Microbiology 4

SUMMARY

Many interventions, protocols, and prevention methods are used to maintain or improve overall human health. The aim of some is to improve quality of life, while others specifically reduce, remove, or eradicate microbial pathogens which would otherwise cause disease.

Many such processes may also result in, or cause, unintended consequences to humans, pathogens, and/or the environment that were not predicted. The most well-known example is that of the rise of multiple antibiotic resistant bacteria following the use (and overuse) of antibiotics.

Each of the papers in this discussion provides an example of interventions originally intended to improve health and prevent disease. The first paper by Alharbi et al concerns restroom electric hand dryers. The second by Nettleton et al discusses artificial sweeteners and their impact on the gut bacteria. The third is a review of the latest findings that trehalose, an artificial sweetener, may have contributed to the current disease epidemic of Clostridium difficile. Finally, McNamara and Levy discuss the current status of triclosan which was first introduced in the 1970s. A background paper which defines and reviews the Hygiene Hypothesis, by Roduit et al, is also provided.

DISCUSSION PROMPTS

· What was the specific original intent of the intervention or procedure described in each of the papers and what was their unintended consequence(s)?

· Can you offer a solution or remediation for any or all of the resulting consequences from these interventions?

· What is the Hygiene Hypothesis (described in the Roduit paper) and how is it related to this discussion?

· Follow the APA format

· 1.5 page paper

 

Reading:

 

· https://elearn.une.edu/bbcswebdav/pid-236273-dt-forum-rid-15646280_1/courses/1015-201900-BIOL-1020L-06N/Antibacterial%20Consumer%20Products%20- %20How%20Reliable%20Are%20They%202017.pdf

 

· https://elearn.une.edu/bbcswebdav/pid-236273-dt-forum-rid-15646282_1/courses/1015-201900-BIOL-1020L-06N/Assessment%20of%20the%20bacterial%20contamination%20of%20hand%20air%20dryer%20in%20washroom.pdf

 

· https://elearn.une.edu/bbcswebdav/pid-236273-dt-forum-rid-15646338_1/courses/1015-201900-BIOL-1020L-06N/Pathogens%20boosted%20by%20food%20additive%202018.pdf

 

· https://elearn.une.edu/bbcswebdav/pid-236273-dt-forum-rid-15646339_1/courses/1015-201900-BIOL-1020L-06N/Reshaping%20the%20gut%20microbiota%20-%20Impact%20of%20low%20calorie%20sweeteners%20and%20the%20link%20to%20insulin%20resistance%202016.pdf

 

· https://elearn.une.edu/bbcswebdav/pid-236273-dt-forum-rid-15646346_1/courses/1015-201900-BIOL-1020L-06N/The%20Hygiene%20Hypothesis%20%20Roduit%20et%20al%202016.pdf

 

· https://elearn.une.edu/bbcswebdav/pid-236273-dt-forum-rid-15646348_1/courses/1015-201900-BIOL-1020L-06N/Triclosan%20-%20An%20Instructive%20Tale%202016.pdf

 
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Effect of substrate concentration on enzyme function

  • Read through the introductory materials below.
  • Open the Unit 2 Experiment Answer Sheet and complete the following Experiment exercises this unit:
    • Experiment 2 Exercise 1A – Effect of substrate concentration on enzyme function (~30 min)
    • Experiment 2 Exercise 1B – Effect of pH on enzyme function (~30 min)
    • Experiment 2 Exercise 2 – Cellular Respiration and Photosynthesis (~1.5 hrs)
  • Save your completed Unit 2 Experiment Answer Sheet and submit it by Midnight Sunday (CT).

Enzymes – Introduction

This unit we will examine enzyme function using a virtual simulation. Be sure to review our online lecture on Energetics and pp 80 – 82 in your book. As we have learned this unit, enzymes are biological catalysts that can lower the activation energy required to allow reactions to proceed. Enzymes are very sensitive to the environment in which they work, meaning changes in substrate concentration, temperature, pH, salts and other chemicals can drastically alter their function. This is one of the reasons the buffers we learned about last unit are so important!

When you are ready to begin these two exercises, go to:

Bioman. No date. Enzymatic (Links to an external site.)

Procedure

  1. Click on “Start a New Game” and follow the on-screen instructions.
  2. When you get to the “Main Menu”, click on “Experiments”.  You will have to click twice.
  3. Click “OK” and follow the on-screen instructions.  Please note that you do not need to submit the answers from the quiz.

You will need an understanding of the different types of experimental variables in order to correctly graph your results. There are three different types of variables:

Independent Variable: This is the variable that the experimenter manipulates and is expected to affect the dependent variable. For example, if you think the amount of sunlight affects plant growth, you would vary the amount of light a plant receives (e.g., 2 hrs/day, 4hrs/day, 6 hrs/day). The amount of sunlight would be the independent variable.

Dependent Variable: This variable is expected to vary depending on the independent variable. In the example above, plant growth would be the dependent variable, because it is dependent on the amount of sunlight it receives.

Control Variable: This type of variable includes factors (there may be many) that could affect the outcome of your experiment. By holding these variables constant in all treatments, the experimenter knows that only the independent variable is affecting the outcome. In the example above, the variables you would want to hold constant would be things such as temperature, water and nutrients.

When graphing your results, the two variables of interest are the independent and dependent variables. The independent variable is always graphed on the x-axis and the dependent variable is always graphed on the y-axis. When you generate a graph, you must also always label each axis and include any units of measure.

When you are ready to begin, use the instructions in the Unit 2 Experiment Answer Sheet to complete these exercises.

Cellular Respiration and Photosynthesis – Introduction

In this exercise, you will have the opportunity to explore the relationship between the air we breathe and the plants around us. Be sure to review our online lecture on Energetics and Chapters 6 and 7 in your book; particularly pp 92-93.

Cellular respiration is the metabolic pathway in which all plants and animals extract usable energy (ATP) from foods either eaten (animals) or synthesized (plants). Yes, plants perform cellular respiration! This is because the energy they generate via photosynthesis is used to produce sugars. It is these sugars that are then broken down by cellular respiration to provide the energy to carry out plant cellular functions, just like in animal cells!

Cellular respiration and photosynthesis are linked by their reactants and products. Here is a chemical summary of the two reactions:

Cellular Respiration:     Oxygen + Glucose » Energy + Carbon dioxide + Water

Photosynthesis:             Energy + Water + Carbon dioxide » Glucose + Oxygen

What do you notice about the reactants and products of these two processes? RIGHT! The reactants of cellular respiration are the products of photosynthesis and the products of cellular respiration are the reactants of photosynthesis. Without photosynthesis and the production of oxygen, aerobic cellular respiration could not occur. And, carbon dioxide levels would increase significantly!

In this exercise, you will demonstrate this relationship between these two important processes using snails and Elodea, a water plant. When you are ready to start this exercise, go to:

Virtual Labs Simulation
http://www.classzone.com/cz/books/bio_09/resources/htmls/virtual_labs/virtualLabs.html (Links to an external site.)

If a link to Carbon Transfer through Snails and Elodea is not directly available, then follow these instructions:

  • Select Missouri as your location and click Go
  • Click on the Go beneath Biology 2010
  • Under the Labs heading, click on Virtual Labs
  • Click on Carbon Transfer through Snails and Elodea

You will need to open the Unit 2 Experiment Answer Sheet and follow the instructions carefully. The simulation is a little clunky to use and if you don’t do things right, you will have to start over. You must complete certain steps before you can proceed.

 
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Monohybrid crosses

How to Proceed

  • Read through the introductory materials below.
  • Open the Unit 6 Experiment Answer Sheet and complete the following Experiment exercises this unit:
    • Experiment 6 Exercise 1 – Monohybrid crosses (~45 min)
    • Experiment 6 Exercise 2 – Dihybrid crosses (~30 min)
    • Experiment 6 Exercise 3 – Inheritance of Human Traits (~30 min)
  • Save your completed Unit 6 Experiment Answer Sheet and submit it no later than Sunday midnight (CT).

Monhybrid and Dihybrid Crosses – Introduction

Mendel crossed true-breeding pea plants in order to develop and understanding of how traits are inherited. True-breeding means that if a plant was crossed with itself, it always generated offspring that looked like the parent. Although Mendel didn’t know this at the time, it meant that the parent plant was homozygous or had two copies of the same allele that controlled the appearance of the trait.

Mendel noticed that when he crossed two true-breeding plants exhibiting different versions of a trait (e.g., green and yellow); the offspring (F1) always looked like only one of the parent plants. We know now that the F1 individuals looked like the parent that carried the dominant trait. But what surprised Mendel, was that when he crossed the F1 individuals with each other, the F2 offspring exhibited BOTH traits! Based on this observation, he concluded that the F1 individuals were hybrids, meaning they carried both alleles for a given trait. Only the dominant trait was expressed in the F1 individuals and the recessive trait, although present, was masked.

monohybrid cross is when you are interested in crossing individuals that vary in only a single trait (e.g., flower color, seed color, stem length). In a dihybrid cross, we are crossing individuals that differ at two traits (e.g., flower color and seed color, flower color and stem length). Obviously, the more traits that vary, the more complex the crosses become!

By examining the distribution of the various traits obtained following different types of crosses, Mendel was able to describe the general pattern of genetic inheritance. Be sure to review the online lecture this unit on Genetics and pp 146-153 in your book before starting these first two exercises.

We will be using the following website for the first exercise. Be sure that you can access it and use it before beginning:

Glencoe-McGraw Hill. No date. Punnett Squares
http://glencoe.mcgraw-hill.com/sites/dl/free/0078759864/383934/BL_05.html (Links to an external site.)

You will need to complete the Tables and answer the questions in the Unit 6 Experiment Answer Sheet for Exercises 1 and 2.

Inheritance of Human Traits – Introduction

Some human traits are controlled by a single gene that has only two alternative alleles. If a characteristic is determined by the dominant allele, one or both parents express that trait and many of the children will as well. Dominant characteristics will most likely be present in every generation, since the expression of these traits requires only one of the dominant alleles in order to be expressed. If the characteristic is determined by the recessive allele, then neither parent may express the trait nor few of the children. This is because two copies of the recessive allele must be present in order for the recessive trait to be expressed. If a trait is X-linked recessive; meaning the gene for the trait is found on the X chromosome, it will be expressed primarily in males.

The application of human genotypes in medicine and genetic counseling is becoming more and more necessary as we discover more about the human genome. Despite our increasing ability to decipher the chromosomes and their genes, an accurate family history remains one of the best sources of information concerning the individual. In this exercise you will determine your genotype for certain characteristics that are controlled by a single gene with two alleles based on your phenotype. We will not be looking at any X-linked traits in this exercise.

Use the information about the traits of interest in the Unit 6 Experiment Answer Sheet to answer the questions found there.

WEEK 6 EXPERIMENT ANSWER SHEET Please submit to the Week 6 Experiment dropbox no later than Sunday midnight.

SUMMARY OF ACTIVITIES FOR WEEK 6 EXPERIMENT ASSIGNMENT

· Experiment 6 Exercise 1 – Monhybrid Crosses

· Experiment 6 Exercise 2 – Dihybrid Cross

· Experiment 6 Exercise 3 – Inheritance of Human Traits

Experiment 6 Exercise 1: Monohybrid Crosses

You will be conducting monohybrid crosses using fruit flies. Open in the following website:

Glencoe-McGraw Hill. No date. Punnett Squares http://glencoe.mcgraw-hill.com/sites/dl/free/0078759864/383934/BL_05.html

Procedure

A. Open the above website and click on the VCR to listen to the introduction. Close the window when done.

B. Click on the Lab Notebook on the lab bench. A breeding scenario will be presented to you that you will need to carry out. Here are the possible phenotypes and genotypes you will using:

a. Normal wings (LL or Ll) or vestigial wings (ll)

b. Gray body (GG or Gg) or black body (gg)

C. Enter the Scenario number in Table 1 below.

D. Based on the Scenario, use the down arrows beneath the Parent 1 and Parent 2 boxes to select the appropriate parents. Look carefully at the flies so that you know which ones to select.

E. Before proceeding, click on the Check Parents button. If necessary, make corrections. If you are correct, the maternal and paternal alleles will be added to the Punnett Square.

F. Next, drag the correct allele combinations and the corresponding fly types to the boxes in the Punnett Square.

G. When you are done, click on Check Offspring. If necessary, make corrections.

H. Record your data in Table 1 below. An example has been given, but note that the example is not using the genotypes and phenotypes used in this exercise.

I. Click on Reset. Repeat steps B – H four more times for a total of five crosses. If a scenario is presented that has already been completed, click Reset again. DO NOT REPEAT a given scenario!

Note that the scenario number you need to record in the Table below is the number associated with the specific scenario you completed.

Table 1. Results of crosses.

 

Parent Genotypes Offspring Genotypes Offspring Phenotype
Scenario # Parent 1 Parent 2 # % # %
Example Rr rr 2 Rr

2 rr

50% Rr

50% rr

2 red

2 white

50% red

50% white

             
             
             
             
             

Questions

1. Which type of cross gave you the greatest number of genotypes? Was the number of phenotypes the same as the number of genotypes or different? If different, why (2 pts)?

2. Can the genotype for a gray-bodied fly be determined? If so, how? (3 pts)?

Experiment 6 Exercise 2: Dihybrid Cross

We will continue to use flies for our crosses, but this time we will examine the inheritance of TWO different traits: body color (gray or black) and wing type (long or vestigial). As with our first crosses, the gray body color is dominant (GG or Gg) over the black body color (gg). And the long wing type is dominant (LL or Ll) over vestigial (ll). Be sure you have reviewed our online Genetics lecture and this week’s reading before proceeding. An example of a dihybrid cross is shown on p 150 in your book.

Recall our flies from the previous exercise. We have the following traits:

· Gray body (GG or Gg) is dominant over black body (gg)

· Long wings (LL or Li) is dominant over vestigial wings (ll)

We will cross a gray bodied fly with long wings which has the genotype GGLl with a gray bodied fly with long wings with a genotype of GgLl . Note that even though the phenotypes are the same, the genotypes of the two parents are different.

Identify the four possible gametes produced by these two individuals. Note that each gamete must consist of two alleles (G or g and L or l):

Parent 1 Parent 2

image1.png image2.png

GGLl GgLl

Parent 1 (GGLl) Gametes: _______ ______ _______ _______ (1 pts)

Parent 2 (GgLl) Gametes: _______ ______ _______ _______ (1 pts)

Create a Punnett square to show the outcome of a cross between these two individuals (GGLl and GgLl) using the gametes you identified above (3 pts).

    Parent 1
           
Parent 2          
           
           
           

Questions

1. What are the possible F1 genotypes (these must now have four alleles) and their percentages (4 pts)?

2. Recall that GG and Gg individuals are gray bodied, while gg individuals are black bodied and that LL and Li individuals have long wings, while ll individuals have vestigial wings. What are the phenotypes of the resulting offspring and what are the percentages of these phenotypes (2 pts)?

Experiment 6 Exercise 3: Inheritance of Human Traits

Read over the Inheritance of Human Traits Introduction under the Week 6 Experiment link in our course before beginning.

Procedure

A. For each of the heritable traits describe below, determine which form you have (dominant form or recessive form). This is your phenotype.

B. Record your phenotype information in Table 2 below. Then, enter the possible genotype(s) you have based on your phenotype.

C. Answer the questions found following Table 2 below.

Description of Heritable Traits

Trait Possible Alleles Dominant Form Recessive

Form

Examples
Ear lobes E or e Detached (Free) Attached  

image3.png 

Hairline W or w Widows peak Straight image4.jpg Widow’s peak Straight
Tongue rolling T or t Able to roll Unable to roll image5.jpg
Hand folding R or r Right thumb on top Left thumb on top image6.jpg
Chin C or c Cleft chin No cleft chin image7.jpg
Tongue folding F or f Can fold tongue backwards Cannot fold tongue backwards image8.jpg
Thumb H or h Straight thumb (cannot bend backwards) Hitchhiker’s thumb (can bend it backwards) image9.jpg
Little Finger B or b Bent inwards Straight image10.jpg
Mid-digital hair M or m Hair on fingers No hair on fingers  

image11.png 

An example is shown as to what should be entered in RED. Please correct the entry for “Ear lobes” based on your personal data. For the Genotypes, please use the letters provided above (8 pts).

Table 2. Your phenotypes and genotypes.

Trait Phenotype Genotype
Ear lobes Unattached OR Detached EE/Ee OR

ee

Hairline    
Tongue Rolling    
Hand Folding    
Chin    
Tongue Folding    
Thumb    
Little Finger    
Mid-digital Hair    

Questions

1.  Which traits did you have that were dominant (1 pts)?

2.  Which traits did you have that were recessive (1 pts)?

3. What does it mean to be homozygous for a trait? Cite source(s) used (1 pts).

4.  What does it mean to be heterozygous for a trait? Cite source(s) used (1 pts).

5.  Define genotype and phenotypeCite source(s) used (1 pts).

6.  Which traits do you know for sure that you were homozygous (1 pts)?

Week 6 Experiment Grading Rubric

Component Expectation Points
Experiment 6 Exercise 1 Correctly perform and record the outcome of five monohybrid crosses (Table 1).

5
 

Demonstrate an understanding of the possible outcomes of monohybrid crosses with respect to genotypes and phenotypes (Questions 1-2).

5
Experiment 6 Exercise 2 Determine the correct parental gametes and conduct a dihybrid cross.

5
 

Correctly evaluate the outcome of a dihybrid cross (Questions 1-2).

6
Experiment 6 Exercise 3

Correctly recognize one’s phenotype and assigns the correct genotype (Table 2).

8
 

Demonstrate an understanding of dominant and recessive traits, genotype vs phenotype and homozygous vs heterozygous (Questions 1-6).

6
TOTAL  

35 pts

Updated October 2013

 
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Video on NPR about how a virus invades your body

Description

Watch this great video on NPR about how a virus invades your body. http://www.npr.org/blogs/krulwich/2011/06/01/114075029/flu-attack-how-a-virus-invades-your-body

Then read the article or listen to the podcast about the spread of an antibiotic resistant bacteria on the following link. http://www.npr.org/2012/09/18/161355297/hospitals-fight-to-stop-superbugs-spread

There are two other links for you to use in this assignment. Those links will be in the questions to which they are associated. It is not necessary that you read the full articles at those links.

Eight of the ten questions in this assignment have answers that are to be gained from the second NPR link (podcast on  Klebsiella pneumoniae).

 

QUESTION 1

What is the scientific name of the bacterial species that has developed “superbug” strains referred to as KPC?

QUESTION 2

According to the talk, what is the name of “the best known” drug-resistant bacteria?

QUESTION 3

According to McKenna, what makes KPS different from other superbugs?

QUESTION 4

In what hospital did the outbreak of KPC featured in this story occur? What’s special / different about this hospital? What type of health care facilities are at risk?

QUESTION 5

Dr. Eli Perencevich explained the two main reasons that KPC and other antibiotic resistant Gram negative pathogens so difficult to eliminate. What are those two reasons?

QUESTION 6

What is the mortality rate for bacteremia (bacteria in blood) from KPC, in this most recent outbreak

QUESTION 7

Although we have not been successful in entirely stopping their spread, what are at least four of the current recommended practices for infection prevention and control regarding these superbug.

QUESTION 8

Why are pharmaceutical companies reluctant to devote resources to developing new classes of antibiotics?

QUESTION 9

At the following peer reviewed journal article http://www.nature.com/emm/journal/v47/n9/full/emm201559a.html  is an description of a specific research project from 2015.

What are these researchers hoping their discoveries can eventually lead to (5 points)?

 

What does EV stand for and what is their general size (5 points)?

QUESTION 10

 

Regarding the superbug recently found in the patient discussed in this article, https://www.rt.com/usa/348637-patient-superbug-new-york/

answer the following 3 questions:

A) What drug is this superbug resistant to?

B) Is this superbug also a type of CRE resistant bacteria?

 

C) What superbug do you know of that is a type of CRE resistant bacteria?

 
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