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https://www.readbyqxmd.com/read/28636461/genice-a-novel-framework-for-gene-network-inference-by-clustering-exhaustive-search-and-multivariate-analysis
#1
Ricardo de Souza Jacomini, David Correa Martins-Jr, Felipe Leno da Silva, Anna Helena Reali Costa
Gene network (GN) inference from temporal gene expression data is a crucial and challenging problem in systems biology. Expression data sets usually consist of dozens of temporal samples, while networks consist of thousands of genes, thus rendering many inference methods unfeasible in practice. To improve the scalability of GN inference methods, we propose a novel framework called GeNICE, based on probabilistic GNs; the main novelty is the introduction of a clustering procedure to group genes with related expression profiles and to provide an approximate solution with reduced computational complexity...
June 21, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28617870/a-novel-genetic-technique-in-plasmodium-berghei-allows-liver-stage-analysis-of-genes-required-for-mosquito-stage-development-and-demonstrates-that-de-novo-heme-synthesis-is-essential-for-liver-stage-development-in-the-malaria-parasite
#2
Upeksha L Rathnapala, Christopher D Goodman, Geoffrey I McFadden
The combination of drug resistance, lack of an effective vaccine, and ongoing conflict and poverty means that malaria remains a major global health crisis. Understanding metabolic pathways at all parasite life stages is important in prioritising and targeting novel anti-parasitic compounds. The unusual heme synthesis pathway of the rodent malaria parasite, Plasmodium berghei, requires eight enzymes distributed across the mitochondrion, apicoplast and cytoplasm. Deletion of the ferrochelatase (FC) gene, the final enzyme in the pathway, confirms that heme synthesis is not essential in the red blood cell stages of the life cycle but is required to complete oocyst development in mosquitoes...
June 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28595540/apicoplast-import-protein-tic20-a-promising-therapeutic-molecular-target-for-plasmodium-falciparum-an-insilico-approach-for-therapeutic-intervention
#3
Pavan C P K Srimath-Tirumala-Peddinti, Sandeep Solmon Kusuma, Deepthi Nammi, Nageswara Rao Reddy Neelapu
Malaria is a lethal disease causing mortality to over millions each year. Drug resistance in the malarial parasite encouraged to discover effective antimalarial drug targets and drugs. An objective of this current study is to identify drug targets for malarial parasite. Genes unique, non-homologous to humans and essential for parasite are identified using BLASTn by comparing genomes between parasite and host. Further open BLASTp was used to filter the targets specific to Plasmodium species and later were subjected to gene property analysis to identify 65 potential targets...
June 5, 2017: Infectious Disorders Drug Targets
https://www.readbyqxmd.com/read/28593938/myosin-dependent-cell-cell-communication-controls-synchronicity-of-division-in-acute-and-chronic-stages-of-toxoplasma-gondii
#4
Karine Frénal, Damien Jacot, Pierre-Mehdi Hammoudi, Arnault Graindorge, Bohumil Maco, Dominique Soldati-Favre
The obligate intracellular parasite Toxoplasma gondii possesses a repertoire of 11 myosins. Three class XIV motors participate in motility, invasion and egress, whereas the class XXII myosin F is implicated in organelle positioning and inheritance of the apicoplast. Here we provide evidence that TgUNC acts as a chaperone dedicated to the folding, assembly and function of all Toxoplasma myosins. The conditional ablation of TgUNC recapitulates the phenome of the known myosins and uncovers two functions in parasite basal complex constriction and synchronized division within the parasitophorous vacuole...
June 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28462015/membrane-and-luminal-proteins-reach-the-apicoplast-by-different-trafficking-pathways-in-the-malaria-parasite-plasmodium-falciparum
#5
Rahul Chaudhari, Vishakha Dey, Aishwarya Narayan, Shobhona Sharma, Swati Patankar
The secretory pathway in Plasmodium falciparum has evolved to transport proteins to the host cell membrane and to an endosymbiotic organelle, the apicoplast. The latter can occur via the ER or the ER-Golgi route. Here, we study these three routes using proteins Erythrocyte Membrane Protein-1 (PfEMP1), Acyl Carrier Protein (ACP) and glutathione peroxidase-like thioredoxin peroxidase (PfTPxGl) and inhibitors of vesicular transport. As expected, the G protein-dependent vesicular fusion inhibitor AlF4(-) and microtubule destabilizing drug vinblastine block the trafficking of PfEMP-1, a protein secreted to the host cell membrane...
2017: PeerJ
https://www.readbyqxmd.com/read/28434971/prevalence-and-genetic-characterization-of-toxoplasma-gondii-in-badgers-melogale-moschata-in-southern-china-by-pcr-rflp
#6
Kai Chen, Si-Yang Huang, Jin-Lei Wang, Rong-Liang Hu, Qiu-Xia Yao, Shou-Feng Zhang, Xing-Quan Zhu, Quan Liu
Toxoplasma gondii is an obligate intracellular apicomplexan parasite which is able to infect almost all warm-blooded animals. There is no information about the prevalence and genetic characterization of T. gondii in badgers (Melogale moschata) in China. Here, a total of 367 badgers were captured from different cities in Jiangxi province, Southern China. Genomic DNA was extracted from brain tissues of each badgers, and 57 (15.45%) of them were positive for T. gondii by semi-nested PCR of the B1 gene. The positive DNA samples were typed at 11 genetic markers, including 10 nuclear loci (SAG1, 5'-SAG2 and 3'-SAG2, alternative SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1) and an apicoplast locus (Apico), with multilocus polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technology...
April 21, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28423214/plasmodium-falciparum-otu-like-cysteine-protease-pfotu-is-essential-for-apicoplast-homeostasis-and-associates-with-non-canonical-role-of-atg8
#7
Gaurav Datta, Mohammad E Hossain, Mohd Asad, Sumit Rathore, Asif Mohmmed
The metabolic pathways associated with the mitochondrion and the apicoplast in Plasmodium, two parasite organelles of prokaryotic origin, are considered as suitable drug targets. In the present study, we have identified functional role of a novel OTU domain containing cysteine protease of Plasmodium falciparum (PfOTU). A C-terminal regulatable fluorescent affinity (RFA) tag on native protein was utilized for its localization and functional characterization. Detailed studies showed vesicular localization of PfOTU, and its association with the apicoplast...
April 18, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/28419631/tgpl2-a-patatin-like-phospholipase-domain-containing-protein-is-involved-in-the-maintenance-of-apicoplast-lipids-homeostasis-in-toxoplasma
#8
Maude F Lévêque, Laurence Berry, Yoshiki Yamaryo-Botté, Hoa Mai Nguyen, Marine Galera, Cyrille Y Botté, Sébastien Besteiro
Patatin-like phospholipases are involved in numerous cellular functions, including lipid metabolism and membranes remodeling. The patatin-like catalytic domain, whose phospholipase activity relies on a serine-aspartate dyad and an anion binding box, is widely spread among prokaryotes and eukaryotes. We describe TgPL2, a novel patatin-like phospholipase domain-containing protein from the parasitic protist Toxoplasma gondii. TgPL2 is a large protein, in which the key motifs for enzymatic activity are conserved in the patatin-like domain...
April 17, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28361906/herbicidal-properties-of-antimalarial-drugs
#9
Maxime G Corral, Julie Leroux, Keith A Stubbs, Joshua S Mylne
The evolutionary relationship between plants and the malarial parasite Plasmodium falciparum is well established and underscored by the P. falciparum apicoplast, an essential chloroplast-like organelle. As a result of this relationship, studies have demonstrated that herbicides active against plants are also active against P. falciparum and thus could act as antimalarial drug leads. Here we show the converse is also true; many antimalarial compounds developed for human use are highly herbicidal. We found that human antimalarial drugs (e...
March 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28344153/plant-hormone-cytokinins-control-cell-cycle-progression-and-plastid-replication-in-apicomplexan-parasites
#10
Syed Bilal Ahmad Andrabi, Michiru Tahara, Ryuma Matsubara, Tomoko Toyama, Hiroka Aonuma, Hitoshi Sakakibara, Makoto Suematsu, Kazuyuki Tanabe, Tomoyoshi Nozaki, Kisaburo Nagamune
Cytokinins are plant hormones that are involved in regulation of cell proliferation, cell cycle progression, and cell and plastid development. Here, we show that the apicomplexan parasites Toxoplasma gondii and Plasmodium berghei, an opportunistic human pathogen and a rodent malaria agent, respectively, produce cytokinins via a biosynthetic pathway similar to that in plants. Cytokinins regulate the growth and cell cycle progression of T. gondii by mediating expression of the cyclin gene TgCYC4. A natural form of cytokinin, trans-zeatin (t-zeatin), upregulated expression of this cyclin, while a synthetic cytokinin, thidiazuron, downregulated its expression...
March 23, 2017: Parasitology International
https://www.readbyqxmd.com/read/28314772/two-phylogenetically-and-compartmentally-distinct-cdp-diacylglycerol-synthases-cooperate-for-lipid-biogenesis-in-toxoplasma-gondii
#11
Pengfei Kong, Christoph-Martin Ufermann, Diana L M Zimmermann, Qing Yin, Xun Suo, J Bernd Helms, Jos F Brouwers, Nishith Gupta
Toxoplasma gondii is among the most prevalent protozoan parasites, which infects a wide range of organisms, including one-third of the human population. Its rapid intracellular replication within a vacuole requires efficient synthesis of glycerophospholipids. Cytidine diphosphate-diacylglycerol (CDP-DAG) serves as a major precursor for phospholipid synthesis. Given the peculiarities of lipid biogenesis, understanding the mechanism and physiological importance of CDP-DAG synthesis is particularly relevant in T...
April 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28260517/capi-computational-model-for-apicoplast-inhibitors-prediction-against-plasmodium-parasite
#12
Surabhi Dixit, Deepak Singla
Background Discovery of apicoplast as a drug target offers a new direction in the development of novel anti-malarial compounds, especially against the drug-resistant strains. Drugs such as azithromycin were reported to block the apicoplast development that leads to unusual phenotypes affecting the parasite. This phenomenon suggeststhat identification of new apicoplast inhibitors will aid in the anti-malarial drug discovery. Therefore, in this study, we developed a computational model to predict apicoplast inhibitors by applying state-of-the-art machine learning techniques...
March 1, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28251546/plasmodium-falciparum-apicoplast-and-its-transcriptional-regulation-through-calcium-signaling
#13
REVIEW
Praveen Rai, Drista Sharma, Rani Soni, Nazia Khatoon, Bhaskar Sharma, Tarun Kumar Bhatt
Malaria has been present since ancient time and remains a major global health problem in developing countries. Plasmodium falciparum belongs to the phylum Apicomplexan, largely contain disease-causing parasites and characterized by the presence of apicoplast. It is a very essential organelle of P. falciparum responsible for the synthesis of key molecules required for the growth of the parasite. Indispensable nature of apicoplast makes it a potential drug target. Calcium signaling is important in the establishment of malaria parasite inside the host...
April 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28163699/a-systematic-review-of-in-vitro-and-in-vivo-activities-of-anti-toxoplasma-drugs-and-compounds-2006-2016
#14
REVIEW
Mahbobeh Montazeri, Mehdi Sharif, Shahabeddin Sarvi, Saeed Mehrzadi, Ehsan Ahmadpour, Ahmad Daryani
The currently available anti-Toxoplasma agents have serious limitations. This systematic review was performed to evaluate drugs and new compounds used for the treatment of toxoplasmosis. Data was systematically collected from published papers on the efficacy of drugs/compounds used against Toxoplasma gondii (T. gondii) globally during 2006-2016. The searched databases were PubMed, Google Scholar, Science Direct, ISI Web of Science, EBSCO, and Scopus. One hundred and eighteen papers were eligible for inclusion in this systematic review, which were both in vitro and in vivo studies...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28100223/surface-attachment-promoted-by-the-actomyosin-system-of-toxoplasma-gondii-is-important-for-efficient-gliding-motility-and-invasion
#15
Jamie A Whitelaw, Fernanda Latorre-Barragan, Simon Gras, Gurman S Pall, Jacqueline M Leung, Aoife Heaslip, Saskia Egarter, Nicole Andenmatten, Shane R Nelson, David M Warshaw, Gary E Ward, Markus Meissner
BACKGROUND: Apicomplexan parasites employ a unique form of movement, termed gliding motility, in order to invade the host cell. This movement depends on the parasite's actomyosin system, which is thought to generate the force during gliding. However, recent evidence questions the exact molecular role of this system, since mutants for core components of the gliding machinery, such as parasite actin or subunits of the MyoA-motor complex (the glideosome), remain motile and invasive, albeit at significantly reduced efficiencies...
January 18, 2017: BMC Biology
https://www.readbyqxmd.com/read/28068997/absence-of-in-vivo-selection-for-k13-mutations-after-artemether-lumefantrine-treatment-in-uganda
#16
Betty Balikagala, Toshihiro Mita, Mie Ikeda, Miki Sakurai, Shouki Yatsushiro, Nobuyuki Takahashi, Shin-Ichiro Tachibana, Mary Auma, Edward H Ntege, Daisuke Ito, Eizo Takashima, Nirianne Marie Q Palacpac, Thomas G Egwang, Joseph Okello Onen, Masatoshi Kataoka, Eisaku Kimura, Toshihiro Horii, Takafumi Tsuboi
BACKGROUND: Individual drug treatment may select resistant parasites in the human body, a process termed in vivo selection. Some single nucleotide polymorphisms in Plasmodium falciparum chloroquine-resistance transporter (pfcrt) and multidrug resistance gene 1 (pfmdr1) genes have been reportedly selected after artemether-lumefantrine treatment. However, there is a paucity of data regarding in vivo selection of P. falciparum Kelch propeller domain (pfkelch13) polymorphisms, responsible for artemisinin-resistance in Asia, and six putative background mutations for artemisinin resistance; D193Y in ferredoxin, T484I in multiple resistance protein 2, V127M in apicoplast ribosomal protein S10, I356T in pfcrt, V1157L in protein phosphatase and C1484F in phosphoinositide-binding protein...
January 9, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28062360/determination-of-glutathione-redox-potential-and-ph-value-in-subcellular-compartments-of-malaria-parasites
#17
Franziska Mohring, Mahsa Rahbari, Bernd Zechmann, Stefan Rahlfs, Jude M Przyborski, Andreas J Meyer, Katja Becker
The malaria parasite Plasmodium falciparum is exposed to multiple sources of oxidative challenge during its complex life cycle in the Anopheles vector and its human host. In order to further elucidate redox-based parasite host cell interactions and mechanisms of drug action, we targeted the genetically encoded glutathione redox sensor roGFP2 coupled to human glutaredoxin 1 (roGFP2-hGrx1) as well as the ratiometric pH sensor pHluorin to the apicoplast and the mitochondrion of P. falciparum. Using live cell imaging, this allowed for the first time the determination of the pH values of the apicoplast (7...
March 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28026138/towards-a-molecular-architecture-of-the-centrosome-in-toxoplasma-gondii
#18
REVIEW
Juliette Morlon-Guyot, Maria E Francia, Jean-François Dubremetz, Wassim Daher
Toxoplasma gondii is the causative agent of toxoplasmosis. The pathogenicity of this unicellular parasite is tightly linked to its ability to efficiently proliferate within its host. Tachyzoites, the fast dividing form of the parasite, divide by endodyogeny. This process involves a single round of DNA replication, closed nuclear mitosis, and assembly of two daughter cells within a mother. The successful completion of endodyogeny relies on the temporal and spatial coordination of a plethora of simultaneous events...
February 2017: Cytoskeleton
https://www.readbyqxmd.com/read/28007455/characterization-of-4-hydroxy-3-methylbut-2-en-1-yl-diphosphate-synthase-ispg-from-plasmodium-vivax-and-it-s-potential-as-an-antimalarial-drug-target
#19
Gagandeep Singh Saggu, Shilpi Garg, Zarna Rajeshkumar Pala, Sushil Kumar Yadav, Sanjay Kumar Kochar, Dhanpat Kumar Kochar, Vishal Saxena
The prokaryotic type Methyl Erythritol phosphate (MEP) pathway functional in the apicoplast of Plasmodium is indispensable for the erythrocytic stages of the parasite. It is the sole process of isoprenoids biosynthesis in the parasite and is different from that in humans. Among the seven enzymes known to be functional in the MEP pathway in prokaryotes, most enzymes from Plasmodium are yet uncharacterized. The penultimate enzyme of this pathway 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (IspG), has been shown to act as a key target molecule in prokaryotes, where its deletion results in impairment of many housekeeping functions...
March 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27916258/the-apicoplast-genomes-of-two-taxonomic-units-of-babesia-from-sheep
#20
Tao Wang, Guiquan Guan, Pasi K Korhonen, Anson V Koehler, Ross S Hall, Neil D Young, Hong Yin, Robin B Gasser
The apicoplast (ap) is a unique, non-photosynthetic organelle found in most apicomplexan parasites. Due to the essential roles that this organelle has, it has been widely considered as target for drugs against diseases caused by apicomplexans. Exploring the ap genomes of such parasites would provide a better understanding of their systematics and their basic molecular biology for therapeutics. However, there is limited information available on the ap genomes of apicomplexan parasites. In the present study, the ap genomes of two operational taxonomic units of Babesia (known as Babesia sp...
January 15, 2017: Veterinary Parasitology
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