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Current Protocols in Microbiology

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https://www.readbyqxmd.com/read/28166387/toxoplasma-gondii-laboratory-maintenance-and-growth
#1
Asis Khan, Michael E Grigg
Toxoplasma gondii is a highly successful apicomplexan protozoan capable of infecting any warm-blooded animal worldwide. In humans, Toxoplasma infections are life-long, with approximately one-third of the world's population chronically infected. Although normally controlled by the host immune system, T. gondii infection can lead to a variety of clinical outcomes in individuals with immature or suppressed immune systems. After penetrating the intestine, parasites rapidly disseminate throughout the body and stimulate production of the cytokines interleukin (IL)-12, IL-18, and interferon (IFN)-γ by immune cells...
February 6, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/28166386/actinomadura-species-laboratory-maintenance-and-ribosome-engineering
#2
Dipesh Dhakal, Nguyen Thanh Chung, Vijay Rayamajhi, Jae Kyung Sohng
Actinomadura spp. are aerobic, Gram-positive, catalase-positive, non-acid fast, non-motile actinomycetes. Some species of Actinomadura are associated with opportunistic infections in humans. However, many bioactive compounds with pharmaceutical applications can be isolated from various Actinomadura spp. This unit includes general protocols for the laboratory maintenance of Actinomadura spp., including growth in liquid medium, growth on solid agar, long-term storage, and generation of a higher producing strain by ribosome engineering...
February 6, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/28166385/virus-hunting-discovery-of-new-episomal-circular-viruses-by-rolling-circle-techniques
#3
Bert Vanmechelen, Annabel Rector, Piet Maes
Many methods for the discovery of novel viruses are based on amplification of the virus using consensus or degenerate PCR primers. A downside of this approach is that it requires prior knowledge of the viral nucleotide sequence to be applicable. Presented in this unit is a method for the sequence-independent amplification of circular viral genomes that is based on the rolling-circle mechanism used by certain viruses in their natural replication cycle. The amplification of the virus of interest is coupled to the isolation of the viral genome by gel extraction following a restriction digestion...
February 6, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/28166384/cryptosporidium-identification-and-genetic-typing
#4
Jan Šlapeta
Cryptosporidium spp. are obligate protozoan parasites of the gastrointestinal tract of vertebrates, including humans. In the majority of human cases, the diarrheal disease cryptosporidiosis is caused by either the human-adapted species Cryptosporidium hominis or the zoonotic Cryptosporidium parvum 'bovine genotype' (also known as Cryptosporidium pestis). The infectious stage, environmentally resilient Cryptosporidium oocysts, are shed by the infected host. Cryptosporidium parasites are transmitted by the fecal-oral route and are one of the major water-borne pathogens...
February 6, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/28166383/efficient-genome-editing-in-the-oomycete-phytophthora-sojae-using-crispr-cas9
#5
Yufeng Fang, Linkai Cui, Biao Gu, Felipe Arredondo, Brett M Tyler
Phytophthora is a filamentous fungus-like microorganism, but belongs to the oomycetes, in the kingdom Stramenopila. Phytophthora species are notorious as plant destroyers, causing multibillion-dollar damage to agriculture and natural ecosystems worldwide annually. For a long time, genome editing has been unattainable in oomycetes, because of their extremely low rate of homologous recombination. The recent implementation of the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system in the soybean pathogen Phytophthora sojae, an experimental model for oomycetes, has opened up a powerful new research capability for the oomycete community...
February 6, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/28166382/saccharopolyspora-species-laboratory-maintenance-and-enhanced-production-of-secondary-metabolites
#6
Dipesh Dhakal, Anaya Raj Pokhrel, Amit Kumar Jha, Nguyen Huy Thuan, Jae Kyung Sohng
Saccharopolyspora spp. are aerobic, Gram-positive, non-acid-fast, and non-motile actinomycetes. Various species of the genus Saccharopolyspora have been reported with an ability to produce various bioactive compounds for pharmaceutical and agricultural uses. This unit includes general protocols for the laboratory maintenance of Saccharopolyspora species, including growth in liquid medium, growth on solid agar, long-term storage, and generation of a higher producer strain by mutagenesis. Saccharopolyspora spinosa ATCC 49460 is used as a prototype for explaining the considerations for efficient laboratory maintenance of Saccharopolyspora spp...
February 6, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/27858973/detection-and-genotyping-of-human-papillomaviruses-from-archival-formalin-fixed-tissue-samples
#7
Koenraad Van Doorslaer, Zigui Chen, Alison A McBride
Pathology departments routinely process and store formalin-fixed, paraffin-embedded (FFPE) tissue samples for clinical diagnosis. These collections often contain decades' worth of samples and represent a treasure trove of specimens that can be analyzed for retrospective epidemiological studies, diagnostics, and pathogen discovery. Accurate amplification and sequencing of DNA from these samples is critical for the usability of these FFPE samples. Here we present a collection of protocols that describe extraction of DNA from FFPE tissues, PCR amplification of human papillomavirus DNA, and subsequent genotyping of the infecting virus...
November 18, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/27858972/a-simple-and-low-cost-procedure-for-growing-geobacter-sulfurreducens-cell-cultures-and-biofilms-in-bioelectrochemical-systems
#8
J Patrick O'Brien, Nikhil S Malvankar
Anaerobic microorganisms play a central role in several environmental processes and regulate global biogeochemical cycling of nutrients and minerals. Many anaerobic microorganisms are important for the production of bioenergy and biofuels. However, the major hurdle in studying anaerobic microorganisms in the laboratory is the requirement for sophisticated and expensive gassing stations and glove boxes to create and maintain the anaerobic environment. This appendix presents a simple design for a gassing station that can be used readily by an inexperienced investigator for cultivation of anaerobic microorganisms...
November 18, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/27858971/molecular-identification-and-subtype-analysis-of-blastocystis
#9
C Rune Stensvold, C Graham Clark
Several typing methods have been used in studies aiming to unravel the molecular epidemiology of Blastocystis, which is one of the most common intestinal parasites in human and many non-human hosts. Such studies have the potential to add to knowledge on Blastocystis transmission, host specificity, phylogeography, and clinical and public health significance, but rely on robust, standardized methods by which data can be generated and compared directly between studies. One of the most used methods is "barcoding,", which involves single-round PCR amplification and sequencing of partial small subunit ribosomal RNA genes of the parasites...
November 18, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/27858970/blastocystis-isolation-xenic-cultivation-and-cryopreservation
#10
C Graham Clark, C Rune Stensvold
Blastocystis is an intestinal parasite that is very easily isolated in culture from fresh stool samples. In fact, the parasite grows so readily in culture that short-term in vitro culture is sometimes used as a diagnostic tool in the absence of DNA-based methods. While axenizing Blastocystis cultures remains a significant challenge, the parasite can be propagated for several months in the presence of metabolically active bacteria (xenic culture). Hence, culture can be used for maintaining live Blastocystis strain libraries...
November 18, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/27858969/zika-virus-quantification-propagation-detection-and-storage
#11
Darrell S Agbulos, Larissa Barelli, Bryan V Giordano, Fiona F Hunter
Zika virus (ZIKV), belonging to the family Flaviviridae, genus Flavivirus, is an arthropod-borne virus that was first discovered from the Zika forest in Uganda in 1947. Recent outbreaks in South America have linked ZIKV to cases of microcephaly and Guillain-Barré syndrome in humans. With the increased interest in ZIKV, protocols must be established to facilitate proper research. Here we describe the laboratory techniques required to quantify, propagate, and store ZIVK. We also review the proper safety protocol for the handling of ZIKV, which is classified as a Biosafety Level 2 pathogen by the United States Centers for Disease Control and Prevention...
November 18, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/27517336/burkholderia-thailandensis-growth-and-laboratory-maintenance
#12
Erin C Garcia, Peggy A Cotter
Burkholderia thailandensis is a nonpathogenic Gram-negative bacterium found in tropical soils. Closely related to several human pathogens, its ease of genetic manipulation, rapid growth in the laboratory, and low virulence make B. thailandensis a commonly used model organism. This unit describes the fundamental protocols for in vitro growth and maintenance of B. thailandensis in the laboratory. © 2016 by John Wiley & Sons, Inc.
August 12, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/26855284/obtaining-high-quality-dna-from-diverse-clinical-samples
#13
Rachael Melton-Kreft, Tracy Spirk
Nucleic acids can be obtained in numerous ways from clinical specimens; however, the quality of the nucleic acid is only as good as the sampling and isolation protocol. While nucleic acids may be extracted they may not be representative of the original source. Large areas of tissue and explanted hardware must be successfully surveyed to reflect the overall clinical picture. Once good sampling technique has been established, successful bacterial nucleic acid isolation is essential. Clinical samples may be difficult to process because of the presence of scar tissue, bone, implants, and bacterial biofilms...
February 8, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/26855283/investigation-of-viral-and-host-chromatin-by-chip-pcr-or-chip-seq-analysis
#14
Thomas Günther, Juliane M Theiss, Nicole Fischer, Adam Grundhoff
Complex regulation of viral transcription patterns and DNA replication levels is a feature of many DNA viruses. This is especially true for those viruses which establish latent or persistent infections (e.g., herpesviruses, papillomaviruses, polyomaviruses, or adenovirus), as long-term persistence often requires adaptation of gene expression programs and/or replication levels to the cellular milieu. A key factor in the control of such processes is the establishment of a specific chromatin state on promoters or replication origins, which in turn will determine whether or not the underlying DNA is accessible for other factors that mediate downstream processes...
February 8, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/26855282/ht-spoti-a-rapid-drug-susceptibility-test-dst-to-evaluate-antibiotic-resistance-profiles-and-novel-chemicals-for-anti-infective-drug-discovery
#15
Cynthia A Danquah, Arundhati Maitra, Simon Gibbons, Jane Faull, Sanjib Bhakta
Antibiotic resistance is one of the major threats to global health and well-being. The past decade has seen an alarming rise in the evolution and spread of drug-resistant strains of pathogenic microbes. The emergence of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis and antimicrobial resistance among the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter species) as well as fungal pathogens (such as certain species of Candida, Aspergillus, Cryptococcus, and Trichophyton) poses a significant 21st century scientific challenge...
February 8, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/26855281/construction-of-a-transcription-map-for-papillomaviruses-using-race-rnase-protection-and-primer-extension-assays
#16
Xiaohong Wang, Zhi-Ming Zheng
Papillomaviruses are a family of small, non-enveloped DNA tumor viruses. Knowing a complete transcription map of each papillomavirus genome can provide guidance for various papillomavirus studies. This unit provides detailed protocols to construct a transcription map of human papillomavirus type 18. The same approach can be easily adapted to other transcription map studies of any other papillomavirus genotype due to the high degree of conservation in genome structure, organization, and gene expression among papillomaviruses...
February 8, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/26855280/genetic-manipulation-of-nocardia-species
#17
Dipesh Dhakal, Amit Kumar Jha, Anaya Pokhrel, Anil Shrestha, Jae Kyung Sohng
Nocardia spp. are aerobic, Gram-positive, catalase positive, and non-motile actinomycetes. They are associated with human infections. However, some species produce important natural products, degrade toxic chemicals, and are involved in biotransformation of valuable products. The lack of robust genetic tools has hindered detailed studies and advanced research. This unit describes the major genetic engineering approaches using Nocardia sp. CS682 as a prototype. These methods will certainly help in understanding the basis of their pathogenicity as well as biosynthetic and biotransforming abilities...
February 8, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/27517337/direct-pcr-of-intact-bacteria-colony-pcr
#18
Michael E Woodman, Christina R Savage, William K Arnold, Brian Stevenson
This protocol describes an efficient method for screening intact bacteria for the presence of desired DNA sequences using the polymerase chain reaction (PCR). This method is commonly referred to as colony PCR. © 2016 by John Wiley & Sons, Inc.
2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/27517335/natural-vaccinia-virus-infection-diagnosis-isolation-and-characterization
#19
Erna Geessien Kroon, Jônatas Santos Abrahão, Giliane de Souza Trindade, Graziele Pereira Oliveira, Ana Paula Moreira Franco Luiz, Galileu Barbosa Costa, Mauricio Teixeira Lima, Rafael Silva Calixto, Danilo Bretas de Oliveira, Betânia Paiva Drumond
Natural infections of Vaccinia virus (VACV)-the prototype species of the Orthopoxvirus genus, from the family Poxviridae and subfamily Chordopoxvirinae-cause an occupational emergent zoonotic disease that is primarily associated with the handling of infected dairy cattle. In humans, VACV infection is characterized by skin lesions, primarily on the hands, and accompanied by systemic symptoms such as fever, myalgia, headache, and lymphadenopathy. The diagnosis of VACV is usually performed according to the methods described for other orthopoxviruses...
2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/27517334/laboratory-cultivation-and-maintenance-of-borrelia-miyamotoi
#20
Brandee L Stone, Catherine A Brissette
Borrelia miyamotoi is a relapsing fever tick-borne pathogen found in Ixodes spp. (hard) ticks. In vitro culturing has proven difficult despite initial reports of cultures maintained in Barbour-Stoenner-Kelly-II (BSK-II) medium. The ability to culture in vitro opens many avenues for investigating the genetics and physiology of bacterial species. This unit describes methods for the maintenance and cultivation of B. miyamotoi in liquid medium. © 2016 by John Wiley & Sons, Inc.
2016: Current Protocols in Microbiology
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