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Background: The Andean condor (Vultur gryphus) is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome. Methods: This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways. Results: Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with Clostridium perfringens, a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for Clostridium perfringens and Plesiomonas shigelloides, respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.
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Falconiformes , Microbioma Gastrointestinal , Animais , Microbioma Gastrointestinal/genética , Metagenômica , Aclimatação , Chile , Clostridium perfringensRESUMO
During its life cycle, Trypanosoma cruzi undergoes physiological modifications in order to adapt to insect vector and mammalian host conditions. Metacyclogenesis is essential, as the parasite acquires the ability to infect a variety of mammalian species, including humans, in which pathology is caused. In this work, the transcriptomes of metacyclic trypomastigotes and epimastigotes were analyzed in order to identify differentially expressed genes that may be involved in metacyclogenesis. Toward this end, in vitro induction of metacyclogenesis was performed and metacyclic trypomastigotes obtained. RNA-Seq was performed on triplicate samples of epimastigotes and metacyclic trypomastigotes. Differential gene expression analysis showed 513 genes, of which 221 were upregulated and 292 downregulated in metacyclic trypomastigotes. The analysis showed that these genes are related to biological processes relevant in metacyclogenesis. Within these processes, we found that most of the genes associated with infectivity and gene expression regulation were upregulated in metacyclic trypomastigotes, while genes involved in cell division, DNA replication, differentiation, cytoskeleton, and metabolism were mainly downregulated. The participation of some of these genes in T. cruzi metacyclogenesis is of interest, as they may be used as potential therapeutic targets in the design of new drugs for Chagas disease.
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Doença de Chagas , Trypanosoma cruzi , Humanos , Animais , Trypanosoma cruzi/fisiologia , Colômbia , Regulação da Expressão Gênica , Diferenciação Celular , MamíferosRESUMO
Aspergillus welwitschiae causes bole rot disease in sisal (Agave sisalana and related species) which affects the production of natural fibers in Brazil, the main worldwide producer of sisal fibers. This fungus is a saprotroph with a broad host range. Previous research established A. welwitschiae as the only causative agent of bole rot in the field, but little is known about the evolution of this species and its strains. In this work, we performed a comparative genomics analysis of 40 Aspergillus strains. We show the conflicting molecular identity of this species, with one sisal-infecting strain sharing its last common ancestor with Aspergillus niger, having diverged only 833 thousand years ago. Furthermore, our analysis of positive selection reveals sites under selection in genes coding for siderophore transporters, Sodiumcalcium exchangers, and Phosphatidylethanolamine-binding proteins (PEBPs). Herein, we discuss the possible impacts of these gene functions on the pathogenicity in sisal.
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Agave , Agave/genética , Brasil , Aspergillus/genéticaRESUMO
Gene Regulatory Networks (GRNs) allow the study of regulation of gene expression of whole genomes. Among the most relevant advantages of using networks to depict this key process, there is the visual representation of large amounts of information and the application of graph theory to generate new knowledge. Nonetheless, despite the many uses of GRNs, it is still difficult and expensive to assign Transcription Factors (TFs) to the regulation of specific genes. ChIP-Seq allows the determination of TF Binding Sites (TFBSs) over whole genomes, but it is still an expensive technique that can only be applied one TF at a time and requires replicates to reduce its noise. Once TFBSs are determined, the assignment of each TF and its binding sites to the regulation of specific genes is not trivial, and it is often performed by carrying out site-specific experiments that are unfeasible to perform in all possible binding sites. Here, we addressed these relevant issues with a two-step methodology using Drosophila melanogaster as a case study. First, our protocol starts by gathering all transcription factor binding sites (TFBSs) determined with ChIP-Seq experiments available at ENCODE and FlyBase. Then each TFBS is used to assign TFs to the regulation of likely target genes based on the TFBS proximity to the transcription start site of all genes. In the final step, to try to select the most likely regulatory TF from those previously assigned to each gene, we employ GENIE3, a random forest-based method, and more than 9,000 RNA-seq experiments from D. melanogaster. Following, we employed known TF protein-protein interactions to estimate the feasibility of regulatory events in our filtered networks. Finally, we show how known interactions between co-regulatory TFs of each gene increase after the second step of our approach, and thus, the consistency of the TF-gene assignment. Also, we employed our methodology to create a network centered on the Drosophila melanogaster gene Hr96 to demonstrate the role of this transcription factor on mitochondrial gene regulation.
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Since 2014, the ISCB Latin American Student Council Symposium (LA-SCS) serves as the main biannual activity where students from all levels, postdocs and early researchers from the entire Latin American region can gather to discuss recent advances in the fields of bioinformatics and computational biology. This time we faced a major unexpected obstacle, a worldwide pandemic that has completely disrupted human activities at a planetary scale. Countless conferences have been either canceled, reprogrammed for the next year or moved to a virtual format. However, thanks to an important strengthening of the Latin American student network and the creation of several new RSGs in the continent, we were able to get together a fearless team that aimed to overcome the pandemic obstacles and still organise the 4th LA-SCS. Here we summarize our experiences in our first virtual symposium.
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COVID-19 , Biologia Computacional/organização & administração , Congressos como Assunto/organização & administração , Humanos , América Latina , Pandemias , EstudantesRESUMO
Staphylococcus aureus represent a serious threat to public health due to food safety, antibiotic resistance, and the potential zoonotic transmission of strains between dairy cattle and humans. Biofilm formation by S. aureus results in chronicity of the infections which confers protection against the immune response and antibiotics. Likewise, biofilm allows the exchange of mobile genetic material among different strains through microbial interactions inside the matrix. In Colombia, where S. aureus continues to be one of the main pathogens isolated from bovine intramammary infections and where milking by hand is highly frequent, there are knowledge gaps on the zoonotic potential of the strains. Therefore, the aim of this work was to characterize genotypically and phenotypically the S. aureus Sa1FB strain with strong biofilm production and to perform genomic and phenotypic comparisons with other relevant S. aureus strains (native and references strains). These results show a highly productive strain of biofilm and a low ability of cell invasion compared to the other two native strains. In addition, high genomic similarity between S. aureus Sa1FB and the reference strains was observed, despite of the differences reported at the clinical level. However, Sa1FB exhibited special features in terms of mobile genetic elements, highlighting its ability to accept foreign genetic material. Indeed, this could increase mutation, pathogenesis, and adaptability to new hosts, representing a risk for people in contact with the milk obtained from animals infected with these strains. These results present the relevance of surveillance for early detection of emergent clones with zoonotic potential, which reduces the risk of occupational exposure and their spread in the community.
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Bacteria inside biofilms are more persistent and resistant to stress conditions found in the production environment of food processing plants, thus representing a constant risk for product safety and quality. Therefore, the aim of this study was to characterize, using 16S rRNA sequencing, the bacterial communities from biofilms found in four food processing plants (P1, P2, P3, and P4). In total, 50 samples from these four processing plants were taken after cleaning and disinfection processes. Four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroides represented over 94% of the operational taxonomic units found across these four plants. A total of 102 families and 189 genera were identified. Two genera, Pseudomonas spp. and Acinetobacter spp., were the most frequently found (93.47%) across the four plants. In P1, Pseudomonas spp. and Lactobacillus spp. were the dominant genera, whereas Lactobacillus spp. and Streptococcus spp. were identified in P2. On the other hand, biofilms found in P3 and P4 mainly consisted of Pseudomonas spp. and Acinetobacter spp. Our results indicate that different bacterial genera of interest to the food industry due to their ability to form biofilm and affect food quality can coexist inside biofilms, and as such, persist in production environments, representing a constant risk for manufactured foods. In addition, the core microbiota identified across processing plants evaluated was probably influenced by type of food produced and cleaning and disinfection processes performed in each one of these.
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Bactérias/genética , Biofilmes , Contaminação de Equipamentos/estatística & dados numéricos , Manipulação de Alimentos/instrumentação , Microbiota , Bactérias/classificação , Bactérias/isolamento & purificação , Colômbia , Desinfecção , Metagenoma , MetagenômicaRESUMO
Systemic sclerosis (SSc) is a rare immune-mediated vasculopathy characterized by fibrosis of the skin and internal organs. Fabry disease (FD) is an X-linked lysosomal storage disorder caused by mutations in the GLA gene producing α-galactosidase-A enzyme (α-Gal A) deficiency. Being a systemic disease, cardiac involvement in FD has a high mortality rate due to heart failure and arrhythmia. The coexistence of these two entities has not been reported previously. We describe the case of a female patient with limited SSc (lcSSc), a diagnosis based on the presence of sclerodactyly, Raynaud phenomenon, microvascular involvement, and positive anti-centromere antibodies. On follow-up, she developed chest pain, a second-degree A-V block, and restrictive cardiomyopathy (without cardiovascular risk factors). Although heart involvement is common in these two entities, the abnormal thickening of lateral and inferior wall, the infiltration pattern and the conduction system disorders presented herein are more characteristic in a heterozygous female with a cardiac variant of FD. The diagnosis of FD was confirmed with high globotriaosylsphingosine (Lyso-Gb3) levels and identification of GLA gene mutation. The patient was treated with enzymatic replacement (agalsidase alpha) following mild improvement in ventricular mass at 6th month, without clinical deterioration. The related literature on SSc associated with FD is also reviewed.
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Cardiomiopatia Restritiva/complicações , Doença de Fabry/complicações , Escleroderma Sistêmico/complicações , Feminino , Humanos , Pessoa de Meia-IdadeRESUMO
The study of molecular host-parasite interactions is essential to understand parasitic infection and adaptation within the host system. As well, prevention and treatment of infectious diseases require a clear understanding of the molecular crosstalk between parasites and their hosts. Yet, large-scale experimental identification of host-parasite molecular interactions remains challenging, and the use of computational predictions becomes then necessary. Here, we propose a computational integrative approach to predict host-parasite protein-protein interaction (PPI) networks resulting from the human infection by 15 different eukaryotic parasites. We used an orthology-based approach to transfer high-confidence intraspecies interactions obtained from the STRING database to the corresponding interspecies homolog protein pairs in the host-parasite system. Our approach uses either the parasites predicted secretome and membrane proteins, or only the secretome, depending on whether they are uni- or multi-cellular, respectively, to reduce the number of false predictions. Moreover, the host proteome is filtered for proteins expressed in selected cellular localizations and tissues supporting the parasite growth. We evaluated the inferred interactions by analyzing the enriched biological processes and pathways in the predicted networks and their association with known parasitic invasion and evasion mechanisms. The resulting PPI networks were compared across parasites to identify common mechanisms that may define a global pathogenic hallmark. We also provided a study case focusing on a closer examination of the human-S. mansoni predicted interactome, detecting central proteins that have relevant roles in the human-S. mansoni network, and identifying tissue-specific interactions with key roles in the life cycle of the parasite. The predicted PPI networks can be visualized and downloaded at http://orthohpi.jensenlab.org.
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Interações Hospedeiro-Parasita , Parasitos/fisiologia , Doenças Parasitárias/parasitologia , Animais , Biologia Computacional/métodos , Interações Hospedeiro-Parasita/genética , Interações Hospedeiro-Parasita/imunologia , Humanos , Modelos Biológicos , Doenças Parasitárias/genética , Doenças Parasitárias/imunologia , Doenças Parasitárias/metabolismo , Mapeamento de Interação de Proteínas , Proteínas de Protozoários/metabolismoRESUMO
In host-parasite systems, protein-protein interactions are key to allow the pathogen to enter the host and persist within the host. The study of host-parasite molecular communication improves the understanding the mechanisms of infection, evasion of the host immune system and tropism across different tissues. Current trends in parasitology focus on unraveling host-parasite protein-protein interactions to aid the development of new strategies to combat pathogenic parasites with better treatments and prevention mechanisms. Due to the complexity of capturing experimentally these interactions, computational approaches integrating data from different sources (mainly "omics" data) become key to complement or support experimental approaches. Here, we focus on the application of experimental and computational methods in the prediction of host-parasite interactions and highlight the potential of each of these methods in specific contexts.
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Simulação por Computador , Interações Hospedeiro-Parasita/fisiologia , Modelos BiológicosRESUMO
Helminths cause a number of medical and agricultural problems and are a major cause of parasitic infections in humans, animals and plants. Comparative analysis of helminth genes and genomes are important to understand the genomic biodiversity and evolution of parasites and their hosts in terms of different selective pressures in their habitats. The interactions between the infective organisms and their hosts are mediated in large part by secreted proteins, known collectively as the "secretome". Proteins secreted by parasites are able to modify a host's environment and modulate their immune system. The composition and function of this set of proteins varies depending on the ecology, lifestyle and environment of an organism. The present study aimed to predict, in silico, the secretome in 44 helminth species including Nematoda (31 species) and Platyhelminthes (13 species) and, understand the diversity and evolution of secretomes. Secretomes from plant helminths range from 7.6% (943 proteins) to 13.9% (2,077 proteins) of the filtered proteome with an average of 10.2% (1,412 proteins) and from free-living helminths range from 4.4% (870 proteins) to 13% (3,121 proteins) with an average of 9.8% (2,126 proteins), respectively, and thus are considerably larger secretomes in relation to animal helminth secretomes which range from 4.2% (431 proteins) to 11.8% (2,419 proteins) of the proteomes, with an average of 7.1% (804 proteins). Across 44 secretomes in different helminth species, we found five conserved domains: (i) PF00014 (Kunitz/Bovine pancreatic trypsin inhibitor domain), (ii) PF00046 (Homeobox domain), (iii) PF00188 (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins), (iv) PF00085 (Thioredoxin) and (v) PF07679 (Immunoglobulin I-set domain). Our results detected secreted proteins associated with invasion, infection, adhesion and immunoregulation processes as protease inhibitors and cytokines, among other functions. In summary, this study will contribute towards the understanding of host-parasite interactions and possibly identify new molecular targets for the treatment or diagnosis of helminthiases.
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Proteínas de Helminto/metabolismo , Helmintos/metabolismo , Animais , Biodiversidade , Sequência Conservada , Genoma , Proteínas de Helminto/química , Proteínas de Helminto/fisiologia , Helmintos/classificação , Helmintos/genética , Helmintos/fisiologia , Interações Hospedeiro-Parasita , Estilo de Vida , Filogenia , Plantas/parasitologia , Domínios Proteicos , Sinais Direcionadores de Proteínas/fisiologia , Especificidade da EspécieRESUMO
INTRODUCTION: Despite efforts to control malaria, around 10% of the world population is at risk of acquiring this disease. Plasmodium falciparum accounts for the majority of severe cases and deaths. Malaria control programs have failed due to the therapeutic failure of first-line antimalarials and to parasite resistance. Thus, new and better therapeutic alternatives are required. Proteomic analysis allows determination of protein expression levels under drug pressure, leading to the identification of new therapeutic drug targets and their mechanisms of action. OBJECTIVE: The aim of this study was to analyze qualitatively the expression of P.falciparum trophozoite proteins (strain ITG2), after exposure to antimalarial drugs, through a proteomic approach. MATERIALS AND METHODS: In vitro cultured synchronized parasites were treated with quinine, mefloquine and the natural antiplasmodial diosgenone. Protein extracts were prepared and analyzed by two-dimensional electrophoresis. The differentially expressed proteins were selected and identified by MALDI-TOF mass spectrometry. RESULTS: The following proteins were identified among those differentially expressed in the parasite in the presence of the drugs tested: enolase (PF10_0155), calcium-binding protein (PF11_0098), chaperonin (PFL0740c), the host cell invasion protein (PF10_0268) and proteins related to redox processes (MAL8P1.17). These findings are consistent with results of previous studies where the parasite was submitted to pressure with other antimalarial drugs. CONCLUSION: The observed changes in the P. falciparum trophozoite protein profile induced by antimalarial drugs involved proteins mainly related to the general stress response.
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Antiprotozoários/farmacologia , Mefloquina/farmacologia , Plasmodium falciparum/efeitos dos fármacos , Proteínas de Protozoários/biossíntese , Quinina/farmacologia , Compostos de Espiro/farmacologia , Triterpenos/farmacologia , Sequência de Aminoácidos , Eletroforese em Gel Bidimensional , Eritrócitos/parasitologia , Regulação da Expressão Gênica/efeitos dos fármacos , Proteínas de Choque Térmico/biossíntese , Proteínas de Choque Térmico/genética , Proteínas de Choque Térmico/isolamento & purificação , Humanos , Técnicas In Vitro , Concentração Inibidora 50 , Dados de Sequência Molecular , Plasmodium falciparum/crescimento & desenvolvimento , Plasmodium falciparum/metabolismo , Proteoma , Proteínas de Protozoários/genética , Proteínas de Protozoários/isolamento & purificação , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por MatrizRESUMO
Introduction: Despite efforts to control malaria, around 10% of the world population is at risk of acquiring this disease. Plasmodium falciparum accounts for the majority of severe cases and deaths. Malaria control programs have failed due to the therapeutic failure of first-line antimalarials and to parasite resistance. Thus, new and better therapeutic alternatives are required. Proteomic analysis allows determination of protein expression levels under drug pressure, leading to the identification of new therapeutic drug targets and their mechanisms of action. Objective: The aim of this study was to analyze qualitatively the expression of P.falciparum trophozoite proteins (strain ITG2), after exposure to antimalarial drugs, through a proteomic approach. Materials and methods: In vitro cultured synchronized parasites were treated with quinine, mefloquine and the natural antiplasmodial diosgenone. Protein extracts were prepared and analyzed by two-dimensional electrophoresis. The differentially expressed proteins were selected and identified by MALDI-TOF mass spectrometry. Results: The following proteins were identified among those differentially expressed in the parasite in the presence of the drugs tested: enolase (PF10_0155), calcium-binding protein (PF11_0098), chaperonin (PFL0740c), the host cell invasion protein (PF10_0268) and proteins related to redox processes (MAL8P1.17). These findings are consistent with results of previous studies where the parasite was submitted to pressure with other antimalarial drugs. Conclusion: The observed changes in the P. falciparum trophozoite protein profile induced by antimalarial drugs involved proteins mainly related to the general stress response.
Introducción. A pesar de los esfuerzos para controlar la malaria, esta sigue siendo un problema de salud pública. Plasmodium falciparum es responsable de la mayoría de los casos graves y de las muertes. Los programas de control de la malaria han sido cuestionados debido al fracaso del tratamiento y a la resistencia del parásito a los antipalúdicos de primera línea, por lo que se requieren nuevas y mejores alternativas. El análisis proteómico permite identificar y determinar los niveles de expresión de las proteínas bajo la presión de los medicamentos, lo que posibilita la identificación de nuevos blancos terapéuticos y mecanismos de acción. Objetivo. Analizar cualitativamente la expresión diferencial de proteínas del citosol del trofozoíto de P. falciparum bajo tratamiento con quinina, mefloquina y el compuesto natural diosgenona mediante una aproximación proteómica. Materiales y métodos. Se trataron trofozoítos sincronizados y cultivados in vitro de P. falciparum (cepa ITG2) con quinina, mefloquina y el compuesto natural diosgenona. Los extractos proteicos se prepararon y analizaron por electroforesis bidimensional. Las proteínas con aparente expresión diferencial se seleccionaron e identificaron mediante espectrometría de masas MALDI-TOF. Resultados. Se encontraron las siguientes proteínas diferencialmente expresadas en el trofozoíto: la enolasa (PF10_0155), la proteína de unión a calcio (PF11_0098), la chaperonina (PFL0740c), la proteína de invasión a la célula del huésped (PF10_0268) y la proteína relacionada con procesos de reducción y oxidación (redox) (MAL8P1.17). Estos hallazgos son congruentes con resultados previos de estudios en los que el parásito fue presionado con otros medicamentos antipalúdicos. Conclusión. Los cambios observados en el perfil de proteínas del trofozoíto de P. falciparum tratado con antipalúdicos involucraron preferencialmente proteínas relacionadas con la respuesta al estrés general.
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Humanos , Antiprotozoários/farmacologia , Mefloquina/farmacologia , Plasmodium falciparum/efeitos dos fármacos , Proteínas de Protozoários/biossíntese , Quinina/farmacologia , Compostos de Espiro/farmacologia , Triterpenos/farmacologia , Sequência de Aminoácidos , Eletroforese em Gel Bidimensional , Eritrócitos/parasitologia , Regulação da Expressão Gênica/efeitos dos fármacos , Proteínas de Choque Térmico/biossíntese , Proteínas de Choque Térmico/genética , Proteínas de Choque Térmico/isolamento & purificação , Técnicas In Vitro , Dados de Sequência Molecular , Proteoma , Plasmodium falciparum/crescimento & desenvolvimento , Plasmodium falciparum/metabolismo , Proteínas de Protozoários/genética , Proteínas de Protozoários/isolamento & purificação , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por MatrizRESUMO
La malaria es una de las enfermedades parasitarias que causa mayor impacto en la salud pública en países en desarrollo. La secuenciación del genoma de Plasmodium falciparum y el desarrollo de la proteómica han permitido un gran avance en el conocimiento de la biología del parásito. La proteómica ha permitido caracterizar cualitativa y cuantitativamente la expresión de proteínas del parásito y ha proveído información de la expresión relativa de proteínas bajo condiciones de estrés como presión por antimaláricos. Dada la complejidad de su ciclo de vida, el cual se lleva a cabo en el hospedero vertebrado y el mosquito, se ha caracterizado la expresión de proteínas para cada estadio del parásito con el fin de determinar el proteoma que media diversos procesos metabólicos, fisiológicos y energéticos. Técnicas de electroforesis bidimensional, cromatografía líquida y espectrometría de masas, han sido útiles para evaluar los efectos de antimaláricos sobre la expresión de proteínas del parásito y caracterizar el proteoma de diferentes formas y organelas de P. falciparum. El propósito de esta revisión es presentar el estado del arte de los avances en proteómica aplicada al estudio de la malaria, y plantear las diferentes estrategias experimentales empleadas para el estudio del proteoma del parásito con el fin de describir las ventajas y desventajas de cada una de estas metodologías.
Malaria is a parasitic disease that has a high impact on public health in developing countries. The sequencing of the Plasmodium falciparum genome and the development of proteomics have enabled a breakthrough in understanding the biology of the parasite. Proteomics have allowed to characterize qualitatively and quantitatively the parasite s expression of proteins and has provided information on protein expression under conditions of estrés induced by antimalarials. Given the complexity of their life cycle, which takes place in the vertebrate host and mosquito vector. It has proven difficult to characterize the protein expression during each stage throughout the infection process in order to determine the proteome that mediates several metabolic, physiological and energetic processes. Two dimensional electrophoresis, liquid chromatography and mass spectrometry have been useful to assess the effects of antimalarials on parasite protein expression and to characterize the proteomic profile of differentt P. falciparum stages and organelles. The purpose of this review is to present state of the art tools and advances in proteomics applied to the study of malaria, and to present different experimental strategies used to study the parasite's proteome in order to show the advantages and disadvantages of each one.
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Objective. Using molecular simulation, we studied the influence of Mg2+ ions on the binding mode of HTLV-I Integrase (IN) catalytic domain (modeled by homology) with the 3,5- Dicaffeoylquinic Acid (DCQA). HTLV-I Integrase homology model was built using template-like crystallographic data of the IN catalytic domain solved for Avian Sarcoma Virus (VSA, pdb: 1VSD). Materials and methods. In order to analyze the role of Mg2+ in the interaction or coupling between 3,5-DCQA and Integrase, three models were created: i) in the absence of Mg2+ ions, ii) with a Mg2+ ion coordinated at Asp15 and Asp72 and iii) model with two Mg2+ ions coordinated at Asp15-Asp72 and Asp72-Glu108. Coupling force and binding free energy between 3,5-DCQA and HTLV-I IN were assessed in the three models. Results. The lowest docking score and free energy binding were obtained for the second model. Mg2+ ion strongly affected the coupling of the inhibitor 3,5-DCQA with HTLV-I catalytic domain of Integrase, thus revealing a strong interaction in the ligand-protein complex regardless of the ligand-catalytic interaction sites for all three models. Conclusion. Altogether, these results strengthen the hypothesis that the presence of one Mg2+ ion could enhance the interaction in the complex by decreasing free energy, therefore increasing the affinity. Moreover, we propose 3,5-DCQA as an important pharmacophore in the rational design of new antiretroviral drugs.
Objetivo: Usando simulación molecular, estudiamos la influencia de los iones Mg2+ en la interacción del dominio catalítico de la integrasa HTLV-I (IN) (modelado por homología) con el ácido 3,5-Dicafeoilquínico (DCQA). Materiales y métodos. El modelo por homología de la HTLV-I IN fue construido usando como molde la estructura cristalina de la IN del virus del sarcoma aviar (VSA, pdb: 1VSD). Para analizar el rol de los iones Mg2+ en la interacción con el DCQA y la integrasa, tres modelos fueron creados: i) en ausencia de iones Mg2+, ii) con un ion Mg2+ coordinado con Asp15 y Asp72 y iii) con dos iones Mg2+ coordinados con Asp15-Asp72 y Asp72-Glu108. Las fuerzas de interacción y la energía libre de unión entre el DCQA y la HTLV-I IN fueron calculadas en los tres modelos. Resultados. El puntaje más bajo en el docking y la menor energía libre fueron obtenidos para el modelo con un solo ion de Mg2+. El Mg2+ afecta fuertemente el acoplamiento del inhibidor DCQA con el dominio catalítico de la HTLV-I IN, revelando una fuerte interacción entre el complejo ligando-proteína que es independiente del sitio catalítico de los tres modelos usados. Conclusión. Los resultados sugieren que la presencia de un ion de Mg² + podría incrementar la interacción en el complejo debido a la disminución de la energía libre, intensificando así la afinidad. Por lo que, proponemos al DCQA como farmacóforo para el diseño de drogas antiretrovirales.
Objetivo. Usando simulação molecular, estudamos a influência dos íons Mg2+ na interação do domínio catalítico da integrase HTLV-I (IN) (modelado por homologia) com o ácido 3,5-dicafeoilquínico (3,5-diCQA). Materiais e métodos. O modelo de homologia da HTLV-I IN foi construído utilizando como fôrma a estrutura cristalina da IN de vírus do sarcoma aviário (VSA, pdb: 1VSD). Para analisar o papel dos íons Mg2+ na interação com o 3,5-diCQA e a integrase, três modelos foram criados: i) na ausência de íons Mg2+, ii) com um íon Mg2+ coordenado com Asp15 e Asp72 e, iii) com dois íons Mg2+ coordenados com Asp15-Asp72 e Asp72-Glu108. As forças de interação e a energia livre de ligação entre o 3,5-diCQA e a HTLV-I IN foram calculadas nos três modelos. Resultados. A pontuação mais baixa no docking e a menor energia livre foram obtidas para o modelo com um único íon de Mg2+. O Mg2+ afeta fortemente o acoplamento do inibidor 3,5-diCQA com o domínio catalítico da HTLV-I IN, revelando uma forte interação entre o complexo ligando-proteína que é independente do sítio catalítico dos três modelos utilizados. Conclusão. Os resultados sugerem que a presença de um íon Mg2+ poderia aumentar a interação no complexo devido à diminuição da energia livre, aumentando assim a afinidade. Assim, propomos ao 3,5-diCQA como farmacóforo para a fabricação de medicamentos antirretrovirais.
Assuntos
Humanos , Antirretrovirais , Integrases , MagnésioRESUMO
Introducción. Aunque la integración del virus linfotrópico humano tipo I no es al azar, se desconocen muchos de los detalles de este proceso. Objetivo. Evaluar las características de la cromatina celular adyacente a secuencias provirales en pacientes con leucemia/linfoma de células T en adultos asociada al virus. Materiales y métodos. Se extrajo el ADN de biopsias de siete pacientes colombianos con leucemia/linfoma de células T en adultos y positivos para el virus linfotrópico humano tipo I. Éste se amplificó mediante reacción inversa en cadena de la polimerasa, para determinar el grado de expansión clónica y su composición de nucleótidos. A partir de 61 secuencias de ADN humano adyacentes a provirus, provenientes de pacientes leucémicos colombianos y japoneses, se efectuó un análisis in silico para obtener datos sobre su integración, las características de la cromatina y sus funciones asociadas. Resultados. La expansión de clones celulares fue predominantemente oligoclónica. De las 61 secuencias de ADN adyacente a provirus, se seleccionaron 155 alineamientos que cumplieron con los criterios de inclusión (homologías≥95%, e-value≤0,05). De éstos, 74,84% fueron secuencias no codificantes repetidas y no repetidas. El 45,95% de las integraciones provirales se localizó en los cromosomas de los grupos A y B. Se observaron tendencias de integración hacia exones de genes que se replican tempranamente, regulan el ciclo celular y participan en la transducción de señales. Conclusiones. Los resultados permiten postular que la integración del virus linfotrópico humano tipo I se dirigiría hacia un ambiente genómico caracterizado por elevado contenido de C:G, genes de replicación temprana que regularían el ciclo celular y la transducción de señales.
Introduction. Although the integration of human T-cell lymphotropic virus type I into the T-cells is not a random process, the mechanistic details are not understood. Objectives. The characteristics of the flanking host chromatin were evaluated at the integration sites in adult T-cell leukaemia/lymphoma (ATLL) patients infected with the virus. Materials and methods. From seven leukemic Colombian patients positive for the human T-cell lymphotropic virus type I (HTLV-I), lymphocyte DNA samples were extracted and amplified by inverse polymerase chain reaction (IPCR). Clonal expansion and human genome nucleotide composition in an extension of 50 bp was determined. To establish the characteristics of the human genome flanking provirus, 61 IPCR sequences from Colombian and Japanese ATLL patients, were analyzed in silico to obtain insights about the genomic structure, functions and nature of associated chromatin. Results. The clonal expansion of cell clones was predominantly oligoclonal. From 61 IPCR sequences, 155 alignments with homology higher than 95% (e-value <0.05) were screened. Seventy-five percent of those sequences corresponded to non coding elements that include repetitive and non-repetitive DNA. Fifty percent of the proviral integrations were associated with chromosomes of A and B groups. Viral DNA integration tended to favor exons of genes that replicated early, controlled the cell cycle, or were involved in signal transduction. Conclusions. The results indicated that HTLV-I integration was preferentially directed towards genomic environments with high C:G content, and toward genes that replicate early, regulate cell cycle or involved with signal transduction.
Assuntos
Biologia Computacional , Genoma Humano , Leucemia , Reação em Cadeia da Polimerase , Integração Viral , Vírus Linfotrópico T Tipo 1 HumanoRESUMO
Objetivo: Analizar las características moleculares y de variación de secuencias de las integrasas del HTLV-I y del VIH-1 y sus variantes poblacionales. Metodología: Análisis de secuencias y estructuras obtenidas de diferentes bases de datos; para ello se utilizaron programas computacionales de modelación de estructuras proteicas e identificación de sustituciones polimórficas en secuencias de aminoácidos de integrasas del HTLV-I y VIH-1 previamente reportadas. Materiales y métodos: Tanto la integrasa del HTLV-I como la del VIH-1 son proteínas compuestas por 288 residuos de aminoácidos. Se encontró un parecido de estructuras terciarias entre los dominios catalíticos de las IN de VIH-1, ASV y RSV con la del HTLV- I. A partir de 103 secuencias completas de la integrasa del VIH-1 se registraron, en 46 codones, un total de 53 sustituciones que se localizaron en diferentes posiciones de la proteína nativa; las más frecuentes fueron: N27G (32,1%), A265V (30,1%), L101I (31,1%) y T123A (27,0%). Ninguna de las sustituciones más frecuentemente encontradas generó un cambio en el plegamiento nativo de la correspondiente región. Conclusión: La estructura tridimensional del dominio central catalítico de la integrasa condicionaría su actividad y su relación con moléculas potencialmente inhibidoras. Las sustituciones observadas fueron neutrales sin alterar la estructura nativa. Los resultados obtenidos confirman que la integrasa es un nuevo y promisorio blanco para el desarrollo de terapias antirretrovirales más efectivas en el siglo XXI...
Objective: To analyze the molecular characteristics and aminoacid sequence variations of HTLV-I and of HIV-1 integrases and their population variants. Materials and methods: Data mining and analysis of integrase sequences and protein structure data bases by using appropriate software for modelling and search for polymorphic substitutions in HTLV-I and HIV-1 integrase amino acid sequences previously reported. Results: HTLV-I and HIV-1 integrases are proteins of 288 amino acid residues. Structural modeling of tertiary folding of HTLV-I integrase catalytic central domains, showed closed structural characteristic with those of HIV-1, ASV and RSV. From 103 full amino acid sequences of HIV-1 integrase, 53 substitutions located in 46 different codons were recorded. The more frequents correspond to N27G (32,1%), L101I (31,1%), A265V (30,1%) and T123A (27,0%). None of these frequent substitutions introduced changes in the folding of HIV-1 native integrase. Conclusion: The tridimensional structure of central catalytic domain would influence the integrase activity and its relationship with potentially inhibitory molecules. Those observed aminoacid substitutions were neutral and do not alter the native protein structure. Our data confirm those previously published, and enable us to propose that IN is a new and promissory target for develop more effective antiviral therapies in the XXI century...
Assuntos
Conformação Proteica , Integrases , Modelos MolecularesRESUMO
INTRODUCTION: Although the integration of human T-cell lymphotropic virus type I into the T-cells is not a random process, the mechanistic details are not understood. OBJECTIVES: The characteristics of the flanking host chromatin were evaluated at the integration sites in adult T-cell leukaemia/lymphoma (ATLL) patients infected with the virus. MATERIALS AND METHODS: From seven leukemic Colombian patients positive for the human T-cell lymphotropic virus type I (HTLV-I), lymphocyte DNA samples were extracted and amplified by inverse polymerase chain reaction (IPCR). Clonal expansion and human genome nucleotide composition in an extension of 50 bp was determined. To establish the characteristics of the human genome flanking provirus, 61 IPCR sequences from Colombian and Japanese ATLL patients, were analyzed in silico to obtain insights about the genomic structure, functions and nature of associated chromatin. RESULTS: The clonal expansion of cell clones was predominantly oligoclonal. From 61 IPCR sequences, 155 alignments with homology higher than 95% (e-value < 0.05) were screened. Seventy-five percent of those sequences corresponded to non coding elements that include repetitive and non-repetitive DNA. Fifty percent of the proviral integrations were associated with chromosomes of A and B groups. Viral DNA integration tended to favor exons of genes that replicated early, controlled the cell cycle, or were involved in signal transduction. CONCLUSIONS: The results indicated that HTLV-I integration was preferentially directed towards genomic environments with high C:G content, and toward genes that replicate early, regulate cell cycle or involved with signal transduction.