Trident BIo101 full course (all cases and SLps)

26 Jun Trident BIo101 full course (all cases and SLps)

Question
Module 1

Video: NOVA Science Now Revealing the Origins of Life. PBS Aired: 02/16/2011http://video.pbs.org/video/1790640610/

PowerPoint slide presentation.trident.edu/content/enforced/53245-BIO101-MAY2015-1/Modules/Module1/Introduction%20to%20the%20Cell.ppt?_&d2lSessionVal=7A4vmMQuIAzFZRvJaVl5laRLC&ou=53245″>Introduction to the Cell.

Basic chemistry involved in biological systems:

Paul Andersen, Bozeman Science: Biological Molecules. Accessed on June 30, 2014 athttp://www.bozemanscience.com/042-biologoical-molecules/

Cell Membrane

Kyrk, John (2014) Accessed February 20, 2014 at:http://www.johnkyrk.com/cellmembrane.html

Transport in and out of cells

Farabee, MJ (2010) Accessed February 20, 2014 at:http://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobooktransp.html

Organelles found in plant and animal cells(be sure to view the animation by clicking on the diagram of the cell):

Sullivan, Jim (1994) Plant, Animal and Bacterial Cell Models. Accessed February 20, 2014, at:http://www.cellsalive.com/cells/3dcell.htm

Additional references:

Terminology:

Pearson Education, Inc. (2007) Glossary of Biological Terms. Accessed February 18, 2014, at:http://www.phschool.com/science/biology_place/glossary/index.html

Microscopy:

Stevenson, John (1998) Types of Microscopes. Accessed February 18, 2014, at:http://www.cas.muohio.edu/mbi-ws/microscopes/types.html

Mithra, S (2003) What are the Different Types of Microscopes? Accessed February 18, 2014, at:http://www.wisegeek.com/what-are-the-different-types-of-microscopes.htm

Structure and function of the cytoskeleton:

Anonymous (2004) The Biology Project: Cytoskeleton Tutorial. Accessed February 20, 2014, at:http://www.biology.arizona.edu/cell_bio/tutorials/cytoskeleton/main.html

Homeostasis

Farabee, MJ (2004) Animal Organ Systems and Homeostasis. Accessed February 25, 2014, at:http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookANIMORGSYS.html

Case

National Ocean and Atmospheric Administration, Accessed February 20, 2014 at:

http://www.gulfspillrestoration.noaa.gov/media-center/videos/

First watch: Deepwater BP Oil Spill – Assessing the Damage Restoring the Coast

Next watch: Shoreline Assessment Webisode

Stanford News Service. Oil Causes Heart Problems for Fish, February 13, 2014. Accessed February 20, 2014 at: https://woods.stanford.edu/news-events/news/oil-causes-heart-problems-fish

Earthsky Presentation: EarthSky Blog, February 18, 2014, “How oil spill chemicals cause heart failure in fish.” Accessed February 20, 2014 at:http://earthsky.org/earth/how-oil-spill-chemicals-cause-heart-failure-in-fish

SLP

Urakawa, H., Garcia, Juan C., Barreto, Patricia D., Molina, Gabriela A., Barreto, Jose C. (2012)..trident.edu/d2l/common/dialogs/quickLink/quickLink.d2l?ou=53245&type=content&rCode=TUI-48086″>A sensitive crude oil bioassay indicates that oil spills potentially induce a change of major nitrifying prokaryotes from the Archaea to the Bacteria.Environmental Pollution. 164:42-45

Biello, David. 2010..trident.edu/d2l/common/dialogs/quickLink/quickLink.d2l?ou=53245&type=content&rCode=TUI-48087″>Clean Up the Deepwater Horizon Oil Spill: Bacteria and other microbes are the only thing that will ultimately clean up the ongoing oil spill in the Gulf of Mexico.Scientific American. May 25, 2010.

In the Case Assignments for this course, you will learn many of the theories of biological science as you learn about current events in the living world around you. In your first Case Assignment, you will watch the following videos to learn about an important environmental event that occurred in 2010 and has had long-lasting effects.

First, watch: Deepwater BP Oil Spill – Assessing the Damage Restoring the Coast

Next, watch: Shoreline Assessment Webisode at

http://www.gulfspillrestoration.noaa.gov/media-center/videos/

Your Assignment:

In the wake of the Deepwater BP Oil Spill, you have been assigned to the Shoreline Assessment Team introduced in this video. You are employed as a junior member of the team responsible for gathering facts and presenting them to the team. For Module 1 you will explain the findings summarized here:

https://woods.stanford.edu/news-events/news/oil-causes-heart-problems-fish

You will develop a report for your team to present to stake-holders in the restoration of the Gulf Coast, including members of BP Oil Corporation. You must assume that these individuals are NOT scientists, and that the relevance of oil within an aquatic environment must be explained to them. You will present the evidence that oil causes physiological damage to vertebrates at the cellular level. Design a PowerPoint presentation to this group that includes:

An introduction that

[Slide 1] Provides a brief background of the Deepwater BP Oil Spill. Include the date, the extent of the spill, and the partnerships working together to address the crisis.
[Slide 2] Outlines the three steps in the damage assessment.
[Slide 3] Explains your role in this assessment (be creative, but stay within the guidelines of the scenario above and the parameters of Assessment Teams explained in the videos).
Now explain the results of one of the studies conducted to assess the effect of oil on ocean life, summarized in this article:https://woods.stanford.edu/news-events/news/oil-causes-heart-problems-fish. To develop your explanation, include:

[Slide 4] A diagram of a hydrocarbon. Explain its relevance to oil in the notes section of the slide.
[Slide 5] A labeled diagram of an animal cell. Label the following: cell membrane, nucleus, cytoplasm, mitochondria, ribosomes, and endoplasmic reticulum. Provide a brief definition of each in the notes section. Review the .pearsoncustom.com/mct-comprehensive/asset.php?isbn=1269879944&id=8524″>tour of the animal celland refer to this labeled diagram of an.pearsoncustom.com/mct-comprehensive/asset.php?isbn=1269879944&id=9093″>animal cell.
[Slide 6] A labeled diagram of a.pearsoncustom.com/mct-comprehensive/asset.php?isbn=1269879944&id=9071″>phospholipid bilayer, AKA the fluid mosaic model of the cell membrane. Click on the link to review the structure and function of the phospholipid bilayer that makes up the cell membrane. Include a brief discussion of the molecules that make up phospholipids and how water facilitates the arrangement of the phospholipid bilayer (Hint: the terms “hydrophobic” and “hydrophilic” are important).
Muscle cells have a specialized cell membrane called the sarcolemma with specialized channels that allow the.pearsoncustom.com/mct-comprehensive/asset.php?isbn=1269879944&id=5247″>ions sodium, Na+, and potassium, K+,to pass, generating an electrical current that signals contractions. Muscle cells in the heart are very similar to the muscle cells that make up your.pearsoncustom.com/mct-comprehensive/asset.php?isbn=1269879944&id=5266″>skeletal muscles (Comparison of skeletal, smooth, and cardiac muscle). The specialized membrane on cardiac cells makes the heart cell contract similar to skeletal muscle cells, and when coordinated with other heart cells, the contractions .pearsoncustom.com/mct-comprehensive/asset.php?isbn=1269879944&id=11370″>push blood out of the heartand throughout the body.

[Slide 7] Include a labeled .pearsoncustom.com/mct-comprehensive/asset.php?isbn=1269879944&id=5273″>diagram of a heart cellusing this link to help you label the following structures: sarcolemma, ion channels, ions responsible for signaling contraction, protein microfibrils that interact to facilitate contraction. Provide a brief definition of each in the notes section.
Next review the steps of muscle contraction:

1) .pearsoncustom.com/mct-comprehensive/asset.php?isbn=1269879944&id=7552″>Events at the neuromuscular junction

2) .pearsoncustom.com/mct-comprehensive/asset.php?isbn=1269879944&id=7585″>Excitation-contraction coupling

3) .pearsoncustom.com/mct-comprehensive/asset.php?isbn=1269879944&id=7590″>Crossbridge cycle

These videos illustrate the steps that occur for skeletal muscle cells, which are very similar to cardiac, heart, muscle cells which contract in a very similar way.

[Slide 8] Now outline how alterations at the chemical level cause complications at the organismal level: How does crude oil interrupt heart cell signaling and overall heart cell function? What does this do to the fish?
[Slide 9] An outline of the research techniques used in this study, including brief description of each technique.
Don’t forget a references Slide that documents the sites you used to complete the assignment!

Assignment Expectations

The Case Assignment is a written description of a problem or situation. Most cases are a “snapshot” of a particular situation within a complex environment. For this Case Assignment you will develop a PowerPoint Presentation that is 10-15 slides in length and addresses the requirements outlined above. Be sure your last slide is a references slide.

The purpose of the Case Assignments in this course is to place the student in a position that will require research, synthesis of information, and critical thought. The student will be asked to distinguish pertinent facts from peripheral facts, identify central alternatives among several issues competing for attention, and formulate strategies and recommendations. This method provides an opportunity to sharpen problem-solving skills and to improve the ability to think and reason rigorously.

Your essay is considered a scholarly work. You will be provided with many scholarly references to begin each assignment. For any additional research you are required to do to complete your assignment, please use scholarly references such as a peer- reviewed journal article or a government sponsored or university sponsored website. As you read through your sources, take notes from your sources and then write your paper in your own words, describing what you have learned from your research. Direct quotes should be limited and must be designated by quotation marks. Paraphrased ideas must give credit to the original author, for example (Murray, 2014). Direct copying from “homework help” websites will not receive credit.

module 2 case and SLP
Module 2 – Case
CELL CHEMISTRY
Case Assignment
Now that you have learned the basics of energy conversion, enzymatic activity, and two important processes used by living organisms, you will focus on cellular respiration for this Case Assignment.

After viewing the videos on.sumanasinc.com/webcontent/animations/content/cellularrespiration.html”>Cellular Respiration, answer the following questions in a 2- to 3-page paper:

1. What is the starting molecule in glycolysis (i.e., what is being metabolized. Be specific)?

2. Define these terms: substrate, enzyme, ATP, and describe why they are important in cellular respiration.

3. What do these enzymes do, generally speaking? Would the reaction occur if they were not present? Why or why not?

4. What are the byproducts of cellular respiration? Where do these byproducts end up (in the organism AND in the environment)?

Assignment Expectations
The Case Assignment is a written description of a problem or situation. Most cases are a “snapshot” of a particular situation within a complex environment.

The purpose of the Case Assignments in this course is to place the student in a position that will require research, synthesis of information, and critical thought. The student will be asked to distinguish pertinent facts from peripheral facts, identify central alternatives among several issues competing for attention, and formulate strategies and recommendations. This method provides an opportunity to sharpen problem-solving skills and to improve the ability to think and reason rigorously.

Your essay is considered a scholarly work. You will be provided with many scholarly references to begin each assignment. For any additional research you are required to do to complete your assignment, please use scholarly references such as a peer reviewed journal article or a government sponsored or university sponsored website. As you read through your sources, take notes from your sources and then write your paper in your own words, describing what you have learned from your research. Direct quotes should be limited and must be designated by quotation marks. Paraphrased ideas must give credit to the original author, for example (Murray, 2014). Direct copying from “homework help” websites will not receive credit.

When you write your essay, please organize your paper to include an introduction (overview of the assignment), body with subtitles (reflecting the requirements of the assignment), and a summary (develop connections between the required topics).

Module 2 – SLP
CELL CHEMISTRY
SLP Assignment Overview
We will continue to analyze our study conducted in the oceans of the Gulf of Mexico in the article by Urakawa et al (2012),A sensitive crude oil bioassay indicates that oil spills potentially induce a change of major nitrifying prokaryotes from the Archaea to the Bacteria.

As you analyze the results in this study, think back to the evolution of life on our planet and the videos you watched in Module 1. One theory of the evolution of life suggests that life evolved in a chemical “soup” of ingredients that under the right conditions facilitated the collection of molecules into primitive cells. In order to maintain organization, these primitive cells needed to acquire resources from their oceanic environment, harvest the energy from these sources, and use it to maintain the structures that worked well and build new structures to accomplish future work and survival. This process is termed “metabolism,” and organisms have evolved many strategies in order to accomplish life-sustaining chemical transformations.

In order to continue your analyses, you must first be able to explain some of the important metabolic pathways described in the study. In this SLP assignment you will compare chemotrophic metabolic pathways to photosynthesis.

Write a 3-4 page paper that addresses each of the following topics. Use subtitles and headings to organize your paper. Research your answers to the questions below using scholarly sources, including national, university, and government websites, publications, and scientific journals. Cite your references throughout, and include a references section at the end.

1. Begin by describing the origin of crude oil deposits in the ocean. What role did photosynthesis play in this process?

2. Using full sentences in paragraph format define:

The difference between an autotroph and a heterotroph

The relationship between a photosynthetic autotroph and a chemotrophic autotroph

Nitrification
Ammonia oxidation

3. Why is nitrogen important to living systems?

4. How are these metabolic pathways similar to photosynthesis?

5. From theUrakawa et al. (2012) paper: Why was nitrite production used to measure the activity of the microbes in the study?

6. What is a bioassay? Why did the scientists use it in this study?

7. Which organisms showed sensitivity to oil toxicity? What happened to nitrite production in these organisms? How did nitrite production relate to growth?

Here is a diagram to help as you consider these metabolic pathways:

.png” alt=”https://tlc.trident.edu/content/enforced/53245-BIO101-MAY2015-1/Metabolic%20Pathways.png?_&d2lSessionVal=aIjeWSyPtE5fWpxaT2DU8aE6d&ou=53245″>

From Wikimedia Commons, the free media repository

SLP Assignment Expectations
The Session Long Project consists of an integrative project emphasizing the personalized application of each module’s concepts. For Modules 1–5, students are required to engage in an original integrative project reflecting their comprehensive knowledge of and ability to apply the course materials. Each component of the SLP will be graded on a modular basis.

Your essay is considered a scholarly work. You will be provided with many scholarly references to begin each assignment. For any additional research you are required to do to complete your assignment, please use scholarly references such as a peer reviewed journal article or a government sponsored or university sponsored website. As you read through your sources, take notes from your sources and then write your paper in your own words, describing what you have learned from your research. Direct quotes should be limited and must be designated by quotation marks. Paraphrased ideas must give credit to the original author, for example (Murray, 2014). Direct copying from “homework help” websites will not receive credit.

When you write your essay, please organize your paper to include an introduction (overview of the assignment), body with subtitles (reflecting the requirements of the assignment), and a summary (develop connections between the required topics).

module 3 case and SLP
From Sea Squirts to Otters…

For the Case Assignment in Module 3, you will compare the taxonomic classification of two organisms within the Phylum Chordata: the sea squirt and the sea otter. Use this site to accomplish your research:

University of California Museum of Paleontology, UC Berkeley

http://www.ucmp.berkeley.edu/exhibit/phylogeny.html

This link will bring you to the “Welcome to the Phylogeny Wing” page where you will begin your orientation to the website.

Follow the links in each of the “four ways to get started” listed on this page. Use your back button to return to the “Welcome to the Phylogeny Wing” page each time.

Read the content on the pages that numbers 1, 2, and 3 link to. Finally, complete your research on the taxonomic classification of sea squirts and sea otters using the link within step 4: Web Lift to Taxa. This is the same link as “tree of life” at the bottom of the page.

Within the Tree of Life/Taxon Lift, you will be able to find information about the classification of the sea squirt and the sea otter, two chordates. First select the appropriate Kingdom that the Phylum Chordata belongs to (you can refer back to our home page – remember, WE are chordates). You will access the rest of the necessary webpages from this list.

Case Assignment

For this Case Assignment, you are required to use the UCMP website and links accessed via this website ONLY. Using this resource write a 3-4 page paper on the taxonomic classification of sea squirts and otters that includes the following for each organism:

Part I: Sea Squirt

Once you find the “Chordata” link within the correct Kingdom page, notice the subphyla listed beneath it. Take note of which subphyla the sea squirt belongs to (you will see it in parentheses next to the correct name). Next click on the “Chordata” link and select “Systematics.”

1. List the Kingdom and Phylum, for the sea squirt and then briefly describe the characteristics that determine the organism’s classification at each taxonomic level.

2. Why is the sea squirt classified in the same phylum as a sea otter?

3. Click on the “Life History & Ecology” tab to read more about Urochordates. What is another name that is used to describe them? Briefly describe the adult versus larval phase of its life cycle.

Part II: Sea Otter

List the Kingdom, Phylum, Class, Order, Family, Genus, and Species. Summarize the descriptions that are provided in each web page for the taxonomic group and use the website address and the TITLE of the page to cite your source. For example, if you summarize the Mammalia page, use this citation after your summary of the content (Hall of Mammals, http://www.ucmp.berkeley.edu/help/taxaform.html).

Use a similar format to describe the taxonomic groups that this individual belong to as was used on the Home page for this Module. Be sure to take notes on each step of your classification as you complete the following instructions:

1. Return to the Tree of Life page using the link at the bottom of the page. Select the correct Kingdom for Phylum Chordata. From this page, now think about what subphyla within Chordata would an otter belong to (HINT: Does it have a vertebral column? Is it more like a koala bear or a primitive fish?).

2. Select the correct subphylum from this list.

3. Now select the correct Class. On the page you will notice links that lead to fish, amphibia, reptiles, and mammals. Think about which best represents the sea otter (HINT: Does it have hair, scales, or a slimy skin? Is it warm-blooded “homeothermic” or cold-blooded “poikilothermic?”). If you can’t decide, try each link until you find characteristics that match those of the sea otter.

4. Once you have selected the correct Class, a list of Orders will open next to it. Consider the sea otter’s diet. Does it eat vegetables such as sea weed, or meat such as oysters, mussels, and clams? Is it more like whale, horse, elephant, bat, or cat? If you can’t decide try some of the links until you narrow it down.

5. Select the corresponding Order and make note of it. Determine which Family, Genus and species describe the otter select “Systematics” at the bottom of the page.

6. When you enter the “Systematics” page for the sea otter, select the link for “International Sea Otter Survival Fund” to learn more about the family and genus characteristics and classification. Use the links “About Otters” and then “Otter Species” from this page to answer the following questions:

To what family do otter-like animals belong?

Using the Species List, what is the difference between the Sea Otter and the Marine otter? List the genus and species for each.

What threats do the Sea Otter and Marine otter face as species?

Part III: Explore the UCMP Site

Follow two additional links within the UCMP website. This is your choice and your opportunity to explore this very cool resource provided by UC Berkeley. The links within UCMP do not have to be related to either sea squirts or otters, but you must include the web address (and it must be within the ucmp.berkeley.edu domain!) and a brief description of what you learned on that page.

Assignment Expectations

This Case Assignment should be entirely completed with the UC Berkeley UCMP website:http://www.ucmp.berkeley.edu/exhibit/phylogeny.html. Points will be deducted for results reported from general Google searches or homework pages. When summarizing the information you read from the UCMP site, be sure to synthesize the information into your own words, and cite the reference using the title of the webpage and its web address. Please use complete sentences and write your paper in essay format using Part I, II, and III as headings, and the topics within each as subheadings.

SLP

Overview
As you have learned in Modules 1 and 2, prokaryotes share many common features that differentiate them from eukaryotes, such as:

Lack of nuclear membrane, unicellularity, division by binary-fission and generally small size.

As introduced on the Home page of Module 3, various species differ and can be classified into taxonomic groups based on several characteristics. One characteristic commonly used to differentiate an organism as belonging to one species or another is the potential for the individuals to reproduce sexually and produce viable offspring. However, this characteristic cannot be applied to prokaryotes, and so their identification and classification is often determined based on:

· Phylogeny: All bacteria stem from a common ancestor and diversified since, consequently possess different levels of evolutionary relatedness

· Metabolism: Different bacteria may have different metabolic abilities

· Environment: Different bacteria thrive in different environments, such as high/low temperature and salt

· Morphology: There are many structural differences between bacteria, such as cell shape, Gram stain (number of lipid bilayers) or bilayer composition

· Pathogenicity: Some bacteria are pathogenic to plants or animals

All microbial metabolisms can be arranged according to three principles:

1. How the organism obtains carbon for synthesizing cell mass:

· autotrophic– carbon is obtained from carbon dioxide (CO2)

· heterotrophic– carbon is obtained from organic compounds

· mixotrophic– carbon is obtained from both organic compounds and by fixing carbon dioxide

2. How the organism obtains reducing equivalents used either in energy conservation or in biosynthetic reactions:

· lithotrophic– reducing equivalents are obtained from inorganic compounds

· organotrophic– reducing equivalents are obtained from organic compounds

3. How the organism obtains energy for living and growing:

· chemotrophic– energy is obtained from external chemical compounds

· phototrophic– energy is obtained from light

In practice, these terms are almost freely combined. Typical examples are as follows:

· chemolithoautotrophsobtain energy from the oxidation of inorganic compounds and carbon from the fixation of carbon dioxide. ie: Nitrifying bacteria

· photolithoautotrophsobtain energy from light and carbon from the fixation of carbon dioxide, using reducing equivalents from inorganic compounds.

For example: Cyanobacteria are photosynthetic autotrophs. Cyanobacteria split water, H2O, molecules and use the electrons to reduce carbon in photosynthesis. Water is the electron donor. However, Chlorobiaceae and Chromatiaceae are also photosynthetic autotrophs, but they use hydrogen sulfide H2S as the electron donor, orreducing equivalent donor.

· chemolithoheterotrophsobtain energy from the oxidation of inorganic compounds, but cannot fix carbon dioxide (CO2).

· chemoorganoheterotrophsobtain energy, carbon, and reducing equivalents for biosynthetic reactions by breaking apart organic compounds (made by photoautotrophs). Examples: most bacteria, e. g.Escherichia coli, Bacillus spp., Actinobacteria

· photoorganoheterotrophsobtain energy from light, carbon and reducing equivalents for biosynthetic reactions from organic compounds. Some species are strictly heterotrophic, many others can also fix carbon dioxide and are mixotrophic. Examples:Rhodobacter,Rhodopseudomonas,Rhodospirillum, Rhodomicrobium, Rhodocyclus,Heliobacterium, Chloroflexus(alternatively to photolithoautotrophy with hydrogen)

For this SLP assignment, you will continue to analyze.trident.edu/d2l/common/dialogs/quickLink/quickLink.d2l?ou=53245&type=content&rCode=TUI-48086″>the paper by Urakawa et al. (2012)by considering the characteristics that allow us to classify the prokaryotic organisms in this study as belonging to different Domains. You will use the website:http://www.ucmp.berkeley.edu/exhibit/phylogeny.html

UC Berkeley’s virtual exhibit hall and resource on taxonomy and phylogeny, to complete this assignment.

SLP Assignment

Review your definitions of Archaea and ammonia-oxidizing bacteria from Module 1. Begin athttp://www.ucmp.berkeley.edu/exhibit/phylogeny.html, webpage titled “Welcome to the Phylogeny Wing. Select the link “Phylogeny of Life” within the first of the “four ways to get started.” You will an overview of the relationship between DNA and the Three Domains of Life. Use this page to begin the research necessary to address these topics in a 3-4 page paper:

1. What general characteristics determine whether a prokaryote belongs to the Archaea or Bacteria domain?

2. Define DNA and RNA. What role do DNA and RNA play in this determination?

3. What role does the metabolism play in classifyingNitrosococcus oceaniandNitrosopumilus maritimusas Archaea or Bacteria?

4. Do either of these organisms normally thrive in an environment where crude oil is abundant? What other microbes live in this type of environment?

Module 4

Case Assignment

In the Module 4 Case assignment you will have the opportunity to explore the new era of personalized medicine that uses genetic mapping to determine medical treatment. Watch the NOVA video:.pbs.org/wgbh/nova/body/cracking-the-code-of-life.html”>Cracking Your Genetic Code to learn more about the genetic technology available to us and what it means for medicine, ethics, and the future of human society.

After watching this video, proceed to the following resource and address the topics below in a 2-3 page paperhttp://www.nature.com/scitable/topicpage/genetic-mutation-1127

1. Explain what a genetic mutation is and the difference between inherited mutations versus point mutations.

2. Describe how the technology explained in “Cracking Your Genetic Code” can be used to detect mutations and predict your health.

3. Form an opinion on whether or not you support utilizing genetic mapping to develop personalized medical treatment. Find evidence to support your opinion and cite your sources. What dangers do you see dangers in knowing our personal genome?

Assignment Expectations

This paper should be approximately 2-3 pages long and reflect the information contained in the resources provided above. When summarizing the information you read from the Nature website, NOVA video, or any resources you use to support your opinions, be sure to synthesize the information into your own words, and cite the references. Please use complete sentences and write your paper in essay format using subheadings to organize the required topics.

Module 4 – SLP
GENETICS AND HEREDITY
Overview
For the Module 4 SLP, you will build on your understanding of the structure of DNA, genetics, and inheritance by exploring some applied genetic engineering techniques. You will review the three papers you have read on the Deepwater Horizon Spill:

Biello D (2010).trident.edu/d2l/common/dialogs/quickLink/quickLink.d2l?ou=53245&type=content&rCode=TUI-48087″>Clean Up the Deepwater Horizon Oil Spill. Scientific America: May 25, 2010.

Urakawa, H., Garcia, Juan C., Barreto, Patricia D., Molina, Gabriela A., Barreto, Jose C. (2012)..trident.edu/d2l/common/dialogs/quickLink/quickLink.d2l?ou=53245&type=content&rCode=TUI-48086″>A sensitive crude oil bioassay indicates that oil spills potentially induce a change of major nitrifying prokaryotes from the Archaea to the Bacteria.Environmental Pollution. 164:42-45

Byrd D (2014).trident.edu/d2l/common/dialogs/quickLink/quickLink.d2l?ou=53245&type=content&rCode=TUI-48090″>How oil spill chemicals cause heart failure in fish.EarthSky Feb 18, 2014.

and consider the effects of toxicity on representative members from three domains:

Archaea -Nitrosopumilus maritimus

Bacteria -Nitrosococcus oceani

Eukarya -Thunnus thynnus(Atlantic Bluefin Tuna)

In order to make connections between the results found in these studies, assess the damage caused by the Deepwater Horizon Oil Spill and move forward in your analysis on how best to remediate the spill.

After analyzing these studies in various assignments in the previous modules, you will now prepare a document for your Shoreline Assessment Team that describes your first interpretation of the data and discusses one approach to remediation that involves genetic engineering.

View these resources to complete this assignment:

Scientific American Instant Egghead Video: Can Microbes clean Up Our Oily Mess?

http://www.scientificamerican.com/video/can-microbes-clean-up-our-oily-mess2013-12-11/

Interview with Professor Barbara Block on BBC News:

http://www.bbc.co.uk/news/science-environment-26184116

Tutorials on Genetic Engineering

Making a Recombinant Plasmid
http://plantandsoil.unl.edu/pages/animation.php?a=making_a_recombinant_plasmid.swf&b=1003514583

Bacteria Transformationhttp://plantandsoil.unl.edu/pages/animation.php?a=Bacteria_Transformation.swf&b=1003514686

Assignment

Prepare a 3-4 page document that outlines your analysis of the effects of the Deepwater Spill on study species in the Gulf of Mexico. In your report include:

Part I – Influence of Crude Oil onNitrosopumilus maritimusandNitrosococcus oceani

1. Which species appeared to be affected by crude oil assays in the Urakawa et al (2012) study? How were they affected in the study?

2. Based on what you know about the metabolism of the organisms, which species was more likely to have been successful in an environment with abundant hydrocarbons?

Part II – Influence of Crude Oil onThunnus thynnus(Atlantic Bluefin Tuna)

1. Provide an overview of the documented effects of crude oil onThunnus thynnus.

2. What stage of development is affected and how could this affect the population?

3. What economic impact would this have on the area?

4. What is a “highly conserved gene?” What relationship do these results have to the effects of hydrocarbons on humans?

Part III – Recommendations for Remediation

Do you recommend genetically engineering a prokaryote to remediate this spill? In your assessment provide reasons for BOTH why and why not this would be a good approach, and describe which genes would need to be targeted and which species would be better suited to be transformed -Nitrosopumilus maritimusorNitrosococcus oceani.

SLP Assignment Expectations
The Session Long Project consists of an integrative project emphasizing the personalized application of each module’s concepts. For Modules 1–5, students are required to engage in an original integrative project reflecting their comprehensive knowledge of and ability to apply the course materials. Each component of the SLP will be graded on a modular basis.

Your essay is considered a scholarly work. You will be provided with many scholarly references to begin each assignment. For any additional research you are required to do to complete your assignment, please use scholarly references such as a peer reviewed journal article or a government sponsored or university sponsored website. As you read through your sources, take notes from your sources and then write your paper in your own words, describing what you have learned from your research. Direct quotes should be limited and must be designated by quotation marks. Paraphrased ideas must give credit to the original author, for example (Murray, 2014). Direct copying from “homework help” websites will not receive credit.

When you write your essay, please organize your paper to include an introduction (overview of the assignment), body with subtitles (reflecting the requirements of the assignment), and a summary (develop connections between the required topics).

Module 5 – Case

NATURAL SELECTION AND ECOLOGY

Case Assignment

In this Case Assignment you will learn about the ecosystems that make up the regions impacted by the Deepwater Horizon Spill. Using resources from the NOAA and your own independent research, write a 4- to 6-page paper that summarizes the characteristics of each ecosystem including organisms commonly found there, potential threats based on their relative location to the spill, and the economic impact of damages in these communities.

Begin your research using diagrams in the report, .trident.edu/content/enforced/53245-BIO101-MAY2015-1/2011NRDA_BWET.pdf?_&d2lSessionVal=ZzRVCa7AwiXSQZMlccW6d5QfW&ou=53245″>Natural Resource Damage Assessment for the Deepwater BP Oil Spillpresented in a B-WET Workshop on April 1, 2011, and the .trident.edu/content/enforced/53245-BIO101-MAY2015-1/FINAL_NRDA_StatusUpdate_April2012.pdf?_&d2lSessionVal=ZzRVCa7AwiXSQZMlccW6d5QfW&ou=53245″>status updatesprovided in April 2012 by the National Oceanic and Atmospheric Administration (NOAA). This and other resources are available on the NOAA website: http://www.gulfspillrestoration.noaa.gov

In your report,

For the following ecosystems:

1. Marine Wetlands

2. Shoreline and Beaches

3. Nearshore benthos

4. Photic zone

5. Deep benthos

Include:

1. An introduction of the characteristics of the ecosytem community

2. The level of the threat posed by the oil spill

3. The affected species

4. The type of surveys conducted to gather the data

5. The economic and environmental cost associated with the damage

For a summary, view the PowerPoint presentation: .trident.edu/content/enforced/53245-BIO101-MAY2015-1/Deepwater%20Oil%20Spill.pptx?_&d2lSessionVal=ZzRVCa7AwiXSQZMlccW6d5QfW&ou=53245″>Deepwater Oil Spill

Assignment Expectations

This paper should be approximately 4-6 pages long and reflect the information contained in the resources provided above. When summarizing the information you read from the NOAA website, or any resources you use, be sure to synthesize the information into your own words, and cite the references. Please use complete sentences and write your paper in essay format using subheadings to organize the required topics.

Module 5 – SLP

NATURAL SELECTION AND ECOLOGY

To complete your SLP, you will complete your analysis of the peer-reviewed article by Urakawa et al (2012) that described the influence of crude oil on two groups of bacteria, Eubacteria,Nitrosococcus oceani, and Archaea, Nitrosopumilus maritimus; that utilize different methods of metabolism. Now that you understand the taxonomic and metabolic differences between these two species, think about how these organisms interact with their environment and how these interactions could potentially affect other populations of organisms. As you prepare to complete this final component of the SLP make sure you think about the nutrients and chemicals that these organisms consume for energy, removing it from their environment, and produce as a byproduct, adding it their environment. By both removing and contributing chemicals and nutrients to their environment, these organisms can alter the availability of nutrients for other organisms.

As we discussed on the Home page of Module 5, the success of individuals, and ultimately of populations of organisms as a whole, is largely determined by their ability to acquire resources from their environment to the extent that they can find a mate, reproduce, and pass their “successful genes” onto their offspring. The term natural selection, describes the role of environmental pressures on determining the success of species. Over long periods of time, the theory of natural selection helps us to understand how species have evolved. Proceed through these brief tutorials developed by the University of California, Berkeley, to understand more about natural selection, and its relevance to your SLP:

Natural Selection http://evolution.berkeley.edu/evolibrary/article/evo_25

Follow the arrows and read the sections on Natural Selection at Work and What About Fitness?

Now complete your research on Nitrosococcus oceani and Nitrosopumilus maritimususing the resources below:

First, visit this website developed by Texas A&M University’s Department of Oceanography:

http://oceanworld.tamu.edu/resources/oceanography-book/microbialweb.htm

to learn more about the marine foodweb, and the relationships between microogranims and larger organisms that inhabit the oceans.

Now read the following article from the University of Washingtonhttp://www.washington.edu/news/2014/02/24/vitamin-water-measuring-essential-nutrients-in-the-ocean/

and this article from the University of Illinois, Urbana-Champaign,

http://news.illinois.edu/news/12/0830methane_WilfredVanDerDonk_WilliamMetcalf.html

to consider additional byproducts and nutrients that these microbes can contribute to the environment, thereby influencing the metabolism
of other species.

After completing your readings, address the following in a 2-3 page paper:

1. What chemicals do Nitrosococcus oceani and Nitrosopumilus maritimus consume from their ocean environment? How does the abundance of these chemicals influence their success and abundance? What is the relationship between nutrient availability and natural selection, in general?

2. What chemical byproducts do each contribute? (Be sure to cite the references above!) How does this relate to the “Greenhouse Effect?”

3. If one group is selected for due to their ability to withstand an abundance of crude oil, what chemical offsets to the environment are possible? How will this affect other organisms in this community? Provide specific examples with references to support your ideas.

SLP Assignment Expectations

The Session Long Project consists of an integrative project emphasizing the personalized application of each module’s concepts. For Modules 1–5, students are required to engage in an original integrative project reflecting their comprehensive knowledge of and ability to apply the course materials. Each component of the SLP will be graded on a modular basis.

Your essay is considered a scholarly work. You will be provided with many scholarly references to begin each assignment. For any additional research you are required to do to complete your assignment, please use scholarly references such as a peer reviewed journal article or a government sponsored or university sponsored website. As you read through your sources, take notes from your sources and then write your paper in your own words, describing what you have learned from your research. Direct quotes should be limited and must be designated by quotation marks. Paraphrased ideas must give credit to the original author, for example (Murray, 2014). Direct copying from “homework help” websites will not receive credit.

When you write your essay, please organize your paper to include an introduction (overview of the assignment), body with subtitles (reflecting the requirements of the assignment), and a summary (develop connections between the required topics).