Microbiology Textbook Overview Quiz
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Microbiology Textbook Overview Quiz

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Questions and Answers

Who are the senior contributing authors of the Microbiology textbook?

Nina Parker, Mark Schneegurt, Anh-Hue Thi Tu, Philip Lister, Brian M. Forster

What year was the original publication of the Microbiology textbook?

2016

What type of organization is OpenStax?

  • A for-profit corporation
  • A nonprofit educational initiative (correct)
  • A government agency
  • A private university

    • OpenStax textbooks can only be accessed through purchase.

    <p>False</p> Signup and view all the answers

    What is the primary focus of the Microbiology textbook?

    <p>Core concepts of microbiology with a focus on applications for careers in allied health.</p> Signup and view all the answers

    Which of the following is NOT part of OpenStax's mission?

    <p>Charge high fees for educational resources</p> Signup and view all the answers

    Where is Rice University located?

    <p>Houston, Texas</p> Signup and view all the answers

    OpenStax textbooks are licensed under a Creative Commons __________ License.

    <p>Attribution 4.0 International</p> Signup and view all the answers

    What type of license is Microbiology licensed under?

    <p>Creative Commons Attribution 4.0 International (CC BY)</p> Signup and view all the answers

    Instructors can customize their OpenStax book to better fit their course.

    <p>True</p> Signup and view all the answers

    What is the main mission of the American Society for Microbiology?

    <p>To promote and advance the microbial sciences.</p> Signup and view all the answers

    Microbiology is produced through a collaborative __________ agreement between OpenStax and the American Society for Microbiology.

    <p>publishing</p> Signup and view all the answers

    Which chapter introduces the overview of the discipline of microbiology?

    <p>Chapter 1: An Invisible World</p> Signup and view all the answers

    What is the focus of Chapter 15 in the Microbiology textbook?

    <p>Microbial pathogenicity.</p> Signup and view all the answers

    Microorganisms provide essential models for understanding __________.

    <p>life processes</p> Signup and view all the answers

    All bacteria in nature live as isolated cells.

    <p>False</p> Signup and view all the answers

    What is the name of the oil-eating marine bacterium that helps clean up oil spills?

    <p>Alcanivorax borkumensis</p> Signup and view all the answers

    What process do microbes use to convert sugars to alcohol and organic acids?

    <p>Fermentation</p> Signup and view all the answers

    What are the potential causes of meningitis as mentioned in the content?

    <p>Bacteria, fungi, viruses, or a reaction to medication or heavy metals</p> Signup and view all the answers

    Most microorganisms are harmful to humans.

    <p>False</p> Signup and view all the answers

    What type of bacterium was used to differentiate between gram-positive and gram-negative bacteria?

    <p>Gram stain</p> Signup and view all the answers

    Who is considered the 'father of Western medicine'?

    <p>Hippocrates</p> Signup and view all the answers

    What was the importance of the Canon of Medicine created by Ibn Sina?

    <p>It included detailed descriptions of the body and mechanisms of contagion.</p> Signup and view all the answers

    What is one piece of evidence suggesting prehistoric humans attempted to treat infections?

    <p>Ötzi the Iceman was found with the woody fruit of the Fomitopsis betulinus fungus.</p> Signup and view all the answers

    Name two foods that have historically been produced with the aid of microbes.

    <p>Bread and cheese</p> Signup and view all the answers

    Who is credited with being the first to develop a lens powerful enough to view microbes?

    <p>Antonie van Leeuwenhoek</p> Signup and view all the answers

    Which chapter addresses the Biochemistry of the Genome?

    <p>10—Biochemistry of the Genome</p> Signup and view all the answers

    The information in the case studies is unrelated to the chapters' topics.

    <p>False</p> Signup and view all the answers

    What is the purpose of the 'Eye on Ethics' feature?

    <p>To explore ethical issues related to chapter content.</p> Signup and view all the answers

    What is included in the Disease Profile feature?

    <p>A table cataloging unique aspects of each disease</p> Signup and view all the answers

    Who is the senior contributing author mentioned in the document?

    <p>Nina Parker</p> Signup and view all the answers

    Where can additional resources for students and instructors be found?

    <p>Online at openstax.org</p> Signup and view all the answers

    The __________ feature provides students with a brief introduction and a link to further explore a topic.

    <p>Link to Learning</p> Signup and view all the answers

    The Comprehensive Art Program is used to support student understanding.

    <p>True</p> Signup and view all the answers

    What is the main theme of the narratives provided in the chapters?

    <p>To highlight the clinical relevance of specific topics.</p> Signup and view all the answers

    What did Leeuwenhoek describe single-celled organisms as?

    <p>Animalcules or wee little beasties</p> Signup and view all the answers

    Which microbiologist invented pasteurization?

    <p>Louis Pasteur</p> Signup and view all the answers

    Robert Koch discovered the bacteria that cause anthrax, cholera, and tuberculosis.

    <p>True</p> Signup and view all the answers

    What is taxonomy?

    <p>The classification, description, identification, and naming of living organisms.</p> Signup and view all the answers

    What are the two main branches in Linnaeus's tree of life?

    <p>Animal and plant kingdoms</p> Signup and view all the answers

    Which kingdom was proposed by Ernst Haeckel for unicellular organisms?

    <p>Protista</p> Signup and view all the answers

    What did Carl Woese and George Fox create based on genetic methods?

    <p>A genetics-based tree of life</p> Signup and view all the answers

    Bergey's Manuals are used for identifying and classifying different prokaryotes.

    <p>True</p> Signup and view all the answers

    In binomial nomenclature, the genus part of the name is always ______.

    <p>capitalized</p> Signup and view all the answers

    What is one challenge in classifying microbes?

    <p>They lack easily observable macroscopic features.</p> Signup and view all the answers

    How do modern scientists determine the relatedness of organisms?

    <p>By comparing nucleic acids or proteins.</p> Signup and view all the answers

    What is binomial nomenclature and why is it a useful tool for naming organisms?

    <p>Binomial nomenclature is a system for naming organisms using two terms, the genus and species names. It is useful because it provides a unique and universal naming system that helps avoid confusion.</p> Signup and view all the answers

    Why would a resource like one of Bergey’s manuals be helpful in identifying a microorganism in a sample?

    <p>Bergey's manuals contain detailed descriptions, classifications, and identification keys for numerous microorganisms.</p> Signup and view all the answers

    What characterizes different strains within the same species of microorganisms?

    <p>They can have very different attributes.</p> Signup and view all the answers

    All strains of E. coli cause disease.

    <p>False</p> Signup and view all the answers

    What is E. coli O157:H7 known for?

    <p>E. coli O157:H7 is known for causing food poisoning and traveler's diarrhea.</p> Signup and view all the answers

    What is the minimum size an object must reach to be visible without a microscope?

    <p>100 micrometers (µm)</p> Signup and view all the answers

    Most bacteria have cell walls that contain ______.

    <p>peptidoglycan</p> Signup and view all the answers

    Which of the following is NOT a shapetype of bacteria?

    <p>Epithelial</p> Signup and view all the answers

    What distinguishes prokaryotes from eukaryotes?

    <p>Prokaryotes lack a true nucleus, while eukaryotes have a nucleus.</p> Signup and view all the answers

    Viruses are classified as prokaryotic microorganisms.

    <p>False</p> Signup and view all the answers

    What is the most common nematode infection in the United States?

    <p>Pinworm (caused by Enterobius vermicularis)</p> Signup and view all the answers

    Which of the following diseases is transmitted by Triatoma spp. (kissing bugs)?

    <p>Chagas' disease</p> Signup and view all the answers

    What are two major groups of parasitic helminths?

    <p>Nematoda (roundworms) and Platyhelminthes (flatworms)</p> Signup and view all the answers

    The Centers for Disease Control and Prevention (CDC) has identified no neglected parasitic infections in the United States.

    <p>False</p> Signup and view all the answers

    What is the causative agent of African trypanosomiasis?

    <p>Trypanosoma brucei</p> Signup and view all the answers

    What type of organism is Trichinella spiralis?

    <p>Nematode</p> Signup and view all the answers

    What are the typical symptoms of hookworm infection?

    <p>Abdominal pain, diarrhea, loss of appetite, weight loss, fatigue, and anemia.</p> Signup and view all the answers

    The __________ is the largest nematode intestinal parasite found in humans.

    <p>Ascaris lumbricoides</p> Signup and view all the answers

    Which of the following is NOT considered a neglected parasitic infection by the CDC?

    <p>Tularemia</p> Signup and view all the answers

    What is the transmission method of Schistosoma spp. to humans?

    <p>Contact with contaminated water.</p> Signup and view all the answers

    What is the effect of the eradication campaign on cases of dracunculiasis?

    <p>It has significantly reduced cases, with only four countries reporting a total of 126 cases in 2014.</p> Signup and view all the answers

    Which of the following are characteristics of fungi? (Select all that apply)

    <p>Fungi have chitin in their cell walls.</p> Signup and view all the answers

    What should Sarah's mother do if the antifungal cream does not work?

    <p>Take Sarah for another visit to the doctor.</p> Signup and view all the answers

    Yeasts reproduce exclusively sexually.

    <p>False</p> Signup and view all the answers

    What is a dimorphic fungus?

    <p>A fungus that can appear as both yeasts and molds depending on environmental conditions.</p> Signup and view all the answers

    All forms of ringworm can be treated with the same antifungal medication.

    <p>False</p> Signup and view all the answers

    What group of organisms are associated with harmful algal blooms?

    <p>Dinoflagellates.</p> Signup and view all the answers

    Which group of fungi includes pathogens that can cause skin infections?

    <p>Ascomycota</p> Signup and view all the answers

    What is the primary cause of histoplasmosis?

    <p>Histoplasma capsulatum.</p> Signup and view all the answers

    The three growth forms of lichens are crustose, foliose, and ______.

    <p>fruticose</p> Signup and view all the answers

    What unique sterols are found in fungal cell membranes?

    <p>Ergosterols</p> Signup and view all the answers

    What is the role of cyanobacteria in some lichens?

    <p>They can fix nitrogen.</p> Signup and view all the answers

    Microsporidia are multicellular fungi.

    <p>False</p> Signup and view all the answers

    Which of the following pigments are found in stramenopiles?

    <p>All of the above</p> Signup and view all the answers

    What type of lichen grows tightly attached to the substrate?

    <p>Crustose lichen.</p> Signup and view all the answers

    What is the significance of the Glomeromycota group?

    <p>They are important symbionts with plant roots, promoting plant growth.</p> Signup and view all the answers

    Fungi are classified by their unique reproductive structures, such as zygospores, ascospores, and ______.

    <p>basidiospores</p> Signup and view all the answers

    What is the primary function of chloroplasts in algal cells?

    <p>Photosynthesis.</p> Signup and view all the answers

    Lichens are a combination of three organisms.

    <p>False</p> Signup and view all the answers

    What does plasmogamy result in?

    <p>A dikaryotic cell with two distinct nuclei.</p> Signup and view all the answers

    Why do humans not have to be concerned about the presence of bacteriophages in their food?

    <p>Bacteriophages specifically infect bacteria and do not harm human cells.</p> Signup and view all the answers

    What are three ways that viruses can be transmitted between hosts?

    <p>Direct contact, indirect contact with fomites, or through a vector.</p> Signup and view all the answers

    Which types of viruses have spikes?

    <p>Enveloped viruses</p> Signup and view all the answers

    What is the main purpose of phage therapy?

    <p>To kill bacteria</p> Signup and view all the answers

    What is the classification criterion used by the International Committee on Taxonomy of Viruses (ICTV)?

    <p>All of the above</p> Signup and view all the answers

    What specific type of virus is known for causing zoonoses?

    <p>Viruses that can be transmitted from an animal host to a human host.</p> Signup and view all the answers

    What coding systems are used alongside ICD codes?

    <p>Healthcare Common Procedure Coding System</p> Signup and view all the answers

    What is the purpose of using ICD codes in medical laboratories?

    <p>To identify tests that must be performed to confirm the diagnosis.</p> Signup and view all the answers

    What technique is used on David's skin biopsy specimen?

    <p>Immunofluorescent staining</p> Signup and view all the answers

    Several tests are available to diagnose rabies in live patients.

    <p>True</p> Signup and view all the answers

    What are the symptoms that raised concerns for David's doctor regarding rabies?

    <p>Prickling and itching at the site of the dog bite.</p> Signup and view all the answers

    What does the lytic cycle of a bacteriophage lead to?

    <p>Cell death through lysis</p> Signup and view all the answers

    Viruses depend on _____ for reproduction and metabolic processes.

    <p>cells</p> Signup and view all the answers

    What is one characteristic of virulent phages?

    <p>They typically lead to the death of the cell through cell lysis.</p> Signup and view all the answers

    Where do most DNA viruses replicate in eukaryotic cells?

    <p>Nucleus</p> Signup and view all the answers

    Which genus includes the causative agent for malaria?

    <p>Plasmodium</p> Signup and view all the answers

    Which protist is a concern because of its ability to contaminate water supplies and cause diarrheal illness?

    <p>Giardia lamblia</p> Signup and view all the answers

    A fluke is classified within which of the following?

    <p>Platyhelminthes</p> Signup and view all the answers

    A nonsegmented worm is found during a routine colonoscopy of an individual who reported having abdominal cramps, nausea, and vomiting. This worm is likely which of the following?

    <p>Nematode</p> Signup and view all the answers

    A segmented worm has male and female reproductive organs in each segment. Some use hooks to attach to the intestinal wall. Which type of worm is this?

    <p>Cestode</p> Signup and view all the answers

    Mushrooms are a type of which of the following?

    <p>Basidiocarp</p> Signup and view all the answers

    Which of the following is the most common cause of human yeast infections?

    <p>Candida albicans</p> Signup and view all the answers

    Which polysaccharide found in red algal cell walls is a useful solidifying agent?

    <p>Agar</p> Signup and view all the answers

    Which is the term for the hard outer covering of some dinoflagellates?

    <p>Theca</p> Signup and view all the answers

    Which protists are associated with red tides?

    <p>Dinoflagellates</p> Signup and view all the answers

    You encounter a lichen with leafy structures. Which term describes this lichen?

    <p>Foliose</p> Signup and view all the answers

    Which of the following is the term for the outer layer of a lichen?

    <p>The cortex</p> Signup and view all the answers

    The fungus in a lichen is which of the following?

    <p>An ascomycete</p> Signup and view all the answers

    The plasma membrane of a protist is called the __________.

    <p>plasmalemma</p> Signup and view all the answers

    Animals belong to the same supergroup as the kingdom __________.

    <p>Animalia</p> Signup and view all the answers

    Flukes are in class __________.

    <p>Trematoda</p> Signup and view all the answers

    Some fungi have proven medically useful because they can be used to produce __________.

    <p>antibiotics</p> Signup and view all the answers

    What are kinetoplastids?

    <p>A group of protozoa distinguished by a unique organelle called a kinetoplast.</p> Signup and view all the answers

    What is the function of the ciliate macronucleus?

    <p>It regulates metabolic functions and governs cell activity.</p> Signup and view all the answers

    What is the best defense against tapeworm infections?

    <p>Properly cooking meat to kill the larvae.</p> Signup and view all the answers

    What other effect might a toxoplasmosis infection have aside from a risk of birth defects?

    <p>It can lead to neuropsychiatric issues.</p> Signup and view all the answers

    What is a distinctive feature of diatoms?

    <p>They have a silica-based cell wall.</p> Signup and view all the answers

    Why are algae not considered parasitic?

    <p>Algae primarily engage in photosynthesis and do not derive nutrients at the expense of other organisms.</p> Signup and view all the answers

    Which groups contain the multicellular algae?

    <p>Chlorophyta, Rhodophyta, and Phaeophyta.</p> Signup and view all the answers

    What are three ways that lichens are environmentally valuable?

    <p>They create soil, provide food, and act as indicators of air pollution.</p> Signup and view all the answers

    What is the role of noncoding DNA?

    <p>Noncoding DNA plays regulatory and structural roles within the genome.</p> Signup and view all the answers

    What is extrachromosomal DNA?

    <p>Extrachromosomal DNA refers to DNA found outside of the main chromosomes within a cell.</p> Signup and view all the answers

    How are plasmids involved in antibiotic resistance?

    <p>Plasmids can carry genes that provide bacteria with resistance to antibiotics.</p> Signup and view all the answers

    What occurs when a bacterium loses one or both of its plasmids?

    <p>The pathogenicity of the bacterium may decrease, losing virulence factors encoded on those plasmids.</p> Signup and view all the answers

    Why do viral genomes vary widely among viruses?

    <p>Viral genomes can vary due to differences in virus structure and replication strategies.</p> Signup and view all the answers

    Which of the following organisms has the largest known genome?

    <p>Plants</p> Signup and view all the answers

    What characterizes plasmids in bacteria?

    <p>They can be exchanged between bacteria.</p> Signup and view all the answers

    What type of genetic material can viral genomes be composed of?

    <p>Both DNA and RNA</p> Signup and view all the answers

    What are the two functions of DNA?

    <p>Inheritance and regulation of protein construction</p> Signup and view all the answers

    What is the central dogma of molecular biology?

    <p>DNA to RNA to protein</p> Signup and view all the answers

    What was the outcome of Frederick Griffith's experiment with mice and bacterial strains?

    <p>The mice will die. Transformation of genetic material from R to S was required.</p> Signup and view all the answers

    What is the difference between genotype and phenotype?

    <p>Genotype is the genetic constitution, while phenotype is the observable characteristics resulting from the genotype.</p> Signup and view all the answers

    Why was the alga Acetabularia a good model organism for Joachim Hämmerling to use?

    <p>After infection with the 32P-labeled viruses and centrifugation, only the pellet would be radioactive.</p> Signup and view all the answers

    How can cells have the same genotype but differ in their phenotype?

    <p>Differences in gene expression and environmental interactions can result in varied phenotypes.</p> Signup and view all the answers

    According to Beadle and Tatum’s 'one gene–one enzyme' hypothesis, which enzymes eliminate transformation of hereditary material from pathogenic bacteria to nonpathogenic bacteria?

    <p>Carbohydrate-degrading enzymes.</p> Signup and view all the answers

    What is semiconservative DNA replication?

    <p>A process where each strand of the double helix serves as a template for a new complementary strand.</p> Signup and view all the answers

    Which of the following is not found within DNA?

    <p>Amino acids</p> Signup and view all the answers

    Why is DNA replication bidirectional?

    <p>DNA replication is bidirectional to allow efficient and simultaneous copying of the DNA in both directions from the origin.</p> Signup and view all the answers

    What are Okazaki fragments?

    <p>Short segments of DNA synthesized on the lagging strand during DNA replication.</p> Signup and view all the answers

    Which of the following types of RNA codes for a protein?

    <p>mRNA</p> Signup and view all the answers

    What is the role of DNA polymerase in DNA replication?

    <p>DNA polymerase synthesizes new DNA strands by adding complementary nucleotides.</p> Signup and view all the answers

    The work of Rosalind Franklin and R.G. Gosling was important in demonstrating the helical nature of DNA.

    <p>True</p> Signup and view all the answers

    The element ____________ is unique to nucleic acids compared with other macromolecules.

    <p>phosphorus</p> Signup and view all the answers

    What was concluded from Meselson and Stahl's experiment if two bands of DNA were found after one generation?

    <p>It would suggest that DNA replication is not semiconservative.</p> Signup and view all the answers

    What is meant by the term 'antiparallel' in the context of DNA?

    <p>The two strands of DNA run in opposite directions.</p> Signup and view all the answers

    Match the correct molecule with its description:

    <p>tRNA = Carries an amino acid to the ribosome rRNA = Is a major component of ribosomes mRNA = Is a copy of the information in a gene</p> Signup and view all the answers

    Why do bacteria and viruses make good model systems for various genetic studies?

    <p>They reproduce quickly and have simple genetic structures.</p> Signup and view all the answers

    What three factors interact with the tRNA molecule?

    <p>Aminoacyl tRNA synthetases, ribosomes, and mRNA.</p> Signup and view all the answers

    What is the CCA amino acid binding end in tRNA?

    <p>A cytosine-cytosine-adenine sequence at the 3' end of the tRNA.</p> Signup and view all the answers

    What is an anticodon?

    <p>A three-nucleotide sequence in tRNA that bonds with an mRNA codon.</p> Signup and view all the answers

    What process links tRNA to its correct amino acid?

    <p>tRNA charging.</p> Signup and view all the answers

    What does the initiator tRNA carry in E. coli?

    <p>N-formyl-methionine (fMet-tRNAfMet).</p> Signup and view all the answers

    Initiation of protein synthesis begins with the assembly of the large ribosomal subunit.

    <p>False</p> Signup and view all the answers

    Which site in the ribosome does the incoming charged aminoacyl tRNA bind to?

    <p>A site</p> Signup and view all the answers

    Peptide bonds are formed between amino acids at the P site during translation.

    <p>True</p> Signup and view all the answers

    How long does the E. coli translation apparatus take to add each amino acid?

    <p>0.05 seconds.</p> Signup and view all the answers

    Match the following components of the ribosome with their functions:

    <p>A site = Binds incoming charged aminoacyl tRNAs P site = Binds tRNAs carrying amino acids forming peptide bonds E site = Releases dissociated tRNAs</p> Signup and view all the answers

    What is the structure formed at the origin of replication?

    <p>Replication bubble</p> Signup and view all the answers

    What prevents single-stranded DNA from rewinding into a double helix?

    <p>Single-stranded binding proteins</p> Signup and view all the answers

    What is the function of the primer in DNA replication?

    <p>Provides a free 3'-OH group</p> Signup and view all the answers

    What enzyme synthesizes the RNA primer?

    <p>RNA primase</p> Signup and view all the answers

    What are the two strands synthesized during DNA replication called?

    <p>Both A and B</p> Signup and view all the answers

    DNA polymerase III can add nucleotides in both 5' to 3' and 3' to 5' directions.

    <p>False</p> Signup and view all the answers

    What are Okazaki fragments?

    <p>Short DNA sequence fragments</p> Signup and view all the answers

    Which enzyme seals the gaps between Okazaki fragments?

    <p>DNA ligase</p> Signup and view all the answers

    What is the role of topoisomerase II during DNA replication?

    <p>Relaxes supercoiled DNA</p> Signup and view all the answers

    Eukaryotic DNA replication occurs at a faster rate than prokaryotic DNA replication.

    <p>False</p> Signup and view all the answers

    What is found at the ends of eukaryotic chromosomes to protect coding sequences?

    <p>Telomeres</p> Signup and view all the answers

    Which enzyme is responsible for removing RNA primers in newly replicated bacterial DNA?

    <p>DNA pol I</p> Signup and view all the answers

    Where does the σ factor of RNA polymerase bind DNA to start transcription?

    <p>at a specific promoter</p> Signup and view all the answers

    What occurs to initiate the polymerization activity of RNA polymerase?

    <p>binding of RNA polymerase to the promoter</p> Signup and view all the answers

    Which of the following is true about the leading strand during replication?

    <p>Synthesized continuously</p> Signup and view all the answers

    Do bacteria have multiple origins of replication?

    <p>No</p> Signup and view all the answers

    Where does the signal to end transcription come from?

    <p>termination signals in the DNA template</p> Signup and view all the answers

    Eukaryotic mRNAs are usually polycistronic.

    <p>False</p> Signup and view all the answers

    Rolling circle replication has a lagging strand.

    <p>False</p> Signup and view all the answers

    How is the RNA transcript from a gene for a protein modified after it is transcribed in eukaryotic cells?

    <p>addition of a 5' cap and a 3' poly-A tail, and splicing of introns</p> Signup and view all the answers

    What are exons and introns?

    <p>exons are coding sequences; introns are non-coding sequences</p> Signup and view all the answers

    Which of the following are characteristics of translation in eukaryotes? (Select all that apply)

    <p>mRNA is monocistronic</p> Signup and view all the answers

    What is the role of tRNA in translation?

    <p>It carries amino acids to the ribosome</p> Signup and view all the answers

    What happens when a stop codon is reached during translation?

    <p>protein synthesis is terminated and the polypeptide is released</p> Signup and view all the answers

    What are the ribosomal subunit sizes in prokaryotes?

    <p>70S</p> Signup and view all the answers

    What signs and symptoms is Michael experiencing?

    <p>Severe headaches and a fever spiking to 40 °C (104 °F)</p> Signup and view all the answers

    What do these signs and symptoms tell us about the stage of Michael's disease?

    <p>They indicate that Michael may be in the illness stage of the disease.</p> Signup and view all the answers

    Explain the difference between signs and symptoms.

    <p>Signs are objective and measurable indicators of disease, while symptoms are subjective experiences reported by the patient.</p> Signup and view all the answers

    What is an infectious disease?

    <p>Any disease caused by the direct effect of a pathogen.</p> Signup and view all the answers

    What is the difference between iatrogenic disease and nosocomial disease?

    <p>Iatrogenic disease occurs as a result of medical procedures, while nosocomial disease is acquired in a hospital setting.</p> Signup and view all the answers

    What are the five periods of disease?

    <p>Incubation, prodromal, illness, decline, and convalescence.</p> Signup and view all the answers

    During which period of disease are signs and symptoms most obvious and severe?

    <p>The period of illness.</p> Signup and view all the answers

    All infectious diseases are contagious.

    <p>False</p> Signup and view all the answers

    What is a zoonotic disease?

    <p>A disease that occurs when a pathogen is transferred from a vertebrate animal to a human.</p> Signup and view all the answers

    Which of the following is an example of a sign of disease?

    <p>Fever</p> Signup and view all the answers

    What type of disease is not caused by pathogens?

    <p>Noninfectious diseases</p> Signup and view all the answers

    A scientist discovers that a soil bacterium he has been studying produces an antimicrobial that kills gram-negative bacteria. What type of antimicrobial is this new version?

    <p>Semisynthetic</p> Signup and view all the answers

    Which of the following antimicrobial drugs is synthetic?

    <p>Sulfanilamide</p> Signup and view all the answers

    Which clinical situation would be appropriate for treatment with a narrow-spectrum antimicrobial drug?

    <p>Treatment of strep throat caused by culture identified Streptococcus pyogenes</p> Signup and view all the answers

    Which of the following terms refers to the ability of an antimicrobial drug to harm the target microbe without harming the host?

    <p>Selective toxicity</p> Signup and view all the answers

    Which of the following is not a type of β-lactam antimicrobial?

    <p>Glycopeptides</p> Signup and view all the answers

    Narrow-spectrum antimicrobials are commonly used for prophylaxis following surgery.

    <p>False</p> Signup and view all the answers

    β-lactamases can degrade vancomycin.

    <p>False</p> Signup and view all the answers

    The group of soil bacteria known for their ability to produce a wide variety of antimicrobials is called the ________.

    <p>Streptomyces</p> Signup and view all the answers

    Where do antimicrobials come from naturally?

    <p>Natural sources such as fungi and bacteria.</p> Signup and view all the answers

    What is the difference between multidrug resistance and cross-resistance?

    <p>Multidrug resistance refers to resistance to multiple drugs, while cross-resistance refers to resistance to drugs that are similar in structure or function.</p> Signup and view all the answers

    What factors can affect the length of the incubation period of a particular disease?

    <p>The pathogen involved, the disease, and the individual infected.</p> Signup and view all the answers

    Explain the difference between latent disease and chronic disease.

    <p>Latent disease involves a dormant pathogen with no active replication, while chronic disease has ongoing pathological changes over an extended period.</p> Signup and view all the answers

    What are Koch's postulates?

    <ol> <li>The suspected pathogen must be found in every case of the disease; 2. It must be isolated and grown in pure culture; 3. A healthy subject must develop the same disease after infection; 4. The pathogen must be re-isolated and identical to the original.</li> </ol> Signup and view all the answers

    What is pathogenicity?

    <p>The ability of a microbial agent to cause disease.</p> Signup and view all the answers

    What is virulence?

    <p>The degree to which an organism is pathogenic.</p> Signup and view all the answers

    What is the ID50?

    <p>The median infectious dose of a pathogen required to infect 50% of the inoculated subjects.</p> Signup and view all the answers

    What is the LD50?

    <p>The median lethal dose of a pathogen required to kill 50% of infected subjects.</p> Signup and view all the answers

    Which of the following statements about Koch's postulates is true?

    <p>Healthy individuals can carry pathogens without disease.</p> Signup and view all the answers

    What does molecular Koch's postulates focus on?

    <p>Identifying a gene that may cause the organism to be pathogenic.</p> Signup and view all the answers

    Virulence is a continuum from avirulent to highly virulent.

    <p>True</p> Signup and view all the answers

    In a complement fixation test, if the serum turns pink, does the patient have antibodies to the antigen or not?

    <p>The patient does not have antibodies to the antigen.</p> Signup and view all the answers

    How is agglutination used to distinguish serovars from each other?

    <p>Agglutination tests use specific antibodies to cause visible clumping of bacteria, indicating the presence of different serovars.</p> Signup and view all the answers

    In a latex bead assay to test for antibodies in a patient's serum, with what are the beads coated?

    <p>The beads are coated with the antigen of interest.</p> Signup and view all the answers

    What has happened when a patient has undergone seroconversion?

    <p>The patient has developed detectable levels of antibodies in their serum.</p> Signup and view all the answers

    What is the mechanism by which viruses are detected in a hemagglutination assay?

    <p>Viruses bind to and cross-link red blood cells, causing agglutination.</p> Signup and view all the answers

    Which hemagglutination result tells us the titer of virus in a sample?

    <p>The highest dilution that produces visible agglutination indicates the viral titer.</p> Signup and view all the answers

    Why does a precipitin ring form in a precipitin ring test?

    <p>A precipitin ring forms when the antigen and antibody diffuse through a gel and interact at an optimal concentration.</p> Signup and view all the answers

    What are some reasons why a precipitin ring might not form?

    <p>A ring might not form due to insufficient antigen or antibody concentration, or the inappropriate pH of the assay.</p> Signup and view all the answers

    What is the main purpose of a radial immunodiffusion assay?

    <p>To precisely quantify antigen concentration in a sample.</p> Signup and view all the answers

    What do flocculation assays involve?

    <p>Flocculation assays involve insoluble antigens, resulting in observable foaming rather than precipitation.</p> Signup and view all the answers

    What is the primary use of the VDRL test?

    <p>The VDRL test is used to diagnose syphilis by detecting anti-treponemal antibodies.</p> Signup and view all the answers

    What indicates a new infection in a neutralization assay?

    <p>A four-fold increase in neutralizing titer in a second serum sample taken two weeks later.</p> Signup and view all the answers

    What does immunoelectrophoresis help diagnose?

    <p>Immunoelectrophoresis is used to diagnose conditions like multiple myeloma.</p> Signup and view all the answers

    What is the function of antibodies in the western blot technique?

    <p>Antibodies are used to identify specific proteins in a gel.</p> Signup and view all the answers

    What role do complement proteins play in the immune response?

    <p>Complement proteins facilitate opsonization and lysis of pathogens.</p> Signup and view all the answers

    What does a clear solution indicate in a complement fixation test?

    <p>A clear solution indicates a positive test for antibodies against the antigen.</p> Signup and view all the answers

    What do fluorescent antibodies bind to in an indirect fluorescent antibody test?

    <p>Antigens fixed to a surface</p> Signup and view all the answers

    What is the ANA test looking for?

    <p>Antinuclear antibodies</p> Signup and view all the answers

    What is the significance of a titer of at least 1:40 in the presence of symptoms involving two or more organ systems?

    <p>Indicates possible systemic lupus erythematosus</p> Signup and view all the answers

    What happens to the CD4 T cell levels in HIV infections?

    <p>They decrease, making the patient more susceptible to infections.</p> Signup and view all the answers

    What does the laser do in a flow cytometer?

    <p>Excites fluorogens to measure fluorescence intensity.</p> Signup and view all the answers

    What is the output from a flow cytometer represented as?

    <p>A histogram</p> Signup and view all the answers

    What is fluorescence-activated cell sorting (FACS) used for?

    <p>To separate cells into purified subpopulations.</p> Signup and view all the answers

    Which of the following best describes the purpose of the VDRL test?

    <p>Determines if an infection is currently active</p> Signup and view all the answers

    Match the following antibody tests with their primary usage:

    <p>DFA = Visualizing bacteria IFA = Diagnosing syphilis and autoimmune diseases Flow cytometry = Counting fluorescently labeled cells FACS = Sorting cells into subpopulations</p> Signup and view all the answers

    For many uses in the laboratory, polyclonal antibodies work well, but for some types of assays, they lack sufficient ________ because they cross-react with inappropriate antigens.

    <p>Specificity</p> Signup and view all the answers

    How are monoclonal antibodies produced?

    <p>Antibody-producing B cells from a mouse are fused with myeloma cells and then the cells are grown in tissue culture.</p> Signup and view all the answers

    The formation of ________ is a positive result in the VDRL test.

    <p>Flocculant</p> Signup and view all the answers

    The titer of a virus neutralization test is the highest dilution of patient serum:

    <p>That completely blocks plaque formation.</p> Signup and view all the answers

    In the Ouchterlony assay, we see a sharp precipitin arc form between antigen and antibody. Why does this arc remain visible for a long time?

    <p>The precipitin lattice is too large to diffuse through the agar.</p> Signup and view all the answers

    We use antisera to distinguish between various ________ within a species of bacteria.

    <p>Serovars</p> Signup and view all the answers

    When using antisera to characterize bacteria, we will often link the antibodies to ________ to better visualize the agglutination.

    <p>Latex beads</p> Signup and view all the answers

    What is the purpose of alcohol treatment when using an EIA to study microtubules or intracellular structures?

    <p>It makes holes in the cell membrane large enough for antibodies to pass.</p> Signup and view all the answers

    What is the purpose of the secondary antibody in a direct ELISA?

    <p>To bind to primary antibodies to quantify the amount of antigen-specific antibody present.</p> Signup and view all the answers

    What do the direct and indirect ELISAs quantify?

    <p>They quantify the presence of antigens or antibodies.</p> Signup and view all the answers

    How accurate is an indirect ELISA test for HIV, and what factors could impact the test’s accuracy?

    <p>The accuracy can be affected by cross-reactivity and the timing of the test after infection.</p> Signup and view all the answers

    What physical process does the lateral flow method require to function?

    <p>Capillary action.</p> Signup and view all the answers

    Explain the purpose of the third strip in a lateral flow assay.

    <p>To serve as a control to verify the validity of the test.</p> Signup and view all the answers

    What is one example of a lateral flow test?

    <p>An in-home pregnancy test.</p> Signup and view all the answers

    The indirect ELISA can yield false-negative results if the infected person is tested too soon after becoming infected.

    <p>True</p> Signup and view all the answers

    What are Koch's postulates used for?

    <p>To prove that a particular microorganism is the cause of a disease.</p> Signup and view all the answers

    Many people support the exploitation of animals for research purposes.

    <p>False</p> Signup and view all the answers

    What is the false-positive rate for many tests?

    <p>0.5% is not unusual.</p> Signup and view all the answers

    The NIH guidelines for the humane treatment of lab animals are based on the principle of the three R's: replace, refine, and ___.

    <p>reduce</p> Signup and view all the answers

    How many false-positive ELISA tests would be expected among 1300 patients?

    <p>Approximately 6.5 false-positive tests.</p> Signup and view all the answers

    What is the role of the Institutional Animal Care and Use Committee (IACUC)?

    <p>To ensure that NIH guidelines for the use of animals in research are being followed.</p> Signup and view all the answers

    What occurs if a western blot yields indeterminate results?

    <p>It neither confirms nor invalidates the results of the indirect ELISA.</p> Signup and view all the answers

    What advantage do fluorescent antibody techniques offer compared to non-fluorescent assays?

    <p>Rapid visualization of target antigens.</p> Signup and view all the answers

    What is agglutination?

    <p>The clumping of cells due to an antigen-antibody reaction</p> Signup and view all the answers

    What is a cross-match assay and why is it performed?

    <p>A cross-match assay checks for compatibility between donor and recipient blood by mixing their blood samples.</p> Signup and view all the answers

    What is the role of direct fluorescent antibody tests?

    <p>To bind and illuminate target antigens for rapid diagnosis.</p> Signup and view all the answers

    What is the purpose of the MMR titer test?

    <p>To determine if an individual has sufficient immunity against measles, mumps, and rubella.</p> Signup and view all the answers

    In a direct fluorescent antibody test, what does the fluorescent antibody bind to?

    <p>The target antigen.</p> Signup and view all the answers

    Match the type of immunoassays with their brief descriptions:

    <p>EIA = Uses antibodies to detect the presence of antigens ELISA = A specific type of EIA used for quantifying antigens Immunohistochemistry = Examines whole tissues for cell types Immunocytochemistry = Visualizes structures inside individual cells</p> Signup and view all the answers

    What is a common application of indirect fluorescent antibody (IFA) tests?

    <p>Diagnosis of syphilis.</p> Signup and view all the answers

    What is the difference between immunohistochemistry and immunocytochemistry?

    <p>Immunohistochemistry examines whole tissues, while immunocytochemistry targets structures within individual cells.</p> Signup and view all the answers

    Study Notes

    About OpenStax

    • OpenStax is a non-profit organization based at Rice University, focused on providing free, peer-reviewed, openly licensed textbooks.
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    About OpenStax Resources

    • OpenStax resources are licensed under a Creative Commons Attribution 4.0 International (CC BY) license, enabling users to distribute, remix, and build upon content while providing attribution.
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    • Instructors have the option to create customized versions of their OpenStax book, tailored to their specific needs.
    • OpenStax provides regular updates and errata changes, ensuring transparency regarding content revisions.

    About Microbiology

    • Microbiology is an OpenStax textbook designed for single-semester Microbiology courses for non-majors.
    • The textbook focuses on applications relevant to careers in allied health, covering core microbiology concepts in an engaging and accessible manner.
    • The content is organized in a logical progression, moving from fundamental to advanced concepts.
    • While focusing on clinical relevance, the textbook also incorporates topics related to environmental and applied microbiology and the history of science.

    Overview

    • This Microbiology textbook is published by OpenStax and the American Society for Microbiology
    • It is aligned with the curriculum guidelines of the American Society for Microbiology for Undergraduate Microbiology Education
    • The textbook is offered free online through openstax.org
    • A physical version, in print or digital form is available through campus bookstores

    Textbook Chapters

    • The first chapters of the textbook provide an overview of microbiology and include information on microscopy and cellular biology
    • Subsequent chapters discuss the classification of microorganisms
    • Later chapters focus on microbial biochemistry, metabolism, and genetics, topics essential for understanding microbial control and combat
    • The middle portion of the book focuses on microbial pathogenicity and emphasizing the role of the immune system in health and disease
    • The final chapters explore medical microbiology, detailing characteristics of microbial diseases categorized by body systems

    ASM's Role

    • The American Society for Microbiology (ASM) is the largest single life science society
    • It promotes and advances the microbial sciences through conferences, publications, certifications and educational opportunities
    • ASM enhances laboratory capacity around the globe through training resources and provides a network for scientists across academia, industry and clinical settings
    • ASM promotes understanding of microbial sciences to diverse audiences
    • They provide free open-access materials through journals, reports and textbooks

    Curriculum Guidelines

    • The traditional concept of species is not easily applied to microbes due to asexual reproduction and horizontal gene transfer
    • The evolutionary relatedness of organisms is best reflected in phylogenetic trees
    • Bacteria have unique cell structures that are targets for antibiotics, immunity, and phage infection
    • Bacteria and Archaea have specialized structures like flagella, endospores, and pili that confer essential capabilities
    • Microorganisms are ubiquitous and live in diverse, dynamic ecosystems
    • Most bacteria live in biofilm communities
    • Microorganisms and their environment interact with and modify each other
    • Microorganisms can interact with human and nonhuman hosts in beneficial, neutral or detrimental ways
    • Microbes are essential for life as we know it and the processes that support life
    • Humans utilize and harness microorganisms and their products.
    • The true diversity of microbial life is largely unknown and its potential benefits haven't been fully explored.

    Competencies and Skills

    • Students must demonstrate an ability to formulate hypotheses and design experiments based on the scientific method.
    • Students must analyze and interpret results from microbiological methods
    • Students must use mathematical reasoning, graphing skills, and solve problems in microbiology.
    • Students must be able to communicate microbiology concepts effectively in written and oral formats
    • Students must identify credible scientific sources and interpret and evaluate the information from these sources.
    • Students must identify and discuss ethical issues in microbiology
    • Students must properly prepare and view specimens for examination using microscopy.
    • Students must use pure culture and selective techniques to enrich for and isolate microorganisms
    • Students must identify microorganisms using media-based, molecular, and serological methods
    • Students must estimate the number of microorganisms in a sample.
    • Students must use appropriate microbiological and molecular lab equipment and methods
    • Students must practice safe microbiology.
    • Students must document and report on experimental protocols, results, and conclusions.

    Engaging Features

    • Clinical Focus: Each chapter includes a multi-part clinical case study that follows a fictional patient, emphasizing applied learning
    • Case in Point: Many chapters include a single-part case study highlighting clinical relevance of a specific topic.
    • Micro Connections: All chapters contain Micro Connections boxes that highlight real-world applications of microbiology
    • Sigma Xi Eye on Ethics: Most chapters feature a Sigma Xi Eye on Ethics box that explores ethical issues related to the chapter content

    What Our Ancestors Knew

    • Microorganisms are small organisms and many are too small to see without a microscope
    • Humans have used microorganisms longer than they have been able to see them

    Clinical Focus

    • A doctor diagnoses Cora with meningitis, a serious infection of the tissue surrounding the brain and spinal cord
    • Meningitis can be caused by bacteria, fungi, viruses, or other factors
    • The doctor orders a lumbar puncture to take cerebrospinal fluid (CSF) samples
    • The CSF is tested in different laboratories
    • The CSF sample is stained with a Gram stain to differentiate between two types of bacteria (gram-positive and gram-negative)
    • The doctor prescribes Cora antibiotics to treat potential bacterial meningitis
    • The bacteria sample is put in special dishes for culturing
    • Some microorganisms take time to reproduce in quantities that can be detected and analyzed

    Fermented Foods and Beverages

    • Humans have enjoyed fermented foods and beverages since ancient times.
    • These foods are created by bacteria, mold, or yeast converting sugars into alcohol, gases, and organic acids.
    • Archeological evidence suggests that ancient Chinese people were fermenting beverages using rice, honey, and fruit as early as 7000 BC.

    The Iceman and Evidence of Early Treatments

    • Ötzi the Iceman was a 5300-year-old mummy found frozen in the Alps.
    • Research suggests that the Iceman was infected with the parasite Trichuris trichiura and the bacteria Borrelia burgdorferi, which causes Lyme disease.
    • The Iceman had the woody fruit of the Fomitopsis betulinus fungus, which has laxative and antibiotic properties, tied to his belongings.
    • The Iceman was covered in tattoos which may have been a form of herbal treatment.

    Early Notions of Disease, Contagion, and Containment

    • Ancient civilizations had some understanding of disease transmission, even without knowing about microbes.
    • The Bible mentions the practice of quarantining individuals with leprosy, indicating an early understanding of communicable diseases.
    • The Indus Valley Civilization, around 2500 BCE, had complex sanitation systems including wells, baths, and drainage systems.
    • Ancient Greeks believed disease was caused by "bad air," which led to hygiene practices.
    • The Romans used aqueducts and the Cloaca Maxima sewage system for fresh water and waste disposal, which may have protected them from waterborne diseases.
    • Hippocrates, thought to be the "father of Western medicine," dismissed supernatural causes of disease and emphasized natural causes.
    • Thucydides, a Greek historian, developed the concept of immunity after observing that survivors of the Athenian plague didn't get re-infected.
    • Marcus Terentius Varro, a Roman writer, proposed that invisible creatures could cause disease centuries before microbes were discovered.
    • Islamic scholars contributed significantly to medicine, with al-Razi distinguishing measles and smallpox using experimental methods.
    • Ibn Sina, or Avicenna, wrote the Canon of Medicine, a comprehensive medical encyclopedia, which included detailed descriptions of contagion and disease transmission.

    The Birth of Microbiology

    • Antonie van Leeuwenhoek developed microscopes powerful enough to view microbes in the 17th century.
    • He observed single-celled organisms, which he called "animalcules," in a drop of rainwater.
    • The Golden Age of Microbiology (1857-1914) saw significant discoveries by Louis Pasteur and Robert Koch.
    • Pasteur demonstrated that fermentation is caused by microorganisms, invented pasteurization, and developed vaccines.
    • Koch was the first to connect specific microbes to human diseases, identifying the bacteria responsible for anthrax, cholera, and tuberculosis.

    Microbiology Toolbox

    • Modern microbiology relies heavily on technology to study microbes.
    • Microscopes allow the viewing of microbes and other small specimens.
    • Stains and dyes are used to color microbes for easier observation.
    • Growth media provide nutrients for microbes to grow and reproduce in a laboratory setting.
    • Petri dishes hold growth media.
    • Test tubes are used to grow microbes in liquid or solid media.
    • Bunsen burners sterilize equipment.
    • Inoculation loops transfer microorganisms.

    The Science of Taxonomy

    • Taxonomy classifies, describes, identifies, and names living organisms.
    • Carolus Linnaeus created the Linnaean taxonomy, a system for categorizing and naming organisms with a consistent format.
    • Linnaeus grouped organisms into kingdoms (animal, plant, mineral), classes, orders, families, genera, and species.
    • Species is the most specific taxonomic unit.

    Evolving Trees of Life (Phylogenies)

    • Advances in technology led to refinements of the Linnaean system.
    • Scientists began to create taxonomies based on the evolutionary relationships between organisms.

    Phylogenetic Tree

    • Phylogenetic trees visualize the relationships between organisms
    • Trees are created by comparing visible similarities (e.g., hair presence, limbs) and more complex analyses like genetic, biochemical, and embryological comparisons
    • Linnaeus initially proposed two kingdoms: Animal and Plant
    • Ernst Haeckel proposed a third kingdom, Protista, for unicellular organisms
    • Haeckel proposed a fourth kingdom, Monera, for unicellular organisms without a nucleus
    • Robert Whittaker added a fifth kingdom, Fungi
    • Whittaker categorized organisms into two empires, Prokaryota and Eukaryota
    • Prokaryota contains Monera
    • Eukaryota contains Fungi, Protista, Plantae, and Animalia
    • Viruses are not included in phylogenetic trees because they are not cellular
    • The tree of life is constantly evolving based on new scientific discoveries

    The Role of Genetics in Modern Taxonomy

    • Molecular genetics revealed new ways to organize phylogenetic trees
    • Genetic methods compare nucleic acids (DNA or RNA) and proteins
    • Similarities between nucleic acids and proteins indicate greater evolutionary relatedness
    • Carl Woese and George Fox created a genetics-based tree using rRNA gene sequences
    • They discovered archaea were distinct from bacteria and eukaryotes
    • Woese and Fox proposed three domains above kingdom level: Archaea, Bacteria, and Eukarya
    • Archaea and Bacteria are prokaryotic organisms, and Eukarya contains eukaryotic organisms
    • Analysis suggests archaea and eukarya are more closely related than archaea and bacteria
    • Horizontal gene transfer (gene transfer between species) complicates phylogenetic relationships
    • Some scientists propose "webs of life" instead of "trees of life"

    Naming Microbes

    • Linnaeus used binomial nomenclature, a two-word naming system (genus and specific epithet)
    • The genus name is capitalized, followed by the specific epithet, which is not capitalized
    • Both names are italicized
    • Modern taxonomic names can be derived from Latin, Greek, or English
    • Names can reflect characteristics of the organism or honor scientists who discovered them
    • The archaeon Haloquadratum walsbyi is an example of this
    • Binomial nomenclature helps to prevent confusion by assigning a unique name to each organism

    Bergey’s Manuals

    • Bergey's Manuals provide standards for identifying and classifying microorganisms
    • Bergey's Manual of Determinative Bacteriology and Bergey's Manual of Systematic Bacteriology are main references
    • Bacteria lack easily observable features, making identification difficult
    • Scientists must study biochemical properties to classify them
    • Biochemical tests identify chemicals unique to specific species
    • Serological tests identify specific antibodies that react with proteins in specific species
    • DNA and rRNA sequencing are used for identification and classification of new species

    Same Name, Different Strain

    • Microorganism species can have different subtypes called strains
    • Strains within the same species may have nearly identical genetics but different attributes
    • Escherichia coli (E. coli) is known for causing food poisoning, but strains vary in disease-causing ability
    • Some E. coli strains are pathogenic, while others are helpful, such as those found in our gut

    Types of Microorganisms

    • Most microbes are unicellular and microscopic, requiring magnification
    • Some unicellular microbes are visible to the naked eye, and some multicellular organisms are microscopic
    • Microorganisms are classified within three domains: Archaea, Bacteria, and Eukarya
    • Bacteria and Archaea are prokaryotic (no nucleus)
    • Eukarya contains eukaryotes (nucleus present)
    • Viruses are acellular (not composed of cells) and do not fit into any of the three domains

    Prokaryotic Microorganisms

    • Bacteria are found in diverse habitats, including within and on humans
    • Some bacteria are pathogenic, causing disease
    • Bacteria are prokaryotic, lacking a true nucleus
    • Most bacteria contain peptidoglycan in their cell walls
    • Common shapes include spherical (coccus), rod-shaped (bacillus), and curved (spirillum, spirochete, or vibrio)
    • Bacteria have diverse metabolic capabilities and can grow in various environments
    • Some bacteria are photosynthetic (e.g., cyanobacteria, green sulfur/nonsulfur bacteria)
    • Photosynthetic bacteria use sunlight for energy and fix carbon dioxide for growth
    • Other bacteria are nonphotosynthetic and obtain energy from other sources

    Unicellular Eukaryotic Parasites

    • Euglena are characterized by a stigma and flagellum.
    • The pellicle gives Euglena its distinct shape and is visible as striations on the cell surface.
    • Trypanosoma brucei causes African trypanosomiasis.
    • Trypanosoma brucei spends part of its life cycle in the tsetse fly and part in humans.
    • Chagas' disease is most prevalent in Latin America and is caused by the insect Triatoma spp.
    • Chagas' disease affects heart tissue and digestive system.
    • The genus Leishmania contains trypanosomes that can cause disfiguring skin disease.
    • Leishmaniasis can cause systemic illness.

    Neglected Parasites

    • Toxoplasmosis, Chagas disease, toxocariasis, cysticercosis, and trichomoniasis are considered neglected parasitic infections (NPIs).
    • The CDC uses a variety of factors when prioritizing diseases.
    • The criteria include the number of people infected, the severity of the illness, and whether the illness is treatable or preventable.

    Parasitic Helminths

    • Parasitic helminths are studied within the discipline of microbiology because of the importance of identifying their microscopic eggs and larvae.
    • There are two major groups of parasitic helminths: roundworms (Nematoda) and flatworms (Platyhelminthes).
    • Parasitic helminths have limited digestive, nervous, and locomotor systems.
    • Parasitic helminths often have complex reproductive cycles and a variety of hosts.
    • Some parasitic worms are monoecious while others are dioecious.

    Nematoda (Roundworms)

    • The phylum Nematoda contains over 15,000 species.
    • Nematodes have a full digestive system.
    • Ascaris lumbricoides is the largest nematode intestinal parasite in humans.
    • Enterobius vermicularis (pinworm) is the most common nematode infection in the U.S.
    • Toxocara canis and T.cati are nematodes found in dogs and cats that can be transmitted to humans.
    • Hookworm infection is caused by Necator americanus and Ancylostoma duodenale.
    • Trichinellosis (trichinosis) is caused by Trichinella spiralis and is contracted by eating undercooked meat.
    • Dirofilaria immitis causes heartworm in dogs and other animals and is transmitted by mosquitoes.

    Platyhelminths (Flatworms)

    • The phylum Platyhelminthes includes flukes, tapeworms, and turbellarians.
    • Flukes (trematodes) are nonsegmented flatworms with an oral sucker.
    • Trematodes have complex life cycles with multiple hosts.
    • Liver flukes, intestinal flukes, and lung flukes are examples of trematodes.
    • Schistosomiasis is caused by Schistosoma mansoni, S.haematobium, and S.japonicum.
    • Tapeworms (cestodes) are segmented flatworms with suckers or hooks at the scolex.
    • Tapeworms attach to the wall of the small intestine.
    • Tapeworms reproduce via segments called proglottids, which detach and release eggs.
    • Taenia saginata (beef tapeworm) and T.solium (pork tapeworm) infect humans through the ingestion of undercooked meat.
    • Diphylobothrium latum is the largest human tapeworm and can be ingested in undercooked fish.
    • Echinococcus granulosus (dog tapeworm) can parasitize humans and uses dogs as an important host.

    Food for Worms

    • Helminth infections are widespread and affect a large portion of the global population.
    • Ascaris lumbricoides, Trichuris, and Necator americanus are common helminth infections.
    • Toxocara is also widespread and found in the U.S.
    • Helminths can cause subclinical illnesses or more severe, chronic problems.

    Eradicating the Guinea Worm

    • Dracunculiasis (Guinea worm disease) is caused by Dracunculus medinensis.
    • Dracunculus medinensis infects humans through the consumption of contaminated water.
    • Guinea worm disease is rarely fatal but causes severe pain and secondary infections.
    • The WHO, CDC, UNICEF, and the Cater Center have collaborated to reduce cases of dracunculiasis.
    • The eradication campaign has been successful due to effective diagnostic methods, readily available control methods, the lack of an animal reservoir, and a commitment from governments in affected areas.

    Fungi

    • Fungi are heterotrophic and typically saprozoic.
    • Fungi are studied within the discipline of microbiology.

    Fungi

    • Fungi include macroscopic organisms like mushrooms and molds, as well as microscopic yeasts and spores.
    • Fungi have medical relevance as some species can cause mycoses (fungal infections).
    • Some fungal pathogens are opportunistic meaning they infect individuals with compromised immune systems.
    • Fungi are decomposers in the environment and are used in the production of foods like cheeses.
    • Fungi are major sources of antibiotics, such as penicillin produced by Penicillium.
    • Most multicellular fungi (molds) are composed of filaments called hyphae.
    • Hyphae can form a network called a mycelium.
    • Hyphae can be septate (with walls between cells) or nonseptate/coenocytic (lacking dividing walls).
    • Yeasts are unicellular fungi.
    • Some fungi are dimorphic, existing in both yeast and mold forms during their life cycle.
    • Dimorphic fungi can alter their appearance in response to environmental changes, such as nutrient availability or temperature fluctuations.
    • Dimorphic yeasts, such as Histoplasma capsulatum and Candida albicans, cause human diseases.
    • Fungal cell walls contain chitin, unlike plant cell walls which contain cellulose.
    • Fungal cell membranes contain ergosterols, unlike animal cell membranes which contain cholesterol.
    • Ergosterols are a target for antifungal drugs.
    • Fungi reproduce sexually through cross- or self-fertilization.
    • Haploid fungi form hyphae with gametes (sex cells) at the tips.
    • Two mating types (+) and (-) are involved in sexual reproduction.
    • Plasmogamy (fusion of cytoplasm), followed by karyogamy (fusion of nuclei) occur during sexual reproduction.
    • Fusion of nuclei forms a diploid zygote which undergoes meiosis to produce spores.
    • Spores germinate to start the haploid stage, leading to the formation of more haploid mycelia.
    • Depending on the taxonomic group, sexually produced spores are called zygospores (Zygomycota), ascospores (Ascomycota), or basidiospores (Basidiomycota).
    • Fungi also reproduce asexually through mitosis, budding, fragmentation of hyphae, and formation of asexual spores.
    • Asexual spores are specialized cells for survival, reproduction, and dispersal.
    • Different types of asexual spores are important for fungal classification.

    Fungal Diversity

    • Fungi are diverse, with seven major groups.
    • Not all groups contain pathogens.
    • Some groups are associated with plants and include plant pathogens.
    • Urediniomycetes are plant rusts and Ustilaginomycetes are smuts, both with significant economic impacts.
    • Glomeromycota include mycorrhizal fungi, symbiotic with plant roots and promoting plant growth.
    • Glomeromycota are obligate symbionts, meaning they can only survive in association with plant roots.
    • Chytridiomycetes (chytrids) are important ecologically and are considered to be involved in amphibian declines.
    • Zygomycota, Ascomycota, Basidiomycota, and Microsporidia are medically important groups.
    • Zygomycota (zygomycetes) are mainly saprophytes with coenocytic hyphae and haploid nuclei.
    • Zygomycetes use sporangiospores for asexual reproduction and zygospores for sexual reproduction.
    • Zygomycetes are important for food science and as crop pathogens.
    • Ascomycota include food sources, food spoilers, and human pathogens.
    • Ascomycota may have septate hyphae, cup-shaped fruiting bodies called ascocarps, and can produce ascospores and conidia.
    • Ascomycota include several bread molds, minor pathogens, and species causing serious mycoses.
    • Aspergillus species are important causes of allergy and infection, and are used in research and food production.
    • Neurospora crassa is a model organism used in genetics research.
    • Penicillium produces the antibiotic penicillin.
    • Many species in Trichophyton, Microsporum, and Epidermophyton are dermatophytes, causing skin infections.
    • Blastomyces dermatitidis is a dimorphic fungus causing blastomycosis, a respiratory infection.
    • Histoplasma capsulatum, associated with birds and bats, is another important respiratory pathogen.
    • Coccidioides immitis causes Valley fever, a serious lung disease.
    • Candida albicans, a common cause of yeast infections, is part of the normal skin, intestinal, and genital microbiota.
    • Ascomycetes also cause plant diseases such as ergot infections, Dutch elm disease, and powdery mildews.
    • Saccharomyces yeasts, including baker’s yeast (S. cerevisiae), are unicellular ascomycetes used for brewing beer.
    • Basidiomycota (basidiomycetes) have basidia (club-shaped structures) that produce basidiospores within fruiting bodies called basidiocarps.
    • Basidiomycota are important decomposers and food sources.
    • Cryptococcus neoformans, found as a yeast in the environment, can cause serious lung infections in immunocompromised individuals.
    • Agricus campestris (edible mushroom) and Amanita phalloides (death cap) are examples of basidiomycetes.
    • Microsporidia are unicellular fungi that are obligate intracellular parasites.
    • Microsporidia lack mitochondria, peroxisomes, and centrioles.
    • Microsporidia spores release a polar tubule that pierces host cell membranes for entry.
    • Enterocystozoan bieneusi is a pathogenic microsporidian that can cause diarrhea, cholecystitis, and respiratory illness.

    Algae

    • Algae are autotrophic protists that can be unicellular or multicellular.
    • Algae are found in the supergroups Chromalveolata (dinoflagellates, diatoms, golden algae, and brown algae) and Archaeplastida (red algae and green algae).
    • Algae are ecologically important due to their production of 70% of oxygen and organic matter in aquatic environments.
    • Algae are a source of food for humans and animals.
    • Algae are the source of agar, agarose, and carrageenan, solidifying agents used in laboratories and food production.
    • While typically not pathogenic, some algae produce toxins.
    • Harmful algal blooms can produce toxins that impact aquatic animals and humans.
    • Algal cells often have complex cell structures like chloroplasts containing pyrenoids for starch synthesis and storage.
    • Chloroplasts differ in their number of membranes, reflecting primary, secondary, or tertiary endosymbiotic events.
    • Different algal groups have different pigments, reflected in names like red algae, brown algae, and green algae.
    • Some algae, the seaweeds, are macroscopic and can be confused with plants.
    • Seaweeds do not have true tissues or organs like plants.
    • Seaweeds do not have a waxy cuticle to prevent desiccation.

    Algae

    • Algae are a diverse group of photosynthetic eukaryotic protists.
    • Algae may be unicellular or multicellular.
    • Large, multicellular algae are called seaweeds, but are not plants and lack plant-like tissues and organs.
    • Algae may be associated with toxic algal blooms which can harm aquatic wildlife and contaminate seafood with toxins that cause paralysis.
    • Algae are important for producing agar, which is used as a solidifying agent in microbiological media, and carrageenan, which is used as a solidifying agent in food.

    Dinoflagellates

    • They belong to the Chromalveolata supergroup.
    • Most are marine and are important components of plankton.
    • They exhibit a variety of nutritional types: phototrophic, heterotrophic, or mixotrophic.
    • Photosynthetic dinoflagellates use chlorophyll a, chlorophyll c2, and other photosynthetic pigments.
    • They generally have two flagella, causing them to whirl.
    • Some have cellulose plates forming a hard outer covering, or theca, for armor.
    • Some dinoflagellates produce neurotoxins that can cause paralysis in humans or fish.
    • When dinoflagellate populations become dense, red tides (harmful algal blooms) can occur.
    • Major red tide toxin producers are Gonyaulax and Alexandrium, which cause paralytic shellfish poisoning.
    • Pfiesteria piscicida is a dinoflagellate species known as a fish killer, producing toxins harming fish and humans.

    Stramenopiles

    • They belong to the Chromalveolata supergroup.
    • They include the golden algae (Chrysophyta), the brown algae (Phaeophyta), and the diatoms (Bacillariophyta).
    • Stramenopiles have chlorophyll a, chlorophyll c1/c2, and fucoxanthin as photosynthetic pigments.
    • They use chrysolaminarin as their storage carbohydrate.
    • While some lack cell walls, others have scales.
    • Diatoms have frustules, outer cell walls made of crystallized silica.
    • Diatoms can reproduce sexually and asexually, and the male gametes of centric diatoms have flagella that propel them to seek female gametes.
    • Brown algae (Phaeophyta) are multicellular marine seaweeds.
    • Some brown algae grow very large, such as the giant kelp (Laminaria).
    • Brown algae have leaf-like blades, stalks, and holdfasts that attach to the substrate, but are not true leaves, stems, or roots.
    • Their photosynthetic pigments include chlorophyll a, chlorophyll c, β-carotene, and fucoxanthine.
    • They store laminarin as their carbohydrate.

    Archaeplastids

    • They include the green algae (Chlorophyta), the red algae (Rhodophyta), another group of green algae (Charophyta), and the land plants.
    • Charaphyta are most similar to terrestrial plants, sharing a cell division mechanism and a biochemical pathway.
    • Like terrestrial plants, Charophyta and Chlorophyta have chlorophyll a and chlorophyll b as photosynthetic pigments, cellulose cell walls, and starch as their carbohydrate storage molecule.
    • Chlamydomonas, a green alga, contains a single large chloroplast, two flagella, and a stigma (eyespot) and is used in molecular biology research.
    • Chlorella is a nonmotile, large, unicellular alga.
    • Acetabularia is a very large unicellular green alga.
    • Volvox is a colonial, unicellular alga.
    • Ulva, also called sea lettuce, is a large, multicellular green alga with edible, green blades.
    • The variety of life forms within the Chlorophyta, ranging from unicellular to multicellular, makes them useful for studying multicellularity evolution.
    • Red algae are mainly multicellular, but some are unicellular.
    • They have rigid cell walls containing agar or carrageenan, used as food solidifying agents and in microbial growth media.

    Lichens

    • Lichens result from a symbiotic relationship between a fungus and an algae or a cyanobacterium.
    • They can be found on diverse surfaces, including rocks and as epiphytes (growing on other plants).
    • This symbiotic relationship is considered a controlled parasitism where the fungus benefits, and the algae or cyanobacterium is harmed.
    • Lichens grow slowly and can survive for centuries.
    • They are used for food and to extract chemicals for dyes or antimicrobial substances.
    • Lichens are sensitive to pollution and serve as environmental indicators.
    • Lichen bodies are called thalli and have an outer fungal cortex and an inner fungal medulla.
    • Rhizines, hyphal bundles, attach lichens to the substrate.
    • Lichens are classified as fungi and the fungal partners belong to the Ascomycota and Basidiomycota.
    • Three major lichen types exist: crustose, foliose, and fruticose.
    • Crustose lichens are tightly attached to the substrate and appear crusty.
    • Foliose lichens have leaf-like lobes attached at one point.
    • Fruticose lichens have rounded, branched structures.

    Viruses

    • Viruses are obligate intracellular parasites meaning they need a host cell to survive and reproduce.
    • Viral genomes are composed of either RNA or DNA, never both.
    • Viruses can infect every type of cell, including plants, animals, fungi, bacteria, and archaea.
    • Viruses are much smaller than prokaryotic and eukaryotic cells, ranging in size from 20 nm to 900 nm.
    • The viral genome enters a host cell and directs the production of viral components, proteins and nucleic acids, needed to form new virus particles called virions.
    • Viruses are composed of a nucleic acid surrounded by a protein coat called a capsid.
    • Viral capsids are composed of protein subunits called capsomeres.
    • Viruses can be transmitted through direct contact, indirect contact with fomites, or through a vector.

    Bacteriophages

    • Bacteriophages can be used as a potential treatment for bacterial infections, particularly antibiotic-resistant strains.
    • They target specific bacteria, unlike antibiotics which can kill beneficial bacteria.
    • Bacteriophages are used to prevent food spoilage by killing bacteria in food, such as Listeria monocytogenes that causes listeriosis.

    Viral Taxonomy

    • Viruses are not included in the tree of life because they are acellular (not consisting of cells).
    • They are classified based on their genome type (RNA or DNA), capsid shape (helical, icosahedral, complex), and the presence or absence of an envelope.

    Viral Life Cycles

    • The viral life cycle begins when the virus attaches to a host cell.
    • The virus then enters the host cell.
    • The viral genome replicates itself using the host cell's machinery.
    • The newly produced viral components assemble into new virions.
    • The new virions are released from the host cell, which may be lysed or remain intact.

    Host Range

    • Viruses typically have a narrow host range, meaning they can only infect a specific type of host.
    • For example, the tobacco mosaic virus only infects tobacco plants.
    • Some viruses have a broader host range and can infect more types of organisms.
    • For example, the influenza virus can infect both humans and animals.
    • Some viruses are zoonotic, meaning they can be transmitted from animals to humans.
    • For example, the avian influenza virus originates in birds, but can cause disease in humans.

    Viral Structures

    • Naked viruses are composed of only a nucleic acid and capsid.
    • Enveloped viruses have a nucleic acid-packed capsid surrounded by a phospholipid membrane studded with viral glycoproteins.
    • Viral proteins play a crucial role in the attachment, entry, replication, assembly, and release of viruses.
    • The glycoprotein spikes on enveloped viruses bind to receptors on the host cell surface to facilitate attachment.
    • The viral genome contains genes for making structural proteins, proteins involved in replication, and proteins that help the virus to spread from one host to another.

    Acellular Pathogens - Viruses

    • Viruses are acellular pathogens that require a host cell for reproduction and metabolic processes.
    • Viruses have a capsid made of protein, which protects the genetic material (DNA or RNA).
    • Some viruses have an outer envelope surrounding the capsid, made of a lipid layer derived from the host cell membrane.
    •  Viruses can be classified based on their shapes, which vary depending on the capsid structure: helical, polyhedral, or complex.
    • Helical capsid is cylindrical or rod-shaped, with the genome fitting inside the capsid (e.g., tobacco mosaic virus, Ebola virus).
    • Polyhedral capsids are many-sided, often in an icosahedron shape, resembling a soccer ball (e.g., poliovirus, rhinovirus).
    • Complex viruses combine features of both helical and polyhedral shapes (e.g., bacteriophages, poxviruses).
    • Bacteriophages have a polyhedral head containing the genome, connected to a sheath that helps with attachment to the host cell.
    • Poxviruses are often brick-shaped with complex surface features.
    • Viruses use spikes, protein structures extending outward from the capsid or envelope, for attachment and entry into host cells.
    • Spikes contain structures for binding to host cells and enzymes that help the virus detach from the cell surface during release (e.g., influenza virus hemagglutinin [H] and neuraminidase [N] spikes).

    Classification and Taxonomy of Viruses

    • Viruses are classified into orders, families, and genera based on genetics, chemistry, morphology, and replication mechanisms.
    • The International Committee on Taxonomy of Viruses (ICTV) develops and maintains the universal virus taxonomy.
    • Viral family names end in -viridae, genus names end in -virus, and species names use a genus and species epithet (e.g., Pandoravirus dulcis).
    • The Baltimore classification system categorizes viruses based on their genomes (DNA or RNA, single or double-stranded, and mode of replication).
    • Viruses are often informally grouped based on their structure (naked or enveloped), genome type (DNA or RNA, single or double-stranded, segmented or nonsegmented), and strand (positive or negative).

    Common Pathogenic Viruses

    • dsDNA, enveloped: Poxviridae (e.g., Orthopoxvirus, Parapoxvirus), Herpesviridae (e.g., Simplexvirus)
    • dsDNA, naked: Adenoviridae (e.g., Atadenovirus), Papillomaviridae (e.g., Papillomavirus), Reoviridae (e.g., Reovirus)
    • ssDNA, naked: Parvoviridae (e.g., Adeno-associated dependoparvovirus A, Adeno-associated dependoparvovirus B)
    • dsRNA, naked: Reoviridae (e.g., Rotavirus)
    • +ssRNA, naked: Picornaviridae (e.g., Enterovirus C, Rhinovirus, Hepatovirus)
    • +ssRNA, enveloped: Togaviridae (e.g., Alphavirus, Rubivirus), Retroviridae (e.g., Lentivirus)
    • −ssRNA, enveloped: Filoviridae (e.g., Zaire Ebolavirus), Orthomyxoviridae (e.g., Influenzavirus A, B, C), Rhabdoviridae (e.g., Lyssavirus)

    Classification of Viral Diseases

    • The ICTV collaborates with the World Health Organization (WHO) to classify viral diseases based on the International Classification of Diseases (ICD).
    • The ICD assigns alphanumeric codes to different viral infections and other health conditions.
    • ICD codes are used in healthcare settings for diagnosis, treatment, insurance reimbursement, and epidemiological studies.
    • ICD codes are also used for vital records (e.g., death certificates).

    The Viral Life Cycle

    • Viruses require host cells for replication because they lack the necessary enzymes for their own reproduction.
    •  Bacteriophages (viruses that infect bacteria) replicate in the cytoplasm of prokaryotes.
    •  Most DNA viruses that infect eukaryotic cells replicate in the nucleus, except for large DNA viruses (e.g., poxviruses) that replicate in the cytoplasm.
    • RNA viruses that infect animal cells typically replicate in the cytoplasm, with exceptions like the influenza virus.

    The Life Cycle of Viruses with Prokaryote Hosts

    • Bacteriophages exhibit two types of life cycles: lytic and lysogenic.
    • Lytic cycle: The phage takes over the host cell, replicates new viral particles, and ultimately destroys the cell.
    • Lysogenic cycle: The phage integrates its genetic material into the host chromosome and replicates with the bacterial genome, remaining dormant until specific conditions trigger the production of new viruses.

    Lytic Cycle

    • Attachment: The phage attaches to specific receptors on the bacterial cell surface.
    • Entry/Penetration: The viral genome is injected into the bacterial cell through the contracted tail sheath.
    • Biosynthesis: The viral genome directs the production of viral components (capsomeres, tail fibers, enzymes) using the host cell's machinery.
    • Maturation: New viral particles are assembled.
    • Release: The bacterial cell is lysed, releasing new progeny viruses.

    Lysogenic Cycle

    • The phage initially integrates its genetic material into the host chromosome (forming a prophage).
    • The prophage replicates along with the host's DNA.
    • The lysogenic cycle can remain dormant for an extended period.
    • Specific environmental cues or stresses can trigger the transition from lysogenic to lytic cycle.

    Extrachromosomal DNA

    • Cells have DNA outside of chromosomes called extrachromosomal DNA.
    • Eukaryotic cells contain extrachromosomal DNA in mitochondria and chloroplasts.
    • Circular chromosomes in organelles are evidence of their prokaryotic origins.
    • DNA viruses can be maintained in host cells during latent infection as extrachromosomal DNA.
    • Human papillomavirus (HPV) can be maintained in infected cells as extrachromosomal DNA.

    Plasmids

    • Prokaryotes can have smaller loops of DNA called plasmids.
    • Plasmids can contain genes not essential for normal growth.
    • Bacteria can exchange plasmids by horizontal gene transfer (HGT).
    • HGT can give microbes new genes for growth and survival.
    • Plasmid-encoded genes can cause disease or antibiotic resistance.
    • Plasmids are used in genetic engineering and biotechnology to move genes between cells.

    Lethal Plasmids

    • Anthrax is caused by the gram-positive bacterium Bacillus anthracis.
    • B. anthracis has two plasmids not found in the similar but less pathogenic bacterium Bacillus cereus which contribute to its virulence.
    • The pX01 plasmid encodes a three-part toxin that suppresses the host immune system.
    • The pX02 plasmid encodes a capsular polysaccharide that protects the bacterium from the host immune system.

    Genome Size Matters

    • Genome sizes vary significantly among organisms.
    • Humans have 46 chromosomes with 3 billion base pairs.
    • Plants can have large genomes with up to 150 billion base pairs.
    • Bacterial genomes are often smaller than eukaryotic genomes.
    • Some bacterial genomes are as small as 112,000 base pairs.
    • Genome size in bacteria relates to their dependence on a host for survival.
    • Obligate and facultative intracellular pathogens often have small genomes due to their dependence on host cells for nutrients.
    • Bacteria with varied metabolic capabilities have larger genomes, such as Pseudomonas aeruginosa.
    • Viral genomes can vary in size from 3,500 to 2.5 million base pairs, exceeding the size of some bacterial genomes.

    Functions of Genetic Material

    • DNA is the genetic material passed down from parents to offspring.
    • DNA is replicated with a high degree of accuracy.
    • DNA is organized into genes, which are located on chromosomes and plasmids.
    • DNA directs and regulates the construction of proteins needed for growth and reproduction.
    • DNA is transcribed into RNA, which is then translated into proteins in a process called gene expression.
    • The central dogma of molecular biology describes the flow of genetic information from DNA to RNA to protein.
    • Gene expression includes three stages: initiation, elongation, and termination.

    Genotype and Phenotype

    • Genotype: the genetic makeup of an organism.
    • Phenotype: the observable characteristics of an organism.
    • Environmental factors can influence phenotype.

    Antibiotic Targets

    • Bacterial DNA gyrase and topoisomerase IV can be targeted by a class of antimicrobial drugs called quinolones
    • They are distinct from their eukaryotic counterparts

    DNA Replication

    • Bacterial DNA replication is a complex process involving multiple enzymes
    • DNA polymerase I removes RNA primers and replaces them with DNA
    • DNA polymerase III is the main enzyme that adds nucleotides
    • Helicase opens the DNA helix by breaking hydrogen bonds
    • Ligase seals gaps between Okazaki fragments on the lagging strand
    • Primase synthesizes RNA primers to start replication
    • Single-stranded binding proteins prevent hydrogen bonding between DNA strands
    • The sliding clamp helps hold DNA polymerase III in place
    • Topoisomerase II (DNA gyrase) relaxes supercoiled chromosomes to make DNA accessible for replication
    • Topoisomerase IV introduces single-stranded breaks into concatenated chromosomes

    Eukaryotic DNA Replication

    • Eukaryotic genomes are larger and more complex than prokaryotic genomes
    • Eukaryotic chromosomes are linear and have multiple origins of replication
    • In humans, there are 30,000 to 50,000 origins of replication
    • Replication occurs at a rate of approximately 100 nucleotides per second
    • Eukaryotic DNA replication involves similar steps as prokaryotic replication
    • The leading strand is continuously synthesized by DNA polymerase δ
    • The lagging strand is synthesized by DNA polymerase ε
    • Ribonuclease H removes the RNA primer in eukaryotes
    • Telomeres protect coding sequences at the ends of chromosomes and consist of noncoding repetitive sequences
    • Telomerase is an enzyme that maintains chromosome ends
    • Telomerase is active in germ cells and adult stem cells but not in adult somatic cells

    Eukaryotic vs Prokaryotic Replication

    • Prokaryotes have a single circular chromosome while eukaryotes have multiple linear chromosomes
    • Prokaryotes have a single origin of replication, while eukaryotes have multiple origins of replication
    • Prokaryotic replication is faster than eukaryotic replication
    • Prokaryotes do not have telomerase, while eukaryotes do
    • Prokaryotes use DNA polymerase I to remove RNA primers, while eukaryotes use RNase H
    • Prokaryotes use DNA polymerase III for strand elongation, while eukaryotes use DNA polymerase δ and ε

    Rolling Circle Replication

    • A method of DNA replication used by some plasmids, bacteriophages, and viruses
    • Begins with the enzymatic nicking of one strand of the circular DNA molecule
    • DNA polymerase III replicates the DNA unidirectionally
    • The nicked strand is displaced and recircularized
    • RNA primase synthesizes a primer at the single-stranded origin to create a double-stranded DNA molecule

    RNA Transcription

    • Transcription is the process of synthesizing RNA using DNA as a template
    • The resulting RNA transcript is a mobile copy of the DNA sequence
    • Transcription requires the DNA double helix to partially unwind
    • The unwound region is called a transcription bubble
    • RNA is synthesized using ribonucleotides containing adenine, cytosine, guanine, and uracil
    • The RNA product is complementary to the template strand of DNA
    • In RNA, T nucleotides are replaced with U nucleotides

    Bacterial Transcription

    • Bacteria use a single RNA polymerase to transcribe all genes
    • RNA polymerase adds nucleotides one by one to the 3’ end of the growing chain
    • RNA polymerase does not require a primer
    • The sigma (σ) factor enables RNA polymerase to bind to a specific promoter

    Initiation of Transcription

    • The promoter is a DNA sequence that binds the transcription machinery
    • The initiation site is the nucleotide pair where the first RNA nucleotide is transcribed
    • Promoters are located upstream of the genes they regulate
    • Conserved promoter sequences include the –10 and –35 positions

    Elongation of Transcription

    • The sigma subunit dissociates from the polymerase and the core enzyme synthesizes RNA
    • The core enzyme synthesizes RNA at a rate of approximately 40 nucleotides per second
    • The DNA is continuously unwound and rewound during elongation

    Termination of Transcription

    • The polymerase dissociates from the DNA template and releases the RNA transcript
    • Repeated nucleotide sequences act as termination signals

    Eukaryotic Transcription

    • Eukaryotes use three RNA polymerases: I, II, and III
    • Eukaryotic mRNAs are monocistronic, meaning they encode a single polypeptide
    • Eukaryotic primary transcripts must undergo processing before translation
    • Eukaryotic mRNAs are protected by RNA-stabilizing proteins
    • A 5’ cap is added to the 5’ end of the primary transcript
    • A poly-A tail is added to the 3’ end of the primary transcript
    • Eukaryotic genes are composed of exons and introns
    • Introns are removed during RNA splicing
    • Introns are excised by a spliceosome containing snRNPs

    Eukaryotic vs Prokaryotic Transcription

    • Prokaryotes can have monocistronic or polycistronic mRNAs, while eukaryotes only have monocistronic mRNAs
    • Prokaryotes use a single RNA polymerase, while eukaryotes use three
    • Prokaryotes do not add a 5’ cap or poly-A tail, while eukaryotes do
    • Prokaryotes do not splice pre-mRNA, while eukaryotes do.
    • Alternative splicing in eukaryotes allows for multiple mRNA transcripts from the same DNA sequence.

    Protein Synthesis

    • Protein synthesis is a cellular process that consumes the most energy.
    • Proteins are essential for virtually all functions of a cell.
    • Protein synthesis is known as translation, the second part of gene expression.

    The Genetic Code

    • Translation is the process of decoding nucleotide-based genetic information into the protein "language" of amino acids.
    • Twenty commonly occurring amino acids make up a protein chain.
    • Each amino acid is defined by a triplet of nucleotides called a codon, found in the mRNA.
    • The relationship between an mRNA codon and its corresponding amino acid is called the genetic code.
    • The three-nucleotide code creates 64 possible combinations, greater than the number of amino acids.
    • One amino acid can be encoded by more than one codon, known as degeneracy.
    • The first two nucleotides of a codon generally determine the amino acid incorporated.
    • The third position, the wobble position, is less critical.
    • Sixty-one of the 64 triplets encode for amino acids.
    • Three codons do not encode an amino acid and terminate protein synthesis: stop codons or nonsense codons.
    • The AUG codon can specify methionine and serve as the start codon to initiate translation.
    • The reading frame for translation is set by the AUG start codon.
    • The genetic code is nearly universal in all species.
    • Selenocysteine and pyrrolysine are unusual amino acids found in archea and bacteria.

    The Protein Synthesis Machinery

    • Translation requires an mRNA template, ribosomes, tRNAs, and enzymatic factors.
    • Ribosomes are complex macromolecules composed of catalytic rRNAs (ribozymes) and structural rRNAs and polypeptides.
    • Prokaryotes have 70S ribosomes, while eukaryotes have 80S ribosomes in the cytoplasm and rough endoplasmic reticulum.
    • The small ribosomal subunit binds to the mRNA template, while the large subunit binds to tRNAs.
    • Ribosomes dissociate into large and small subunits when not synthesizing proteins and reassociate during initiation.
    • Each mRNA can be simultaneously translated by multiple ribosomes, forming a polyribosome or polysome.
    • Transcription and translation happen concurrently in prokaryotes, forming polyribosomes.
    • This occurs because both processes are in the same direction, occur in the cytoplasm, and the RNA transcript is not processed immediately in prokaryotes.
    • Eukaryotes do not have concurrent transcription and translation.

    Transfer RNAs

    • tRNAs are structural RNA molecules that serve as adaptors.
    • They bind to a specific codon on the mRNA template and add the corresponding amino acid to the polypeptide chain.
    • tRNAs "translate" the language of RNA into the language of proteins.
    • tRNAs have specific three-dimensional structures due to base pairing.
    • The CCA amino acid binding end is located at the 3’ end of the tRNA.
    • The anticodon is a three-nucleotide sequence that bonds with an mRNA codon through complementary base pairing.
    • Aminoacyl tRNA synthetases link each tRNA molecule to its correct amino acid.

    The Mechanism of Protein Synthesis

    • Initiation begins with the formation of an initiation complex that varies in prokaryotes and eukaryotes.
    • In E. coli, the initiation complex includes the 30S ribosome, mRNA template, initiation factors, GTP, and initiator tRNA carrying N-formyl-methionine (fMet-tRNAfMet).
    • The initiator tRNA interacts with the AUG start codon and carries formylated methionine (fMet), which is inserted at the N terminus of every E.coli polypeptide chain.
    • The Shine-Dalgarno sequence in the mRNA interacts with the rRNA in the ribosome, anchoring the 30S subunit to the mRNA.
    • The 50S subunit then binds to the initiation complex, forming an intact ribosome.
    • In eukaryotes, the initiation complex has different features:
      • The initiator tRNA is Met-tRNAi.
      • The initiation complex recognizes the 5’ cap of the mRNA and tracks along it until reaching the AUG start codon.
    • Elongation proceeds with single-codon movements of the ribosome, called translocation events.
    • Three ribosomal sites are involved: A (aminoacyl) site, P (peptidyl) site, and E (exit) site.
    • During initiation complex formation, bacterial fMet−tRNAfMet or eukaryotic Met-tRNAi directly enters the P site.
    • Each translocation event involves:
      • Charged tRNAs enter the A site.
      • The tRNA shifts to the P site.
      • Finally, the tRNA moves to the E site and is released.
    • Ribosomal movements are powered by conformational changes that move the ribosome by three bases in the 3’ direction.
    • Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA.
    • Peptidyl transferase, an RNA-based ribozyme in the 50S subunit, catalyzes peptide bond formation.
    • The amino acid bound to the P-site tRNA is linked to the growing polypeptide chain.
    • As the ribosome moves across the mRNA, the former P-site tRNA enters the E site, detaches from the amino acid, and is expelled.
    • Elongation steps require energy from GTP hydrolysis, catalyzed by specific elongation factors.
    • Termination occurs when the ribosome encounters a stop codon.
    • Release factors then bind to the A site, causing the polypeptide to detach from the tRNA in the P site.
    • The ribosome separates from the mRNA, and subunits dissociate.

    Characteristics of Infectious Disease

    • A disease is any condition that damages or impairs the body's normal structure or functions.
    • A disease can be caused by factors including infection by a pathogen, genetics, noninfectious environmental causes, or inappropriate immune responses.
    • An infection is the successful colonization of a host by a microorganism.
    • Infections can lead to disease.
    • Microorganisms that can cause disease are known as pathogens.
    • Signs of disease are objective and measurable, and can be observed directly by a clinician.
    • Vital signs are used to measure the body's basic functions and include body temperature, heart rate, breathing rate, and blood pressure.
    • Changes in vital signs may be indicative of disease.
    • Other observable conditions seen by a clinician can also be considered signs of disease.

    Signs and Symptoms

    • Signs are objective and measurable
    • Examples are antibodies found in blood serum
    • Symptoms are subjective and felt by patients
    • Examples include nausea, loss of appetite, and pain

    Syndrome

    • A specific group of signs and symptoms that characterize a disease
    • Many are named based on signs, symptoms, or disease location
    • Examples include "cytopenia", "hepatitis", "colitis", "hemolysis", "keratoderma"

    Disease Classification

    • Infectious Disease: Caused by pathogens (cellular or acellular)
    • Communicable Disease: Spreadable from person to person
    • Contagious Disease: Easily spread from person to person
    • Iatrogenic Disease: Acquired due to medical procedures (e.g., wound treatments, surgery)
    • Nosocomial Disease: Acquired in hospital settings
    • Zoonotic Disease: Transmitted from animals to humans
    • Noncommunicable Infectious Disease: Not spread from person to person
    • Noninfectious Disease: Not caused by pathogens, can be caused by genetics, environment, immune system dysfunction

    Periods of Disease

    • Incubation Period: Pathogen multiplies but does not cause symptoms
    • Prodromal Period: General symptoms of illness occur
    • Period of Illness: Most severe signs and symptoms manifest
    • Period of Decline: Pathogen numbers decrease, symptoms subside
    • Period of Convalescence: Return to normal function

    Acute and Chronic Diseases

    • Acute Disease: Rapid onset, short duration
    • Chronic Disease: Gradual onset, long duration, often persistent or recurring
    • Latent Disease: Pathogen lies dormant, may reactivate later

    Koch's Postulates

    • Significance: Link a specific pathogen to a specific disease
    • Limitations: Not all pathogens can be grown in culture, some diseases are polymicrobial, ethical considerations

    Stages of Pathogenesis

    • Attachment/Adhesion: Pathogen attaches to host cells
    • Invasion: Pathogen enters host tissues
    • Multiplication: Pathogen replicates within the host
    • Spread: Pathogen disseminates throughout host
    • Evasion of Host Defenses: Pathogen evades the immune system
    • Damage: Pathogen causes tissue damage, disease symptoms

    Portals of Entry and Exit

    • Portals of Entry: Ways pathogens enter the body (e.g., respiratory tract, gastrointestinal tract, skin)
    • Portals of Exit: Ways pathogens leave the body (e.g., respiratory secretions, feces, blood)

    Koch’s Postulates

    • Robert Koch established a systematic approach to identify pathogens responsible for specific diseases.
    • Koch’s postulates are used to determine if a particular microorganism causes a specific disease
    • These postulates are tested on laboratory animals.
    • The suspected pathogen must be found in diseased animals.
    • The suspected pathogen must be isolated and grown in a pure culture.
    • Healthy animals infected with the suspected pathogen must develop the same symptoms as the diseased animals in the first step.
    • The pathogen must be re-isolated from the infected animals, and must be identical to the pathogen from the second step.

    Limitations to Koch’s Postulates

    • Pathogens are not exclusively found in diseased individuals.
    • For example, H. pylori is found in both healthy and gastritis sufferers.
    • All individuals do not have the same susceptibility to disease.
    • Microbiota compositions can influence a person’s susceptibility to infection.
    • Some pathogens cannot be grown in pure culture.
    • Some diseases do not have suitable animal models.

    Molecular Koch’s Postulates

    • Identifying a gene that causes pathogenicity helps to identify pathogenic microorganisms.
    • Molecular Koch’s postulates are used to identify pathogenic strains of microorganisms typically considered harmless.
    • For example, pathogenic forms of E. coli result from genetic changes that allow them to produce toxins and cause illness.

    Pathogenicity and Virulence

    • The ability of a microbial agent to cause disease is called pathogenicity.
    • The degree to which an organism is pathogenic is called virulence.
    • Virulence is a continuum with avirulent (non-harmful) organisms on one end and highly virulent organisms on the other.
    • Virulence can be quantified using controlled experiments with laboratory animals.
    • The median infectious dose (ID50) represents the number of pathogen cells or virions required to cause infection in 50% of inoculated animals.
    • The median lethal dose (LD50) represents the number of pathogenic cells or virions, or amount of toxin required to kill 50% of infected animals.

    Factors Affecting Infective Dose

    • The actual infective dose for an individual can vary.
    • Factors influencing the infective dose include:
      • Route of entry
      • Age and health of the host
      • Immune status of the host
      • Environmental and pathogen-specific factors, such as susceptibility to the pH of the stomach.
    • A pathogen’s infective dose does not necessarily correlate with disease severity.
    • For example, Salmonella enterica serotype Typhimurium can cause gastroenteritis with low mortality, while S. enterica serotype Typhi has a much higher ID50 but causes more severe typhoid fever with a higher mortality rate.

    Detecting Antigen-Antibody Complexes

    • Ouchterlony assay: This assay is used to determine the presence of antibodies to antigens.
      • The antigen and antibody are placed in different wells in a gel.
      • The antibodies and antigens diffuse through the gel.
      • A precipitin arc forms at the zone of equivalence.
      • Presence of the precipitin arc suggests antibodies against the antigen.
    • Radial Immunodiffusion (RID) assay: This assay helps in quantifying the antigen concentration by measuring the zones of precipitation.
      • Antiserum is mixed with tempered agar and placed in petri dishes.
      • Wells are made in agar and antigen is delivered into the wells.
      • As the antigen and antibody interact, they form zones of precipitation.
      • The square of the diameter of the zone of precipitation is directly proportional to the concentration of antigen.
      • This assay is helpful in determining the concentration of serum proteins such as C3 and C4 complement proteins.
    • Flocculation assay: This assay involves antigens that are insoluble, specifically lipids.
      • The interaction of insoluble antigens and antibodies leads to flocculation, meaning the formation of a visible lattice of antigens and antibodies.
      • It is used to diagnose syphilis.
      • VDRL test: This test is a modification to Wasserman's original test.
        • It uses cardiolipin, lecithin, and cholesterol.
        • A flocculant is formed when anti-treponemal antibodies bind to cardiolipin.
        • It is more specific but can have false-positives in patients with autoimmune diseases.
    • Neutralization assay: This assay detects and quantifies antibodies by observing their effect on viral infection.
      • This assay helps in determining whether a patient is infected or was infected in the past with a specific virus.
      • Antibodies bind to viruses and neutralize their ability to infect cells by blocking virus-cell binding.
      • This assay uses plaques, indicating cell damage, to measure the effect of antibodies on viral infections.
      • A decrease in plaques indicates an increase in neutralizing antibody titer in the patient's serum.
    • Immunoelectrophoresis (IEP): This assay identifies specific serum proteins by using precipitin arcs.
      • First, perform protein gel electrophoresis.
      • Then, antisera against serum proteins are added to troughs that run parallel to the electrophoresis track.
      • Precipitin arcs are formed similar to the Ouchterlony assay.
      • It helps in identifying abnormal immunoglobulin proteins in the sample.
      • It is particularly useful in diagnosing multiple myeloma.
        • Multiple myeloma is a cancer of antibody-secreting cells.
        • Multiple myeloma patients have elevated serum protein levels.
        • The antibody-secreting cells in multiple myeloma patients produce monoclonal proteins.
        • That is why patients with multiple myeloma will present with elevated serum protein levels that show a distinct band in the gamma globulin region.
    • Western blot: It identifies proteins of interest in a sample by using antibodies.
      • First, perform protein gel electrophoresis.
      • Then, transfer the proteins to a nitrocellulose membrane.
      • The membrane is exposed to a specific primary antibody that binds to the protein of interest.
      • Then, expose the membrane to a secondary antibody that binds to the primary antibody.
      • The secondary antibody is coupled with an enzyme.
      • This enzyme aids in the visualization of the target protein band.
      • This assay is highly sensitive and uses polyclonal antibodies which can bind to different epitopes of the antigen.
    • Complement fixation test: This test helps in detecting the presence of antibodies against a specific antigen.
      • This test can be used to identify antibodies against pathogens difficult to culture in the lab.
      • The antigen from the pathogen is added to the patient’s serum.
      • If antibodies are present in the serum, they will bind to the antigen.
      • This binding activates the complement cascade.
      • Red blood cells are added to the mix.
      • If the solution stays clear, it is a positive test, meaning antibodies against the pathogen are present.
      • If the solution turns pink, it is a negative test, indicating no antibodies against the pathogen.
      • The change in color is due to the release of hemoglobin from lysed red blood cells.
      • The lysis of red blood cells happens only if there is no previous complement activation by antigen-antibody complexes.

    Precipitation Assays

    • Precipitation assays involve antibodies binding to soluble antigens, forming visible precipitates.
    • Examples of precipitation assays include:
      • Precipitin ring test
      • Immunoelectrophoresis
      • Ouchterlony assay
      • Radial immunodiffusion assay

    Flocculation Assays

    • Flocculation assays involve antibodies binding to insoluble molecules in suspension, forming visible aggregates.
    • Example of flocculation tests is the VDRL test for syphilis.

    Neutralization Assays

    • Neutralization assays involve antibodies binding to viruses, blocking viral entry into target cells and preventing plaque formation.
    • Example of neutralization assays is the plaque reduction assay for detecting neutralizing antibodies in patient sera.

    Complement Activation Assays

    • Complement activation assays use antibodies binding to antigens, inducing complement activation and leaving no complement to lyse red blood cells.
    • An example is the complement fixation test for patient antibodies against hard-to-culture bacteria such as Chlamydia.

    Agglutination Assays

    • Agglutination involves antibodies clumping together cells or particles (e.g., antigen-coated latex beads).
    • Agglutination assays are quick and easy to perform on a glass slide or a microtiter plate.
    • Agglutination assays can identify antibodies against bacteria or red blood cells.

    Agglutination of Bacteria and Viruses

    • Direct agglutination assays use bacterial cells themselves to agglutinate.
    • Indirect agglutination assays (or latex fixation assays) use antibodies attached to inert latex beads to visualize agglutination.
    • Indirect assays can detect the presence of both antibodies and specific antigens.

    Hemagglutination

    • Agglutination of red blood cells is called hemagglutination.
    • The direct Coombs’ test (or direct antihuman globulin test) detects nonagglutinating antibodies and complement attached to red blood cells.
    • The Coombs’ test is used for newborn jaundice, hemolytic transfusion reactions, autoimmune hemolytic anemia, infectious mononucleosis, syphilis, and Mycoplasma pneumonia.
    • The indirect Coombs’ test (or indirect antiglobulin test) detects unbound antibodies against red blood cell antigens in a patient's serum.

    Hemagglutination Assays: Detecting Viruses

    • Some viruses cause hemagglutination by binding to red blood cells and cross-linking them.
    • Hemagglutination assays (HA) are used to detect the presence of viruses like influenza, mumps, and rubella.
    • A serial dilution viral agglutination assay is used to measure the titer of virus in cell culture or for vaccine production.
    • Viral hemagglutination inhibition assays (HIA) are used to determine the titer of antiviral antibodies.

    Blood Typing

    • Blood typing is crucial during transfusions to ensure compatibility between donor and recipient.
    • The ABO and Rh blood groups are the most critical for transfusions.
    • Commercial antibodies against A, B, and Rh antigens are used to confirm blood types.
    • Agglutination (clumping) of red blood cells with specific antibodies indicates the presence of corresponding antigens.
    • Antibodies against other blood group antigens, while less common, can develop due to multiple pregnancies or transfusions.

    Cross-Matching

    • Cross-matching involves mixing donor red blood cells with recipient serum to detect antibodies against donor blood.
    • Agglutination during cross-matching indicates incompatibility and prevents transfusion.
    • Coombs' reagent facilitates visualization of antibody-red blood cell interactions in cases of weak agglutination.

    Antibody Screen Test

    • The antibody screen test checks for antibodies against other red blood cell antigens beyond ABO and Rh.
    • It involves mixing patient serum with pooled type O red blood cells that express various antigens.
    • Agglutination indicates the presence of antibodies against specific antigens, requiring further investigation for donor compatibility.

    Immunoassays: EIA, ELISA, and Immunostaining

    • EIAs involve enzyme-linked antibodies to detect the presence of antigens.
    • EIAs utilize chromogens or fluorogens to create a detectable signal.
    • Immunohistochemistry (IHC) uses EIA to stain whole tissue sections, visualizing cell types and structures.
    • Immunocytochemistry (ICC) uses EIA to stain individual cells, visualizing intracellular components.

    Enzyme-Linked Immunosorbent Assays (ELISAs)

    • ELISAs are widely used EIAs for detecting and quantifying antigens or antibodies.
    • Direct ELISAs involve immobilizing antigens to a plate, binding with enzyme-conjugated antibodies, and detecting the enzyme's activity.
    • Sandwich ELISAs utilize capture antibodies to bind target antigens, followed by enzyme-conjugated detection antibodies.
    • Indirect ELISAs are used to detect and quantify antigen-specific antibodies in patient serum.
    • They involve immobilizing known antigens, binding with primary antibodies from patient serum, and detecting primary antibodies using enzyme-conjugated secondary antibodies.

    Immunofiltration and Immunochromatographic Assays

    • Immunofiltration techniques are used to detect or quantify antigens or antibodies present in low concentrations.
    • They involve passing fluids through a porous membrane with attached antigens or antibodies to capture the target molecules.
    • Immunochromatographic assays, often known as lateral flow tests, are rapid and convenient for point-of-care or home use.

    Lateral Flow Tests

    • Lateral flow tests use capillary action to move a sample through a strip containing reagents
    • Reagents are present in a dried state and are rehydrated by the sample
    • Antibody-coated beads bind to antigens in the sample
    • Antibody-antigen complexes are captured by a stripe containing immobilized antibody
    • A positive test is indicated by a colored line at the test line
    • A negative test is indicated by a colored line at the control line only
    • Lateral flow tests are fast, inexpensive, and don't require special equipment
    • Lateral flow tests can be performed anywhere by anyone
    • Concerns exist about the use of self-administered tests due to potential for false-positive results

    Immunochromatographic Assays

    • Immunochromatographic assays are also known as lateral flow tests
    • These tests use the capture of flowing antigen-antibody complexes to detect disease
    • Examples include rapid strep tests, malaria dipsticks, and pregnancy tests

    Direct Fluorescent Antibody Techniques

    • Direct fluorescent antibody (DFA) tests use a fluorescently labeled monoclonal antibody (mAb) to bind and illuminate a target antigen
    • DFA tests are useful for rapid diagnosis of bacterial diseases
    • DFA techniques can be used to diagnose bacterial infections such as strep throat, pneumonia, and Legionnaires' disease

    Indirect Fluorescent Antibody Techniques

    • Indirect fluorescent antibody (IFA) tests use a secondary antibody to detect antibodies in patient serum
    • IFA tests are used for the diagnosis of syphilis and autoimmune diseases such as systemic lupus erythematosus (SLE)
    • The IFA test for syphilis is a complement to the VDRL test
    • The IFA test for ANA can be a valuable tool for diagnosing SLE

    Flow Cytometry

    • Flow cytometry uses fluorescently labeled antibodies to quantify cells of a specific type in a complex mixture
    • The technique uses a laser to activate the fluorogen and detect fluorescent light emitted by cells
    • Flow cytometry is used to monitor levels of CD4 T cells in HIV infections

    Fluorescence-Activated Cell Sorter

    • Fluorescence-activated cell sorters (FACS) use flow cytometry to separate unique types of cells
    • FACS works by directing fluorescently labeled cells into specific containers based on their fluorescence properties
    • FACS allows the isolation of specific cell populations for further research

    Flow Cytometry

    • Flow cytometry uses a laser to excite fluorescently labeled antibodies bound to cells
    • Cells are passed through a laser beam one by one
    • The fluorescence intensity of each cell is measured by a detector
    • The information is compiled into a histogram that shows the number of cells at each level of fluorescence

    Antibody Expression

    • The peak on the left of a flow cytometry histogram represents cells that do not express the target protein
    • The peak on the right of a flow cytometry histogram represents cells that express the target protein
    • The area under each peak is proportional to the number of cells in each population

    Fluorescence Activated Cell Sorting (FACS)

    • FACS is a type of flow cytometry that physically separates cells into populations based on their fluorescence intensity
    • Cells are passed through a laser beam, and their fluorescence intensity is measured
    • A charge is applied to droplets containing the cells
    • The charge is specific to the wavelength of the fluorescent light, allowing for differential sorting
    • The charged droplets are deflected into different collection vessels
    • FACS provides highly purified populations of cells for research purposes

    Uses of FACS

    • FACS can be used to separate different cell types from a mixed population
    • FACS can be used to isolate cells that express a specific protein

    Limitations of FACS

    • FACS can only be used to sort cells that are already isolated
    • FACS can only be used to sort cells into two populations based on their fluorescence intensity
    • FACS can only be used on isolated cells.
    • Therefore, researchers can only study tissues using FACS after isolating cells from the tissue

    Immunofluorescence

    • Immunofluorescence assays use fluorogen-antibody conjugates to illuminate antigens for detection

    Types of Immunofluorescence Assays

    • Direct immunofluorescence uses fluorogen-antibody conjugates to label antigens directly
    • Indirect immunofluorescence uses fluorogen-antibody conjugates to detect antigen-specific antibodies in patient sera
    • Flow cytometry is a type of immunofluorescence that is used to quantify specific subsets of cells in complex mixtures
    • FACS is an extension of flow cytometry that is used to physically separate cells into different populations based on their fluorescence intensity

    Applications of Immunofluorescence Assays

    • Direct immunofluorescence can be used to detect the presence of bacteria in clinical samples
    • Indirect immunofluorescence can be used to detect the presence of antigen-specific antibodies in patient sera
    • Flow cytometry can be used to quantify the number of CD4 or CD8 cells in a sample
    • FACS can be used to sort cancer cells
    • Indirect immunofluorescence assays to detect antinuclear antibodies (ANA) are important in the diagnosis of diseases, such as lupus and other autoimmune diseases

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