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Methods for Gene Silencing With RNAi
Time of Update: 2021-02-12
This chapter describes a technique for synthesizing and transfecting double stranded RNA (dsRNA) for RNA interference in Sf-21 cell culture.
Transfection with dsRNA only requires 1 h and the cells are usually recovered within 12 h.
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Determination of Substrate Utilization Rates by Mycoplasmas
Time of Update: 2021-02-12
Within these groups, patterns and rates of substrate utilization have been shown to distinguish certain species and subspecific taxa ( 4 – 6 ), and may be applied to the biochemical characterization and identification of isolates.
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Application of Two-Step Quantitative Reverse-Transcription PCR to Bacterial Diagnostics
Time of Update: 2021-02-12
The opportunity to only detect viable cells by targeting labile RNA transcripts may create an opportunity for “real-time” monitoring of pathogen load in response to a treatment regimen, while the natural amplification provided by the relative abundance of the RNA target compared with its corresponding gene opens a door to potential nonamplified direct detection technologies.
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Conductimetric Method for Evaluating Inhibition of Listeria monocytogenes
Time of Update: 2021-02-12
One of the major problems in the food industry, particulary in dairy products, is the occasional presence of the pathogen Listeria monocytogenes , which has been associated with food-borne disease outbreaks ( 1 ).
monocytogenes .
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Transposon Mutagenesis in Clostridium difficile
Time of Update: 2021-02-12
Genetic manipulation ofClostridium difficile is notoriously difficult, currently there is only one reliable method for generating random mutations in the organism and that is to use the conjugative transposon Tn 916 .
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Using MCL to Extract Clusters from Networks
Time of Update: 2021-02-12
MCL is a general purpose cluster algorithm for both weighted and unweighted networks.
The algorithm utilises network topology as well as edge weights, is highly scalable and has been applied in a wide variety of bioinformatic methods.
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Dynamic Analysis of Viral Populations by Direct DNA Sequencing and Solid-Phase Technology
Time of Update: 2021-02-12
Among the most important developments towards automated systems has been the introduction of the polymerase chain reaction ( PCR ) and the replacement of isotopic labels by fluorescent dyes and on-line monitoring of the DNA sequence.
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Use of the Hollow Fiber Assay for the Discovery of Novel Anticancer Agents from Fungi
Time of Update: 2021-02-12
The hollow fiber assay (HFA) is a drug discovery tool to aid investigators in the prioritization of lead compounds identified by in vitro testing for further development in animal models of disease.
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Using the NeAT Toolbox to Compare Networks to Networks, Clusters to Clusters, and Network to Clusters
Time of Update: 2021-02-12
Next, we show how to map functional classes (e.g., GO categories, sets of regulons or complexes) onto a biological network.
A third protocol explains how to compare two sets of functional classes, e.g., to assess statistically the biological relevance of some computationally returned groups of genes (clustering).
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Bacterial Genome Annotation
Time of Update: 2021-02-12
This is done in an effort to construct accurate gene models, so understanding function or evolution of genes among organisms is not impeded.
Functional annotation is dependent on sequence similarity to other known genes or proteins in an effort to assess the function of the gene.
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Plasmid Vectors
Time of Update: 2021-02-12
This is in large part due to the impenetrable nature of the cell wall, resulting in difficulty both in introducingDNA into the bacterium and subsequent isolation of intact plasmid DNA.
In addition, the mycobacterial cell wall contains complex lipids and polysaccharides that can contaminate DNA preparations.
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Serological diagnosis of Helicobacter pylori infection in children
Time of Update: 2021-02-12
We tested serological HP antibody IgG on 72 children with recurrent abdominal pain, anorexia and chronic diarrhea, 54 of whom were positive (75%).
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Isolation of CpG Islands From BAC Clones Using a Methyl-CpG Binding Column
Time of Update: 2021-02-12
Vertebrate genomes are globally heavily methylated at the sequence CpG with the exception of short patches of GC-rich DNA , usually between 1–2 kb in size, which are free of methylation and these are known as CpG islands ( see refs.
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Bioassays of Quorum Sensing Compounds Using Agrobacterium tumefaciens and Chromobacterium violaceum
Time of Update: 2021-02-12
In most bacteria, a global level of regulation exists involving intercellular communication via the production and response to cell density-dependent signal molecules.
Chromobacterium violaceum , a Gram-negative bacterium commonly found in soil and water, produces the characteristic purple pigment violacein, the production of which is regulated by acyl HSL-mediated QS.
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Production of cDNA Libraries by Electroporation
Time of Update: 2021-02-12
In addition to small molecules, such as sucrose and dyes,DNA could be introduced into these electropermeabilized cells ( 5 – 7 ).
More recently, the electroporation process has been used to transform bacterial cells with plasmid DNA efficiently ( 8 , 9 ).
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Analysis of Herbicides in Water by On-Line In-Tube Solid-Phase Microextraction Coupled With Liquid Chromatography-Mass Spectrometry
Time of Update: 2021-02-12
We have developed a method using in-tube solid-phase microextraction coupled with liquid chromatography-mass spectrometry (SPME-LC-MS) for the assay of herbicides in water samples.
The automated in-tube SPME-LC-MS system can continuously extract herbicides from aqueous samples, followed by LC-MS.
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Mixed Infections with Rotaviruses: Protocols for Reassortment, Complementation, and Other Assays
Time of Update: 2021-02-12
The conditional-lethality of thets mutations allows the use of selective conditions in the analysis of the progeny of the mixed infections, so that the results of genetic and nongenetic interactions can be easily revealed.
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Ribozymes as a Novel Approach for the Treatment of Human Pancreatic carcinoma
Time of Update: 2021-02-12
Recently, gene modulation using specific oligonucleotides have been developed and defined as an effective strategy for suppressing the function of genes ( 1 – 4 ).
The types of oligonucleotides used to modulate specific gene expression include triplexDNA , antisense DNA/RNA and ribozymes (catalytic RNAs; for a reviewsee ref.
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Generation of Langerhans Cell-Like Dendritic Cells from Murine Fetal Skin
Time of Update: 2021-02-12
In contrast, interdigitating DC in lymphoid tissue display a mature phenotype, i.e., they have limited phagocytic and antigen-processing capacity, but express high levels of MHC antigen and costimulatory molecules and are very effective stimulators of naive T cells ( 2 ).
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Isolation of Genomic DNA from Mycobacteria
Time of Update: 2021-02-12
However, research on these bacteria has focused primarily on the pathogensMycobacterium bow, Mycobacterium tuberculosis , andMycobacterium leprae , and opportunistic pathogens such as theMycobacterium avium complex andMycobacterium kansasil .
