The aim of this course is to give the students insight and practical skills in Microbiology at an advanced level. The following areas will be covered:
1. Cell structure and function in Bacteria and Archaea
2. Mechanisms involved in bacterial biofilms. Review of adhesions involved in dental plaque biofilms as well as the structure and formation of these biofilms
3. Study of recent research on the molecular mechanisms of pathogenesis of a selected group of pathogenic microorganisms as well as the advanced molecular techniques in clinical microbiology
4. Mechanism of bacterial damage and bacterial toxins
5. Practical applications of immunology and vaccines
6. General principles of antimicrobial drug action and means by which bacteria become resistant to antimicrobial drugs
7. Wastewater treatment, water purification, and waterborne microbial diseases
8. Bioinformatics principles, sequence analysis and how to interpret data from microbiology experiments.
Textbook :
Brock Biology of Microorganisms, 12 ed., by Madigan, Martinko, Dunlap and Clark Pearson Publishers (ISBN-10: 0132324601; ISBN-13: 978-0132324601)
Cell structure and Function in Bacteria and Archae
Introduction :
In this chapter we will study the structures of the cell wall and the cell membrane of bacterial cells in both Bacteria and Archaea and describe the roles played by each of the major components. Also, we will discuss briefly the features of the cell well that are targets for current drugs and those which offer new targets for antimicrobial drugs. Other topics include endotoxins, endospores and microbial locomotion.
Objectives :
1. The membrane lipids of Bacteria and Archaea similar, and how do they differ?
2. The cell wall structure and function in Bacteria and Archaea
3. Endotoxin properties
4. Endospore structure, sporulation, dipicolinic acid and SASPs and their functions
5. Microbial Locomotion
Plan:
Step 1: There is a Portable Document Format (PDF) file, 37 pages, 16,210 KB, which you can review and print using the Acrobat portable document format reader. I recommend that you have Adobe Reader on your computer to access this file.
The title of the file is Cell structure and function in Bacteria and Archaea,
Step 2: Please check your assignment folder to find out assignment no. 1. Please take the time to answer it and send back.
Step 3: Attached please find a short video about flagellar motion.
In this topic we will study the structure of biofilm communities, the pattern of plaque biofilm formation. Also, we will discuss briefly the role of adherence in formation of biofilms and some features of control and removal of dental plaque biofilms.
Objectives
1. Understand the components that make up the structure of biofilm and its biochemistry
2. Understand the process resulting in biofilm formation and maturation, including the role of adhesion
3. Describe the mechanisms proposed to explain bacterial adhesion to the acquired pellicle.
4. Understand how to educate patients and what information is most needed to help prevent and fight the development of dental biofilm
Plan:
Step1. There is a Microsoft Power Point (PPT) file, 26 pages, 3.4 MB andPortable Document Format (pdf) file, 6 pages, 2.2 MB, which you can review and print. Also, I recommend that you have Adobe Reader and Microsoft PowerPoint installed on your computer to access to these files.
Step1. Please check your assignment folder to find out assignment no. 2. Please take the time to answer it and send it back.
Step 3. Attached please find a short video about Dental Plaque Biofilm.
In this topic we will study the virulence factors, laboratory diagnosis, clinical manifestations, mechanism of resistance to methicillin and vancomycin. Also, we will discuss briefly the staphylococcal cassette chromosome mec (SCCmec) and molecular techniques for MRSA typing.
ObjectiveS :
1. Understand the epidemiology and various virulence factors associated with MRS infections
2. Understand the mechanism of resistance to methicillin and vancomycin antibiotics
3. Describe the differences between health-care acquired and community acquired MRSA strains
4. Understand the staphylococcal cassette chromosome mec (SCCmec) gene and molecular techniques used to type MRSA
Plan:
Step1. There is a Microsoft Power Point (PPT) file, 26 pages, 3.4 MB and Portable Document Format (pdf) file, 6 pages, 2.2 MB, which you can review and print. Also, I recommend that you have Adobe Reader and Microsoft PowerPoint installed on your computer to access to these files.
Step 2. Attached please find a recent published article on the molecular epidemiology MRSA in Palestine. Please take the time to read so we can discuss the data in the class.
Step 3. Attached please find a short video about MRSA.
Molecular mechanisms of Escherichia coli pathogenicity
Topic Number Four
Molecular Mechanisms of Escherichia Coli Pathogenicity
Introduction :
Escherichia coli are normal inhabitants of the human gastrointestinal tract. When E. coli strains acquire certain genetic material, they can become pathogenic. E. coli are among the most frequent bacterial causes of diarrhea and are classified by clinical syndrome they produce.
In this topic we will study the toxin secretion systems in both Gram-Negative and Gram-Positive bacteria. The characteristics of diarrheal illness caused by enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC, also called Shiga toxin-producing E. coli or STEC), enteroinvasive E. coli (EIEC), and enteroaggregative E. coli (EAEC) is also discussed in greater detail separately.
Objectives :
Understand the various toxin secretion systems in both Gram-Negative and Gram-Positive bacteria.
Describe the characteristics of diarrheal illness caused by E. coli pathotypes
Understand how to identify samples containing pathogenic E. coli
Plan :
Step 1. There is study text folder containing a Microsoft Power Point (PPT) file, 38 pages, and Portable Document Format (pdf) file, 22 pages, 2.5 MB, which you can review and print. Also, I recommend that you have Adobe Reader and Microsoft PowerPoint installed on your computer to access to these files.
Step 2. Please check your assignment folder to find out assignment no. 1. Please take the time to answer it and send it back.
Step 3. Attached please find a short video about .
The First exam is on Tuesday, February 26 at 2:00 P.M. in the normal lecture room. It will cover the following topics:
Cell structure and function in Bacteria and Archaea
Dental Plaque: A Microbial Biofilm
Methicillin-resistant Staphylococcus aureus Introduction and literature review
Molecular analysis and susceptibility patterns of methicillin-resistant Staphylococcus aureus (MRSA) strains causing community- and healthcare-associated infections in the northern region of Palestine (article)
Molecular mechanisms of Escherichia coli pathogenicity-Part-1: Toxin secretion systems.
The exam consists of 3 parts:
Part I is objective questions [17 points],
Part II is short answer question type [19 points] and
Part III is long answer question type [24 points].
In part III, there will be 4 possible long answer questions, you should answer 3 of them for 24 points. If you answer more than 3 questions, I will simply grade the first 3 and ignore the rest
Molecular techniques in clinical microbiology
Topic Number Five
Molecular Techniques in Clinical Microbiology
Introduction :
Identifying and reporting out pathogenic organisms in a timely manner is one of the greatest challenges of a clinical microbiologist. Although the advent of automation and rapid methods has reduced turn-around times considerably, there are still fastidious organisms that may not grow well on conventional media making identification virtually impossible. This topic provides a comprehensive and up-to-date description of advanced methods that have evolved for the diagnosis of infectious diseases in the routine clinical microbiology laboratory
Objectives :
1. Describe some of the advantages of molecular methods over traditional microbiology.
2. Describe the principles of the basic methods of molecular techniques. These include: DNA sequencing, restriction fragment length polymorphism (RFLP), nucleic acid hybridization, amplification techniques and DNA microarrays
Plan :
Step1. There is study text folder containing a Microsoft Power Point (PPT) file, 26 pages, 2.2 MB which you can review and print. Also, I recommend that you have Adobe Reader and Microsoft PowerPoint installed on your computer to access to these files.
Step 2. Please check your assignment folder to find out assignment no. 3. Please take the time to answer it and send it back.
In this topic we will first briefly review basic topics critical to understanding diagnostic testing and then discuss how these concepts can be applied in the diagnosis of infectious diseases. How to evaluate diagnostic tests also will be discussed .
Objectives :
1. Brief review of reliability, validity, sensitivity and specificity, positive predictive value (PPV) and negative predictive value (NPV)
2. The land of agreement or disagreement (no gold standard for diagnosis): Kappa
Plan :
Step 1. There is study text folder containing 2 Portable Document Format (pdf) files, which you can review and print. Also, I recommend that you have Adobe Reader and Microsoft PowerPoint installed on your computer to access to these files.
Step 2. Please check your assignment folder to find out assignment no. 4. Please take the time to answer it and send it back.
Step 3. Attached please find a short video about .
The Second exam is on Tuesday, March 26 at 2:00 P.M. in the normal lecture room. It will cover the following topics:
1. Topic number four: Molecular mechanisms of Escherichia coli pathogenicity-Part-2: Pathogenic E. coli.
2. Topic number five: Molecular techniques in clinical microbiology
3. Topic number six: Evaluation of diagnostic tests
4. Topic number four: Article "Isolation, identification and molecular characterization of Brucella strains isolated from small ruminants in the West bank, Palestine".
The exam consists of 3 parts.
PartI is objective questions [15 points].
PartII is short answer question type [29 points]
and Part III is long answer question type [16 points].
In part III, there will be 2 long answer questions, you should answer both.
Mechanism of Bacterial Damage and Bacterial Toxins
Toipc seven
Mechanism of Bacterial Damage and Bacterial Toxins
Introduction:
In this topic we will take a look at some of the specific properties of microorganisms that contribute to pathogenicity, the ability to cause disease by overcoming the defenses of a host, and virulence, the degree or extent of pathogenicity
Objectives:
1. Describe the function of siderophores.
2. Contrast the nature and effects of exotoxins and endotoxins.
3. Outline the mechanisms of action of A-B toxins, membrane-disrupting toxins, and superantigens.
Plan
Step1. There is study text folder containing a Microsoft Power Point (PPT) file, 25 pages, which you can review and print. Also, I recommend that you have Adobe Reader and Microsoft PowerPoint installed on your computer to access to these files.
Step 2. Attached please find a short video about .
Practical Applications of Immunology and Vaccination
Toipc eight
Practical Applications of Immunology and Vaccination
Introduction
In this topic, we will discuss some useful tools that have been developed from knowledge of the basics of the immune system. We will expand our discussion on immunologic-based diagnostic tests. Also, we will discuss briefly the principles and effects of vaccination
Objectives:
1. Define vaccine and differentiate the following, and provide an example of each: attenuated, inactivated, toxoid, subunit, and conjugated vaccines.
2. Understanding the functions and applications of many common immunologic-based diagnostic tests.
Plan :
Step1. There is study text folder containing a Portable Document Format (pdf) file, 18 pages, which you can review and print. Also, I recommend that you have Adobe Reader and Microsoft PowerPoint installed on your computer to access to these files.
Step 2. Attached please find a short video about some common immunologic-based diagnostic tests.
This short animation demonstrates enzyme-linked immunosorbent assay (ELISA) to measure specific antibodies
Antibiotics mode of action and mechanisms of resistance
Toipc Number Nine
Antibiotics Mode of Action and Mechanisms of Resistance
Introduction :
Antibiotics have saved millions of lives since the 1940’s. However, overuse and misuse of antibiotics have led to the development of antibiotic resistances. If the spread of antibiotic resistance is not brought under control, common bacterial infections may once again be responsible for the deaths of untold numbers of people. In this topic we will study the mode of action and mechanisms of resistance to Beta lactam and aminoglycoside antibiotics
Objective :
1. Describe the mode of action and mechanisms of resistance.to Beta lactam antibiotics
2. Describe the mode of action and mechanisms of resistance.to aminoglycoside
Plan :
Step1. There is study text folder containing a Microsoft Power Point (PPT) file, 25 pages, and Portable Document Format (pdf) file, -- pages, which you can review and print. Also, I recommend that you have Adobe Reader and Microsoft PowerPoint installed on your computer to access to these files.
Step 2. Attached please find a short video about the mechanism of resistance to these antibiotics.
Clean water, free of biological and chemical contaminants, is essential for public health. Standard procedures to disinfect drinking water and remediate wastewater are in place in developed countries to achieve water quality. Water quality, however is sometimes compromised, even in large-scale public wastewater and drinking water systems. This topic describes standard methods of testing fecal coliforms. We will also study the standard methods of wastewater monitoring and treatment
Objectives:
1. Describe the standard methods of testing fecal coliforms
2. Describe the standard methods of water monitoring and treatment
Plan:
Step1. There is study text folder containing a Microsoft Power Point (PPT) file, 17 pages, which you can review and print. Also, I recommend that you have Microsoft PowerPoint installed on your computer to access to these files.
Step 2.Attached please find 2 short videos about the standard methods of wastewater treatment
1.The following video describe the tertiary sewage treatment process in 3D animation view
2. Video about Konya waste-water treatment plant flow diagram .
The Immune System
Topic Number Eleven
The Immune System
Introduction
The immune system is a complex network of organs containing cells that recognize foreign substances in the body and destroy them. It protects vertebrates against infectious agents, such as viruses, bacteria, fungi, and other parasites. The human immune system is the most complex.This topic describes the innate Immunity and the adaptive immunity, major events in the local inflammatory response, clonal selection theory and the allergic response.
Objectives :
1. Describe the innate Immunity and the adaptive immunity
2. Describe the major events of inflammatory response, clonal selection theory and the allergic response
Plan:
Step1. There is study text folder containing a Microsoft Power Point (PPT) file, 36 pages, which you can review and print. Also, I recommend that you have Microsoft PowerPoint installed on your computer to access to these files.
Step 2. Attached please find a short video about the clonal selection theory
Roughly, bioinformatics describes any use of computers to handle biological information. Bioinformatics is a synonym for “computational molecular biology” –the mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information. In this topic we will study the basics of bioinformatics