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 Drosophila

Abstract (5 points)

 DrosophilaIn a short paragraph describe the experiment that was done as well as the major findings. Clarity is essential. The abstract is usually written last and is limited to 200 words.

Introduction (14 points)

Provide ALL background information a reader would need to understand the purpose, results and analysis of the experiment. Must include:

  1. Why it is important to know the locations of genes in the genome.
  2. A description a crossing-over during meiosis, linkage, recombination frequency (RF), and how RF relates to map units? How does RF change for closely linked versus distantly linked and unlinked, genes?
  3. Why is it advantageous to map three (or more) genes at once instead of mapping each pair of genes separately
  4. The benefits of Drosophila for genetic analyses
  5. The hypotheses for this experiment
  • RF measured in lab will be similar to the expected RF based on known map distances.
  • Reciprocal classes will occur and survive in equal numbers.
  • Interference will be a positive value.

Methods (14 points)

This section should provide enough information so that the reader could carry out the experiment independently.

  1. Explain the experimental strategy: P, F1 and F2. Describe all genotypes and expected phenotypes.
  2. Describe the different traits that were scored.
  3. Why was it unnecessary to determine the sex of the F2?
  4. Describe calculations for RF, map units, and Interference.
  5. Describe the Chi-Square tests that were done and the highest acceptable Chi-Square value for a corresponding p value of 0.05 or lower for relevant degrees of freedom used in your different Chi-Square tests. (Measured vs. published map distances; reciprocal classes)

 Results (14 points)

In this section, the data are shown in tables AND explained in coherent paragraphs.

  1. Produce a table with the counts of each F2 phenotype for: your group’s data, your lab section’s data, data provided by the fly experts. (Note to TA’s: This lab has a long history of terrible data, so each lab instructor will invent a dataset for each of her/his lab sections. These data sets MUST change each semester!)
  2. Produce THREE genetic maps, each based on each of the data sets in the Table. Calculate Interference for each data set. Show the equation for calculation of interference.
  3. Compare expected and observed data for pairwise map distances among the three genes and for reciprocal crosses using Chi-Square values. Report p-values for all comparisons, and state whether differences between expected and observed data can be attributed to chance. Do this for all data sets. (There will be 18 Chi-square calculations, 6 per data set.)
  4. A narrative must describe the table, mapping calculations and Chi-Square calculations. You must interpret your Chi-Square results.  Can deviations from expected values be attributed to chance?  Explain your reasoning.

 Discussion (14 points)

The results are summarized in this section and the reasons WHY data were significantly different than expected are considered.

  1. How do map units calculated from the three data sets (one small and two large) compare to published distances?
    1. What happened for the shorter y-cv distance?
    2. What happened for the longer cv-f distance?
    3. What happened with the 4 reciprocal classes? In the case of reciprocal classes, were any trends observed (certain reciprocals tend to be near equal while others were quite different)? How do mutations affect viability?
    4. Did these results match the hypotheses stated earlier?
  2. Why is it difficult to accurately measure long map distances by RF?
    1. What can be done for more accurate measurements of long map distances?
  3. What difficulties arose when assigning phenotypes when scoring the F2?
    1. What could be done to reduce these difficulties?

 Overall Conclusions (4 points)

Keep this section short, one paragraph at the most. Do not repeat yourself over and over when writing this paragraph!

What do the data demonstrate?

Why is a statistical analysis important?

Summarize ways to improve the outcome of the three point testcross mapping experiment; describe “tricks” for evaluating phenotypes.

PLAGIARISM: Remember, you must use your own words, even if you work with others to discuss what the content of your paper will be.  Do not use quotations; read material, figure out what it means, and then explain in your own words. If you do use material not found in the lab manual or the textbook, be sure to cite it. Instructions for citations are found in the oral presentation section of the Genetics Lab Manual.  All papers must be .doc or .docx files, and will be submitted to your lab’s BeachBoard Dropbox and will be subject to plagiarism detection using TurnitinA strict ZERO policy (on the entire write-up) will apply to all plagiarism that goes beyond a shared, common phrase.  If two students’ papers are found to be highly similar, BOTH students will receive a ZERO.  Do not give your word file to a friend to help them out at the last minute; they will likely take both of you down. Papers must be uploaded to the lab BeachBoard Dropbox BEFORE your lab starts on the designated due date. Please see http://philosophy.tamu.edu/~gary/intro/plagiarism.index.html for some examples of plagiarism.

Citations

To respond to question 1 of the Introduction, you will need to look up papers. Cite these as described in the group oral presentation instructions in the Genetics Lab Manual.

Writing Tips

Many students feel that if they write something in complicated language, they sound more intelligent.  This results in awful sentences such as, “A significant frequency of DNA is made of gene.” “Genes are made of DNA.” makes a lot more sense!  Also, the term “significant” is only used with an accompanying statistical test.  See below for more helpful writing tips:

1) The phrasing, “, so…” is conversational English, and not appropriate for written English.
2) The word “very” has little meaning.  Use a stronger adjective. Four letter V-WORD.
3) Use the passive voice, not “We define recombination frequency as…”  Instead use:  “Recombination frequency is defined ..”
4) Separate different sections into paragraphs so the overall organization is clear to the reader.

5) If you want to use “it” or “they” in a sentence, be certain that the subject referred to is clear.

6) Omit needless words.  Go through each sentence to reduce wordiness.

7)” it’s” = it is; “its” is the possessive.

8) Do not keep using the word “it” in your complex sentences.  Re-word the sentence so the subject is clear.

9) Avoid meaningless sentences such as “Chromosomes are interesting molecules that are found in Drosophila.”  Think of a real point you want to make, and use meaningful language.

10) Avoid contractions; don’t use them!  I cannot emphasize this enough; they’re too informal.

11) Semicolons separate two independent clauses; independent clauses can serve as their own sentence.

12) A colon separates one independent and one dependent clause: as in this sentence.

13) The possessive is rarely used in scientific writing and comes off as awkward and unprofessional.  Do not write, “The gene’s location is not known.”  Instead, write, “The location of the gene is not known.”v

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Climate Change Examining the science 

Objective

–     Climate Change Examining the science     Students will be able to identify how energy is obtained by organisms (how it enters ecosystems).

–           Students will be able to relate changes in C02 to changing temperatures on earth and identify future research needed with regard to C02 and carbon footprints.

–          Students will be able to form an opinion on whether or not they support the “global myth” documentary.

**Please note: The opinions of scientists on documentary are not necessarily shared by your instructor. I want you all to make YOUR decision on controversial issues. Your job is to not simply answer the questions, but question the answers!

 

Part I: Why do we care? (Literature search and background information)  (20 points)

Before watching the documentary, Search the internet to answer the following questions. Include  your website after each question.  State why you chose the source you did (is it trustworthy?) Please use bolded letters or another color for your responses for ease in grading. Thanks!

1.       We have discussed photosynthesis in lab and lecture. What is the purpose of photosynthesis? (2 points)

2.        What gas is necessary for plants to absorb in order for photosynthesis to take place? What gas does photosynthesis provide in order for respiration to take place? (2 points)

 

 

3.       How does the greenhouse effect work on Earth? What would Earth be like without the greenhouse effect?  (4  points)

4.       How do scientists study Earth’s past climate? (3 points)

5.       List the 4 major greenhouse gases ( 2 points)

6.       Why do we care about climate change? (What are some possible consequences or impacts of global warming?) (5 points)

7.       What is current belief in media ( daily news)  about climate change? (2 points)

Part II  Climate skeptics –  Examining the science – Can we believe everything we hear? Can science always provide the answers?  (40 points) each questions is worth one point unless otherwise noted. 

View the following film: “The Great Global Warming Swindle”

https://www.youtube.com/watch?v=52Mx0_8YEtg

Answer the following questions with a brief paragraph. Location for answers will be found in green. Point values will follow questions.

(1) “People have decided you have to convince other people: Since no scientists disagree, then you shouldn’t disagree either”  Professor Richard Lindzen, IPCC & MIT “The Great Global Warming Swindle”

How does this line of thinking compare to that of the scientific method?  What are your thoughts? (2 points) 

(2) “This is a story about how a theory on climate turned into a political ideology…” The Great Global Warming Swindle

“I don’t even like to call it an environmental movement anymore.  What it really is, is a political activist movement” Patrick Moore: Co-founder of Greenpeace from “The Great Global Warming Swindle”

  1. Why would Patrick Moore, co-founder of Greenpeace, question that this is an environmental issuee?
  1. According to the video, when and who actually started this “political activist” movement? (37)

(3) “It is a story of distortion of a whole area of science” The Great Global Warming Swindle

According to the video, what has been distorted?

(4) When did the “Little Ice Age” occur ? When did the Medieval warm period occur? What were temperatures like during the Holocene era? (7)  (2 points)

(5) According to the hypothesis of man made global warming, industrialization should cause the temperature to rise.

  1. What data does the video provide to support or reject this?
  2. What happened to temperatures during the post War Economic Boom ? (11)

(6) If Greenhouse gasses are causing the increase in temperature where should you find the highest temperature readings? (15)

There are two ways to take the temperature in the earth’s atmosphere.  What are they? (2 points)

(8) What did John Christy’s research show regarding temperature at the surface of the earth verses temperature in the troposphere? (16:50) Does his data support the current climate models? (2 points)

(9) (18:32) Al Gore’s argument of man-made Global warming  rests on one all important piece of evidence taken from ice core surveys in which scientists drill deep into the ice to look back into the earth’s climate history hundreds of thousands of years.  What they found was a clear correlation between Carbon dioxide and temperature .  What important information did Gore not mention? (21) (2 points)

(10) (23) The biggest source of CO2 output on earth comes from where?

(11) What happens when you heat the surface of the ocean? (what gas is emitted?) (24)  What happens to this gas when the surface of the ocean cools?  (2 points)

12) Why is there a lag of 100 years for the increase in CO2 after temperature increases? (24:20) (2 points)

(13) Solar Physicist Piers Corbyn predicted climate changes based on what? (2 points)

(14) In 1991 Senior scientists from the Danish meteorological institute decided to compare a record of sunspots in the 20th century to temperature what did they find?  (28:55) (2 points)

(15) According to Shaviv and Veltzer’s research,and Data collected independently from NASA and  the National Oceanic and Atmospheric Admisistration, what is the relationship between Cosmic rays, the formation of clouds and temperature? (31)  (3 points)

(16) In 1974, the BBC warned of impending disaster….What was the perceived threat at that time?

(17) Computer-based models all assume what hypothesis? Dr. Roy Spencer (NASA)(46:22 (2 points)

(18) According to the video, there is a powerful bias within the media and the science community itself toward what type of results? (2 points)

(19 )(52:45) According to Professor Akasofu, what has been happening to glaciers throughout history?

(20)  (54:24) What causes sea levels to change?  (2 points)

(21)According to the researech presented in the film,  does an increase in global temperature increase the liklihood of malaria?

(22) “This is a story  about westerners evoking the threat of climatic disaster to hinder vital industrial progress in the developing world” 

What evidence (or examples) does the video provide regarding a threat to industrialization of developing countries? (1:04:40)  (2 points)art III: Meeting the scientists- (5 points)

Visit the following website: http://www.centredaily.com/2014/03/20/4093680/john-r-christy-climate-science.html

Write a  paragraph stating your reaction to Dr. Christi’s comments in this blog. Do you agree or disagree?  Why?

Part IV: Refining your viewpoint – Digging deeper into the science – Defending your viewpoint (20 points)

  1. Search for scientific evidence ( a peer reviewed article or data from credible scientists 2012 or later) that might refute “Skepticism about Global Warming”.
  • Post the website and results of your search here. (2 points)
  • include the name of the scientists performing the research. (2 points)
  • Write your reaction to the research being conducted. (8 points)
  1. What is your final analysis on global Warming? Who will you believe?  Can you do anything about it? (8 points)

 

 

 

 

 

 

 

 

 

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The effect of manuka honey on the structure of Pseudomonas aeruginosa.

Structure Pseudomonas Aeruginosa

Structure Pseudomonas AeruginosaMaterials and methods. General A culture of Ps. aeruginosa ATCC 27853 was tested with a sample of manuka honey (M109) that was a gift from Prof. Molan of the University of Waikato, New Zealand. Antibacterial potency of the sample was equivalent to 18% (wlv) phenol using a bioassay developed in New Zealand [15]. Minimum inhibitory concentrations and minimum bactericidal concentrations The minimum inhibitory concentration (MIC) was determined in 96-well, flat bottomed microtitre plates (Nuno, Roskilde, Denmark) using double strength nutrient broth (oxoid,of 200 HL overnight broth cultures of the test organism (1 was used as an inocu without dilution, and total viable cell counts were performed to check retrospectively that each well had received approximately 100 cells. Plates were incubated at 37 C for 24 hours and turbidity measured at 400 nm in a plate reader (Anthos btec Instruments) Positive (broth and inoculum) and negative (broth and honey) controls were included Wells with the lowest concentration without growth were recorded as MIC. MBC was determined by plating 20 HL from wells without growth onto nutrient agar (oxoid. Basingstoke, UK) and incubating at 37 c for 24 hours to find the lowest concentration without viable bacteria. Experiments were performed in duplicate on each of three occasions.

Time-kill curve

A time-kill study was performed by inoculating 40 uL of an overnight culture of Ps. aeruginosa ATCC 27853 into 20 mL nutrient broth with and without 20% (wlv) M109 and incubating at 37°c for 24 hours in a shaking water bath (120 cycles min (the honey concentration was approximately twice the MIC value). Samples were removed at known intervals and Miles and Misra surface drop counts were performed by serial decimal dilution in quarter-strength Ringers solution, plating onto nutrient agar and incubating at 37°C for 24 hours

 Electron microscopy

Electron microscopy was performed using the test organism in either the exponential or stationary phase of growth following cultivation in isosensitest broth (oxoid, Basingstoke, UK at 37ec in a shaking water bath for either 3 hours or overnight, respectively. Cells were harvested by centrifugation at 3000 g for 30 minutes (MSE harrier 15/80 centrifuge, Sanyo) at room temperature and suspended in MoPs buffer (pH 7.2) with and without 20% (wlv) manuka honey for 8 hours, or in MoPS buffer containing 20% (wlv) artificial

honey solution to determine the effect of sugars in honey in ce structure (Cooper, Halas & Molan, 2002: Cooper, Molan & Harding, 2002). cells were examined in scanning (SEM) (520OLv Jeol, Herts, Uky and transmission electron microscopy mEM) (1210 Jeol. H uk by the method of Lemar, Turner & Lloyd 16), except that harvested cell pellets for TEM were embedded in Araldite resin. not Spurr.

 Analysis of images

Electron micrographs of untreated and treated cells were examined to identify structural changes such as altered shape, modified surface layers, the presence of electron dense material, and cellular debris. Typically at least six photographs, each with approximately 160 cells were observed, so that more than 1000 cells were counted in total for each sample. Data was analysed for statistically significant differences by the Mann-Whitney test using Minitab (version 15)

Results.

Inhibition studies MIC and MBC were found to be 9.5 and 12 (wlv) manuka honey, respectively. The close proximity of these two values indicates a bactericidal mode of inhibition. This was confirmed by time-kill studies (Fig. 1) where cells exposed to manuka honey were found to lose viability with time yet numbers of untreated cells increased. The time estimated to achieve a 5 log reduction of test organism incubated with nutrient broth containing 20% (wlv) manuka honey was 257 minutes.

 Structural studies

The effect of manuka oney on cell structure was investigated in both exponential and stationary phase cultures because stationary phase cells are often less susceptible to antimicrobial agents than exponential cells. However the structural changes observed in both of these stages of growth were similar and therefore only electron micrographs of exponential cells are presented here. Using scanning electron microscopy the smooth surface layers of untreated cells (Fig 2a) and cells exposed to 20% (w/v) artificial honey (Fig 2b) contrasted with those of honey treated Ps aeruginosa cells, which exhibited marked cell surface changes as furrows and blebs (Fig. 2c). Honey-treated cells also appeared to be shortened and to have distorted shapes (Fig. 2c). In untreated samples 2% of cells were found to have structural irregularities, whereas 80 and 60 cells of exponential and stationary cultures, respectively exhibited irregular cell structure. These differences were statistically significant Table 1). For exponential phase cells exposed to 20% (wlv) artificial honey, 7% cells were found to exhibit structural irregularities. This suggests that the effect of manuka honey on Ps aeruginosa is not due exclusively to the sugars contained in honey. Using TEM, untreated cells (Fig. 3a) and cells incubated in MoPs containing 20% (wlv) artificial honey (Fig. 3b) were entire cells with relatively densely stained contents. In TEM images of honey-treated P aeruginosa (Fig. 3c) cellular debris was clearfy evident and whole cells with evacuated areas were observed.