Infectious Disease Organisms Research Articles

Stanley Falkow. 24 January 1934—5 May 2018

Our understanding of infectious disease and disease-causing organisms has been broadly shaped by two revolutions. The first was the advent of clinical microbiology of the nineteenth and early twentieth centuries, which saw the isolation, identification and classification of disease-causing organisms. In the middle of the twentieth century, the emerging field of molecular biology transformed our understanding of genes and their regulation. Starting in 1960, Stanley Falkow fused clinical microbiology with molecular biology, founding the new discipline of molecular microbial pathogenesis. Over the next half century, he led and shaped this new discipline, revolutionizing our understanding of how pathogenic bacteria cause disease and become resistant to antibiotics.

Profiling endogenous, environmental, and infectious disease mutational signatures in blastic plasmacytoid dendritic cell neoplasms.

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare hematopoietic disease derived from plasmacytoid dendritic lineage cells. The disease typically shows skin as well as frequent bone marrow and peripheral blood involvement. However, the pathogenesis of this disease is still not well understood. While somatic point mutations and genetic rearrangements have been described in BPDCN, the types and origins of these mutations and relationships to other cancer types is not well understood. To probe the origins of BPDCN, we analyzed the exome sequence data of 9 tumor-normal pair cases of BPDCN. We utilized SignatureAnalyzer, SigProfiler and a custom microbial analysis pipeline to understand the relevance of endogenous and environmental mutagenic processes. Our results identified a significant tobacco exposure and aging genetic signature as well as signatures related to nucleotide excision repair deficiency, ultra violet (UV) exposure, and endogenous deamination in BPDCN. We also assessed the samples for microbial infectious disease organisms but did not find a link to a microbial etiology. The identification of a tobacco exposure and aging genetic signature in patients with BPDCN suggests that environmental and endogenous genetic changes may be central to the oncogenesis of BPDCN.

Epigenetic dysregulation of host gene expression in Toxoplasma infection with specific reference to dopamine and amyloid pathways

Recent interest has focussed on the influence of infectious disease organisms on the host epigenome. Toxoplasma gondii infection acquired congenitally or in early life is associated with severe ocular and brain developmental anomalies, while persistent asymptomatic infection is a proposed risk factor for neurodegenerative and psychiatric disorders, including Parkinson's and Alzheimer's Diseases, and schizophrenia. Genome-wide analysis of the host methylome and transcriptome following T. gondii infection in a retinal cell line identified genes (132, 186 and 128 genes at 2, 6 and 24 h post-infection) concordant for methylation and expression, i.e. hypermethylated and decreased expression or hypomethylated and increased expression. Pathway analyses showed perturbation of two neurologically-associated pathways: dopamine-DARPP32 feedback in cAMP signalling (p-value = 8.3 × 10−5; adjusted p-value = 0.020); and amyloid processing (p-value = 1.0 × 10−3; adjusted p-value = 0.043). Amyloid Precursor Protein (APP) decreased in level following T. gondii infection. These results are of interest given the expression of APP early in nervous system development affecting neural migration and the role of amyloid processing in Alzheimer's disease, while dopamine has roles in the developing retina as well as in Parkinson's disease and schizophrenia. Our results provide a possible functional link between T. gondii infection and congenital/early life and adult neurological clinical signs.

Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms

Aminoacyl-tRNA synthetases (aaRSs) charge tRNAs with their cognate amino acid, an essential precursor step to loading of charged tRNAs onto the ribosome and addition of the amino acid to the growing polypeptide chain during protein synthesis. Because of this important biological function, aminoacyl-tRNA synthetases have been the focus of anti-infective drug development efforts and two aaRS inhibitors have been approved as drugs. Several researchers in the scientific community requested aminoacyl-tRNA synthetases to be targeted in the Seattle Structural Genomics Center for Infectious Disease (SSGCID) structure determination pipeline. Here we investigate thirty-one aminoacyl-tRNA synthetases from infectious disease organisms by co-crystallization in the presence of their cognate amino acid, ATP, and/or inhibitors. Crystal structures were determined for a CysRS from Borrelia burgdorferi bound to AMP, GluRS from Borrelia burgdorferi and Burkholderia thailandensis bound to glutamic acid, a TrpRS from the eukaryotic pathogen Encephalitozoon cuniculi bound to tryptophan, a HisRS from Burkholderia thailandensis bound to histidine, and a LysRS from Burkholderia thailandensis bound to lysine. Thus, the presence of ligands may promote aaRS crystallization and structure determination. Comparison with homologous structures shows conformational flexibility that appears to be a recurring theme with this enzyme class.

Ex vivo antigen-pulsed PBMCs generate potent and long lasting immunity to infection when administered as a vaccine

Numerous studies have demonstrated that administration of antigen (Ag)-pulsed dendritic cells (DCs) is an effective strategy for enhancing immunity to tumors and infectious disease organisms. However, the generation and/or isolation of DCs can require substantial time and expense. Therefore, using inactivated F. tularensis (iFt) Ag as a model immunogen, we first sought to determine if DCs could be replaced with peripheral blood mononuclear cells (PBMCs) during the ex-vivo pulse phase and still provide protection against Ft infection. Follow up studies were then conducted using the S. pneumoniae (Sp) vaccine Prevnar ®13 as the Ag in the pulse phase followed by immunization and Sp challenge. In both cases, we demonstrate that PBMCs can be used in place of DCs when pulsing with iFt and/or Prevnar ®13 ex vivo and re-administering the Ag-pulsed PBMCs as a vaccine. In addition, utilization of the i.n. route for Ag-pulsed PBMC administration is superior to use of the i.v. route in the case of Sp immunization, as well as when compared to direct injection of Prevnar ®13 vaccine i.m. or i.n. Furthermore, this PBMC-based vaccine strategy provides a more marked and enduring protective immune response and is also capable of serving as a multi-organism vaccine platform. The potential for this ex-vivo vaccine strategy to provide a simpler, less time consuming, and less expensive approach to DC-based vaccines and vaccination in general is also discussed.

Nanoarchitecture Based SERS for Biomolecular Fingerprinting and Label-Free Disease Markers Diagnosis.

ConspectusSurface-enhanced Raman spectroscopy (SERS) fingerprinting is highly promising for identifying disease markers from complex mixtures of clinical sample, which has the capability to take medical diagnoses to the next level. Although vibrational frequency in Raman spectra is unique for each biomolecule, which can be used as fingerprint identification, it has not been considered to be used routinely for biosensing due to the fact that the Raman signal is very weak. Contemporary SERS has been demonstrated to be an excellent analytical tool for practical label-free sensing applications due its ability to enhance Raman signals by factors of up to 108–1014 orders of magnitude. Although SERS was discovered more than 40 years ago, its applications are still rare outside the spectroscopy community and it is mainly due to the fact that how to control, manipulate and amplify light on the “hot spots” near the metal surface is in the infancy stage.In this Account, we describe our contribution to develop nanoachitecture based highly reproducible and ultrasensitive detection capability SERS platform via low-cost synthetic routes. Using one-dimensional (1D) carbon nanotube (CNT), two-dimensional (2D) graphene oxide (GO), and zero-dimensional (0D) plasmonic nanoparticle, 0D to 3D SERS substrates have been designed, which represent highly powerful platform for biological diagnosis. We discuss the major design criteria we have used to develop robust SERS substrate to possess high density “hot spots” with very good reproducibility. SERS enhancement factor for 3D SERS substrate is about 5 orders of magnitude higher than only plasmonic nanoparticle and more than 9 orders of magnitude higher than 2D GO. Theoretical finite-difference time-domain (FDTD) stimulation data show that the electric field enhancement |E|2 can be more than 2 orders of magnitude in “hot spots”, which suggests that SERS enhancement factors can be greater than 104 due to the formation of high density “hot spots” in 3D substrate. Next, we discuss the utilization of nanoachitecture based SERS substrate for ultrasensitive and selective diagnosis of infectious disease organisms such as drug resistance bacteria and mosquito-borne flavi-viruses that cause significant health problems worldwide. SERS based “whole-organism fingerprints” has been used to identify infectious disease organisms even when they are so closely related that they are difficult to distinguish. The detection capability can be as low as 10 CFU/mL for methicillin-resistant Staphylococcus aureus (MRSA) and 10 PFU/mL for Dengue virus (DENV) and West Nile virus (WNV). After that, we introduce exciting research findings by our group on the applications of nanoachitecture based SERS substrate for the capture and fingerprint detection of rotavirus from water and Alzheimer’s disease biomarkers from whole blood sample. The SERS detection limit for β-amyloid (Aβ proteins) and tau protein using 3D SERS platform is several orders of magnitude higher than the currently used technology in clinics. Finally, we highlight the promises, major challenges and prospect of nanoachitecture based SERS in biomedical diagnosis field.

Structural Genomics Support for Infectious Disease Drug Design.

Structural Genomics Support for Infectious Disease Drug Design.

Fc receptor-targeting of immunogen as a strategy for enhanced antigen loading, vaccination, and protection using intranasally administered antigen-pulsed dendritic cells

Dendritic cells (DCs) play a critical role in the generation of adaptive immunity via the efficient capture, processing, and presentation of antigen (Ag) to naïve T cells. Administration of Ag-pulsed DCs is also an effective strategy for enhancing immunity to tumors and infectious disease organisms. Studies have also demonstrated that targeting Ags to Fcγ receptors (FcγR) on Ag presenting cells can enhance humoral and cellular immunity in vitro and in vivo. Specifically, our studies using a Francisella tularensis (Ft) infectious disease vaccine model have demonstrated that targeting immunogens to FcγR via intranasal (i.n.) administration of monoclonal antibody (mAb)-inactivated Ft (iFt) immune complexes (ICs) enhances protection against Ft challenge. Ft is the causative agent of tularemia, a debilitating disease of humans and other mammals and a category A biothreat agent for which there is no approved vaccine. Therefore, using iFt Ag as a model immunogen, we sought to determine if ex vivo targeting of iFt to FcγR on DCs would enhance the potency of i.n. administered iFt-pulsed DCs. In this study, bone marrow-derived DCs (BMDCs) were pulsed ex vivo with iFt or mAb-iFt ICs. Intranasal administration of mAb-iFt-pulsed BMDCs enhanced humoral and cellular immune responses, as well as protection against Ft live vaccine strain (LVS) challenge. Increased protection correlated with increased iFt loading on the BMDC surface as a consequence of FcγR-targeting. However, the inhibitory FcγRIIB had no impact on this enhancement. In conclusion, targeting Ag ex vivo to FcγR on DCs provides a method for enhanced Ag loading of DCs ex vivo, thereby reducing the amount of Ag required, while also avoiding the inhibitory impact of FcγRIIB. Thus, this represents a simple and less invasive strategy for increasing the potency of ex vivo-pulsed DC vaccines against chronic infectious diseases and cancer.

Selected Abstracts From the 2013 International Neuroethics Society Annual Meeting

Selected Abstracts From the 2013 International Neuroethics Society Annual Meeting

Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei

Published biological data suggest that the methyl erythritol phosphate (MEP) pathway, a non-mevalonate isoprenoid biosynthetic pathway, is essential for certain bacteria and other infectious disease organisms. One highly conserved enzyme in the MEP pathway is 2C-methyl-d-erythritol 2,4-cyclodiphosphate synthase (IspF). Fragment-bound complexes of IspF from Burkholderia pseudomallei were used to design and synthesize a series of molecules linking the cytidine moiety to different zinc pocket fragment binders. Testing by surface plasmon resonance (SPR) found one molecule in the series to possess binding affinity equal to that of cytidine diphosphate, despite lacking any metal-coordinating phosphate groups. Close inspection of the SPR data suggest different binding stoichiometries between IspF and test compounds. Crystallographic analysis shows important variations between the binding mode of one synthesized compound and the pose of the bound fragment from which it was designed. The binding modes of these molecules add to our structural knowledge base for IspF and suggest future refinements in this compound series.

Fc receptor-targeting of immunogen as a strategy for enhanced antigen loading, vaccination, and protection using intranasally-administered ex vivo antigen-pulsed dendritic cells (P4292)

Abstract Dendritic cells play a critical role in the generation of an effective adaptive immune response. This is primarily due to their ability to capture, process, and present Ag to naïve T cells. Administration of Ag-pulsed DCs has proven to be an effective strategy for enhancing immunity to both tumors and infectious disease organisms. In addition, our own studies using an F. tularensis infectious disease vaccine model have demonstrated that targeting immunogens to FcγR via intranasal administration of inactivated F. tularensis-mAb complexes enhances protection against F. tularensis challenge. Therefore, we sought to determine if ex vivo targeting of Ag to FcγR would enhance the potency of intranasally administered Ag-pulsed DCs. In this study, bone marrow-derived DCs were pulsed ex vivo with inactivated F. tularensis alone or complexed to mAb. Immunization of mice, via intranasal injection of F. tularensis-mAb-pulsed DCs, enhanced humoral and cellular immune responses, as well as protection against F. tularensis infection. These observations correlated with increased loading of Ag on the DCs as a consequence of FcR targeting. Importantly, engagement of the inhibitory receptor FcγRIIB had no impact on this enhancement. In conclusion, targeting Ag ex vivo via FcγR on DCs provides a method for enhanced Ag loading of DCs, while bypassing the inhibitory impact of FcγRIIB. Thus, this represents an important strategy for increasing the potency of ex vivo-pulsed DC vaccines.

The Pomegranate: Effects on Bacteria and Viruses That Influence Human Health

Pomegranates have been known for hundreds of years for their multiple health benefits, including antimicrobial activity. The recent surge in multidrug-resistant bacteria and the possibility of widespread global virus pandemics necessitate the need for additional preventative and therapeutic options to conventional drugs. Research indicates that pomegranates and their extracts may serve as natural alternatives due to their potency against a wide range of bacterial and viral pathogens. Nearly every part of the pomegranate plant has been tested for antimicrobial activities, including the fruit juice, peel, arils, flowers, and bark. Many studies have utilized pomegranate peel with success. There are various phytochemical compounds in pomegranate that have demonstrated antimicrobial activity, but most of the studies have found that ellagic acid and larger hydrolyzable tannins, such as punicalagin, have the highest activities. In some cases the combination of the pomegranate constituents offers the most benefit. The positive clinical results on pomegranate and suppression of oral bacteria are intriguing and worthy of further study. Much of the evidence for pomegranates' antibacterial and antiviral activities against foodborne pathogens and other infectious disease organisms comes from in vitro cell-based assays, necessitating further confirmation of in vivo efficacy through human clinical trials.

Structural genomics of infectious disease drug targets: the SSGCID.

The Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium of researchers at Seattle BioMed, Emerald BioStructures, the University of Washington and Pacific Northwest National Laboratory that was established to apply structural genomics approaches to drug targets from infectious disease organisms. The SSGCID is currently funded over a five-year period by the National Institute of Allergy and Infectious Diseases (NIAID) to determine the three-dimensional structures of 400 proteins from a variety of Category A, B and C pathogens. Target selection engages the infectious disease research and drug-therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. The protein-expression systems, purified proteins, ligand screens and three-dimensional structures produced by SSGCID constitute a valuable resource for drug-discovery research, all of which is made freely available to the greater scientific community. This issue of Acta Crystallographica Section F, entirely devoted to the work of the SSGCID, covers the details of the high-throughput pipeline and presents a series of structures from a broad array of pathogenic organisms. Here, a background is provided on the structural genomics of infectious disease, the essential components of the SSGCID pipeline are discussed and a survey of progress to date is presented.

SAD phasing using iodide ions in a high-throughput structural genomics environment

The Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures. Thus, many SSGCID targets are expected to be solved by molecular replacement (MR), and reflective of this, all proteins are expressed in native form. However, many community request targets do not have homologs with known structures and not all internally selected targets readily solve by MR, necessitating experimental phase determination. We have adopted the use of iodide ion soaks and single wavelength anomalous dispersion (SAD) experiments as our primary method for de novo phasing. This method uses existing native crystals and in house data collection, resulting in rapid, low cost structure determination. Iodide ions are non-toxic and soluble at molar concentrations, facilitating binding at numerous hydrophobic or positively charged sites. We have used this technique across a wide range of crystallization conditions with successful structure determination in 16 of 17 cases within the first year of use (94% success rate). Here we present a general overview of this method as well as several examples including SAD phasing of proteins with novel folds and the combined use of SAD and MR for targets with weak MR solutions. These cases highlight the straightforward and powerful method of iodide ion SAD phasing in a high-throughput structural genomics environment.Electronic supplementary materialThe online version of this article (doi:10.1007/s10969-011-9101-7) contains supplementary material, which is available to authorized users.

BEI Resources: a biological resource center for parasitologists

BEI Resources: a biological resource center for parasitologists

Considerations for minimising the spread of infectious disease in Antarctic seabirds and seals

ABSTRACTBefore 1998, concern was raised over the potential for human activities in Antarctica to introduce infectious disease organisms to native wildlife. A workshop was held that year to address this issue. In the last decade, there has been a dramatic increase in human traffic to the Antarctic and the number of commercial tourists visiting the Antarctic has steadily risen. Personnel of national science programmes, though relatively few in numbers, have the most intimate contact with wildlife and thus the greater potential to introduce organisms through their research activities. Many visitors are now able to arrive in the Antarctic from temperate regions within hours by aircraft, and from northern polar regions within 24 to 36 hours. Tourists, by their high numbers, also have the potential to transfer infectious disease agents among commonly visited sites. As of 2009, no outbreaks of infectious diseases in the Antarctic reported in the literature have been directly attributed to human activity, but the ameliorating climate may break down the barriers that have kept Antarctic wildlife relatively free of infectious diseases. Several agents of infectious diseases reported in Antarctic seabirds and seals are assessed for their likelihood to occur more frequently in terms of the characteristics of the agent, the behaviour of Antarctic wildlife, and the effects of an ameliorating climate (regional warming) in conjunction with continued increasing human activities.

The Role of Medical Structural Genomics in Discovering New Drugs for Infectious Diseases

The Role of Medical Structural Genomics in Discovering New Drugs for Infectious Diseases

A path to discovery: the career of Maclyn McCarty.

Maclyn McCarty, who devoted his life as a physician-scientist to studying infectious disease organisms, was best known for his part in the monumental discovery that DNA, rather than protein, constituted the chemical nature of a gene. Uncovering the molecular secret of the gene in question—that for the capsular polysaccharide of pneumococcal bacteria—led the way to studying heredity not only through genetics but also through chemistry, and initiated the dawn of the age of molecular biology. McCarty was the youngest and longest surviving member of the research team responsible for this feat, which also included Oswald T. Avery and Colin MacLeod; he died on January 2, 2005, from congestive heart failure.

Trite but True, Better Safe Than Sorry

Trite but True, Better Safe Than Sorry

Plant-Based Vaccines for Protection Against Infectious and Autoimmune Diseases

Referee: Dr. Yoedono Sovyanhadi, Department of Biological Sciences, Oakwood College, 7000 Adventist Boulevard, NW, Huntsville, AL 35896Over the last 2 decades, the number of emergent infectious diseases has increased at an alarming rate. Also disheartening is the rise of known infectious pathogens that have acquired extensive drug resistance and reemerged with greater virulence. More recently, the threat of bioweapons has rekindled an urgency for the development of mass immunization programs. In response to this increased infectious disease threat, efforts have been intensified to identify more effective, inexpensive, and more easily deliverable mucosal vaccination methods. One area of research currently under development is the genetic modification of plants for production of immunoprotective proteins. The ability of plants to synthesize complex proteins using the elements of sunlight, soil, air, and water makes them ideal organisms for harvesting large quantities of therapeutic proteins. The introduction of antigen or antibody encoding genes into the genome of a plant through stable transformation enables them to manufacture vaccine proteins that are directly applicable for use in disease treatment, unlike yeast, bacterial, insect or other expression systems that require purification steps before delivery. As an alternative to stable transformation, plants can be used to generate large quantities of vaccines by acting as hosts for genetically altered plant viruses in which antigen proteins can be expressed and later purified from infected plant tissues. In this review, we survey current experimental strategies for using edible plants to achieve passive and active immunization against infectious disease organisms. In addition, methods are described for the construction of transformed plants that can provide protection against autoimmune diseases. Concerns and present obstacles to effective immunization with plant-based vaccines for animals and humans are presented.