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    Principles of Taxonomy

    Principles of Taxonomy

    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:
    *chemolithoautotrophs obtain energy from the oxidation of inorganic compounds and carbon from the fixation of carbon dioxide. ie: Nitrifying bacteria

    *photolithoautotrophs obtain 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, or reducing

    equivalent donor.
    *chemolithoheterotrophs obtain energy from the oxidation of inorganic compounds, but cannot fix carbon dioxide (CO2).
    *chemoorganoheterotrophs obtain 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  *photoorganoheterotrophs obtain 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 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 at http://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 classifying Nitrosococcus oceani and Nitrosopumilus maritimus as 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?

    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.

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    Genetics and Heredity

    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) 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). 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) 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 Transformation http://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 on Nitrosopumilus maritimus and Nitrosococcus 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 on Thunnus thynnus (Atlantic Bluefin Tuna)  1.Provide an overview of the documented effects of crude oil on Thunnus 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 maritimus or Nitrosococcus

    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.

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    Natural Selection and Ecology

    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 maritimus using 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 Washington http://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.

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    Healthcare

    Healthcare

    The topic of the research paper will be any disease or condition of the body.  The paper must include a thorough description of the disease/condition; current

    statistics of those affected; explanations on how the various body systems are affected; and any medications/treatments that are available, if any. The paper should be

    complete and the main body should be 1000-1500 words in length (excluding cover page, references, etc.).

    Research Paper Guidelines
    •    Utilize APA Style format and references.  See the Owl at Purdue site for help with APA formatting principles:  http://owl.english.purdue.edu/owl/resource/560/01/
    •    Utilize at least five references (two of which must be from credible scientific organizations).  You can use Internet articles, journals, text books, etc. In

    fact, I strongly recommend that you utilize the APUS Online Library for your research as they offer a plethora of reliable and pertinent research sources. You may

    access the Online Library by clicking on the “Online Library” link on the menu inside the electronic classroom. However, you should NEVER use Wikipedia for your

    research as anyone can alter the information on this site making it a poor source of accurate information.
    •    Paper must be typed in MS Word.  **PLEASE NOTE that you must submit your assignments as a “Microsoft Word” document rather than a Word Pad, Works, etc. type of

    document, otherwise you will not receive credit for your work.
    •    Utilize one inch margins on all sides.
    •    Double-space your paper.
    •    Use either an Arial or Times New Roman font in a 10 or 12 point font.
    •    Include a cover page, an abstract, page headers, in-text citations, and a reference page.
    •    Submit a high-quality paper, free of spelling and grammatical errors; use your Spelling and Grammar checker in Word AND proofread your final draft!!!
    •    Should be written in your own words; answers should not be copied from other sources – see section on plagiarism.  Properly formatted in- text citations and

    references are required as noted above.

    Students will be graded on format, content, and grammar using the SCIN132 Research Paper Grade Sheet.

    **Evaluation/Grading of the Research Paper: Points are allocated as follows (Total of 100 points):

    A.  Content/Subject Knowledge and Analysis – (65 points possible). Your paper should be pertinent to the subject matter and demonstrate knowledge and understanding of

    the subject with an appropriate introduction, supporting paragraphs, and conclusions. The paper itself should be between 1000-1500 words (not including cover page,

    references, etc.).  Your paper should be written in your own words using proper in-text citations when indicated.  Please review the “Plagiarism” section located

    inside the APUS classroom under the “Policy” link for details.  You should use a minimum of five current and reliable sources for your research.

    B.  Format – (20 points possible). Your paper should contain a cover page, an abstract, a main body and a reference page. References should be cited and properly

    listed in APA format. Whenever you write a paper based on the research of someone else’s work, you must give credit to the original author. If you do not cite and

    document your sources carefully, you run the risk of plagiarism. In addition, when you document papers correctly, you provide others with a way to find the sources you

    have used. I recommend you visit the following web site (The Owl at Purdue) to learn how to properly cite your sources in the APA format:

    http://owl.english.purdue.edu/owl/resource/560/01/.  Your paper should be typewritten in double-spaced format using Arial or Times New Roman styles in a 10 or 12-point

    black font. All page margins (left, right, top, and bottom) should be set to 1 inch.

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    CELL CHEMISTRY

    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.

    Begin by describing the origin of crude oil deposits in the ocean. What role did photosynthesis play in this process?
    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
    Why is nitrogen important to living systems?
    How are these metabolic pathways similar to photosynthesis?
    From the Urakawa et al. (2012) paper: Why was nitrite production used to measure the activity of the microbes in the study?
    What is a bioassay? Why did the scientists use it in this study?
    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:

    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.

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    Cellular Respiration

    Cellular Respiration

    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 Assignment.

    (Videos on Cellular Respiration) http://www.sumanasinc.com/webcontent/animations/content/cellularrespiration.HTML

    After viewing the videos on Cellular Respiration, answer the following questions in a 2-3 page paper:

    What enzymes are named in the videos (provide at least 5)?
    What do these enzymes do, generally speaking?  Would the reaction occur if they were not present? Why or why not?
    Define these terms: substrate, enzyme, ATP, and describe why they are important in cellular respiration.
    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.

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    Oswalt text, “The Bible Among the Myths, ”

    Oswalt text, “The Bible Among the Myths, ”

    Project instructions:
    Book Summary:

    The first Book Summary will be a summary of the Oswalt text, The Bible Among the Myths, and must be at least 11 pages, not including the title page. Please be sure to

    summarize each chapter, as well as the introduction and conclusion. This assignment is due by 11:59 p.m. (ET) on Sunday of Module/Week 3.

    General Instructions:

    Write a one-page summary for each introduction, chapter, conclusion, and postscript found in the books. The summaries can be written as the reading is being done then

    collected into one coherent paper for submission in Modules/Weeks 3 and 7. Each section should have its own heading in the papers. The major topics discussed in each

    section of the books should be summarized. These are not intended to be book reviews, but summary re-statements of the authors? works in your own words.

    Please use the following guidelines:

    ? Limit direct quotations from the books. Summarize the authors? concepts in your own words.
    ? Add a title page in Turabian format for each Book Summary. The title page does not count toward the total number of pages.
    ? With the exception of the title page, use 1-inch margins all around throughout the body of the papers.

    Oswalt, John. N. The Bible Among the Myths: Unique Revelation of Just Ancient Literature. Grand Rapids, MI: Zondervan, 2009.

    Writer please follow the instructions as listed above to every detail stated.

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    Spain’s cultural perspective

    Spain’s cultural perspective

    Project instructions:
    to save space and pages , no writing format or spacing required.
    In this assignment we look at Spain?s cultural perspective, traditional food habits, and staple foods. Watch the videos: the history of saffron and olive oil. Spain is

    the main olive oil producer in the world. This video shows Spanish olive oil from the tree to the table. Find out more at www.foodsfromspain.com. Answer the following

    questions:

    a.) Name 2 additional Spanish cuisine special ingredients that are not normally found in the average American supermarket?

    b.) Find a Mediterranean market in your area, or on the web, (I noticed at least 6 stores near Falls Church and in Fairfax county) that do sell these ingredients you

    mentioned that are used in cuisine from the north or south of Spain?

    c.) Did you find interesting ingredients that you have not used before? Describe the 2 ingredients and tell us how YOU would use them?

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    Few injustices deeper than the denial of an opportunity to strive or even to hope

    Few injustices deeper than the denial of an opportunity to strive or even to hope

    The   lecture (on Race) ended with the following quote which summarized Stephen Jay Gould’s view of the consequences of bio-determinism (race).

    ‘We pass through this life but once
    Few tragedies can be more extensive than the stunting of life
    Few injustices deeper than the denial of an opportunity to strive or even to hope,
    By a limit imposed from without, but falsely identified as lying within’

    Gould, S.J. 1981. The  Mismeasure of Man [W.W Norton New York].

    Write a reflective account of your own understanding and view of ‘race’, and discuss whether or not you think the concept of race has any validity.

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    Industry Analysis

    Industry Analysis

    Research an airline company and give a brief overview of the company, identify the industry it is a part of, and complete a Five Forces Industry Analysis.
    Research the airline company and be sure to include company information as well as industry information. Write a two-page (500-word) paper to include the following:
    ? A brief company background of the company
    ? Identification of the industry the company is a part of and give a brief overview of that industry
    ? Complete a Five Forces Industry Analysis of the industry identified to include:
    o A one or two sentence explanation of each force
    o Indication if the force is high or low for the industry
    o A brief justification of why you believe the force to be high or low
    CSU requires that students use the APA style for papers and projects. Therefore, the APA rules for formatting, quoting, paraphrasing, citing, and listing of sources

    are to be followed.

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