applied bacte 2

• Hybridization is the process in which two complementary single-stranded DNA and/or RNA molecules bond together to form a double-stranded molecule
• Hybridization plays a role in DNA replication where the new strand hybridizes to the old strand
• In the laboratory, small pieces of DNA can be made to screen for the presence or absence of certain DNA or RNA molecules in the cell
• Hybridization is important in the polymerase chain reaction (PCR) procedure for amplifying specific gene regions used in clinical testing
• Fluorescence in Situ Hybridization (FISH) is a molecular cytogenetic technique that allows the localization of specific DNA sequences or entire chromosomes in a cell
• FISH is used for diagnosing genetic diseases, gene mapping, identifying chromosomal abnormalities, and studying chromosome arrangements in related species
• FISH involves unwinding the double helix structure and binding DNA probes attached to a fluorescent molecule with a specific sequence of sample DNA
• Multiplex PCR is a technique to amplify multiple target DNA sequences simultaneously in a single PCR reaction
• Multiplex PCR uses multiple sets of primers, each targeting a specific region of interest
• Advantages of PCR amplification include simplicity and not requiring special reagents or equipment
• Hybridization capture is a technique to selectively capture and enrich target DNA sequences in a sample
• Hybridization capture uses biotinylated probes complementary to target regions, which are captured and isolated using streptavidin-coated magnetic beads
• Compared to PCR amplification, hybridization capture allows capturing larger target regions without interference between capture probe sets
• Sensitivity is the proportion of subjects correctly identified as positive out of all subjects truly positive for the outcome of interest
• Specificity is the proportion of subjects correctly identified as negative out of all subjects truly negative for the outcome of interest
• Positive predictive value reflects the proportion of subjects with a positive test result who truly have the outcome of interest
• Negative predictive value reflects the proportion of subjects with a negative test result who truly do not have the outcome of interest
• Genome sequencing, particularly bacterial whole genome sequencing, is used for high-resolution characterization of bacterial pathogens in research, clinical diagnostics, and public health laboratories
• Next-generation sequencing (NGS) is applied to understanding and managing infectious diseases, including sequencing microbial genomes for laboratory identification of infectious agents, detection of antibiotic resistance markers, and public health surveillance of epidemics
• NGS protocol involves steps like extraction of bacterial genomic DNA, quantification, tagmentation, PCR amplification, library preparation, and bioinformatic analyses
• Antigen specificity is the ability of host cells to recognize an antigen specifically and distinguish it from others due to side-chain conformations
• Affinity is the strength of a single bond between an antibody's paratope and an antigen's epitope, while avidity is the total binding strength of all binding sites on a single antibody molecule
• Affinity increases as the immune response adapts to an antigen, while avidity is determined by binding affinity, valency, and structural arrangement
• Affinity and avidity tests are valuable in research and medicine, including diagnostic applications like avidity assays
• Avidity tests are used in diagnostic medicine to exclude or identify pathogens such as HIV, rubella virus, and hepatitis viruses
• Binding affinity is crucial in developing new pharmaceuticals to understand how a drug candidate interacts with the desired target
• Avidity and affinity tests are utilized in cancer research to identify the activity and success of anticancer therapeutics, especially in tumor targeting
• Affinity chromatography is used for purifying specific molecules or groups of molecules from a mixture based on the relationship between two molecules, such as antigen and antibody
• Antibodies functions include neutralization of pathogens and toxins, agglutination of particulate antigens, opsonization, complement activation, antibody-dependent cell-mediated cytotoxicity, and degranulation
• Specificity measures how well the immune system differentiates between different antigens, while cross-reactivity measures the extent to which different antigens appear similar to the immune system
• Antibodies have a variable region with paratopes that define complementary regions of shape and charge, allowing a single paratope to bind to unrelated epitopes and vice versa
• Monoclonal antibodies are laboratory-produced molecules used to mimic the immune system's attack on unwanted cells like cancer cells
• Complement fixation assays are used to demonstrate the presence of antibodies in patient serum by testing for the lysis of indicator sheep red blood cells
• Enzyme immunoassays, such as ELISA, utilize enzymes to detect and quantify immunologic reactions, commonly used in clinical analyses
• Lateral flow assays involve the movement of a liquid sample containing the analyte of interest through polymeric strips to detect interactions with attached molecules
• Western blotting is a laboratory technique used to detect specific proteins in blood or tissue samples by separating proteins through gel electrophoresis
• Immunohistochemistry is used to selectively identify antigens in cells of a tissue section by exploiting antibodies binding specifically to antigens in biological tissues
• Immunohistochemical staining is widely used in diagnosing abnormal cells like those found in cancerous tumors and in basic research to understand biomarker distribution and localization in biological tissues
• Pointers for medical testing include paired samples for acute vs convalescence, titer demonstration of activity, seroconversion on a fourfold rise in titer, and IgM response indicating acute infection