Publications by authors named "Travis Harrison"

26 Publications

  • Page 1 of 1

The MG-RAST API explorer: an on-ramp for RESTful query composition.

BMC Bioinformatics 2019 Nov 8;20(1):561. Epub 2019 Nov 8.

Argonne National Laboratory, Lemont, IL, USA.

Background: The MG-RAST API provides search capabilities and delivers organism and function data as well as raw or annotated sequence data via the web interface and its RESTful API. For casual users, however, RESTful APIs are hard to learn and work with.

Results: We created the graphical MG-RAST API explorer to help researchers more easily build and export API queries; understand the data abstractions and indices available in MG-RAST; and use the results presented in-browser for exploration, development, and debugging.

Conclusions: The API explorer lowers the barrier to entry for occasional or first-time MG-RAST API users.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-019-2993-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842160PMC
November 2019

GCC Consolidated Feedback to ICH on the 2019 ICH M10 Bioanalytical Method Validation Draft Guideline.

Bioanalysis 2019 Sep 30;11(18s):1-228. Epub 2019 Sep 30.

WuXi Apptec, Shanghai, China.

The 13 GCC Closed Forum for Bioanalysis was held in New Orleans, Louisiana, USA on April 5, 2019. This GCC meeting was organized to discuss the contents of the 2019 ICH M10 Bioanalytical Method Validation Draft Guideline published in February 2019 and consolidate the feedback of the GCC members. In attendance were 63 senior-level participants from eight countries representing 44 bioanalytical CRO companies/sites. This event represented a unique opportunity for CRO bioanalytical experts to share their opinions and concerns regarding the ICH M10 Bioanalytical Method Validation Draft Guideline and to build unified comments to be provided to the ICH.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.4155/bio-2019-0207DOI Listing
September 2019

Patterns of mercury and selenium exposure in minnesota common loons.

Environ Toxicol Chem 2019 03 4;38(3):524-532. Epub 2019 Feb 4.

Minnesota Department of Natural Resources, St. Paul, Minnesota, USA.

Common loons (Gavia immer) are at risk of elevated dietary mercury (Hg) exposure in portions of their breeding range. To assess the level of risk among loons in Minnesota (USA), we investigated loon blood Hg concentrations in breeding lakes across Minnesota. Loon blood Hg concentrations were regressed on predicted Hg concentrations in standardized 12-cm whole-organism yellow perch (Perca flavescens), based on fish Hg records from Minnesota lakes, using the US Geological Survey National Descriptive Model for Mercury in Fish. A linear model, incorporating common loon sex, age, body mass, and log-transformed standardized perch Hg concentration representative of each study lake, was associated with 83% of the variability in observed common loon blood Hg concentrations. Loon blood Hg concentration was positively related to standardized perch Hg concentrations; juvenile loons had lower blood Hg concentrations than adult females, and blood Hg concentrations of juveniles increased with body mass. Blood Hg concentrations of all adult common loons and associated standardized prey Hg for all loon capture lakes included in the study were well below proposed thresholds for adverse effects on loon behavior, physiology, survival, and reproductive success. The fish Hg modeling approach provided insights into spatial patterns of dietary Hg exposure risk to common loons across Minnesota. We also determined that loon blood selenium (Se) concentrations were positively correlated with Hg concentration. Average common loon blood Se concentrations exceeded the published provisional threshold. Environ Toxicol Chem 2019;38:524-532. Published 2018 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/etc.4331DOI Listing
March 2019

MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis.

Brief Bioinform 2019 07;20(4):1151-1159

As technologies change, MG-RAST is adapting. Newly available software is being included to improve accuracy and performance. As a computational service constantly running large volume scientific workflows, MG-RAST is the right location to perform benchmarking and implement algorithmic or platform improvements, in many cases involving trade-offs between specificity, sensitivity and run-time cost. The work in [Glass EM, Dribinsky Y, Yilmaz P, et al. ISME J 2014;8:1-3] is an example; we use existing well-studied data sets as gold standards representing different environments and different technologies to evaluate any changes to the pipeline. Currently, we use well-understood data sets in MG-RAST as platform for benchmarking. The use of artificial data sets for pipeline performance optimization has not added value, as these data sets are not presenting the same challenges as real-world data sets. In addition, the MG-RAST team welcomes suggestions for improvements of the workflow. We are currently working on versions 4.02 and 4.1, both of which contain significant input from the community and our partners that will enable double barcoding, stronger inferences supported by longer-read technologies, and will increase throughput while maintaining sensitivity by using Diamond and SortMeRNA. On the technical platform side, the MG-RAST team intends to support the Common Workflow Language as a standard to specify bioinformatics workflows, both to facilitate development and efficient high-performance implementation of the community's data analysis tasks.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/bib/bbx105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781595PMC
July 2019

The MG-RAST metagenomics database and portal in 2015.

Nucleic Acids Res 2016 Jan 9;44(D1):D590-4. Epub 2015 Dec 9.

Argonne National Laboratory, Mathematics and Computer Science Division, 60439 Argonne, IL, USA University of Chicago, Chicago 60637, IL, USA

MG-RAST (http://metagenomics.anl.gov) is an open-submission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. The system currently hosts over 200,000 datasets and is continuously updated. The volume of submissions has increased 4-fold over the past 24 months, now averaging 4 terabasepairs per month. In addition to several new features, we report changes to the analysis workflow and the technologies used to scale the pipeline up to the required throughput levels. To show possible uses for the data from MG-RAST, we present several examples integrating data and analyses from MG-RAST into popular third-party analysis tools or sequence alignment tools.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv1322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702923PMC
January 2016

A RESTful API for accessing microbial community data for MG-RAST.

PLoS Comput Biol 2015 Jan 8;11(1):e1004008. Epub 2015 Jan 8.

Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http://kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase's microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1004008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287624PMC
January 2015

Novel human radiation exposure biomarker panel applicable for population triage.

Int J Radiat Oncol Biol Phys 2014 Nov 29;90(3):612-9. Epub 2014 Jul 29.

SRI International, Menlo Park, California. Electronic address:

Purpose: To identify a panel of radiation-responsive plasma proteins that could be used in a point-of-care biologic dosimeter to detect clinically significant levels of ionizing radiation exposure.

Methods And Materials: Patients undergoing preparation for hematopoietic cell transplantation using radiation therapy (RT) with either total lymphoid irradiation or fractionated total body irradiation were eligible. Plasma was examined from patients with potentially confounding conditions and from normal individuals. Each plasma sample was analyzed for a panel of 17 proteins before RT was begun and at several time points after RT exposure. Paired and unpaired t tests between the dose and control groups were performed. Conditional inference trees were constructed based on panels of proteins to compare the non-RT group with the RT group.

Results: A total of 151 patients (62 RT, 41 infection, 48 trauma) were enrolled on the study, and the plasma from an additional 24 healthy control individuals was analyzed. In comparison with to control individuals, tenascin-C was upregulated and clusterin was downregulated in patients receiving RT. Salivary amylase was strongly radiation responsive, with upregulation in total body irradiation patients and slight downregulation in total lymphoid irradiation patients compared with control individuals. A panel consisting of these 3 proteins accurately distinguished between irradiated patients and healthy control individuals within 3 days after exposure: 97% accuracy, 0.5% false negative rate, 2% false positive rate. The accuracy was diminished when patients with trauma, infection, or both were included (accuracy, 74%-84%; false positive rate, 14%-33%, false negative rate: 8%-40%).

Conclusions: A panel of 3 proteins accurately distinguishes unirradiated healthy donors from those exposed to RT (0.8-9.6 Gy) within 3 days of exposure. These findings have significant implications in terms of triaging individuals in the case of nuclear or other radiologic events.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijrobp.2014.05.046DOI Listing
November 2014

Metazen - metadata capture for metagenomes.

Stand Genomic Sci 2014 8;9:18. Epub 2014 Dec 8.

Computation Institute, University of Chicago, 5735 S Ellis Ave, Chicago, IL 60637, USA ; Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA ; Biological Sciences Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA.

Background: As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. Unfortunately, these tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools.

Results: Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata.

Conclusions: Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1944-3277-9-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334943PMC
March 2015

A metagenomics portal for a democratized sequencing world.

Methods Enzymol 2013 ;531:487-523

Argonne National Laboratory, Lemont, Illinois, USA; University of Chicago, Chicago, Illinois, USA.

The democratized world of sequencing is leading to numerous data analysis challenges; MG-RAST addresses many of these challenges for diverse datasets, including amplicon datasets, shotgun metagenomes, and metatranscriptomes. The changes from version 2 to version 3 include the addition of a dedicated gene calling stage using FragGenescan, clustering of predicted proteins at 90% identity, and the use of BLAT for the computation of similarities. Together with changes in the underlying software infrastructure, this has enabled the dramatic scaling up of pipeline throughput while remaining on a limited hardware budget. The Web-based service allows upload, fully automated analysis, and visualization of results. As a result of the plummeting cost of sequencing and the readily available analytical power of MG-RAST, over 78,000 metagenomic datasets have been analyzed, with over 12,000 of them publicly available in MG-RAST.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/B978-0-12-407863-5.00022-8DOI Listing
April 2014

β-Carotene Biosynthesis in Probiotic Bacteria.

Probiotics Antimicrob Proteins 2013 Jun;5(2):69-80

Biosciences Division, SRI International, Harrisonburg, VA, 22802, USA.

Susceptibility to deadly diarrheal diseases is partly due to widespread pediatric vitamin A deficiency. To increase vitamin A coverage in malnourished children, we propose to engineer a probiotic bacterium that will produce β-carotene in the intestine, which will be metabolized to vitamin A. Such a therapy has the potential to broadly stimulate mucosal immunity and simultaneously reduce the incidence and duration of diarrheal disease. To that end, a β-carotene-producing variant of the probiotic Escherichia coli strain Nissle 1917 (EcN-BETA) was generated. Notably, the strain produces β-carotene under anaerobic conditions, reflective of the gut environment. EcN-BETA also retains β-carotene production capability after lyophilization, suggesting that it may be amenable to dry formulation. Moreover, EcN-BETA activates murine dendritic cells in vitro, suggesting that the presence of β-carotene may not diminish the immunostimulatory capacity of EcN. Finally, we present a framework through which further improvements may enable approaches such as the one described in this report to yield innovative life-saving therapies for the developing world.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12602-013-9133-3DOI Listing
June 2013

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools.

BMC Bioinformatics 2012 Jun 21;13:141. Epub 2012 Jun 21.

Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.

Background: Computing of sequence similarity results is becoming a limiting factor in metagenome analysis. Sequence similarity search results encoded in an open, exchangeable format have the potential to limit the needs for computational reanalysis of these data sets. A prerequisite for sharing of similarity results is a common reference.

Description: We introduce a mechanism for automatically maintaining a comprehensive, non-redundant protein database and for creating a quarterly release of this resource. In addition, we present tools for translating similarity searches into many annotation namespaces, e.g. KEGG or NCBI's GenBank.

Conclusions: The data and tools we present allow the creation of multiple result sets using a single computation, permitting computational results to be shared between groups for large sequence data sets.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-13-141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3410781PMC
June 2012

A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE.

PLoS Comput Biol 2012 7;8(6):e1002541. Epub 2012 Jun 7.

Argonne National Laboratory, Argonne, Illinois, United States of America.

We provide a novel method, DRISEE (duplicate read inferred sequencing error estimation), to assess sequencing quality (alternatively referred to as "noise" or "error") within and/or between sequencing samples. DRISEE provides positional error estimates that can be used to inform read trimming within a sample. It also provides global (whole sample) error estimates that can be used to identify samples with high or varying levels of sequencing error that may confound downstream analyses, particularly in the case of studies that utilize data from multiple sequencing samples. For shotgun metagenomic data, we believe that DRISEE provides estimates of sequencing error that are more accurate and less constrained by technical limitations than existing methods that rely on reference genomes or the use of scores (e.g. Phred). Here, DRISEE is applied to (non amplicon) data sets from both the 454 and Illumina platforms. The DRISEE error estimate is obtained by analyzing sets of artifactual duplicate reads (ADRs), a known by-product of both sequencing platforms. We present DRISEE as an open-source, platform-independent method to assess sequencing error in shotgun metagenomic data, and utilize it to discover previously uncharacterized error in de novo sequence data from the 454 and Illumina sequencing platforms.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1002541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369934PMC
October 2012

Nociceptin/orphanin FQ inhibition with SB612111 ameliorates dextran sodium sulfate-induced colitis.

Eur J Pharmacol 2012 May 16;683(1-3):285-93. Epub 2012 Mar 16.

SRI International, Biosciences Division, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA.

Inflammatory bowel diseases, primarily Crohn's disease and ulcerative colitis, are chronic inflammatory disorders of the gastrointestinal tract with unknown etiology. The majority of current therapeutic agents focus on controlling proinflammatory molecules. The neuropeptide nociceptin/orphanin FQ (N/OFQ) has been described as a potential immunomodulator for inflammatory bowel diseases. In this study, we asked whether the small molecule N/OFQ antagonist (-)-cis-1-methyl-7-[[4-(2,6-dichlorophenyl)piperidin-1-yl]methyl]-6,7,8,9-tetrahydro-5H-benzocyclohepten-5-ol (SB612111) would inhibit the development of dextran sodium sulfate-induced colitis in C57BL/6 mice. Inhibition of the N/OFQ receptor (NOP) by SB612111 significantly ameliorated the clinical disease course in these animals, as indicated by reduced fecal bleeding, improved recovery from diarrhea and weight loss, and a reduction in histopathological alterations. In addition, the inflammatory response in the colon was diminished, as demonstrated by reduced cytokine protein and messenger RNA expression for CXCL1/keratinocyte-derived chemokine, interferon-γ, interleukin-1β, interleukin-6, and tumor necrosis factor-α, some of which are known targets for the treatment of this devastating disease. Our results strongly support a role for the receptor-ligand pair NOP-N/OFQ in the pathogenesis of colitis. We conclude that inhibition of NOP receptors with small molecule inhibitors may constitute a novel, urgently needed approach for the treatment of inflammatory bowel diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ejphar.2012.03.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582657PMC
May 2012

Increased CCL2 expression and macrophage/monocyte migration during microbicide-induced vaginal irritation.

Curr HIV Res 2009 Nov;7(6):639-49

Biosciences Division, SRI International, Menlo Park, CA 94025, USA.

Despite availability of successful prevention strategies, HIV continues to spread at alarming rates, especially among women in developing countries. Vaginal microbicides offer a promising approach for blocking transmission of HIV when condom use cannot be negotiated with male partners. A major problem in the development of vaginal microbicides is chemically induced vaginal irritation, which can enhance the risk of HIV transmission. Evaluation of vaginal irritation prior to clinical trials typically uses an expensive and animal-intensive rabbit vaginal irritation model, which could be supplemented by measuring additional inflammatory biomarkers. We studied several immunological parameters as potential biomarkers of vaginal irritation, using the spermicides nonoxynol-9 and benzalkonium chloride as test microbicides. We measured amounts of cytokines, as well as inflammatory cells, in vaginal tissue lysates and on the vaginal surface. We observed that treatment with the selected microbicides increases quantities of the inflammatory cytokines interleukin-1beta, CXCL8, and CCL2 in the vaginal tissue parenchyma, and of CCL2 on the vaginal surface. This observation was correlated with increases in macrophages in the vaginal parenchyma. We suggest that measurements of CCL2 and macrophages can serve as new inflammatory biomarkers to evaluate the safety of promising novel microbicides for prevention of HIV.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892884PMC
http://dx.doi.org/10.2174/157016209789973682DOI Listing
November 2009

Immunotoxicity of gallium arsenide on antigen presentation: comparative study of intratracheal and intraperitoneal exposure routes.

J Immunotoxicol 2005 Jan;2(1):1-9

Department of Microbiology and Immunology, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA, USA.

Gallium arsenide (GaAs) is a semiconductor utilized in electronics and computer industries. GaAs exposure of animals causes local inflammation and systemic immune suppression. Mice were administered 2 to 200 mg/kg GaAs. On day 5, intratracheal instillation increased lung weights in a dose-dependent manner and induced pulmonary inflammation exemplified by mononuclear cell infiltration and mild epithelial hyperplasia. No fibrosis, pneumocyte hyperplasia, proteinosis, or bronchial epithelial damage was observed in the lungs. Splenic cellularity and composition were unaffected. GaAs' effect on antigen presentation by macrophages was similar after intratracheal and intraperitoneal exposure, although the lowest observable adverse effect levels differed. Macrophages from the exposure site displayed an enhanced ability to activate an antigen-specific CD4(+) helper T-cell hybridoma compared with vehicle controls, whereas splenic macrophages were defective in this function. The chemical's impact on peritoneal macrophages depended on the exposure route. GaAs exposure augmented thiol cathepsins B and L activities in macrophages from the exposure site, but decreased proteolytic activities in splenic macrophages. Alveolar macrophages had increased expression of major histocompatibility complex (MHC) Class II molecules, whereas MHC Class II expression on splenic and peritoneal macrophages was unaffected. Modified thiol cathepsin activities statistically correlated with altered efficiency of antigen presentation, whereas MHC Class II expression did not. Our study is the first one to examine the functional capability of alveolar macrophages after intratracheal GaAs instillation. Therefore, thiol cathepsins may be potential target molecules by which GaAs exposure modulates antigen presentation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/15476910590930083DOI Listing
January 2005

The malaria secretome: from algorithms to essential function in blood stage infection.

PLoS Pathog 2008 Jun 13;4(6):e1000084. Epub 2008 Jun 13.

Department of Pathology, Northwestern University, Chicago, Illinois, United States of America.

The malaria agent Plasmodium falciparum is predicted to export a "secretome" of several hundred proteins to remodel the host erythrocyte. Prediction of protein export is based on the presence of an ER-type signal sequence and a downstream Host-Targeting (HT) motif (which is similar to, but distinct from, the closely related Plasmodium Export Element [PEXEL]). Previous attempts to determine the entire secretome, using either the HT-motif or the PEXEL, have yielded large sets of proteins, which have not been comprehensively tested. We present here an expanded secretome that is optimized for both P. falciparum signal sequences and the HT-motif. From the most conservative of these three secretome predictions, we identify 11 proteins that are preserved across human- and rodent-infecting Plasmodium species. The conservation of these proteins likely indicates that they perform important functions in the interaction with and remodeling of the host erythrocyte important for all Plasmodium parasites. Using the piggyBac transposition system, we validate their export and find a positive prediction rate of approximately 70%. Even for proteins identified by all secretomes, the positive prediction rate is not likely to exceed approximately 75%. Attempted deletions of the genes encoding the conserved exported proteins were not successful, but additional functional analyses revealed the first conserved secretome function. This gave new insight into mechanisms for the assembly of the parasite-induced tubovesicular network needed for import of nutrients into the infected erythrocyte. Thus, genomic screens combined with functional assays provide unexpected and fundamental insights into host remodeling by this major human pathogen.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1000084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408878PMC
June 2008

Erythrocyte G protein as a novel target for malarial chemotherapy.

PLoS Med 2006 Dec;3(12):e528

Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America.

Background: Malaria remains a serious health problem because resistance develops to all currently used drugs when their parasite targets mutate. Novel antimalarial drug targets are urgently needed to reduce global morbidity and mortality. Our prior results suggested that inhibiting erythrocyte Gs signaling blocked invasion by the human malaria parasite Plasmodium falciparum.

Methods And Findings: We investigated the erythrocyte guanine nucleotide regulatory protein Gs as a novel antimalarial target. Erythrocyte "ghosts" loaded with a Gs peptide designed to block Gs interaction with its receptors, were blocked in beta-adrenergic agonist-induced signaling. This finding directly demonstrates that erythrocyte Gs is functional and that propranolol, an antagonist of G protein-coupled beta-adrenergic receptors, dampens Gs activity in erythrocytes. We subsequently used the ghost system to directly link inhibition of host Gs to parasite entry. In addition, we discovered that ghosts loaded with the peptide were inhibited in intracellular parasite maturation. Propranolol also inhibited blood-stage parasite growth, as did other beta2-antagonists. beta-blocker growth inhibition appeared to be due to delay in the terminal schizont stage. When used in combination with existing antimalarials in cell culture, propranolol reduced the 50% and 90% inhibitory concentrations for existing drugs against P. falciparum by 5- to 10-fold and was also effective in reducing drug dose in animal models of infection.

Conclusions: Together these data establish that, in addition to invasion, erythrocyte G protein signaling is needed for intracellular parasite proliferation and thus may present a novel antimalarial target. The results provide proof of the concept that erythrocyte Gs antagonism offers a novel strategy to fight infection and that it has potential to be used to develop combination therapies with existing antimalarials.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pmed.0030528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716186PMC
December 2006

Lipid rafts and malaria parasite infection of erythrocytes.

Mol Membr Biol 2006 Jan-Feb;23(1):81-8

Department of Pathology and Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.

Infection of human erythrocytes by the malarial parasite, Plasmodium falciparum, results in complex membrane sorting and signaling events in the mature erythrocyte. These events appear to rely heavily on proteins resident in erythrocyte lipid rafts. Over the past five years, we and others have undertaken a comprehensive characterization of major proteins present in erythrocyte detergent-resistant membrane lipid rafts and determined which of these proteins traffic to the host-derived membrane that bounds the intraerythrocytic parasite. The data suggest that raft association is necessary but not sufficient for vacuolar recruitment, and that there is likely a mechanism of active uptake of a subset of erythrocyte detergent-resistant membrane proteins. Of the ten internalized proteins, few have been evaluated for a role in malarial entry. The beta(2)-adrenergic receptor and heterotrimeric G protein G(s) signaling pathway proteins regulate invasion. The implications of these differences are discussed. In addition, the latter finding indicates that erythrocytes possess important signaling pathways. These signaling cascades may have important influences on in vivo malarial infection, as well as on erythrocyte membrane flexibility and adhesiveness in sickle cell anemia. With respect to malarial infection, host signaling components alone are not sufficient to induce formation of the malarial vacuole. Parasite proteins are likely to have a major role in making the intraerythrocytic environment conducive for vacuole formation. Such interactions should be the focus of future efforts to understand malarial infection of erythrocytes since host- and parasite-targeted interventions are urgently needed to combat this terrible disease.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/09687860500473440DOI Listing
May 2006

A host-targeting signal in virulence proteins reveals a secretome in malarial infection.

Science 2004 Dec;306(5703):1934-7

Departments of Pathology and Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA.

Malaria parasites secrete proteins across the vacuolar membrane into the erythrocyte, inducing modifications linked to disease and parasite survival. We identified an 11-amino acid signal required for the secretion of proteins from the Plasmodium falciparum vacuole to the human erythrocyte. Bioinformatics predicted a secretome of >320 proteins and conservation of the signal across parasite species. Functional studies indicated the predictive value of the signal and its role in targeting virulence proteins to the erythrocyte and implicated its recognition by a receptor/transporter. Erythrocyte modification by the parasite may involve plasmodial heat shock proteins and be vastly more complex than hitherto realized.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1102737DOI Listing
December 2004

Erythrocyte detergent-resistant membrane proteins: their characterization and selective uptake during malarial infection.

Blood 2004 Mar 30;103(5):1920-8. Epub 2003 Oct 30.

Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.

Infection of human erythrocytes by the apicomplexan malaria parasite Plasmodium falciparum results in endovacuolar uptake of 4 host proteins that reside in erythrocyte detergent-resistant membranes (DRMs). Whether this vacuolar transport reflects selective uptake of host DRM proteins remains unknown. A further complication is that DRMs of vastly different protein and cholesterol contents have been isolated from erythrocytes. Here we show that isolated DRMs containing the highest cholesterol-to-protein ratio have low protein mass. Liquid chromatography, mass spectrometry, and antibody-based studies reveal that the major DRM proteins are band 3, flotillin-1 and -2, peroxiredoxin-2, and stomatin. Band 3 and stomatin, which reflect the bulk mass of erythrocyte DRM proteins, and all tested non-DRM proteins are excluded from the vacuolar parasite. In contrast, flotillin-1 and -2 and 8 minor DRM proteins are recruited to the vacuole. These data suggest that DRM association is necessary but not sufficient for vacuolar recruitment and there is active, vacuolar uptake of a subset of host DRM proteins. Finally, the 10 internalized DRM proteins show varied lipid and peptidic anchors indicating that, contrary to the prevailing model of apicomplexan vacuole formation, DRM association, rather than lipid anchors, provides the preferred criteria for protein recruitment to the malarial vacuole.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1182/blood-2003-09-3165DOI Listing
March 2004

Cooperative domains define a unique host cell-targeting signal in Plasmodium falciparum-infected erythrocytes.

Proc Natl Acad Sci U S A 2003 Oct 26;100(21):12402-7. Epub 2003 Sep 26.

Departments of Pathology and Microbiology-Immunology, The Feinberg School of Medicine, Northwestern University, 303 Chicago Avenue, Chicago, IL 60611, USA.

When the malaria parasite Plasmodium falciparum infects an erythrocyte, it resides in a parasitophorous vacuole and remarkably exports proteins into the periphery of its host cell. Two of these proteins, the histidine-rich proteins I and II (PfHRPI and PfHRPII), are exported to the erythrocyte cytoplasm. PfHRPI has been linked to cell-surface "knobby" protrusions that mediate cerebral malaria and are a frequent cause of death. PfHRPII has been implicated in (i) the production of hemozoin, the black pigment associated with disease, as well as (ii) interactions with the erythrocyte cytoskeleton. Here we show that a tripartite signal that is comprised of an endoplasmic reticulum-type signal sequence followed by a bipartite vacuolar translocation signal derived from HRPII and HRPI exports GFP from the parasitophorous vacuole to the host cytoplasm. The bipartite vacuolar translocation signal is comprised of unique, peptidic (approximately equal to 40-aa) sequences. A domain within it contains the signal for export to "cleft" transport intermediates in the host erythrocyte and may thereby regulate the pathway of export to the host cytoplasm. A signal for posttranslational, vacuolar exit of proteins has hitherto not been described in eukaryotic secretion.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.2133080100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC218770PMC
October 2003

Erythrocyte G protein-coupled receptor signaling in malarial infection.

Science 2003 Sep;301(5640):1734-6

Department of Pathology, Feinberg School of Medicine, Northwestern University, 303 Chicago Avenue, Chicago, IL 60611, USA.

Erythrocytic mechanisms involved in malarial infection are poorly understood. We have found that signaling via the erythrocyte beta2-adrenergic receptor and heterotrimeric guanine nucleotide-binding protein (Galphas) regulated the entry of the human malaria parasite Plasmodium falciparum. Agonists that stimulate cyclic adenosine 3',5'-monophosphate production led to an increase in malarial infection that could be blocked by specific receptor antagonists. Moreover, peptides designed to inhibit Galphas protein function reduced parasitemia in P. falciparum cultures in vitro, and beta-antagonists reduced parasitemia of P. berghei infections in an in vivo mouse model. Thus, signaling via the erythrocyte beta2-adrenergic receptor and Galphas may regulate malarial infection across parasite species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1089324DOI Listing
September 2003

Impact of in vitro gallium arsenide exposure on macrophages.

Toxicol Appl Pharmacol 2003 Jan;186(1):18-27

Department of Microbiology and Immunology, Virginia Commonwealth University, Ricchmond, VA 23298-0678, USA.

The semiconductor gallium arsenide (GaAs) is classified as an immunotoxicant and a carcinogen. We previously showed that GaAs in vivo induces several phenotypic changes in macrophages located at the exposure site, indicative of an activated state. These physiological alterations may be a primary or secondary consequence of chemical exposure. To discern primary influences, our current study examined the in vitro effects of the chemical on macrophage cell lines and murine peritoneal macrophages. GaAs augmented cathepsins L and B proteolytic activities in all three sources of macrophages. Expression of the two mature isoforms of invariant chain and its cleavage fragment was also significantly increased, indicating that the chemical directly affects macrophages. However, GaAs did not alter the overall cell surface expression of major histocompatibility complex class II molecules on macrophages nor influence their ability to stimulate antigen-specific helper T cell hybridomas to respond to intact antigens that require processing. These findings raise the possibility that the chemical's complete in vivo impact may involve cytokines. Further, GaAs in vitro enhanced steady-state cathepsin L protein, and cathepsins L and B mRNA expression in macrophages, indicating that GaAs may alter gene expression, which may contribute to the chemical's adverse biological effects.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/s0041-008x(02)00020-0DOI Listing
January 2003

Protein and lipid trafficking induced in erythrocytes infected by malaria parasites.

Cell Microbiol 2002 Jul;4(7):383-95

Department of Pathology, Northwestern University, 303 E. Chicago Avenue, Chicago, IL 60611, USA.

The human malaria parasite Plasmodium falciparum develops in a parasitophorous vacuolar membrane (PVM) within the mature red cell and extensively modifies structural and antigenic properties of this host cell. Recent studies shed significant new, mechanistic perspective on the underlying processes. There is finally, definitive evidence that despite the absence of endocytosis, transmembrane proteins in the host red cell membrane are imported in to the PVM. These are not major erythrocyte proteins but components that reside in detergent resistant membrane (DRM) rafts in red cell membrane and are detected in rafts in the PVM. Disruption of either erythrocyte or vacuolar rafts is detrimental to infection suggesting that raft proteins and lipids are essential for the parasitization of the red cell. On secretory export of parasite proteins: an ER secretory signal (SS) sequence is required for protein secretion to the PV. Proteins carrying an additional plastid targeting sequence (PTS) are also detected in the PV but subsequently delivered to the plastid organelle within the parasite, suggesting that the PTS may have a second function as an endocytic sorting signal. A distinct but yet undefined peptidic motif underlies protein transport across the PVM to the red cell (although all of the published data does not yet fit this model). Further multiple exported proteins transit through secretory 'cleft' structures, suggesting that clefts may be sorting compartments assembled by the parasite in the red cell.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1046/j.1462-5822.2002.00204.xDOI Listing
July 2002

Trans expression of a Plasmodium falciparum histidine-rich protein II (HRPII) reveals sorting of soluble proteins in the periphery of the host erythrocyte and disrupts transport to the malarial food vacuole.

J Biol Chem 2002 Aug 22;277(32):28923-33. Epub 2002 May 22.

Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.

The heme polymer hemozoin is produced in the food vacuole (fv) of the parasite after hemoglobin proteolysis and is the target of the drug chloroquine. A candidate heme polymerase, the histidine-rich protein II (HRPII), is proposed to be delivered to the fv by ingestion of the infected-red cell cytoplasm. Here we show that 97% of endogenous Plasmodium falciparum (Pf) HRPII (PfHRPII) is secreted as soluble protein in the periphery of the red cell and avoids endocytosis by the parasite, and 3% remains membrane-bound within the parasite. Transfected cells release 90% of a soluble transgene PfHRPIImyc into the red cell periphery and contain 10% membrane bound within the parasite. Yet these cells show a minor reduction in hemozoin production and IC(50) for chloroquine. They also show decreased transport of resident fv enzyme PfPlasmepsin I, the endoplasmic reticulum (ER) marker PfBiP, and parasite-associated HRPII to fvs. Instead, all three proteins accumulate in the ER, although there is no defect in protein export from the parasite. The data suggest that novel mechanisms of sorting (i) soluble antigens like HRPII in the red cell cytoplasm and (ii) fv-bound membrane complexes in the ER regulate parasite digestive processes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.M201968200DOI Listing
August 2002

Targeting the malarial plastid via the parasitophorous vacuole.

J Biol Chem 2002 May 28;277(18):16265-77. Epub 2002 Jan 28.

Department Pathology, Northwestern University, Chicago, Illinois 60611, USA.

The malarial "apicoplast" derived from an algal plastid, has stimulated interest for its novel evolutionary biology and potential as a drug target. An endoplasmic reticulum-type signal sequence followed by a plastid targeting sequence are required to target proteins to the apicoplast but the pathway by which proteins are transported to the organelle is unknown. By stage regulating the expression of transgenes we show that early (0-12 h) in the parasite's development in red cells, newly synthesized green fluorescent protein that contains the plastid targeting sequence (plastid targeting sequence-green fluorescent protein (PTS-GFP)) is recruited into the parasite's secretory pathway. PTS-GFP in 0-12-h parasites is found released into the parasitophorous vacuole (PV) and in apposition with the Golgi. However, import into the apicoplast and processing to GFP does not occur until 18-36 h in development. In intermediate, 18-h parasites PTS-GFP resides in the PV. Quantitative exit of PTS-GFP from the PV and its conversion to GFP is seen at 36 h. The data suggest that: (i) import into the apicoplast is stage regulated and (ii) the PTS can signal endomembrane targeting from the PV to the apicoplast.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.M109331200DOI Listing
May 2002