Curr Protoc Microbiol
· 2013 Oct · PMID 24510894
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Streptococcus pyogenes (the Group A Streptococcus, GAS) is a Gram-positive bacterium responsible for a wide spectrum of diseases ranging from mild superficial infections (pharyngitis, impetigo) to severe, often life-thre...Streptococcus pyogenes (the Group A Streptococcus, GAS) is a Gram-positive bacterium responsible for a wide spectrum of diseases ranging from mild superficial infections (pharyngitis, impetigo) to severe, often life-threatening invasive diseases (necrotizing fasciitis, streptococcal toxic shock syndrome) in humans. This unit describes molecular techniques for the genetic manipulation of S. pyogenes with detailed protocols for transformation, gene disruption, allelic exchange, transposon mutagenesis, and genetic complementation.
Curr Protoc Microbiol
· 2013 Oct · PMID 24510893
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Full text
Streptococcus pyogenes is a Gram-positive bacterium that strictly infects humans. It is the causative agent of a broad spectrum of diseases accounting for millions of infections and at least 517,000 deaths each year worl...Streptococcus pyogenes is a Gram-positive bacterium that strictly infects humans. It is the causative agent of a broad spectrum of diseases accounting for millions of infections and at least 517,000 deaths each year worldwide. It is a nutritionally fastidious organism that ferments sugars to produce lactic acid and has strict requirements for growth. To aid in the study of this organism, this unit describes the growth and maintenance of S. pyogenes.
Metronidazole and vancomycin remain the front-line therapies for most Clostridium difficile infections (CDI). However, recurrent CDI occurs in ∼ 25% of patients, causing significant morbidity and mortality and healthcare...Metronidazole and vancomycin remain the front-line therapies for most Clostridium difficile infections (CDI). However, recurrent CDI occurs in ∼ 25% of patients, causing significant morbidity and mortality and healthcare costs. For this population, traditional antibiotic therapies fail and new treatment options are greatly needed. The US Food and Drug Administration recently approved fidaxomicin for CDI treatment. This narrow-spectrum antibiotic preserves the normal gut microbiota and shows promise as a treatment for severe and recurrent CDI. Monoclonal antibodies and vaccines directed against toxin are currently in clinical trials and represent alternative, non-antibiotic therapies. Less traditional therapeutic interventions include bacteriotherapy with non-toxigenic C. difficile and fecal transplant. This commentary will provide an overview of current and forthcoming CDI therapies.
Curr Protoc Microbiol
· 2013 Oct · PMID 24510891
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Full text
Virus-like particles (VLPs) are large particles, the size of viruses, composed of repeating structures that mimic those of infectious virus. Since their structures are similar to that of viruses, they have been used to s...Virus-like particles (VLPs) are large particles, the size of viruses, composed of repeating structures that mimic those of infectious virus. Since their structures are similar to that of viruses, they have been used to study the mechanisms of virus assembly. They are also in development for delivery of molecules to cells and in studies of the immunogenicity of particle-associated antigens. However, they have been most widely used for development of vaccines and vaccine candidates. VLPs can form upon the expression of the structural proteins of many different viruses. This chapter describes the generation and purification of VLPs formed with the structural proteins, M, NP, F, and HN proteins, of Newcastle disease virus (NDV). Newcastle disease virus-like particles (ND VLPs) have also been developed as a platform for assembly into VLPs of glycoproteins from other viruses. This chapter describes the methods for this use of ND VLPs.
Curr Protoc Microbiol
· 2013 Oct · PMID 24510890
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Selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) provides a means to investigate RNA structure with better resolution and higher throughput than has been possible with traditional methods. We present...Selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) provides a means to investigate RNA structure with better resolution and higher throughput than has been possible with traditional methods. We present several protocols, which are based on a variety of previously published methods and were adapted and optimized for the analysis of poliovirus RNA in the Andino laboratory. These include methods for nondenaturing RNA extraction, RNA modification and primer extension, and data processing in ShapeFinder.
Curr Protoc Microbiol
· 2014 Feb · PMID 24510849
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Staphylococcus aureus is a facultative anaerobic Gram-positive coccus and a member of the normal skin flora, as well as that of the nasal passages of humans. However, S. aureus can also gain entry into the host and cause...Staphylococcus aureus is a facultative anaerobic Gram-positive coccus and a member of the normal skin flora, as well as that of the nasal passages of humans. However, S. aureus can also gain entry into the host and cause life-threatening infections or persist as disease foci that develop into suppurative abscesses. While genetically tractable, the manipulation of S. aureus remains challenging. This unit describes methods developed in our laboratory for gene disruption by allelic replacement and transposition. We also provide a protocol for bacteriophage-mediated transduction of mutants marked with selectable alleles and describe plasmid utilization for complementation studies.
Curr Protoc Microbiol
· 2014 Feb · PMID 24510848
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Stenotrophomonas maltophilia is a ubiquitous soil bacterium that is increasingly recognized as an emerging nosocomial pathogen. This unit includes protocols for the in vitro growth and maintenance of S. maltophilia.Stenotrophomonas maltophilia is a ubiquitous soil bacterium that is increasingly recognized as an emerging nosocomial pathogen. This unit includes protocols for the in vitro growth and maintenance of S. maltophilia.
This unit describes how to use several gene-finding programs from the GeneMark line developed for finding protein-coding ORFs in genomic DNA of prokaryotic species, in genomic DNA of eukaryotic species with intronless ge...This unit describes how to use several gene-finding programs from the GeneMark line developed for finding protein-coding ORFs in genomic DNA of prokaryotic species, in genomic DNA of eukaryotic species with intronless genes, in genomes of viruses and phages, and in prokaryotic metagenomic sequences, as well as in EST sequences with spliced-out introns. These bioinformatics tools were demonstrated to have state-of-the-art accuracy, and have been frequently used for gene annotation in novel nucleotide sequences. An additional advantage of these sequence-analysis tools is that the problem of algorithm parameterization is solved automatically, with parameters estimated by iterative self-training (unsupervised training).
The microscopic agglutination test (MAT) is the gold standard for sero-diagnosis of leptospirosis because of its unsurpassed diagnostic specificity. It uses panels of live leptospires, ideally recent isolates, representi...The microscopic agglutination test (MAT) is the gold standard for sero-diagnosis of leptospirosis because of its unsurpassed diagnostic specificity. It uses panels of live leptospires, ideally recent isolates, representing the circulating serovars from the area where the patient became infected. A dilution series of the patient's serum is mixed with a suspension of live leptospires in microtiter plates. After incubating for about 2 hr at 30°C, results are read under the dark-field microscope. The titer is the last dilution in which ≥ 50% of the leptospires have remained agglutinated. Seroconversion or ≥ 4-fold titer rise in paired sera is consistent with current leptospirosis. The significance of a titer in a single sample depends on the frequency of residual titers due to past infections and cross-reacting other diseases in the population. Full standardization of the MAT is not possible, but quality assurance can be achieved by participation in the international MAT proficiency testing scheme.
The importance of laboratory mice in experimental microbiology and biomedical research is indisputable, and their care and handling is a contributing factor to the quality of the science resulting from their use. This un...The importance of laboratory mice in experimental microbiology and biomedical research is indisputable, and their care and handling is a contributing factor to the quality of the science resulting from their use. This unit provides guidelines for practical housing, handling, and the methodology for sample collection to ensure animal health and minimize variable experimental parameters.
Curr Protoc Microbiol
· 2013 Nov · PMID 24510293
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Listeria monocytogenes causes foodborne disease in humans that ranges in severity from mild, self-limiting gastroenteritis to life-threatening systemic infections of the blood, brain, or placenta. The most commonly used...Listeria monocytogenes causes foodborne disease in humans that ranges in severity from mild, self-limiting gastroenteritis to life-threatening systemic infections of the blood, brain, or placenta. The most commonly used animal model of listeriosis is intravenous infection of mice. This systemic model is highly reproducible, and thus, useful for studying cell-mediated immune responses against an intracellular bacterial pathogen, but it completely bypasses the gastrointestinal phase of L. monocytogenes infection. Intragastric inoculation of L. monocytogenes produces more variable results and may cause direct bloodstream invasion in some animals. The foodborne transmission model described here does not require specialized skills to perform and results in infections that more closely mimic human disease. This natural feeding model can be used to study both the host- and pathogen-derived factors that govern susceptibility or resistance to orally acquired L. monocytogenes.
Curr Protoc Microbiol
· 2013 Nov · PMID 24510292
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This unit describes general procedures for the lab cultivation and storage of the Gram-positive facultative intracellular bacterium Listeria monocytogenes. The basic protocols are relevant for a wide scope of application...This unit describes general procedures for the lab cultivation and storage of the Gram-positive facultative intracellular bacterium Listeria monocytogenes. The basic protocols are relevant for a wide scope of applications including microbial genetics and both in vitro and in vivo infection studies. Commonly used L. monocytogenes strains, serotypes, and growth parameters are also discussed.
Curr Protoc Microbiol
· 2013 Nov · PMID 24510291
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DNA immunization was discovered in early 1990s, and its use has been expanded from vaccine studies to a broader range of biomedical research areas, such as the generation of high-quality polyclonal and monoclonal antibod...DNA immunization was discovered in early 1990s, and its use has been expanded from vaccine studies to a broader range of biomedical research areas, such as the generation of high-quality polyclonal and monoclonal antibodies as research reagents. In this unit, three common DNA immunization methods are described: needle injection, electroporation, and gene gun. In addition, several common considerations related to DNA immunization are discussed.
Curr Protoc Microbiol
· 2013 Nov · PMID 24510290
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Human noroviruses constitute a significant worldwide disease burden. Each year, noroviruses cause over 267 million infections, deaths in over 200,000 children under the age of five, and over 50% of U.S. food-borne illnes...Human noroviruses constitute a significant worldwide disease burden. Each year, noroviruses cause over 267 million infections, deaths in over 200,000 children under the age of five, and over 50% of U.S. food-borne illness. Due to the absence of a tissue culture model or small animal model to study human norovirus, virus-like particles (VLPs) and ELISA-based biological assays have been used to answer questions about norovirus evolution and immunity as well to provide a potential vaccine platform. This chapter outlines the protocols for norovirus detection in stool, as well as norovirus VLP design, production, purification, and storage using a Venezuelan equine encephalitis virus (VEE)-based virus replicon particle (VRP) expression system.
West Nile virus (WNV) is a member of the Flaviviridae family of enveloped, single-stranded, positive-sense RNA viruses. WNV, an emerging viral pathogen, is transmitted by mosquitoes to birds and mammals and is responsibl...West Nile virus (WNV) is a member of the Flaviviridae family of enveloped, single-stranded, positive-sense RNA viruses. WNV, an emerging viral pathogen, is transmitted by mosquitoes to birds and mammals and is responsible for an increasing incidence of human disease in North America and Europe. Due to its ease of use in the laboratory and the availability of robust mouse models of disease, WNV provides an excellent experimental system for studying molecular virology and pathogenesis of infection by flaviviruses. Here, we describe common laboratory techniques used to propagate, quantify, detect, and store WNV. We also briefly describe appropriate safety precautions required for the laboratory use of WNV, which is classified as a Biosafety Level 3 pathogen by the United States Centers for Disease Control and Prevention.
Curr Protoc Microbiol
· 2013 · PMID 23686830
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Poliovirus (PV) is the prototypical picornavirus. It is a non-enveloped RNA virus with a small (~7.5-kb) genome of positive polarity. It has long served as a model to study RNA virus biology, pathogenesis, and evolution....Poliovirus (PV) is the prototypical picornavirus. It is a non-enveloped RNA virus with a small (~7.5-kb) genome of positive polarity. It has long served as a model to study RNA virus biology, pathogenesis, and evolution. cDNA clones of several strains are available, and infectious virus can be produced by the transfection of in vitro transcribed viral genomes into an appropriate host cell. PV infects many human and non-human primate cell lines including HeLa and HeLa S3 cells, and can grow to high titer in culture. Protocols for the production, propagation, quantification, and purification of PV are presented.
Curr Protoc Microbiol
· 2013 · PMID 23686829
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Poliovirus (PV) is the prototypical picornavirus. It is a non-enveloped RNA virus with a small (~7.5-kb) genome of positive polarity. cDNA clones of several strains are available, and infectious virus can be produced by...Poliovirus (PV) is the prototypical picornavirus. It is a non-enveloped RNA virus with a small (~7.5-kb) genome of positive polarity. cDNA clones of several strains are available, and infectious virus can be produced by the transfection of in vitro-transcribed viral genomes into an appropriate host cell. The ease of genetic studies in poliovirus is a primary reason that it has long served as a model to study RNA virus biology, pathogenesis, and evolution. Protocols for the generation and characterization of PV mutants are presented.
Curr Protoc Microbiol
· 2013 · PMID 23686828
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The incorporation of a fluorescent reporter gene into a replication-competent influenza A virus (IAV) has made it possible to trace IAV infection in vivo. This protocol describes the process of inserting a green fluoresc...The incorporation of a fluorescent reporter gene into a replication-competent influenza A virus (IAV) has made it possible to trace IAV infection in vivo. This protocol describes the process of inserting a green fluorescent protein (GFP) reporter into the IAV genome using the established reverse genetics system. The strategy begins with the reorganization of segment eight of the IAV genome, during which the open reading frames of nonstructural protein 1 (NS1) and the nuclear export protein (NEP) are separated to allow for GFP fusion to the NS1 protein. The NS1, GFP, and NEP open reading frames (ORF) are then cloned into the IAV rescue system backbone. Upon construction of the GFP-encoding segment eight rescue plasmid, recombinant NS1-GFP influenza virus can be rescued via co-transfection with the remaining seven rescue plasmids. The generated NS1-GFP IAV can subsequently be used to visualize infected cells, both in vitro and in vivo.
Influenza viruses are negative-sense, single-stranded, enveloped RNA viruses belonging to the family Orthomyxoviridae. Three types exist, influenza A, B, and C. All infect humans, but only A and B are major human pathoge...Influenza viruses are negative-sense, single-stranded, enveloped RNA viruses belonging to the family Orthomyxoviridae. Three types exist, influenza A, B, and C. All infect humans, but only A and B are major human pathogens. Influenza type A viruses are divided into subtypes based on genetic and antigenic differences in the two surface spike proteins, hemagglutinin (HA) and neuraminidase (NA). The appropriate cell lines to be used for isolation of influenza A or B viruses depend on the clinical information and the host of origin. MDCK cells are the preferred cell line for isolation of human influenza viruses from clinical specimens.
Ahmed SS, Li J, Godwin J
… +2 more, Gao G, Zhong L
Curr Protoc Microbiol
· 2013 · PMID 23686826
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Liver-directed gene transfer and gene therapy are rapidly gaining attention primarily because the liver is centrally involved in a variety of metabolic functions that are affected in various inherited disorders. Recombin...Liver-directed gene transfer and gene therapy are rapidly gaining attention primarily because the liver is centrally involved in a variety of metabolic functions that are affected in various inherited disorders. Recombinant adeno-associated virus (rAAV) is a popular gene delivery vehicle for gene therapy, and intravenous delivery of some rAAV serotypes results in very efficient transduction in the liver. rAAV-mediated gene transfer to the liver can be used to create somatic transgenic animals or disease models for studying the function of various genes and miRNAs. The liver is the target tissue for gene therapy of many inborn metabolic diseases and may also be exploited as a "biofactory" for production of coagulation factors, insulin, growth hormones, and other non-hepatic proteins. Hence, efficient delivery of transgenes and small RNAs to the liver by rAAV vectors has been of long-standing interest to research scientists and clinicians alike. This unit describes methods for delivery of rAAV vectors by several injection routes, followed by a range of analytical methods for assessing the expression, activity, and effects of the transgene and its product.