MSc (Biochemistry) / Department of Biochemistry / Sustaining proteostasis is essential for the survival of the cell and altered protein regulation leads to many cellular pathologies. Heat shock proteins (Hsps) are involved in the regulation of the protein quality control. Hsps are a group of molecular chaperones that are upregulated in response to cell stress and some are produced constitutively. The Hsp70 family also known as DnaK in Escherichia coli (E. coli) is the most well-known group of molecular chaperones. Structurally, Hsp70s consist of a nucleotide binding domain (NBD) and a substrate binding domain (SBD) conjugated by a linker sub-domain. ATP binding and hydrolysis is central to the Hsp70 functional cycle. Hsp70s play a role in cytoprotection especially during heat stress in E. coli. Hsp70s from different organisms are thought to exhibit specialized cellular functions. As such E. coli Hsp70 (DnaK) is a molecular chaperone that is central to proteostasis in E. coli. On the other hand, Plasmodium falciparum Hsp70s are structurally amenable to facilitate folding of P. falciparum substrates. The heterologous production of P. falciparum proteins in E. coli towards drug discovery has been a challenge. There is need to develop tools that enhance heterologous expression and proper folding of P. falciparum proteins in an E. coli expression system. To this end, a chimeric Hsp70, KPf consisting of E. coli DnaK NBD and P. falciparum Hsp70-1 (PfHsp70-1) SBD was previously designed. KPf was shown to confer cytoprotection to E. coli DnaK deficient cells that were subjected to heat stress. In this study it was proposed that KPf has an advantage over E. coli DnaK and PfHsp70-1 in its function as a protein folding chaperone. Therefore, the main aim of this study was to characterize the chaperone function of KPf relative to the function of wild type E. coli and P. falciparum Hsp70s. The recombinant forms of KPf, DnaK and PfHsp70-1 proteins were successfully expressed and purified using nickel affinity chromatography. Circular Dichroism (CD) structural study demonstrated that KPf and PfHsp70-1 are predominantly α-helical and are also heat stable. Tertiary structure studies of PfHsp70-1 and KPf using tryptophan fluorescence revealed that both confirmations of recombinant proteins are perturbed by the presence of ATP more than ADP. Interestingly, the substrate binding capabilities of these proteins were comparable both in the absence or presence of nucleotides ATP/ADP. KPf is an independent chaperone, that exhibit nucleotide binding and hydrolysis. The current study has established unique structure-function features of KPf that distinguishes it from its “parental” forms, DnaK and PfHsp70-1. / NRF

Introducción: La malaria es una enfermedad metaxénica producida por Plasmodium spp. Las especies que causan más daño en salud pública son P. vivax y P. falciparum. Malaria severa se refiere a un cuadro de malaria en presencia de alteraciones de signos físicos y laboratoriales definidos por la OMS. Aunque la malaria severa se ha relacionado tradicionalmente con malaria por P. falciparum, también está asociada a malaria por P. vivax. La prevalencia de malaria severa por P. vivax no ha sido bien estudiada. Por ello, el objetivo de este estudio fue identificar algunos factores epidemiológicos y clínicos asociados a malaria severa en los pacientes con malaria por Plasmodium vivax y Plasmodium falciparum, en la población de la provincia de Maynas entre los años 2014-2019. Métodos: Estudio observacional analítico de tipo transversal. Se revisaron todas las historias clínicas de pacientes con diagnóstico confirmado de malaria por P. vivax o P. falciparum del hospital Regional de Loreto en el periodo 2014-2019. Se determinó malaria severa por los criterios de la OMS y se estratificaron los casos por especie. Luego, se realizaron análisis univariados, bivariados, y multivariados; en las que los factores asociados a malaria severa eran las variables independientes, y tener malaria severa por una u otra especie eran las variables dependientes. Para realizar el análisis multivariado se usó el modelo lineal generalizado de la familia Poisson para obtener razones de prevalencia crudas y ajustadas (RP). Resultados: Se revisaron 590 historias clínicas de pacientes con malaria del Hospital Regional de Loreto. De estas, 456 historias tenían información sobre algún criterio para evaluar malaria severa. Se encontró malaria severa en 55 (16,2%) pacientes con malaria por P. vivax, y en 22 (19%) pacientes con malaria por P. falciparum. En los análisis multivariados, no se encontraron asociación entre malaria severa ni por P. vivax ni por P. falciparum, con la edad, sexo, episodios previos de malaria, ocupación ni número de leucocitos en sangre. Conclusiones: En el Hospital Regional de Loreto, la frecuencia de malaria de malaria severa por P. vivax y P. falciparum fue de 16,2% y 19,0%, respectivamente. Los criterios de malaria severa más prevalentes fueron anemia severa (9,3%) e injuria renal aguda (14,5%). No se encontró asociación entre malaria severa ni por P. vivax ni por P. falciparum, y la edad, sexo, episodios previos de malaria, ocupación ni número de leucocitos en sangre. / Introduction: Malaria is a vector-borne disease caused by Plasmodium spp. The most important species and that cause more damage in Public Health are P. vivax and P. falciparum. Severe malaria refers to malaria episodes with altered physical and laboratory signs defined by the WHO. Although severe malaria has traditionally been associated with P. falciparum, it is also associated with P. vivax malaria. The prevalence of severe P. vivax malaria has not been well studied. Therefore, the objective of this study was to identify some epidemiological and clinical factors associated with severe malaria in patients with malaria caused by Plasmodium vivax and Plasmodium falciparum, in the population of the province of Maynas between the years 2014-2019. Methods: Cross-sectional and analytical observational study. All the medical records of patients with a confirmed diagnosis of P. vivax or P. falciparum malaria from the “Hospital Regional de Loreto” in the period 2014-2019 were reviewed. Severe malaria was determined by the 2015 WHO criteria and cases were stratified by species. Then, univariate, bivariate, and multivariate analyzes were performed; in which factors associated with severe malaria were the independent variables, and having severe malaria due to one or another species were the dependent variables. To perform the multivariate analysis, the generalized linear model of the Poisson family was used to obtain crude and adjusted prevalence ratios (PR). Results: We reviewed 590 medical charts of patients with malaria from the “Hospital Regional de Loreto”. Out of them, 456 charts had some criteria to evaluate severe malaria. Severe malaria was found in 55 (16.2%) patients with P. vivax malaria, and in 22 (19%) patients with P. falciparum malaria. In the multivariate analyzes, no association was found between severe malaria neither by P. vivax nor by P. falciparum, and age, sex, previous malaria episodes, occupation or leukocytes count. Conclusions: The prevalence of severe malaria due to P. vivax and P. falciparum was 16.2% and 19,0%, respectively. No association was found between severe malaria neither by P. vivax nor by P. falciparum, and age, sex, previous malaria episodes, occupation or leukocytes count. / Tesis

Duplications and deletions are a major source of genomic variation. Duplications, specifically, have a significant impact on gene genesis and dosage, and the malaria parasite P. falciparum has developed resistance to a growing number of anti-malarial drugs via gene duplication. It also contains highly duplicated families of antigenically variable allelic genes. While specific genes and families have been studied, a comprehensive analysis of duplications and deletions within the reference genome and population has not been performed. We analyzed the extent of segmental duplications (SD) in the reference genome for P. falciparum, primarily by a whole genome self alignment. We discovered that while 5% of the genome identified as SD, the distribution within the genome was partition clustered, with the vast majority localized to the subtelomeres. Within the SDs, we found an overrepresentation of genes encoding antigenically diverse proteins exposed to the extracellular membrane, specifically the var, rifin, and stevor gene families. To examine variation of duplications and deletions within the parasite populations, we designed a novel computational methodology to identify copy number variants (CNVs) from high throughput sequencing, using a read depth based approach refined with discordant read pairs. After validating the program against in vitro lab cultures, we analyzed isolates from Senegal for initial tests into clinical isolates. We then expanded our search to a global sample of 610 strains from Africa and South East Asia, identifying 68 CNV regions. Geographically, genic CNV were found on average in less than 10% of the population, indicating that CNV are rare. However, CNVs at high frequency were almost exclusively duplications associated with known drug resistant CNVs. We also identified the novel biallelic duplication of the crt gene – containing both the chloroquine resistant and sensitive allele. The synthesis of our SD and CNV analysis indicates a CNV conservative P. falciparum genome except where drug and human immune pressure select for gene duplication.

Each year countless lives are affected and about half a million people die from malaria, a disease caused by parasites originating from the Plasmodium family. The most virulent species of the parasite is Plasmodium falciparum (P. falciparum).   Calmodulin (CaM) is a small, 148 amino acid long, highly preserved and essential protein in all eukaryotic cells. Previous studies have determined that CaM is important for the reproduction and invasion of P. falciparum in host cells. The primary structure of human CaM (CaMhum) and CaM from P. falciparum (CaMpf) differ in merely 16 positions, making differences in their structures and ligand affinity interesting to study. Especially since possible inhibitors of CaMpf in favor of CaMhum, in extension, could give rise to new malaria treatments.   Some antagonists, functioning as inhibitors of CaM, have already been analysed in previous studies. However, there are also compounds that have not yet been studied in regards to being possible antagonists of CaM. This study regards three known antagonists; trifluoperazine (TFP), calmidazolium (CMZ) and artemisinin (ART) and also three recently created fentanyl derivatives; 3-OH-4-OMe-cyclopropylfentanyl (ligand 1), 4-OH-3OMe-4F-isobutyrylfentanyl (ligand 2) and 3-OH-4-OMe-isobutyrylfentanyl (ligand 3).   Bioinformatic methods, such as modelling and docking, were used to compare the structures of CaMhum and CaMpf as well as observe the interaction of the six ligands to CaM from both species. In addition to the differences in primary structure, distinguished with ClustalW, disparities in tertiary structure were observed. Structure analysis of CaMhum and CaMpf in PyMOL disclosed a more open conformation as well as a larger, more defined, hydrophobic cleft in CaMhum compared to CaMpf. Simulated binding of the six ligands to CaM from both species, using Autodock 4.2, indicated that TFP and ART bind with higher affinity to CaMhum which is expected. Ligand 2 and ligand 3 also bound with higher affinity and facilitated stronger binding to CaMhum, which is reasonable since their docking is based on how TFP binds to CaM. However, ligand 1 as well as CMZ both bound to CaMpf with higher affinity. Despite promising results for ligand 1 and CMZ, no decisive conclusion can be made solely based on bioinformatic studies.    To gain a better understanding on the protein-ligand interactions of the six ligands to CaMhum and CaMpf, further studies using e.g. circular dichroism and fluorescence would be advantageous. Based on the results from this study, future studies on the binding of CMZ and ligand 1 to CaM as well as ligands with similar characteristics would be especially valuable. This is because they, based on the results from this study, possibly are better inhibitors of CaMpf than CaMhum and thereby could function as possible antimalarial drugs.

Previously it has been shown that cultures of Plasmodium falciparum died following exposure to a febrile temperature of 40°C, as demonstrated by a decrease in parasitemia of the following generation. In the current study, the effect of 40°C treatment on culture media, erythrocytes, and parasite glucose consumption, were ruled out as possible influences on parasite death, demonstrating that 40°C impacted the parasites directly. Metabolic profiling of DNA synthesis, protein synthesis, and glucose utilization during exposure to 40°C clearly indicated that febrile temperatures had direct effect on major metabolic pathways and parasite development, beginning 20-24 hr after erythrocyte invasion. The ring stages were relatively refractory to heat and recovered completely if returned to 37°C. The mechanism of parasite death was investigated for evidence of an apoptosis-like pathway in cells treated with 40°C, chloroquine, and staurosporine. Lack of typical physiological hallmarks, namely, caspase activation, characteristic mitochondrial membrane potential changes, and DNA degradation as indicated by DNA laddering, eliminated ‘classical’, apoptosis as a mechanism of parasite death. Parasites dying under the influence of 40°C, staurosporine, and chloroquine initially appeared pyknotic in light and electron microscopy, as in apoptosis, but eventual swelling and lysis of the food vacuole membrane led to secondary necrosis. Initially, chloroquine did induce DNA laddering, but it was later attributed to occult white blood cell contamination. While not apoptosis, the results do not rule out other forms of temperature-induced programmed cell death.

Association of Commonwealth Universities. Commonwealth Scholarship Commission. United Kingdom.

Malaria, caused by the parasite Plasmodium falciparum, has a long history as a global health threat. The vector-borne disease causes millions of deaths yearly, especially in developing countries with tropical climates that facilitate transmission. Compounding the problem is the emergence of drug-resistant strains due to overuse of outdated treatments. New compounds with antiplasmodial activity are needed to be developed as effective drugs against malaria. The hypothesis for this project is that marine microorganisms have a high likelihood of yielding novel antiplasmodial chemotypes because of their high diversity, which has not yet been explored for antimalarial development. In this project, microbes harvested and fermented by the Harbor Branch Oceanographic Institute in Fort Pierce, Florida were explored as sources for antiplasmodial natural products. Using a SYBR Green I fluorescence-based assay, 1,000 microbial extracts were screened for inhibition of the multidrug-resistant Plasmodium falciparum strain Dd2. Dose-response analysis was performed on 46 fractions from isolates whose extracts demonstrated greater-than or equal to] 70% inhibition of Dd2 at 1 micro]g/mL. To evaluate cytotoxicity, the MTS cell viability assay was used to calculate IC50 of extracts from active isolates in NIH/3T3 embryonic mouse fibroblasts. Several extracts demonstrated low IC50 in Dd2 and high IC50 in 3T3, suggesting that they contain potential lead antimalarial compounds. Extracts with high selectivity indices (potent plasmodial inhibition with low mammalian toxicity) have been prioritized for dereplication, with the goal of identifying novel active components that can be developed as antimalarial drugs.

Female adults of many mosquito species possess distinct physiological features adapting to blood feeding for successful reproduction. The disease pathogens that are transmitted by mosquitoes have evolved to take advantages of the indispensable blood feedings to complete their transmission cycles and to survive attacks from the mosquito's innate immune system. Normal egg development and mosquito immunity are tightly controlled by tissue- and stage-specific gene expression and coordinated by many signal molecules in the mosquito. Understanding gene regulation affecting mosquito reproduction and malaria parasites infection is of paramount importance for developing novel malaria control strategies. A growing body of evidence indicates that microRNAs (miRNAs) are involved in egg maturation and immune reactions against invading pathogens in mosquitoes. However, the molecular mechanisms by which specific miRNAs selectively modulate reproduction and the survival of pathogens are largely unknown. The miRNA-induced gene-silencing pathway in mosquitoes was mostly extrapolated from the studies of flies. To explore the dynamics of miRNAs in reproduction, I used small RNAs sequencing to monitor miRNAs expression and their association with Argonaute 1 (Ago1) and Argonaute 2 (Ago2) in the malaria mosquito Anopheles gambiae (An. gambiae) during the 72-h period immediately after blood feeding. I found the abundance and Ago loading of most of the mature miRNAs were relatively stable after blood ingestion. However, miRNAs of the miR-309/286/2944 cluster were considerably upregulated after blood feeding. I confirmed that miR-309 is essential for normal egg development by depletion of endogenous miR-309 with a specific antagomir. In addition, my results showed that the Ago association of some miRNAs was not proportional to their cellular abundance implying additional regulation at miRNA integration. To investigate the functional roles of miRNAs and define context-dependent miRNA-mRNA interactions during the reproductive process, I have applied an innovative experimental approach to study miRNA-mRNA interactome. CLEAR (covalent ligation of endogenous Argonaute-bound RNAs)-CLIP can generate miRNA-mRNA chimeras from UV-irradiation stabilized Ago-miRNA-mRNA complex. My results have defined tens of thousands of miRNA-mRNA interactions in mosquitoes, including novel targets for mosquito-specific miRNAs. Verification of the predicted interactions using mRNA-seq, ribosome-profiling, and luciferase reporter assay revealed a reliable miRNA-mRNA interaction network. Based on the detected interactions, I refined the paring rules for mosquito miRNAs and illustrated the dynamic pairing between different regions of miRNAs with their targets in vivo. The miRNA-mRNA interactions were compared using this approach at multiple time points before and after blood feeding. Importantly, this study showed that the interactions were dynamic and enriched in genes that are involved in metabolisms, supporting the proposed functions of miRNAs in coordinating the gene regulation in mosquito reproduction. Plasmodium falciparum (P. falciparum) is a major human malaria parasite. To understand the functions of miRNAs in the mosquito resistance to Plasmodium infection, we analyzed the miRNA-mRNA interactions after female mosquitoes taking a P. falciparum-infected blood meal or an uninfected blood meal. Comparison of the interactions revealed enhanced miRNA-mRNA interactions after P. falciparum infection involving a group of immunity-related genes. In summary, this study has provided a systematic view and significantly advanced our understanding of the miRNA functions in mosquito reproduction and P. falciparum infection. / PHD / Female mosquito is able to transmit lots of disease to the human when it bites for blood. The blood meal provides necessary nutrient for mosquito reproduction and spread the pathogens such as malaria and Zika at the same time. Thus understanding the molecular mechanism behind this process would be greatly helpful to develop novel vector control strategy. Here, we found a distinct class of RNAs contributing to the regulation of mosquito blood meal and parasite infection. We used a novel biochemical method to decoding the special role of these kinds of RNAs in these processes. We found them regulating mosquito metabolism and immunity. This study significantly deepened our knowledge about the process of mosquito reproduction and transmitting diseases.

Neste estudo avaliamos a resposta imune humoral de indivíduos naturalmente expostos à malária em áreas endêmicas no Brasil. Os anticorpos IgG, IgG1, IgG2, IgG3, IgG4, IgM, IgE e IgA anti-formas eritrocitárias de Plasmodium falciparum foram determinadas por ELISA. Anticorpos IgG, IgG1, IgG2 de alta avidez e IgG3 de baixa avidez predominaram nos indivíduos sem complicações de malária ou assintomáticos, enquanto anticorpos IgG4, IgE e IgM predominaram nos indivíduos com complicações clínicas por malária. Os resultados mostram que mesmo em regiões com transmissão instável de malária pode ser observado o desenvolvimento de imunidade protetora quando anticorpos apropriados são produzidos / In this study, we have evaluated the humoral immune response of individuals naturally exposed to malaria living in endemic areas of Brazil. We determined IgG, IgG1, IgG2, IgG3, IgG4, IgM, IgE and IgA antibodies against Plasmodium falciparum blood stages by ELISA. We observed that the level of high avidity IgG, IgG1 and IgG2 and low avidity IgG3 antibodies were higher in asymptomatic individuals or with uncomplicated malaria, while IgG4, IgE and IgM antibodies were higher in individuals with complicated malaria. Taken together the results showed that even in unstable malaria regions it can be observed the development of protective immunity against malaria when appropriate antibodies are produced

Neste estudo avaliamos a resposta imune humoral de indivíduos naturalmente expostos à malária em áreas endêmicas no Brasil. Os anticorpos IgG, IgG1, IgG2, IgG3, IgG4, IgM, IgE e IgA anti-formas eritrocitárias de Plasmodium falciparum foram determinadas por ELISA. Anticorpos IgG, IgG1, IgG2 de alta avidez e IgG3 de baixa avidez predominaram nos indivíduos sem complicações de malária ou assintomáticos, enquanto anticorpos IgG4, IgE e IgM predominaram nos indivíduos com complicações clínicas por malária. Os resultados mostram que mesmo em regiões com transmissão instável de malária pode ser observado o desenvolvimento de imunidade protetora quando anticorpos apropriados são produzidos / In this study, we have evaluated the humoral immune response of individuals naturally exposed to malaria living in endemic areas of Brazil. We determined IgG, IgG1, IgG2, IgG3, IgG4, IgM, IgE and IgA antibodies against Plasmodium falciparum blood stages by ELISA. We observed that the level of high avidity IgG, IgG1 and IgG2 and low avidity IgG3 antibodies were higher in asymptomatic individuals or with uncomplicated malaria, while IgG4, IgE and IgM antibodies were higher in individuals with complicated malaria. Taken together the results showed that even in unstable malaria regions it can be observed the development of protective immunity against malaria when appropriate antibodies are produced