Malaria is a leading cause of death in some developing countries. The malaria parasite has been around for over a century, and has coevolved with humans. Coming up with an effective vaccine for P. falciparum will save millions of lives and reduce the morbidity and mortality of malaria globally. Understanding the role of exported parasite proteins i.e PfEMP1 a virulence factor and major cause of malarial pathogenesis, has been of great interest to vaccine researchers in the last decade. The focus of this review is to provide a literature review on PfEMP1s, their interaction with the human immune system, and their role in helping P. falciparum parasite to evade the immune system. This review will primarily focus on the intra-erythrocytic stage, which is the stage that results in the symptoms of malaria. A review is necessary to understand the antigenic variation of PfEMP1s, and how PfEMP1s challenge the different arms of the immune response, both the innate and adaptive. This review is unique in touching on the major parts of the immune system's interaction with the PfEMP1 antigen. Furthermore, the review explores the discussion of future research and therapeutic opportunities based on our knowledge of PfEMP1 antigens.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Dichloro-diphenyl-trichloroethane (DDT) was extensively used in agriculture pest control and is still used for indoor residual spraying to control malaria. The lipophylicity of DDT and its breakdown product dichloro-diphenyl-dichloroethylene (DDE) dictates that they associate with membranes, lipids and hydrophobic proteins in the biological environment. Their poor degradable nature causes DDT and DDE to persist for decades in the environment and in individuals who are or were in contact with the pesticide. In many countries the synchronised resistance of the mosquito vector to insecticides and the malaria parasite towards antimalarial drugs led to a drastic rise in malaria cases and to malaria epidemics. This study assesses the influence of low level exposure of DDT and DDE on chloroquine (CQ) resistance of the dire human malaria parasite, Plasmodium falciparum. The in vitro activity of p,p’-DDT and p,p’-DDE towards blood stages of chloroquine sensitive (CQS) P. falciparum D10 and chloroquine resistant (CQR) P. falciparum Dd2 was determined using two complementary in vitro assays (Malstat and SYBR Green 1). The 50% inhibition concentrations (IC50s) of p,p’-DDT and p,p’-DDE were found to be ±14 to 38 μM (5-12 μg/mL) and highly similar towards CQS and CQR P. falciparum strains. This result indicated that the proteins involved in CQ resistance have no effect on the activity of the insecticide DDT and it breakdown product DDE. In order to assess the influence of DDT and DDE on CQ activity, in vitro fixed ratio drug combination assays were performed, as well as isobologram analysis. We found that CQ works in synergy with p,p’-DDT and p,p’-DDE against CQS P. falciparum D10. However, both p,p’-DDT and p,p’-DDE were antagonistic toward CQ activity in CQR P. falciparum Dd2. This indicated that p,p’-DDT and p,p’-DDE do have an effect on CQ resistance or on the action of CQ via a target other than hemozoin polymerization. The observation of reciprocal synergism of p,p’-DDT and p,p’-DDE with CQ against CQS D10 and antagonism against CQR Dd2 strain is highly significant and strongly indicates selection of CQ resistant strains in the presence of p,p’-DDT and p,p’-DDE. People who have low levels of circulating DDE and/or DDT could be at a high risk of contracting CQR malaria. However, medium term (nine days) DDE exposure of CQS P. falciparum D10 did not induce resistance, as no significant change in activity of CQ, p,p’-DDT and p,p’-DDE towards blood stages the CQS strain was observed. This exposure was, however, shorter than expected for a malaria infection and would be addressed in future studies. From our results on the interaction of CQ with p,p’-DDT and p,p’-DDE, it was important to assess the residual DDT and DDE variable and how much of residual p,p’-DDT and/or p,p’- DDE would enter into or remain in the different compartments (the RPMI media, erythrocytes and infected erythrocytes) over time. In combination with liquid-liquid extraction, we developed a sensitive GC-MS analyses method and a novel HPLC-UV analysis method for measuring DDT and DDE levels in malaria culturing blood and media. Whilst the HPLC-UV method was relatively cheaper, faster, and effective in determining high DDT and DDE concentrations, the optimised GC-MS method proved to be effective in detecting levels as low as 78 pg/mL (ppt) DDE and 7.8 ng/mL (ppb) DDT in biological media. Using both the HPLC and GC-MS methods we observed that malaria parasites influence distribution of the compounds between the erythrocytic and media fractions. P. falciparum D10 infection at ±10% parasitemia lead to must faster equilibration (less than 8 hours) between compartments. Equimolar distribution of p,p’-DDE was observed, but the parasites lead to trapping of the largest fraction of p,p’-DDT in the erythrocyte compartment. These results indicate that a substantial amount would reach the intra-erythrocytic parasite and could influence the parasite directly, possibly leading to either synergistic or antagonistic drug interactions. This study is the first to illustrate the “good and bad” of the insecticide DDT in terms of CQ resistance and sensitivity toward the human malaria parasite P. falciparum. These results will hopefully have an important influence on how future policies on malaria control and treatment particularly in endemic areas will be addressed and could also have an impact on the anti-malarial drug discovery approach. / AFRIKAANSE OPSOMMING: Dichlorodifenieltrichloroetaan (DDT) is op groot skaal in landbouplaagbeheer gebruik en word nog steeds gebruik vir binnenshuise oppervlakbespuiting om malaria te beheer. Die lipofilisiteit van DDT en sy afbraakproduk dichlorodifenieldichloroetileen (DDE) dikteer dat hulle met membrane, lipiede en hidrofobiese proteïene in die biologiese omgewing assosieer. Stadige afbraak veroorsaak dat DDT en DDE vir dekades in die omgewing agterbly, asook in individue wat in kontak is, of was met die insekdoder. In baie lande het gesinkroniseerde weerstand van die muskietvektor teenoor insekdoders en die malariaparasiet teenoor antimalariamiddels gelei tot 'n drastiese styging in malariagevalle en tot malariaepidemies. In hierdie studie word die invloed van lae vlak blootstelling van DDT en DDE op chlorokien (CQ) weerstand van die mens malariaparasiet, Plasmodium falciparum, geëvalueer. Die in vitro aktiwiteit van p,p'-DDT en p,p'-DDE teenoor die bloedstadia van chlorokiensensitiewe (CQS) P. falciparum D10 en chlorokien-weerstandbiedende (CQW) P. falciparum Dd2 is bepaal deur gebruik te maak van twee komplementêre in vitro toetse (Malstat en SYBR Groen toetse). Die 50% inhibisie konsentrasies (IC50s) van p,p'-DDT en p,p'-DDE is bepaal as ±14 to 38 μM (5-12 μg/mL) en was hoogs vergelykbaar tussen CQS en CQW P. falciparum stamme. Hierdie resultaat het aangedui dat die proteïene betrokke by CQ weerstand geen effek op die aktiwiteit van die insekdoder DDT en die afbraakproduk DDE het nie. Om die invloed van DDT en DDE op CQ aktiwiteit te evalueer, is die aktiwiteit van kombinasies van die verbindings in vaste verhoudings getoets, tesame met isobologram ontleding. Ons het gevind dat CQ sinergisties saam met p, p'-DDT en p, p'-DDE teen CQS P. falciparum D10 werk. Daarteenoor het beide p, p'-DDT en p, p'-DDE antagonistiese werking getoon teenoor CQ aktiwiteit met CQW P. falciparum Dd2 as teiken. Dit het aangedui dat p,p'-DDT en p, p'-DDE wel 'n invloed op CQ weerstand het of ‘n aktiwiteit van CQ, anders as hemozoin polimerisasie, beïnvloed. Die waarneming van resiproke sinergisme en antagonisme van p, p'-DDT en p, p'-DDE in kombinasie met CQ teenoor die CQS D10 en CQW DD2 stamme respektiewelik, is hoogs betekenisvol en dui op seleksie van CQweerstandige stamme in die teenwoordigheid van p, p'- DDT en p, p'-DDE. Mense wat lae vlakke van sirkulerende DDE/DDT het, het dus 'n hoër risiko om CQW malaria te kry. Verder is gevind dat medium termyn (nege dae) DDE blootstelling van CQS P. falciparum D10 nie weerstand nie veroorsaak nie, want geen beduidende verandering in die aktiwiteit van CQ, p,p'-DDT en p,p'-DDE teenoor die bloed stadiums van die CQS stam is waargeneem nie. Hierdie blootstelling is egter korter as in 'n malaria-infeksie en sal verder bestudeer word in toekomstige studies. Vanuit die interaksie resultate van CQ met p, p'-DDT en p, p'-DDE was dit belangrik om die residuele DDT en DDE veranderlike te evalueer, asook die distribusie van p,p'-DDT en p,p'- DDE tussen die verskillende kompartemente (die kultuurmedium, eritrosiete en geïnfekteerde rooibloedselle) oor verloop van tyd. In kombinasie met vloeistof-vloeistof ekstraksie, het ons 'n sensitiewe GC-MS en nuwe HPLC-UV analisemetode ontwikkel vir die meet van DDT en DDE-vlakke in bloed (normale en geïnfekteerde eritrosiete) en die kultuurmedium. Terwyl die HPLC-UV metode relatief goedkoper, vinniger en effektief in die bepaling van hoë DDT en DDE-konsentrasies is, was die geoptimaliseerde GC-MS metode doeltreffend in die opsporing van vlakke so laag as 78 pg/mL (dpt) DDE en 7.8 ng/mL (dpb) DDT in biologiese media. Met behulp van beide die HPLC-UV en GC-MS metodes is waargeneem dat die malariaparasiet die ekwilibrasie van die verbindings tussen die eritrosiet- en media kompartemente beïnvloed. P. falciparum D10 infeksie met ± 10% parasitemia lei tot vinniger ekwilibrasie (minder as 8 uur) tussen die kompartemente. Ekwimolêre verspreiding van p,p'- DDE is waargeneem, maar die parasiete het die grooste fraksie van p,p'-DDT in die eritrosiet kompartement vasgevang. Hierdie resultate wys dat 'n aansienlike fraksie die intraeritrositiese parasiet kan bereik en sodoende die parasiet direk kan beïnvloed en moontlik kan lei tot sinergistiese of antagonistiese middel interaksies. Hierdie studie is die eerste om die "goed en sleg" van die insekdoder DDT in terme van CQ weerstand en sensitiwiteit teenoor die menslike malariaparasiet P. falciparum te illustreer. Hierdie resultate sal hopelik 'n belangrike invloed hê op die toekomstige beleid oor die beheer van malaria en behandeling, veral in endemiese gebiede, en mag ook 'n impak hê op die antimalariamiddel navorsing.

Thesis (MSc (Biochemistry))--University of Stellenbosch, 2009. / ENGLISH ABSTRACT: In Africa alone, Plasmodium, the causative agent of malaria is estimated to kill a child, under the age of five every thirty seconds140. The ability of the parasite to rapidly attain resistance, has resulted in immunity of the parasite to all, except one group of frontline drugs. The need to develop novel drugs, vaccines and prevention strategies that are accessible and affordable for third world countries is of the utmost importance to prevent needless human suffering and death. The glycolytic pathway is an attractive drug target since it is the principal source of ATP for the parasite. Many of the glycolytic enzymes have been studied and proposed as drug targets, but the importance of these enzymes for the function of the pathway as a whole has not been considered. It is known, from the frameworks of metabolic control analysis, that control of the flux and metabolite concentration can be divided among the individual steps. Differential control analysis of Plasmodium and erythrocyte glycolysis may reveal potential drug targets. These analyses require a detailed kinetic model of Plasmodium glycolysis, and the feasibility of constructing and validating such a model was the aim of this study. In this work we determined the feasibility of constructing and validating a detailed kinetic model for the Plasmodium falciparum glycolytic pathway. Whether the construction and validation of this kinetic model was feasible or not was decided on the basis of the ability to: i) culture and isolate sufficient asexual parasites for enzymatic and steady state assays , ii) obtain kinetic parameters such as Km and Vmax for each glycolytic enzyme, either from literature or experimentally, iii) measure glycolytic fluxes, iv) determine glycolytic intermediate concentrations, v) construct a kinetic model from the kinetic parameters and vi) validate it with steady state glycolytic fluxes and metabolite concentrations Each of the above criteria were successfully addressed. In summary, the kinetic parameters and glycolytic fluxes that were measured experimentally, were used to construct and partially validate a detailed kinetic model, respectively. Further validation of the model by means of steady state metabolite concentrations was shown to be possible with the development of a suitable protocol to measure the glycolytic intermediate concentrations. The model presented in this work may play an important role in drug target identification and improving the current understanding of host-parasite interactions and glycolytic regulation. / AFRIKAANSE OPSOMMING: Plasmodium, die parasiet wat malaria veroorsaak, is in Afrika alleen elke dertig sekondes verantwoordelik vir die afsterwe van ’n kind jonger as vyf jaar. Die parasiet se vermoë om vinnig weerstand op te bou het daartoe gelei dat Plasmodium weerstandbiedend is teen byna alle nuwe teen-malaria middels, behalwe vir ’n enkele toonaangewende groep. Die ontwikkeling van nuwe malaria teen-middels is van uiterste belang om lyding te voorkom. ’n Goeie teiken vir teen-malaria middels is die glikolitiese padweg omdat die metaboliese padweg essensieël is vir die produksie van ATP, die energiebron van die parasiet. Desondanks die feit dat meeste van die glikolitiese ensieme al goed bestudeer en as teiken voorgestel is, is dit steeds onduidelik hoe hierdie ensieme saam funksioneer om die metaboliese weg, as geheel, tot stand te bring. Metaboliese kontrole analise het aangetoon dat die glikolitiese beheer verdeel is tussen die onderskeie glikolitiese ensieme, m.a.w. geen enkele ensiematiese stap het volledige beheer oor die fluksie van die glikolitiese padweg nie. Die afsonderlike analise en vergelyking van Plasmodium - en rooibloedselglikolise met behulp van differensiële metaboliese kontrole analise sal moontlik gebruik kan word om gasheervriendelike teikens vir nuwe middels aan te toon. So ’n analise benodig ’n omvattende kinetiese model van Plasmodium glikolise. Derhalwe was die doel van hierdie studie om vas te stel hoe uitvoerbaar dit is om ’n kinetiese model van Plasmodium glikolise te konstrueer en te valideer. Die uitvoerbaarheid van die konstruksie en validering van die kinetiese model was geasseseer op grond van die vermoë om: i) parasietkulture te kweek en genoegsame parasiete, wat in die aseksuele fase is, te isoleer sodat ensiembepalings en bestendige toestand-bepalings gedoen kan word, ii) kinetiese parameters soos Km - en Vmax-waardes vir elke glikolitiese ensiem, hetsy vanuit literatuur of eksperimentele werk, te verkry, iii) glikolitiese fluksie te meet, iv) glikolitiese intermediaatkonsentrasies te bepaal, v) ’n kinetiese model van die bepaalde kinetiese parameters op te stel en vi) die model te valideer met glikolitiese flukswaardes en metaboliet- konsentrasies wat in die bestendige toestand verkry is. Elk van die bogenoemde kriteria was met sukses in hierdie studie aangespreek. Ter opsomming, die eksperimenteel bepaalde kinetiese parameters en glikolietiese flukswaardes was gebruik om onderskeidelik ’n gedetaileerde kinetiese model te konstrueer en gedeeltelik te valideer. Daar was getoon dat verdere validering van die model deur middel van bestendige toestand metabolietkonsentrasies moontlik is met die ontwikkeling van ’n geskikte protokol om glikolitiese intermediaatkonsentrasies te meet. Die model, soos opgestel in hierdie studie, kan moontlik ’n belangrike rol speel om teikens vir nuwe malaria teen-middels te identifiseer en om gasheer-parasiet interaksies en glikolitiese regulering beter te verstaan.

<p>The action of Mung Bean Nuclease (MBN) on DNA makes it possible to clone intact gene fragments from genes of the malaria parasite, Plasmodium. This &ldquo / genease&rdquo / activity has provided a foundation for further investigation of the coding elements of the Plasmodium genome. MBN has been reported to cleave genomic DNA of Plasmodium preferentially at positions before and after genes, but not within gene coding regions. This mechanism has overcome the difficulty encountered in obtaining genes with low expression levels because the cleavage mechanism of the enzyme yields sequences of genes from genomic DNA rather than mRNA. However, as potentially useful as MBN may be, evidence to support its genease activity comes from analysis of a limited number of genes. It is not clear whether this mechanism is specific to certain genes or species of Plasmodia or whether it is a general cleavage mechanism for Plasmodium DNA .There have also been some projects (Nomura et al., 2001 / van Lin, Janse, and Waters, 2000) which have identified MBN generated fragments which contain fragments of genes with both introns and exons, rather than the intact genes expected from MBN-digestion of genomic DNA, which raises concerns about the efficiency of the MBN mechanism in generating complete genes.</p> <p><br /> Using a large-scale, whole genome mapping approach, 7242 MBN generated genome survey sequences (GSSs) have been mapped to determine their position relative to coding sequences within the complete genome sequences of the human malaria parasite Plasmodium falciparum and the incomplete genome of a rodent malaria parasite Plasmodium berghei. The location of MBN cleavage sites was determined with respect to coding regions in orthologous genes, non-coding /intergenic regions and exon-intron boundaries in these two species of Plasmodium. The survey illustrates that for P. falciparum 79% of GSSs had at least one terminal mapping within an ortholog coding sequence and 85% of GSSs which overlapped coding sequence boundaries mapped within 50 bp of the start or end of the gene. Similarly, despite the partial nature of P.berghei genome sequence information, 73% of P.berghei GSSs had at least one terminal mapping within an ortholog coding sequence and 37% of these mapped between 0-50 bp of the start or end of the gene. This indicates that a larger percentage of cleavage sites in both P.falciparum and P.berghei were found proximal to coding regions. Furthermore, 86% of P.falciparum GSSs had at least one terminal mapping within a coding exon and 85% of GSSs which overlapped exon-intron boundaries mapped within 50bp of the exon start and end site. The fact that 11% of GSSs mapped completely to intronic regions, suggests that some introns contain specific cleavage sites sensitive to cleavage and this also indicates that MBN cleavage of Plasmodium DNA does not always yield complete exons.</p> <p><br /> Finally, the results presented herein were obtained from analysis of several thousand Plasmodium genes which have different coding sequences, in different locations on individual chromosomes/contigs in two different species of Plasmodium. Therefore it appears that the MBN mechanism is neither species specific nor is it limited to specific genes.</p>

Intermittent fevers caused by Plasmodium parasites have been known for millennia, and have caused untold human suffering. Today, millions of people are afflicted by malaria each year, and hundreds of thousands die. Historically, the most successful synthetic antimalarial drug was chloroquine, as it was safe, inexpensive, and highly efficacious. However, plasmodial resistance to chloroquine now greatly limits its utility. Previously in our laboratories it has been shown that attachment of a "reversal agent moiety" to the side chain of chloroquine can result in the restoration of activity against chloroquine-resistant strains of P. falciparum malaria. In the first part of the work presented here, a study has been made of the importance of the quinoline ring substitution pattern to the activity of such reversed chloroquines. The compounds presented here include those bearing a substituent in the 2-, 5, 6-, 7-, and/or 8- position, and include those with chloro, bromo, iodo, fluoro, nitro, trifluoromethyl, methyl, and methoxy substituents. For reversed chloroquines, 2-, 5-, and 8- substituents have been found to decrease in vitro antiplasmodial activity against P. falciparum relative to 7-chloro substitution, whereas 6- and 7- substituted compounds with various substituents have in many cases similar activity to that of 7-chloro substituted compounds. Little difference has been observed between 6- and 7- substitution, or between chlorine and a methyl group in position 6. In most cases these effects on activity are directionally similar to those observed for chloroquine analogs without an attached reversal agent, but the magnitude of the effect is generally smaller, suggesting that the activities of reversed chloroquines are less affected by modifications to the quinoline ring system than is true for chloroquine analogs without an attached reversal agent. The second portion of this work presents an asymmetrical bis-quinoline (PL241) that is highly active against P. falciparum malaria, with an IC50 of less than 0.1 nM for all strains tested. Mechanistic studies have been performed in which the substitution patterns of the two quinoline rings of PL241 are modified in ways that indicate that either ring system is equally capable of participating in the antimalarial activity of these compounds. The excellent in vitro antiplasmodial activity of PL241 makes this a compound of great interest for further development as a potential antimalarial drug. In the third part of this work, a survey has been made of antimalarial treatments recommended in the European medical literature from the time of Pliny the Elder (active in the first century A.D.) through the advent of modern malaria chemotherapy in the early twentieth century. In the fifteen primary sources utilized in this study, 251 distinct substances - primarily plants - were identified as having likely been used in the treatment of malaria. Of the 38 substances that were described in three or more sources, at least fifteen have been examined by other workers for antiplasmodial activity; in many cases, they were found to have antiplasmodial activity in vitro or in vivo. However, the majority of the phytotherapies for malaria identified in this project have not yet been tested against Plasmodium species, and may provide valuable leads in the search for new compounds active against drug-resistant malaria.

The virulence of Plasmodium falciparum is largely attributed to the ability of asexual blood-stage parasites to cytoadhere to the microvascular endothelium of the human host. This pathogenic behavior is mediated by the primary parasite virulence factor P. falciparum erythrocyte membrane protein 1 (PfEMP1), an understanding of which is crucial to develop interventions to ameliorate the morbidity and mortality of P. falciparum malaria. The work presented in this thesis describes the application of a phenotype-to-genotype experimental approach to identify novel parasite proteins involved in the trafficking and display of PfEMP1. Guided by the overall hypothesis that the in vitro culture-adapted parasite line 3D7 harbors 1 or more genetic determinants of impaired PfEMP1 trafficking, surface PfEMP1 levels were first measured in 3D7, the presumably trafficking-competent parasite line HB3, and 16 unique progeny from an HB3 x 3D7 genetic cross (chapter 2). These phenotypes were then combined with genome-wide SNP data in QTL analysis to identify genetic polymorphisms potentially responsible for the impaired trafficking in 3D7 (chapter 3). A near-significant QTL containing a single protein-coding gene, the putative kinesin Pf3D7_1245600, was identified, characterized, and investigated in CRISPR-Cas9-driven allele-exchange parasite transfection experiments to establish a causal link between the gene and PfEMP1 trafficking (chapter 4). The parasite transfections were unsuccessful, but the potential role of Pf3D7_1245600 in PfEMP1 trafficking was indirectly assessed through the disruption of microtubules with colchicine (chapter 4), which significantly impacted the surface PfEMP1 levels of HB3 but not 3D7. The findings of this thesis suggest that kinesins and microtubules may play previously unconsidered roles in the regulation, production, or trafficking of PfEMP1.

El objetivo de esta investigación retrospectiva, fue determinar la asociación existente entre mutaciones puntuales en los genes dihidrofolato reductasa (Pfdhfr) y dihidropteroato sintasa (Pfdhps) de Plasmodium falciparum y la respuesta clínica en pacientes con diagnóstico de malaria no complicada causada por P. falciparum, admitidos en un estudio de eficacia in vivo de sulfadoxina-pirimetamina (SP) llevado a cabo en dos áreas de la región Loreto en 1999. Se tomaron muestras de sangre de 86 pacientes antes de administrarles SP, las que se analizaron usando PCR-anclado específico de alelo para estudiar a los codones S108N/T, N51I, C59R, I164L y C50R del gen Pfdhf y los codones A436G, A437G, K540E, A581G y A613S/T del gen Pfdhps, encontrándose que las infecciones causadas por parásitos con 3 mutaciones en Pfdhfr (108Asn/51Ile/164Leu) y 2 (581Gli/437Gli) ó 3 mutaciones en Pfdhps (581Gli/437Gli/540Glu) denominados el quíntuple mutante y el séxtuple mutante, respectivamente, se encontraban asociadas con la falla del tratamiento con SP. Además, se estableció que cuanto más alto era el número de mutaciones tanto en Pfdhfr como en Pfdhps, más alto era el riesgo de fallar al tratamiento con SP, según resultado del análisis de regresión logística empleado para asociar a estas dos variables. Este estudio contribuye en brindar evidencias científicas de la asociación existente entre las variables en la región Loreto contribuyendo a su validación y su futuro uso para estudios de vigilancia de fármaco resistencia a SP no solo en el Perú sino en general para los países de América del Sur que comparten territorio de la selva Amazónica. / -- The objective of this retrospective study was to determine the asociation between point mutations in dihydrofolate reductase (Pfdhfr) and dihydropteroate synthase (Pfdhps) Plasmodium falciparum genes, and clinical outcome of patients with non complicated P.falciparum malaria diagnosis, admitted to a in vivo sulphadoxine-pirymethamine (SP) drug efficacy study conducted in 1999, in two areas of Loreto region. We used allelic specific-nested PCR to analize 86 blood samples collected before SP treatment, and study mutations at codons S108N/T, N51I, C59R, I164L and C50R in Pfdhfr and codons A436G, A437G, K540E, A581G y A613S/T in Pfdhps genes, and found that Infections caused by parasites harbouring 3 mutations in Pfdhfr (108Asn/51Ile/164Leu) and either 2 or 3 mutations in Pfdhps (581Gly/437Gly and 540Glu) called the quintuple and sextuple mutants, respectively, were associated to failure with SP treatment. Logistic regression analysis was used to look for association between the variables, helping to establish the higher the number of mutations in both Pfdhfr and Pfdhps genes, the higher the risk of treatment failures when using SP.The contribution of this study is to provide scientific evidences of the association between both variables in Loreto region supporting its validation and future application in surveillance studies for SP drug resistance, that can be conducted not only in Peru but also in South American countries that share the Amazon basin territory.

In der vorliegenden Arbeit haben wir unter Nutzung bioinformatischer Methoden eine innovative Strategie zur Eindämmung der Malaria entwickelt. Die genetische Modifikationsstrategie beinhaltet sowohl Manipulationen aufseiten des gefährlichsten Erregers, Plasmodium falciparum, als auch des Hauptvektors, Anopheles gambiae. In den Genomen beider Spezies wurden eine Reihe neuer konkreter targets identifiziert. Auch bereits beschriebene targets und Ansätze wurden in die Strategie einbezogen bzw. weiter ausgestaltet. Bezüglich der Vektormoskitos wird die Verbreitung eines gegenüber Plasmodien resistenten Genotyps angestrebt. Es werden einerseits effiziente natürliche und künstliche Resistenzgene diskutiert und andererseits eine bekannte Strategie zur Fixierung natürlicher Resistenzallele in natürlichen Populationen verbessert. Auf der Seite der Plasmodien erweiterten wir einen bereits von A. Burt (2003) beschriebenen Eradikationsansatz um weitere targets. Aus ethischen und evolutionsbiologischen Erwägungen bevorzugen wir jedoch eine alternative Strategie, welche die Etablierung von in ihrer Virulenz gemilderten Parasiten zum Ziel hat. Der attenuierte Genotyp wird unter anderem durch komplexe Pathway-Remodellierungen beschrieben (Löwe, Sauerborn, Schirmer, Dandekar, A refined genome engineering strategy against parasites and vectors, Manuskript beim Journal „Genome Biology“ eingereicht). Da sich Mutanten in der Natur gegen Wildtyp-Organismen kaum durchsetzen können, werden zwei drive-Systeme beschrieben, welche für die Implementierung der genetischen Manipulationsstrategie entwickelt wurden. Beide Konstrukte wurden zur Patentierung angemeldet (Patentanmeldung U30010 DPMA bzw. Aktenzeichen 102006029354.1). Zusätzlich zur deutschen wurde für eines der beiden Konstrukte eine PCT-Anmeldung eingereicht, welche in Zukunft einen internationalen Patentschutz ermöglichen soll. Es werden Kalkulationen vorgelegt, welche die Verbreitungstendenzen der Konstrukte in natürlichen Populationen vorhersagen. Die Beschreibung der entwickelten Konstrukte beschränkt sich nicht auf das primäre Anwendungsgebiet der Arbeit (Malaria), sondern beinhaltet auch andere Anwendungsgebiete, vor allem im Bereich der Medizin und Molekularbiologie. / Background: Gene drive strategies are an important alternative to control tropical diseases such as malaria. Results: Here we introduce a new gene drive strategy based on gene conversion constructs. We identify a gene drive strategy both for plasmodia and for anopheles including design of an inducible modification vector. Our constructs are based on group II introns or homing endonuclease genes. They include besides the intron to modify vector or parasite genome sites inducible promoters for gene activation. We thus separate gene modification from activation of the modified gene. Moreover, we provide a detailed list of suitable targets in vector and plasmodia for the modification strategy. Finally, we discuss the control effect of an eradication strategy versus a mild strategy of the gene construct for vector and parasite populations. Conclusions: A new eukaryotic vector and parasite control strategy using gene drive systems is presented and discussed.

In Säugetieren existieren im wesentlichen zwei Abwehrsysteme gegen oxidativen Streß, in welchen die Glutathionreduktase (GR) und Thioredoxinreduktase (TrxR) Schlüsselenzyme sind. Ein einzelnes Gen der Taufliege, genannt dmtrxr-1, kodiert sowohl für die durch alternatives Splicing entstehende cytoplasmatische und mitochondriale Form der DmTrxR-1. Zum Teil innerhalb des dmtrxr-1-Gens findet sich auf dem Komplementärstrang ein weiteres Gen, welches sniffer genannt wurde. In Kooperation wurde nachgewiesen, daß dieses Gen essentiell zur Verhinderung alterungsbedingter Neurodegeneration ist. Durch biochemische Charakterisierung konnte das rekombinant hergestellte Produkt dieses Gens in der vorliegenden Arbeit als Carbonylreduktase, ein zu den Kurzketten-Dehydrogenasen (short-chain dehydrogenases) gehörendes Enzym, identifiziert werden. Sniffer weist das für Carbonylreduktasen typische Substratspektrum mit Phenanthrenequinone als bestem Substrat auf und wird von Flavonoiden wie Quercetin und Rutin sowie Hydroxymercuribenzoat gehemmt. In verschiedenen Ansätzen konnten Kristalle des rekombinanten Proteins gewonnen werden, die inzwischen in Kooperation vermessen wurden und so zu einer Kristallstruktur mit einer Auflösung von 1,7 Angström führten. Durch diese Arbeiten konnte zum ersten Mal eine Verbindung zwischen einem charakterisierten Gen (snifffer), oxidativem Streß und neurodegenerativen Effekten auf molekularer Ebene nachgewiesen werden. Parasiten haben während ihres Lebenszyklus einen hohen Bedarf an Energie und sind abhängig von einer starken Syntheseleistung. Zur Bewältigung dieses Stresses benötigen sie hohe Aktivitäten an Adenylatkinase (AK; ATP + AMP &#61683; 2 ADP) und GTP-AMP-Phosphotransferase (GAK; GTP + AMP &#61683; GDP + ADP). Beide Enzyme wurden in Blutstadien des Malariaparasiten Plasmodium falciparum identifiziert und die entsprechenden Gene der PfAK und PfGAK auf den Chromosomen 10 und 4 respektive lokalisiert. Klonierung und heterologe Expression in E. coli ergab enzymatisch aktive Proteine mit einer Größe von 28,9 (PfAK), bzw. 28,0 kDa (PfGAK). Das rekombinante Protein der PfAK entspricht in seinen biochemischen Charakteristika denen der authentischen PfAK. Dies gilt auch für eine mögliche Assoziation mit einem stabilisierenden Protein mit einem Molekulargewicht von ca. 70 kDa und der hohen Substratspezifität für das Monophosphat-Nukleotid AMP. Die Spezifität für das Triphosphat-Substrat ist weniger stringent. Das beste Triphosphat-Substrat ist ATP mit einem Vmax-Wert von 75 U/mg und einem kcat von 2800 min-1. Die Sequenz der PfAK enthält eine amphiphatische Helix, welche als notwendig für die Translokation zytosolischer Adenylatkinasen in den Intermembranraum der Mitochondrien beschrieben wurde. Die PfGAK bevorzugt GTP und AMP als Substrat (100 U/mg; kcat = 2800 min-1 bei 25°C) und zeigt als Besonderheit keine messbare Aktivität mit ATP. Im Gegensatz zu ihrem Ortholog im Menschen (AK3) enthält die Sequenz der PfGAK ein Zinkfinger-Motiv und bindet Eisenionen. Erste Immunfluoreszenz-Analysen lokalisieren die PfGAK in den Mitochondrien. PfAK und PfGAK werden von den Dinukleosid-Pentaphosphat-Verbindungen AP5A beziehungsweise GP5A gehemmt. Die Ki-Werte liegen mit ca. 0.2 µM ungefähr 250-fach niedriger als die KM-Werte der entsprechenden Nukleotidsubstrate. Zur Lösung der vor allem im Rahmen einer rationalen Medikamentenentwicklung notwendigen Kristallstruktur des Zielmoleküls konnten bereits Kristalle der PfGAK erhalten werden. / In mammalia, two major systems with glutathione reductase (GR) and thioredoxin reductase (TrxR) as key enzymes defend the organism against oxidative stress. The single copy gene dmtrxr-1 codes for both the cytoplasmic and mitochondrial form of DmTrxR-1, generated by alternative splicing. Another gene, located on the complementary strand partially within the dmtrxr-1 gene, could be identified and was named sniffer. This gene is essential for prevention of age-related neuro-degeneration, as could be shown in a cooperation with the group of Prof. Schneuwly. In this thesis, biochemical characterization of the recombinant protein identified sniffer as a carbonyl reductase, an enzyme belonging to the short-chain-dehydrogenases. Sniffer shows the typical substrate spectrum of carbonyl reductases with phenthrenequinone as best substrate and is inhibited by the flavonoids quercetin and rutin and also by hydroxymercurybenzoate (HMB). Protein crystals could be obtained under different conditions. In a cooperation with the group of Prof. Klebe, these already lead to a crystal structure with a resolution of 1.7 angstrom. The work on sniffer is the first that directly links a characterized gene (sniffer), oxidative stress and neurodegeneration on the molecular level. For coping with energetic and synthetic challenges, parasites require high activities of adenylate kinase (AK; ATP + AMP &#61683; 2 ADP) and GTP:AMP phosphotransferase (GAK; GTP + AMP &#61683; 2 ADP). These enzymes were identified in bloodstream stages of Plasmodium falciparum. The genes encoding PfAK and PfGAK are located on chromosomes 10 and 4, respectively. Molecular cloning and heterologous expression in E. coli yielded enzymatically active proteins of 28.9 (PfAK) and 28.0 kDa (PfGAK). Recombinant PfAK resembles authentic PfAK in its biochemical characteristics including the possible association with a stabilizing protein and the high specificity for AMP as the mononucleotide substrate. Specificity is less stringent for the triphosphate, with ATP as the best substrate (75 U/mg; kcat = 2160 min-1). PfAK contains the sequence of the amphiphatic helix that is known to mediate translocation of the cytosolic protein into the mitochondrial intermembrane space. PfGAK exhibits substrate preference for GTP and AMP (100 U/mg; kcat = 2800 min-1); notably, there is no detectable activity with ATP. In contrast to its human orthologue (AK3), PfGAK contains a zinc finger motif and binds ionic iron. The dinucleoside pentaphosphate compounds AP5A and GP5A inhibited PfAK and PfGAK, respectively, with Ki values of appr. 0.2 µM which is more than 250-fold lower than the KM values determined for the nucleotide substrates. The disubstrate inhibitors are useful for studying the enzymatic mechanism of PfAK and PfGAK as well as their function in adenine nucleotide homeostasis; in addition, the chimeric inhibitors represent interesting lead compounds for developing nucleosides to be used as antiparasitic agents. To elucidate the structure which is necessary for the use as a drug target, crystallization studies have been performed and the first crystals could be obtained.

Diese Arbeit untersucht zelluläre Netzwerke mit dem Ziel, die so gewonnenen Einsichten medizinisch beziehungsweise biotechnologisch zu nutzen. Hierzu müssen zunächst Proteindomänen und wichtige regulatorische RNA Elemente erkannt werden. Dies geschieht für regulatorische Elemente in Nukleinsäuren am Beispiel von Iron Responsive Elements (IREs) in Staphylococcus aureus, wobei sich solche Elemente in viel versprechender Nähe zu exprimierten Sequenzen finden lassen (T. Dandekar, F. Du, H. Bertram (2001) Nonlinear Analysis 47(1): 225-34). Noch bedeutsamer als Ziele zur Medikamentenentwicklung gegen Parasiten sind Domänenunterschiede in Struktur und Sequenz bei Proteinen (T. Dandekar, F. Du, H. Bertram (2001) Nonlinear Analysis 47(1): 225-34). Ihre Identifikation wird am Beispiel eines potentiellen Transportproteins in Plasmodium falciparum exemplarisch dargestellt. Anschließend wird das Zusammenwirken von regulatorischen Elementen und Domänen in Netzwerken betrachtet (einschließlich experimenteller Daten). Dies kann einerseits zu allgemeineren Schlussfolgerungen über das Netzwerkverhalten führen, andererseits für konkrete Anwendungen genutzt werden. Als Beispiel wählten wir hier Redoxnetzwerke und die Bekämpfung von Plasmodien als Verursacher der Malaria. Da das gesamte Redoxnetzwerk einer lebenden Zelle mit Methoden der pH Wert Messung nur unzureichend zu erfassen ist, werden als alternative Messmethode für dieses Netzwerk Mikrokristalle der Glutathionreduktase als Indikatorsystem nach digitaler Verstärkung experimentell genutzt (H. Bertram, M. A. Keese, C. Boulin, R. H. Schirmer, R. Pepperkok, T. Dandekar (2002) Chemical Nanotechnology Talks III - Nano for Life Sciences). Um komplexe Redoxnetzwerke auch bioinformatisch zu modulieren, werden Verfahren der metabolischen Fluxanalyse vorgestellt und verbessert, um insbesondere ihrer Verzahnung besser gerecht zu werden und solche Netzwerke mit möglichst wenig elementaren Flussmoden zutreffend beschreiben zu können. Die Reduktion der Anzahl von Elementarmoden bei sehr großen metabolischen Netzwerken einer Zelle gelingt hier mit Hilfe unterschiedlicher Methoden und führt zu einer vereinfachten Darstellungsmöglichkeit komplexer Stoffwechselwege von Metaboliten. Dabei dient bei jeder dieser Methoden die biochemisch sinnvolle Definition von externen Metaboliten als Grundlage (T. Dandekar, F. Moldenhauer, S. Bulik, H. Bertram, S. Schuster (2003) Biosystems 70(3): 255-70). Allgemeiner werden Verfahren der Proteindomänenklassifikation sowie neue Strategien gegen mikrobielle Erreger betrachtet. In Bezug auf automatisierte Einteilung von Proteinen in Domänen wird ein neues System von Taylor (2002b) mit bekannten Systemen verglichen, die in unterschiedlichem Umfang menschlichen Eingriffs bedürfen (H. Bertram, T. Dandekar (2002) Chemtracts 15: 735-9). Außerdem wurde neben einer Arbeit über die verschiedenen Methoden aus den Daten eines Genoms Informationen über das metabolische Netzwerk der Zelle zu erlangen (H. Bertram, T. Dandekar (2004) it 46(1): 5-11) auch eine Übersicht über die Schwerpunkte der Bioinformatik in Würzburg zusammengestellt (H. Bertram, S. Balthasar, T. Dandekar (2003) Bioforum 1-2: 26-7). Schließlich wird beschrieben, wie die Pathogenomik und Virulenz von Bakterien der bioinformatischen Analyse zugänglich gemacht werden können (H. Bertram, S. Balthasar, T. Dandekar (2003) Bioforum Eur. 3: 157-9). Im letzten Teil wird die metabolische Fluxanalyse zur Identifikation neuer Strategien zur Bekämpfung von Plasmodien dargestellt: Beim Vergleich der Stoffwechselwege mit Glutathion und Thioredoxin in Plasmodium falciparum, Anopheles und Mensch geht es darum, gezielte Störungen im Stoffwechsel des Malariaerregers auszulösen und dabei den Wirt zu schonen. Es ergeben sich einige interessante Ansatzpunkte, deren medizinische Nutzung experimentell angestrebt werden kann. / The objective of this thesis is to obtain information, which may be advantageous for biotechnical and medical purposes. In order to achieve this aim it is first necessary to identify protein domains and essential regulatory RNA elements. In case of regulatory RNA elements this is accomplished by investigating Iron Responsive Elements (IREs) in Staphylocuccus aureus as a model. In this case these elements are found in much promising vicinity to open reading frames coding for proteins (T. Dandekar, F. Du, H. Bertram (2001) Nonlinear Analysis 47(1): 225-34). Even more significant for the purpose of developing pharmaceuticals against parasites are differences of structure and sequence in protein domains (T. Dandekar, F. Du, H. Bertram (2001) Nonlinear Analysis 47(1): 225-34). Their identification is shown in a potential transport protein in Plasmodium falciparum. Subsequently the interaction of regulatory elements and domains in networks is considered (including experimental data). The resulting observations may lead to general conclusions concerning network reaction, as well as specific applications. Our example and field of interest are redox networks and Plasmodia causing malaria. It is not possible to cover the redox network state of a living cell using only pH measurements. Therefore small crystals of glutathione reductase are employed as a more suitable indicator, whose signal is digitally amplified (H. Bertram, M. A. Keese, C. Boulin, R. H. Schirmer, R. Pepperkok, T. Dandekar (2002) Chemical Nanotechnology Talks III - Nano for Life Sciences). In order to bioinformatically modulate complex redox networks techniques of metabolic flux analysis are presented. They are also improved particularly to advance the understanding of interdependences and to facilitate the correct comprehension of such networks with as few elementary flux modes as possible. In this thesis the reduction of the number of elementary modes of large and intertwined metabolic networks succeeds with various methods. This leads to a simpler model of complex metabolic functions. For each of the methods used in this process the biochemically justified definition of external and internal metabolites constitutes the basis (T. Dandekar, F. Moldenhauer, S. Bulik, H. Bertram, S. Schuster (2003) Biosystems 70(3): 255-70). In a more general sense methods of protein domain classification and new strategies for the control of microbial pathogens are considered. In reference to automated classification of protein domains a new system by Taylor (2002b) is compared with traditional systems, which require a varying degree of human intervention (H. Bertram, T. Dandekar (2002) Chemtracts 15: 735-9). In addition different methods of acquiring information on the cellular metabolic network from genomic data is discussed (H. Bertram, T. Dandekar (2004) it 46(1): 5-11). Furthermore a survey of the main fields of bioinformatic research in Würzburg is given (H. Bertram, S. Balthasar, T. Dandekar (2003) Bioforum 1-2: 26-7). Finally it is outlined how pathogenicity and virulence of bacteria may be made accessible to bioinformatic analysis (H. Bertram, S. Balthasar, T. Dandekar (2003) Bioforum Eur. 3: 157-9). In the conclusion metabolic flux analysis is used for the identification of new strategies in the battle against Plasmodia: The comparison of metabolic pathways with glutathione and thioredoxin in Plasmodium falciparum, Anopheles and man aims at raising planned dysfunctions in the metabolism of Plasmodium or Anopheles without harming the human host. Valuable suggestions for medical applications and pharmacological targets are obtained.