâce à une collection de mutants des poches catalytiques. HDQ s'est avéré être un inhibiteur du site Qi. Il pourrait être utilisé avec un inhibiteur du site Qo afin de limiter l'apparition de mutations de résistance. D12 est un inhibiteur du site Qo qui est capable notamment de court-circuiter la mutation de résistance à des fongicides du site Qo G143A. Cette dernière a été trouvée chez de nombreux phytopathogènes, mais n'est cependant pas apparue chez des champignons possédant un intron immédiatement après le codon codant pour la glycine 143. En utilisant la levure, nous avons montré que la mutation empêche l'épissage de l'intron en altérant la structure exon/intron. Nous avons également identifié des mécanismes de " by-pass " qui permettent de restaurer la fonction respiratoire du mutant et qui pourraient apparaître chez les pathogènes. Les mutants créés au cours de ma thèse pourront aider à identifier, concevoir et caractériser de nouveaux antimicrobiens et à étudier l'apparition de mutations de résistance.

Plateau pika (Ochotonidae: Ochotona curzoniae) is widespread in Qinghai-Tibetan Plateau (QTP). It is endemic to QTP and restricted to high altitude area, ranging from 3,000 to 5,200 m above sea level. In this study, I examined the genetic structure of O. curzoniae along the Qinghai-Tibetan Railway (QTR) using mitochondrial cytochrome b sequences, and investigated whether QTR had become a barrier of gene flow to populations of O. curzoniae on its two sides. In total, I found 26 haplotypes of cyt b sequences from 29 individuals, of which the mean length was 1,190 bp including 68 informative sites, and the mean genetic distance was 1.7%. Two major clades were revealed in phylogenetic trees as well as TCS haplotype network. In general, the relative positions of haplotypes in the clades were corresponded to their geographic distribution. Most haplotypes of clade I were from east side, while all the haplotypes of clade II were from west side of QTR. Significant population differentiation was revealed between populations from the opposite sides of QTR, but not the same side. Due to the far smaller geographical distances between sampling sites between opposite sides than those of the same side, the differentiation pattern was not consistent with the theory of isolation by distance. Therefore, QTR might have resulted as a barrier to gene flow between populations of O. curzoniae living on opposite sides of QTR. The degree of genetic differentiation between populations of O. curzoniae on opposite sides of QTR will probably further increase in the future.

Phylogeny of 25 Hemidactylus frenatus populations from Taiwan and adjecent islands were resloved by mitochondrial cytochrome b nucleotide sequences and morphological characters. A total of 327 bp were sequenced. Using neighbor-joining and maximum parsimony methods, the phylogenetic trees divide Hemidactylus frenatus into 8 regional groups: Tungshia group; Chiaohsi group; northwest group; central group; Chiayi-Tainan group; south-Penghu group; east-Hengchun group; and southeast group. The results suggest that, the dispersal center should be in the northwest, and then dispersed to the east and the south. Phylogenetic state of Chiaohsi population is not clear. It may be immigrated from northwest or outside of Taiwan. The Penghu and Kaohsiung populations have a short genetic distance, maybe caused from frequently genetic interflow, as well as the Chihpen, Tunghe, Lutao and Lanyu populations. The Principle Component Analysis and Canonical Discriminate Analysis of 16 morphological characters, showed that no differences exist populations.

L'apparition récurrente de Plasmodium falciparum résistant aux antipaludiques est un obstacle majeur au contrôle du paludisme. Introduite en 2000, une nouvelle association très bien tolérée, l'atovaquone-proguanil est rapidement devenue le traitement de choix des accès palustres simples dans certains hôpitaux français. Ce travail de recherche avait pour objectif d'approfondir les connaissances sur la résistance à cette association. Nous n'avons détecté aucune résistance naturelle à l'atovaquone-proguanil en Afrique de l'Ouest et dans l'Océan Indien parmi 477 isolats. La majorité des rechutes précoces sont liées à une malabsorption des principes actifs alors que les échecs tardifs sont liés à la présence de parasites hautement résistants in vitro présentant, au moment de la rechute, une mutation au niveau du codon 268 du cytochrome b (Y268S ou Y268C) sans augmentation du nombre de copies de ce gène, évalué par PCR en temps réel à 16 ± 9 copies par parasite. Le séquençage du génome mitochondrial et l'analyse de marqueurs microsatellites chromosomiques des parasites isolés avant et après la rechute parasitaire montrent que la mutation associée à cette résistance est apparue indépendamment chez chacun des six patients en échec étudiés. L'atovaquone-proguanil est efficace pour le traitement des voyageurs avec moins de 0,1% de résistance. Le risque actuel de dispersion des résistances est négligeable puisqu'elles émergent chez des patients traités hors de zone de transmission. Par contre, si cette association devait être déployée en zone d'endémie, il serait indispensable de la combiner avec d'autres molécules.

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 124-142).

The number of non-parasitic (brook) lamprey species in the genus Lampetra is underestimated since isolated populations are generally considered one species due to their relatively conserved body form. The phylogeographic and phylogenetic structure was estimated among and within Lampetra species along the Pacific coast of North America (presumed to represent Lampetra richardsoni; L. pacifica – which is currently regarded as a junior synonym of L. richardsoni; L. ayresii; and L. hubbsi) using up to three mitochondrial and three nuclear genetic markers. These data show that L. richardsoni as currently recognized is polyphyletic when lampreys (some of which show up to 8 K2P% sequence divergence) from Siuslaw River and Fourmile Creek (Oregon) and Mark West, Paynes, and Kelsey creeks (California) are included; Lampetra pacifica is a valid species; the population from Kelsey Creek almost certainly represents a new species; and those from Siuslaw, Fourmile, and Mark West may also be distinct species.