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Sanger-led Team Sequences Patient's Brain Tapeworm - GenomeWeb

Sanger-led Team Sequences Patient's Brain Tapeworm - GenomeWeb | parasitegenome | Scoop.it
Researchers sequenced the genome of Spirometra erinaceieuropaei with DNA from tapeworm that had been living in the patient's brain for several years.
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Penn and UGA Awarded $23.4 Million Contract for Pathogen Genomics Database - Penn: Office of University Communications

Penn and UGA Awarded $23.4 Million Contract for Pathogen Genomics Database - Penn: Office of University Communications | parasitegenome | Scoop.it
At the turn of the millennium, the cost to sequence a single human genome exceeded $50 million, and
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Genome editing in the human malaria parasite Plasmodium falciparum using the CRISPR-Cas9 system

Genome editing in the human malaria parasite Plasmodium falciparum using the CRISPR-Cas9 system | parasitegenome | Scoop.it
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Genome and transcriptome of the porcine whipworm Trichuris suis : Nature Genetics

Genome and transcriptome of the porcine whipworm Trichuris suis : Nature Genetics | parasitegenome | Scoop.it
Aaron Jex and colleagues report whole-genome sequencing of adult male and female whipworm, Trichuris suis, from experimentally infected pigs. They also report stage-, sex- and tissue-specific transcriptomes and provide insights into host-parasite interactions.
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Retroviruses, the Placenta, and the Genomic Junk Drawer

Retroviruses, the Placenta, and the Genomic Junk Drawer | parasitegenome | Scoop.it
by Jamie Henzy | By now, many of us are aware that a considerable portion (45% or more) of the human genome consists of transposable elements. These are ...
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Methylated glycans as conserved targets of animal and fungal innate defense

Methylated glycans as conserved targets of animal and fungal innate defense | parasitegenome | Scoop.it

Defense mechanisms against predators, parasites, and pathogens are a hallmark of all multicellular life forms. A conserved defense mechanism is the production of toxic proteins. Because of the limited number of innate defense effectors in a specific host organism, the target epitopes of such toxins are usually highly conserved or occur in different molecular contexts to cover a large spectrum of antagonists. Because glycan epitopes are part of different surface-displayed glycoconjugates in different organisms, carbohydrate-binding proteins (lectins) are the prevailing type of protein toxins in many multicellular organisms. Here we provide evidence that defense lectins can be specific for secondary glycan modifications, such as O-methylation, thereby broadening the range of target organisms.


Via Francis Martin
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Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and Plants

Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and Plants | parasitegenome | Scoop.it

Abstract: Genomic characteristics discriminating parasitic and mutualistic relationship of bacterial symbionts with plants are poorly understood. This study comparatively analyzed the genomes of 54 mutualists and pathogens to discover genomic markers associated with the different phenotypes. Using metabolic network models, we predict external environments associated with free-living and symbiotic lifestyles and quantify dependences of symbionts on the host in terms of the consumed metabolites. We show that specific differences between the phenotypes are pronounced at the levels of metabolic enzymes, especially carbohydrate active, and protein functions. Overall, biosynthetic functions are enriched and more diverse in plant mutualists whereas processes and functions involved in degradation and host invasion are enriched and more diverse in pathogens. A distinctive characteristic of plant pathogens is a putative novel secretion system with a circadian rhythm regulator. A specific marker of plant mutualists is the co-residence of genes encoding nitrogenase and ribulose bisphosphate carboxylase/oxygenase (RuBisCO). We predict that RuBisCO is likely used in a putative metabolic pathway to supplement carbon obtained heterotrophically with low-cost assimilation of carbon from CO2. We validate results of the comparative analysis by predicting correct phenotype, pathogenic or mutualistic, for 20 symbionts in an independent set of 30 pathogens, mutualists, and commensals.


Via Bradford Condon
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Mechanisms Of Antigenic Variation In Borrelia Hermsii And African ...

Mechanisms Of Antigenic Variation In Borrelia Hermsii And African ... | parasitegenome | Scoop.it
Two pathogens particularly adept at using this strategy are Borrelia hermsii, a prokaryotic spirochete that causes relapsing fever in the western United States and Canada(2), and African trypanosomes, eukaryotic protozoan parasites that cause...
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The genomes of four tapeworm species reveal adaptations to parasitism : Nature : Nature Publishing Group

The genomes of four tapeworm species reveal adaptations to parasitism : Nature : Nature Publishing Group | parasitegenome | Scoop.it
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David Roos (U Penn) Part 1: Biology of Apicomplexan Parasites

http://ibioseminars.org/lectures/global-health-a-energy/david-s-roos.html There are more than 5000 species of single-celled eukaryotes in the biological phyl...
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The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families : Nature Genetics : Nature Publishing Group

The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families : Nature Genetics : Nature Publishing Group | parasitegenome | Scoop.it
Erich Schwarz and colleagues report whole-genome sequencing of the zoonotic hookworm Ancylostoma ceylanicum. They also analyze the transcriptome through the course of infection in golden hamsters and identify groups of genes showing differential regulation across different stages.
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Genomic analysis of the causative agents of coccidiosis in domestic chickens

Genomic analysis of the causative agents of coccidiosis in domestic chickens | parasitegenome | Scoop.it

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.

Jason Tsai's insight:

Very nice and comprehensive study by former colleagues.

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5.2 Pathogen Evolution: Evasion of Host Defenses

Prof. Stearns explains how pathogens exploit every chink in the host's armor in this second lecture in the pathogen evolution series.
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Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction : Nature Genetics

Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction : Nature Genetics | parasitegenome | Scoop.it
Matthew Berriman and colleagues report the whole-genome sequences of the human-infective whipworm Trichuris trichiura and the mouse-infective laboratory model Trichuris muris. Their transcriptome analyses and examination of T. muris infection in mice provide insights into host response to infection and potential drug targets for this major soil-transmitted helminth.
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Symbiotic root fungus promotes growth in plants

Symbiotic root fungus promotes growth in plants | parasitegenome | Scoop.it
Researchers at the University of Tübingen have discovered a microscopic fungus which promotes growth in certain plants. "This fungus, native to Europe, is an organic fertilizer with the potential to increase yields of crops such as wheat and maize," says Sigisfredo Garnica of the Institute of Evolution and Ecology.

Read more at: http://phys.org/news/2014-06-symbiotic-root-fungus-growth.html#jCp

Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, June 8, 2014 8:15 PM

Commentary on Kai Riess, Franz Oberwinkler, Robert Bauer, Sigisfredo Garnica (2014): "Communities of endophytic Sebacinales associated with roots of herbaceous plants in agricultural and grassland ecosystems are dominated by Serendipita herbamans sp. nov." PLoS ONE 9(4): e94676.

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The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes

The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes | parasitegenome | Scoop.it

Phytophthora infestans is a destructive plant pathogen best known for causing the disease that triggered the Irish potato famine and remains the most costly potato pathogen to manage worldwide. Identification of P. infestan’s elusive center of origin is critical to understanding the mechanisms of repeated global emergence of this pathogen. There are two competing theories, placing the origin in either South America or in central Mexico, both of which are centers of diversity of Solanum host plants. To test these competing hypotheses, we conducted detailed phylogeographic and approximate Bayesian computation analyses, which are suitable approaches to unraveling complex demographic histories. Our analyses used microsatellite markers and sequences of four nuclear genes sampled from populations in the Andes, Mexico, and elsewhere. To infer the ancestral state, we included the closest known relatives Phytophthora phaseoli, Phytophthora mirabilis, andPhytophthora ipomoeae, as well as the interspecific hybrid Phytophthora andina. We did not find support for an Andean origin of P. infestans; rather, the sequence data suggest a Mexican origin. Our findings support the hypothesis that populations found in the Andes are descendants of the Mexican populations and reconcile previous findings of ancestral variation in the Andes. Although centers of origin are well documented as centers of evolution and diversity for numerous crop plants, the number of plant pathogens with a known geographic origin are limited. This work has important implications for our understanding of the coevolution of hosts and pathogens, as well as the harnessing of plant disease resistance to manage late blight.


Via Francis Martin
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Biswapriya Biswavas Misra's curator insight, June 4, 2014 10:57 PM

Phytophthora infestans is a destructive plant pathogen best known for causing the disease that triggered the Irish potato famine and remains the most costly potato pathogen to manage worldwide. Identification of P. infestan’s elusive center of origin is critical to understanding the mechanisms of repeated global emergence of this pathogen. There are two competing theories, placing the origin in either South America or in central Mexico, both of which are centers of diversity of Solanum host plants. To test these competing hypotheses, we conducted detailed phylogeographic and approximate Bayesian computation analyses, which are suitable approaches to unraveling complex demographic histories. Our analyses used microsatellite markers and sequences of four nuclear genes sampled from populations in the Andes, Mexico, and elsewhere. To infer the ancestral state, we included the closest known relatives Phytophthora phaseoli, Phytophthora mirabilis, andPhytophthora ipomoeae, as well as the interspecific hybrid Phytophthora andina. We did not find support for an Andean origin of P. infestans; rather, the sequence data suggest a Mexican origin. Our findings support the hypothesis that populations found in the Andes are descendants of the Mexican populations and reconcile previous findings of ancestral variation in the Andes. Although centers of origin are well documented as centers of evolution and diversity for numerous crop plants, the number of plant pathogens with a known geographic origin are limited. This work has important implications for our understanding of the coevolution of hosts and pathogens, as well as the harnessing of plant disease resistance to manage late blight.

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Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States


Via Bradford Condon
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Bradford Condon's curator insight, June 2, 2014 12:38 PM

Abstract: Native tallgrass prairie once dominated much of the midwestern United States, but this biome and the soil microbial diversity that once sustained this highly productive system have been almost completely eradicated by decades of agricultural practices. We reconstructed the soil microbial diversity that once existed in this biome by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum that appears to dominate many prairie soils. Shotgun metagenomic data suggested that these spatial patterns were associated with strong shifts in carbon dynamics. We show that metagenomic approaches can be used to reconstruct below-ground biogeochemical and diversity gradients in endangered ecosystems; such information could be used to improve restoration efforts, given that even small changes in below-ground microbial diversity can have important impacts on ecosystem processes

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Sleeping sickness and tsetse flies - Scientific American (blog)

Sleeping sickness and tsetse flies - Scientific American (blog) | parasitegenome | Scoop.it
Sleeping sickness and tsetse flies Scientific American (blog) One topic that I haven't covered nearly enough is the protozoan pathogens; the unicellular organisms that are not bacterial, but are responsible for some of the deadliest diseases in the...
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PLOS Genetics: Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8 (2014)

PLOS Genetics: Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8 (2014) | parasitegenome | Scoop.it

Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA. We also observed SNP-level “hypermutation” of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the R. solani genome sequence may prove to be a useful resource in future comparative analysis of plant pathogens.


Via Kamoun Lab @ TSL, Jie Wang
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David Roos (U Penn) Part 2: The apicomplexan plastid

http://ibioseminars.hhmi.org/lectures/global-health-a-energy/david-s-roos.html Antibiotics are effective because they kill bacteria without harming humans an...
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A Gut Feeling: Studying the Bugs in Bees - LiveScience.com

A Gut Feeling: Studying the Bugs in Bees - LiveScience.com | parasitegenome | Scoop.it
A Gut Feeling: Studying the Bugs in Bees
LiveScience.com
Waldan Kwong (doctoral student) and Amanda Macenido (undergraduate student) are working on the genomics and diversity of bacteria living in guts of honeybees and bumblebees.
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