Hepatitis B virus
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Evolution of Cell-Autonomous Effector Mechanisms in Macrophages versus Non-Immune Cells
- Authors: Ryan G. Gaudet, Clinton J. Bradfield, John D. MacMicking
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Citation: Gaudet R, Bradfield C, MacMicking J. 2016. Evolution of cell-autonomous effector mechanisms in macrophages versus non-immune cells. 4(6): doi:10.1128/microbiolspec.MCHD-0050-2016
- DOI 10.1128/microbiolspec.MCHD-0050-2016
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Abstract:
Specialized adaptations for killing microbes are synonymous with phagocytic cells including macrophages, monocytes, inflammatory neutrophils, and eosinophils. Recent genome sequencing of extant species, however, reveals that analogous antimicrobial machineries exist in certain non-immune cells and also within species that ostensibly lack a well-defined immune system. Here we probe the evolutionary record for clues about the ancient and diverse phylogenetic origins of macrophage killing mechanisms and how some of their properties are shared with cells outside the traditional bounds of immunity in higher vertebrates such as mammals.
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Obituaries:
- Authors: Lynne M. Sehulster, Jennie Hunter-Cevera, Douglas Eveleigh, Joachim Messing, and David Pramer
- Publication Date : September 2016
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Authors: Lynne M. Sehulster, Jennie Hunter-Cevera, Douglas Eveleigh, Joachim Messing, and David PramerNo descriptions available.
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Viral Infection Studied over 15 Years
- Publication Date : July 2016
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How do chronic infections change over time? This is the broad question addressed in recent research published in the Journal of Virology. In their study, a team of scientists headed by Fabio Luciani from the University of New South Wales in Sydney, Australia, investigated a hepatitis B virus (HBV) infection at different time points over a 15-year infection in a single patient. Viruses were sequenced using Pacific Bioscience single-molecule sequencing technology, which allows full-length HBV genomes in a single read. First author B. D. Betz-Stablein used this technology to show that viral deletion variants missing internal genomic content (called splice variant HBV genomes, or spHBVs) are more diverse than previously measured. The team also found that most fixation mutants occurred in the genomic region containing the HBV reverse transcriptase, which is a region known to contain resistance variations, and that evolution of resistant variants changed with the therapeutic regimen.
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Laboratory Safety
- Authors: James J. Dunn, David L. Sewell
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Source: Clinical Laboratory Management, Second Edition , pp 515-544
Publication Date :
January 2014
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Abstract:
This chapter defines the essential components of a laboratory safety program. The key to a safe laboratory environment is the development, implementation, and enforcement of a high-quality safety management program that considers worker safety as a responsibility of the facility. The risk from biological, chemical, physical, and radiological hazards is related to exposure levels, duration of exposure, toxicity or pathogenicity of the hazardous material, safety controls present, and other factors such as the general health or age of the laboratory worker. The Occupational Safety and Health Administration (OSHA) identifies a number of practices that should be implemented to protect the worker from exposure to blood-borne pathogens, including an exposure control and risk assessment plan. The chapter describes various modes of hazard prevention such as handwashing, barrier protection and immunization. While disinfectants destroy all microorganisms, but not necessarily their spores on inanimate surfaces, sterilants are agents that kill all microbial life, including spores, on inanimate surfaces. The chapter provides discusses spill management, both for biological and chemical spills. A training program should include recognition and evaluation of fire hazards, planning to reduce the risk of fire, and all actions to take when a fire occurs. For effective and efficient management of infectious wastes, a comprehensive management plan is essential to ensure the safety of the employees handling the waste, and implementation of cost-effective strategies for waste disposal.
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Outreach Implementation Requirements: A Case Study
- Authors: Frederick L. Kiechle, Jack Shaw, Joseph E. Skrisson
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Source: Clinical Laboratory Management, Second Edition , pp 740-758
Publication Date :
January 2014
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Abstract:
A variety of methods have been designed to reduce cost per procedure, which include increased test volume through hospital laboratory mergers, consolidation, and integration and/or development of an outreach program that markets laboratory services to physician offices, nursing homes, and other hospitals. An intrapreneur must convert the illusion of revenue consisting of clad coinage created by delusional, magical thinking to a coherent outreach program generating genuine profits. Numerous potential barriers may be encountered during a change process, including myths, active inertia, lack of incentive, insufficient support from financial analysis and other groups, a slow approval process, conflicting visions, and others. This chapter describes the implementation of a hospital-based clinical laboratory outreach program, Beaumont Reference Laboratory (BRL), and its affiliation with a regional hospital laboratory network, Joint Venture Hospital Laboratories (JVHL), to secure provider status with major local and regional insurance carriers. A section of the chapter reviews the development of the sales and marketing department, as well as courier services for BRL. The chapter shows how BRL built success through affiliation with JVHL. The key factor to success in this network affiliation is the ability of the laboratory network to win provider status for its members with the major managed-care organizations. The implementation of the outreach program led to many benefits, including using spare capacity and thus achieving economies of scale, generating a new revenue stream, lowering unit costs, enhancing the test menu, and creating a new avenue for customer (physician) bonding.
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The Future of Pathology and Laboratory Medicine: Political, Social, Economic, and Regulatory Impacts
- Author: Paul Bachner
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Source: Clinical Laboratory Management, Second Edition , pp 897-906
Publication Date :
January 2014
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Abstract:
This chapter discusses the major features of the current healthcare environment. It describes the current regulations affecting laboratory practice. The chapter explains future regulations and political and economic events impacting pathology and laboratory practice. A high level of volatility and uncertainty, reflecting the political, economic, and social instability of our current environment, characterizes healthcare in the United States in the second decade of the 21st century. Funding and support for healthcare are diminishing, and the economic future of healthcare is hostage to some identifiable trends and concerns that include: a growing federal deficit and concerns about the future sustainability of Medicare and Medicaid; and a healthcare insurance and delivery system plagued by problems of access, quality, and safety. The “four horsemen” of federal laws and regulations that are particularly pertinent to pathology and laboratory medicine services are CLIA ’88, HIPAA, the Occupational Safety and Health Administration (OSHA) standards for occupational exposure to blood-borne pathogens, and the so-called Stark regulations that prohibit self-referral by healthcare providers. The increasing research and clinical demands for validated biospecimens can be expected to lead to significant growth in the number and size of biorepositories. Two other areas of concern to research and clinical laboratory practice are restrictive patents and excessive restraints on the use of human tissue and data for research and clinical purposes.
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Index
- Publication Date : January 2014
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No descriptions available.
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Hepatitis B and D Viruses
- Authors: Rebecca T. Horvat, Gary E. Tegtmeier
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Source: Manual of Clinical Microbiology, 10th Edition , pp 1659-1676
Publication Date :
January 2011
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Abstract:
Hepatitis B virus (HBV) was identified and characterized after the discovery of the Australia antigen by Blumberg and colleagues in 1965. The Australia antigen, now designated hepatitis B surface antigen (HBsAg), is detected in the sera of patients with both acute and chronic HBV. HBV infects hepatocytes, leading to an acute infection that resolves or a chronic infection lasting years. Safe and effective vaccines against HBV have been available since 1982. HBV infection is diagnosed by serological and molecular markers using serum or plasma. The laboratory diagnosis of HBV uses a combination of tests that detect virus-specific protein and nucleic acid as well as the host immune response to infection. The methods for identification of HBV infection use a combination of molecular, antigenic, and serological methods. Serologic tests for HBV-specific antibodies are used to determine the stage of disease and to establish immunity due to vaccination. Patients with chronic hepatitis that are hepatitis B e antigen (HBeAg) negative are more likely to have more advanced liver disease in spite of lower serum HBV DNA levels. The majority of individuals vaccinated for HBV have detectable levels of anti-HBs, but some test negative due to waning levels of anti-HBs. Hepatitis D virus (HDV) is a defective RNA virus that requires the presence of HBV for its replication. The laboratory diagnosis of HDV depends on the detection of specific antibodies, HDAg, and HDV RNA.
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Procedures for the Storage of Microorganisms *
- Authors: Cathy A. Petti, Karen C. Carroll
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Source: Manual of Clinical Microbiology, 10th Edition , pp 124-131
Publication Date :
January 2011
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Abstract:
This chapter presents methods that can be used for the storage of bacteria, protozoa, fungi, and viruses. There are two types of cryoprotective agents: those that enter the cell and protect the intracellular environment and others that protect the external milieu of the organism. Glycerol and dimethyl sulfoxide (DMSO) are most often used for the former; sucrose, lactose, glucose, mannitol, sorbitol, dextran, polyvinylpyrrolidone, polyglycol, and skim milk are used for the latter. To protect microorganisms from damage during the freezing process, during storage, and during thawing, cryoprotective agents are often added to the culture suspension. Whereas most bacteria, fungi, and viruses survive better with such additives, studies have shown that cryoprotective agents significantly damage others. Freeze-drying is considered to be the most effective way to provide long-term storage of most bacteria, yeasts, sporulating molds, and viruses. The preparation is then used in smaller volumes as described above for freezing. All of the material presented in this chapter applies primarily to the preservation of bacteria. Subculturing is the simplest method of maintaining living fungi and involves serial transfer to fresh solid or liquid media. Storage is accomplished usually at room or refrigerator temperature. All of the techniques described have been applied to the storage of yeasts and fungi. Viruses tend to be more stable than other microorganisms because of their small size and simple structure, and the absence of free water. Many viruses can be stored for months at refrigerator temperatures or for years by ultralow-temperature freezing or freeze-drying.
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CONTENTS
- Publication Date : January 2011
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No descriptions available.
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Quantitative Molecular Methods
- Authors: Donna M. Wolk, Randall T. Hayden
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Source: Molecular Microbiology , pp 83-105
Publication Date :
January 2011
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Abstract:
Quantitative molecular methods provide information about the concentration of microbial nucleic acid target present in a sample. The evolution of various quantitative methods includes PCR and commercial alternatives to PCR. Quantitative methods that rely on target amplification include transcription-mediated amplification (TMA) and nucleic acid sequenced-based amplification (NASBA). Commercially available quantitative signal and probe amplification methods include the branched DNA (bDNA) method and the Invader assay, respectively. Quantitative methods based on PCR include three broad categories: quantitative PCR (Q-PCR) is typically used to determine the microbial density or ‘‘load’’ of DNA in clinical specimens; (ii) quantitative reverse transcriptase PCR (QRT-PCR) is used to determine the density of RNA viruses, an approach commonly called ‘‘viral load’’ testing; and (iii) in what are often referred to as ‘‘gene expression’’ assays, QRT-PCR can be used to determine relative mRNA expression levels for different disease states. This chapter concentrates on the technological features unique to quantitative molecular assays. The advantages and limitations of these methods are reviewed in the chapter. For microbial quantitation, whole-organism comparisons are best but not always feasible; therefore, plasmids or oligonucleotides are often used as substitutes. The chapter talks about general issues for viral load measurement, and other general considerations and tips for quantitative methods. Speed, accuracy, and utilization of results will be paramount to the future of quantitative technology as new methods extend our understanding of pathogenesis and advance our ability to improve diagnosis and disease management.
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Diagnostic Molecular Virology: Current Practice and Future Trends
- Author: Frederick S. Nolte
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Source: Molecular Microbiology , pp 537-539
Publication Date :
January 2011
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Abstract:
Molecular methods are now firmly established as new diagnostic gold standards for most of the clinically important viruses. Molecular methods have changed the face of clinical virology and created new opportunities for laboratories to impact diagnosis and management of patients with viral infections. This chapter discusses the thoughts and impressions on the current practice and future trends in diagnostic molecular virology. Real-time PCR methods have largely replaced conventional, end-point PCR methods in clinical laboratories, with the attendant benefits of speed, broad dynamic range and increased precision for target quantitation, and reduced contamination. Multiplex, real-time amplification methods are limited to three to four different targets by the small number of available fluorescent reporter dyes. These new uses for hepatitis C virus (HCV) viral load measurements provide motivation for patients to complete therapy and permit the individualization of therapy duration. There has also been significant progress in the development of specifically targeted antiviral therapy for hepatitis C, such as NS5 polymerase and NS3/4 protease inhibitors. Phylogenetic genotyping has a more limited role in the clinical management of patients with chronic hepatitis B than it does in patients with chronic hepatitis C .
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Molecular Method Verification
- Authors: Donna M. Wolk, Elizabeth M. Marlowe
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Source: Molecular Microbiology , pp 861-883
Publication Date :
January 2011
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Abstract:
This chapter talks about aspects of molecular method verification as well as the common statistical analyses that are used during this process. Stevenson et al. showed how polymorphisms in the probe target can affect the performance of an herpes simplex virus (HSV) real-time PCR assay. Such polymorphisms can result in decreased sensitivity of an assay, which is critical for a cerebrospinal fluid (CSF) specimen. In this study using the crossing threshold (CT) as a cutoff for assay sensitivity, it was estimated that as many as 15% of the HSV type 1 (HSV-1)-positive and 7% of the HSV-2-positive specimens would be missed when comparing two real-time HSV PCRs based on commercially available analyte specific reagents (ASRs). The author's clinical laboratory research is, in essence, translational research, in which their purpose is to describe, explain, predict outcomes, and control their systems. The chapter focuses on those aspects of biostatistics that are relevant to the verification and validation of new laboratory assays. Clinical Laboratory Improvement Act (CLIA) has clear guidelines on the verification and validation of laboratory-developed tests (LDTs) and other non-FDA-approved/ cleared assays. Choices of statistical methods and methods for drawing conclusions on the accuracy are less defined. Analysis of method verification data may require collaboration with a statistician or use of software specifically designed for CLIA method verification such as EP Evaluator.
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Molecular Test Validation, Monitoring, and Quality Control
- Author: Matthew J. Bankowski
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Source: Molecular Microbiology , pp 885-890
Publication Date :
January 2011
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Abstract:
Test validation is the ongoing process of ensuring that the expected performance of an assay is consistently met in testing clinical specimens. Test (or assay) validation is an integral part of quality assessment (QA), which includes quality control, quality improvement, and method validation. QA encompasses routine quality control, proficiency testing, technical staff competency, instrument calibration, and clinical correlation. Quality management of molecular testing begins with the test request and continues through specimen collection, transport, processing, analytical testing, result generation, result review, test interpretation, and reporting. This chapter focuses mainly on the analytical phase of testing. The types of molecular testing included in the chapter are qualitative, quantitative, multiplex, and microarray methods. Quantitative molecular testing consists of numeric values with defined units in the test result. Quality assurance includes quality control, quality improvement, and method validation. Validation of the analytical phase not only includes ensuring adequate and acceptable training on the test but also relies upon evaluation by actual observation of the technologist performing the test on a recurrent basis (operator competency assessment). This should include validation of staff adherence to the standard operating procedure (SOP) exactly as stated, biosafety, patient confidentiality, result interpretation, reporting, and quality control documentation. The use of quality controls, proficiency testing, and monitoring of technical staff competency and equipment and instrument performance are all essential parts of this process.
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Contents
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Source: Molecular Microbiology
Publication Date :
January 2011
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No descriptions available.
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Natural Killer Cell Response against Viruses
- Authors: Joseph C. Sun, Lewis L. Lanier
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Source: The Immune Response to Infection , pp 197-207
Publication Date :
January 2011
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Abstract:
During viral infection, cells of the innate immune system such as monocytes, dendritic cells (DCs), natural killer (NK) cells, and polymorphonuclear leukocytes serve several functions: alerting the host to invading pathogens, providing early containment of pathogens, mediating antimicrobial effects against pathogens, directing the nature of the immune response, and participating in wound healing and tissue repair. During viral infection, antigen-presenting cells (APCs) sense viral nucleic acids via members of the Toll-like receptor family (TLR3, 7, 8, and 9) and intracellular sensors such as the RNA helicases RIG-I, mda5, and LGP2. Ablating the pleiotropic activity of type I interferons (IFNs) during viral infection in mice containing a genetic deletion of the type I interferon receptor resulted in higher virus replication and severe pathology or death. The potent antiviral responses of NK cells that directly clear certain viral infections to promote host survival unmistakably demonstrate how crucial these cytotoxic cells are; at the same time, the importance of NK cell activity is equally demonstrated by the discovery of the many strategies different viruses employ to specifically evade detection by NK cells. Although viruses evolve because of the pressures exerted by cells of the immune system, there is evidence that the mammalian immune system also adapts in response to viral evasion mechanisms. As more viral ligands of activating NK cell receptors are uncovered, we will have a greater appreciation of the evolution of mammalian receptors on NK cells at the population level driven by viruses.
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Acquired Immunity against Virus Infections
- Authors: Eva Szomolanyi-Tsuda, Michael A. Brehm, Raymond M. Welsh
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Source: The Immune Response to Infection , pp 239-254
Publication Date :
January 2011
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Abstract:
The importance of acquired immunity against viruses is demonstrated by fatal or persistent infections of viruses in severe combined immunodeficient (SCID) mice, which lack functional T and B cells, under conditions where normal immunocompetent mice would clear the infection without apparent disease or mortality. Most of our present understanding of antiviral immune mechanisms comes from experiments performed with inbred laboratory mice, because different components of the immune system can be easily manipulated in this animal model. This chapter describes the dynamics of T- and B-cell responses elicited by virus infections and illustrates the functions and importance of these cells with examples from well-studied viral models. Immunodominant epitopes are highly immunogenic and therefore elicit T-cell responses that are easily detectable, whereas T cells specific for weakly immunogenic, subdominant epitopes are often difficult to detect. Studies with poliovirus have indicated that virus-specific CD8 T cells can recognize antigen presenting cells (APC) class I MHC-presented peptides derived from exogenous proteins. FcγRIII, which are expressed on natural killer (NK) cells in addition to monocytes and macrophages, bind mainly IgG2a, IgG2b, and IgG1 antibodies, and have the potential to mediate antibody-dependent cell-mediated cytotoxicity (ADCC) of virus-infected cells.
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Pathology and Pathogenesis of Virus Infections
- Authors: Carmen Baca Jones, Matthias Von Herrath
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Source: The Immune Response to Infection , pp 383-389
Publication Date :
January 2011
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Abstract:
While the term immunopathology was originally used to describe an aberrant immune response to autoantigen resulting in pathology, more recent developments in our understanding of virus-induced immunopathology have revealed that this can be linked to both an aberrant immune response to the virus itself as well as unfavorable virus-induced changes to the immune response as a whole; for example, lymphopenia following certain types of infections as well as the specific loss of CD4 T cells in HIV infection. Perhaps the most common virus-induced pathology is T-cell-induced destruction of host tissues. T-cell mediated pathologies occur through both direct and indirect mechanisms including the targeted cytolysis of the infected cell by effector T cells, the induction of apoptosis in infected cells and generalized tissue damage due to bystander effects of T-cell activation. Difficulties in establishing an animal model of hantavirus pulmonary syndrome (HPS) had greatly hampered progress in understanding the factors involved in pathogenesis. Perhaps the most widely examined example of antibody dependent enhancement (ADE) can be found in dengue virus infections. The process by which viruses may induce or enhance autoimmunity is hypothesized to occur by a number of mechanisms. Recent clinical trials for several different vaccines, where vaccinated groups had elevated risk for infection and or disease than their naive cohorts, have highlighted the necessity for continued basic science research into the precise mechanisms of virus-induced immunopathology. One example of this can be found in the vastly different outcomes achieved with different strategies in respiratory syncytial virus (RSV) vaccination.
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Genomics of Aspergillus flavus Mycotoxin Production
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Source: Genomes of Foodborne and Waterborne Pathogens , pp 259-270
Publication Date :
January 2011
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Abstract:
Food microbiologists often overlook the importance of fungi as a threat to food safety and security even though fungi produce a wide array of toxic compounds. Aspergillus flavus is known to produce over 14 described mycotoxins. It is common for strains of A. flavus to produce both aflatoxin and cyclopiazonic acid (CPA) and for commodities to contain both mycotoxins. Other than A. flavus and A. minisclerotigenes, no other fungal genera are known to produce aflatrem; however, structurally related tremorgenic mycotoxins, such as penitrem from Penicillium spp., are prevalent in other fungi and likely share common enzymes. Fungi have the capacity to produce many diverse secondary metabolites, and over 300 fungal secondary metabolites are described as mycotoxins. It is now possible to predict whether potential toxins produced by secondary metabolism clusters may be present in food. With respect to the regulation of aflatrem biosynthesis, researchers have shown that the gene called veA, previously shown to control aflatoxin and sclerotial production in A. parasiticus was found to not only be necessary for the production of aflatoxins B1 and B2 and sclerotia, but also regulated the synthesis of the mycotoxins cyclopiazonic acid and aflatrem. New tools for genomewide gene profiling and functional analysis will surely reveal additional information on aflatoxin production and the regulation of the process. This knowledge will empower researchers to find effective strategies for controlling aflatoxin contamination of food and feed. Gradually, newly developed next-generation sequencing technologies will become common research tools for functional genomics studies.
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The Global Impact of Hepatitis E: New Horizons for an Emerging Virus
- Authors: Alain B. Labrique, Mark H. Kuniholm, Kenrad E. Nelson
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Source: Emerging Infections 9 , pp 53-93
Publication Date :
January 2010
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Abstract:
An appreciation of the role of the fifth human hepatitis virus, hepatitis E virus (HEV), as an important cause of acute, and occasionally chronic, hepatitis in humans has increased in recent years. Hepatitis viruses have long been implicated as the cause of substantial morbidity and mortality in the developing world, through both sporadic and epidemic disease. The predictable seasonal outbreaks, coincident with the monsoon rains, have provided numerous opportunities to study risk factors for HEV infection, the clinical course of hepatitis E disease, and the characteristics of the virus. In 1980, by excluding hepatitis A virus (HAV) and hepatitis B virus (HBV) as causes of a large 1955 to 1956 hepatitis epidemic in India, two groups independently reported the hypothesis of a novel, enterically transmitted non-A, non-B (ET-NANB) virus. As HEV shares certain morphologic and biophysical properties with members of the Caliciviridae family, it was initially classified as a calicivirus. Electron microscopy has been used to detect virus-like particles in the livers of patients with HEV-attributable fulminant hepatitis. The age- and gender-matched control group in a case control study in Sudan found a high (18%) anti-HEV IgG seroprevalence among children in the general population. Immunologic changes of pregnancy, such as the down-regulation of TH1 cytokines, and hormonal changes may also influence pathogenesis. A recent case report of fulminant hepatitis due to infection with an HEV genotype 3 strain in a patient in Spain has suggested that an important cofactor was the usage of hormonal contraceptives.