GENETIC VARIABILITY, MUTATIONS AND SEXUAL REPRODUCTION

Hi Guys:

Use the following information to check the basis for writing an essay, which is our next exercise.

Writing Your Essay

Write a first draft

Your first draft will help you work out:

• the structure and framework of your essay
• how you will answer the question
• which evidence and examples you will use
• how your argument will be logically structured.

Your first draft will not be your final essay; think of it as raw material you will refine through editing and redrafting. Once you have a draft, you can work on writing well.

Structure

Structure your essay in the most effective way to communicate your ideas and answer the question.

All essays should include the following structure

Essay paragraphs

A paragraph is a related group of sentences that develops one main idea. Each paragraph in the body of the essay should contain:

• A topic sentence that states the main or controlling idea
• Supporting sentences to explain and develop the point you’re making
• Evidence. Most of the time, your point should be supported by some form of evidence from your reading, or by an example drawn from the subject area.
• Analysis. Don’t just leave the evidence hanging there - analyse and interpret it! Comment on the implication/significance/impact and finish off the paragraph with a critical conclusion you have drawn from the evidence.
• a concluding sentence that restates your point, analyses the evidence or acts as a transition to the next paragraph.

Tips for effective writing

• Start writing early - the earlier the better. Starting cuts down on anxiety, beats procrastination, and gives you time to develop your ideas.
• Keep the essay question in mind. Don’t lose track of the question or task. Keep a copy in front of you as you draft and edit and work out your argument.
• Don’t try to write an essay from beginning to end (especially not in a single sitting). Begin with what you are ready to write - a plan, a few sentences or bullet points. Start with the body and work paragraph by paragraph.
• Write the introduction and conclusion after the body. Once you know what your essay is about, then write the introduction and conclusion.
• Use 'signpost' words in your writing. Transition signals can help the reader follow the order and flow of your ideas.
• Integrate your evidence carefully. Introduce quotations and paraphrases with introductory phrases.
• Revise your first draft extensively. Make sure the entire essay flows and that the paragraphs are in a logical order.
• Put the essay aside for a few days. This allows you to consider your essay and edit it with a fresh eye.

Paraphrasing, Summarising and Quoting

Much of the work you produce at university will involve the important ideas, writings and discoveries of experts in your field of study. The work of other writers can provide you with information, evidence and ideas, but must be incorporated into your work carefully. Quoting, paraphrasing and summarising are all different ways of including the works of others in your assignments.

Your lecturers expect you to demonstrate an understanding of the major ideas/concepts in the discipline. Paraphrasing and summarising allow you to develop and demonstrate your understanding and interpretation of a text and to avoid plagiarism.

They are important tools for reshaping information to suit the many varied university writing tasks. They require analytical and writing skills which are crucial to success at university.

What are the differences?

Paraphrasing

• does not match the source word for word
• involves putting a passage from a source into your own words
• changes the words or phrasing of a passage, but retains and fully communicates the original meaning
• must be attributed to the original source

Summarising

• does not match the source word for word
• involves putting the main idea(s) into your own words, but including only the main point(s)
• presents a broad overview, so is usually much shorter than the original text
• must be attributed to the original source

Quotations

• match the source word for word
• are usually a brief segment of the text
• appear between quotation marks
• must be attributed to the original source

• Example of a reference list

  Banerjee, A. and Watson, T.F. (2011) Pickard’s manual of operative dentistry. 9th edn. Oxford: Oxford University Press. 

  Davidson, A. (2013) ‘The Saudi Marathon Man’, The New Yorker, 16 April. Available at: http://www.newyorker.com/news/daily-comment/the-saudi-marathon-man (Accessed: 22 June 2015).

And use this articles to understand the topic.

http://faculty.evansville.edu/de3/b10004/PDFs/13b_Sources_variation.pdf

http://www.uwyo.edu/bio1000skh/lecture35.htm

You can look for more information if you consider as necessary

See you at class!!

SEXUAL REPRODUCTION AND GENETIC VARIABILITY

Hi students:

This week we will work in understanding the concepts related to the sexual reproduction and how this type  lead to the genetic variation that produces new species.

First of all watch this video and take some notes, this will be used as a support for a short quiz during the classes of this week.




Secondly, watch this video about the importance of sexual reproduction in organisms.




And finally, bring one exam paper.

See you at class!!!!!

GEL ELECTROPHORESIS VIRTUAL LAB

Hi guys:

This week we will work in a Virtual Lab related to Gel Electrophoresis.

First it is important to check what are the parts of the Lab Report, so here you have a template to remember each one.

Lab Report Template

Title: * a brief, concise, yet descriptive title

Example: "Types of Invertebrates Found in Pond Water"

Introduction: (State the problem or question to be answered)

* What question(s) are you trying to answer?
* Not all experiments start with a question, some start with an observation and questions develop from further observations
* Include any preliminary observations or background information about the subject

Example: How many different types of insects are found in pond water? Does the location of the pond change the types of insects that live there? Does water quality affect the number of organisms?

Hypothesis:

* Write a possible solution for the problem or an explanation for the observation
* Make sure this possible solution is a complete sentence.
* Make sure the statement is testable, an if-then statement is recommended to illustrate what criteria will support your hypothesis (and what data would not support the hypothesis).
* Identify the manipulated (independent) variable and the responding (dependent) variable.

Example: Ponds located near populated areas will have less organisms than ponds found in isolated areas. The manipulated variable is the pond location, the responding variable is the number of organisms.

Materials:

* Make a list of ALL items used in the lab. Draw the to be sure you recognize each of them. Alternatively, materials can be included as part of the procedure.

Example: Pond water, strainers, microscopes, field guides, petri dishes

Procedure:

* Write a paragraph (complete sentences) which explains what you did in the lab as a short summary.
* You may choose to add details (step-by-step) of your procedure in such a way that anyone else could repeat the experiment.

Example: Water was sampled from each pond and examined under the microscope. A field guide was used to identify the types of organisms found and estimations of numbers were recorded.

Data:

* This section should include any data tables, observations, or observations
* You may attach a separate sheet(s) if necessary.
* All tables, graphs and charts should be labeled appropriately (X and Y axis)

Conclusions:

* Accept or reject your hypothesis.
* EXPLAIN why you accepted or rejected your hypothesis using data from the lab.
* Include a summary of the data - averages, highest, lowest..etc to help the reader understand your results. Try not to copy your data here, you should summarize and reference KEY information.
* List one thing you learned and describe how it applies to a real-life situation.
*Discuss possible errors that could have occurred in the collection of the data (experimental errors) and suggest ways the experiment could be improved.

After this please open , READ and print the worksheet in the following link.

WORKSHEET ON LAB ON ELECTROPHORESIS 

Later, enter into the Virtual Lab 

VIRTUAL LAB LINK

Finally, this information taken from: https://www.khanacademy.org/science/biology/biotech-dna-technology/dna-sequencing-pcr-electrophoresis/a/gel-electrophoresis
will help you to understand the characteristics and uses of this procedure.

Gel electrophoresis

A technique used to separate DNA fragments and other macromolecules by size and charge.

Key points:

• Gel electrophoresis is a technique used to separate DNA fragments according to their size.
• DNA samples are loaded into wells (indentations) at one end of a gel, and an electric current is applied to pull them through the gel.
• DNA fragments are negatively charged, so they move towards the positive electrode. Because all DNA fragments have the same amount of charge per mass, small fragments move through the gel faster than large ones.
• When a gel is stained with a DNA-binding dye, the DNA fragments can be seen as bands, each representing a group of same-sized DNA fragments.

Introduction

Suppose you have just done a PCR reaction, making many copies of a target DNA region. Or perhaps you’ve done some DNA cloning, trying to "paste" a gene into a circular DNA plasmid.

Now, you want to check and see whether your PCR worked, or whether your plasmid has the right gene in it. What technique can you use to visualize (directly observe) the fragments of DNA?

Gel electrophoresis

Gel electrophoresis is a technique used to separate DNA fragments (or other macromolecules, such as RNA and proteins) based on their size and charge. Electrophoresis involves running a current through a gel containing the molecules of interest. Based on their size and charge, the molecules will travel through the gel in different directions or at different speeds, allowing them to be separated from one another. 

[Where does the name "electrophoresis" come from?]

$^1$start superscript, 1, end superscript

All DNA molecules have the same amount of charge per mass. Because of this, gel electrophoresis of DNA fragments separates them based on size only. Using electrophoresis, we can see how many different DNA fragments are present in a sample and how large they are relative to one another. We can also determine the absolute size of a piece of DNA by examining it next to a standard "yardstick" made up of DNA fragments of known sizes. 

[More info]

What is a gel?

As the name suggests, gel electrophoresis involves a gel: a slab of Jello-like material. Gels for DNA separation are often made out of a polysaccharide called agarose, which comes as dry, powdered flakes. When the agarose is heated in a buffer (water with some salts in it) and allowed to cool, it will form a solid, slightly squishy gel. At the molecular level, the gel is a matrix of agarose molecules that are held together by hydrogen bonds and form tiny pores.

At one end, the gel has pocket-like indentations called wells, which are where the DNA samples will be placed:

Before the DNA samples are added, the gel must be placed in a gel box. One end of the box is hooked to a positive electrode, while the other end is hooked to a negative electrode. The main body of the box, where the gel is placed, is filled with a salt-containing buffer solution that can conduct current. Although you may not be able to see in the image above (thanks to my amazing artistic skills), the buffer fills the gel box to a level where it just barely covers the gel.

The end of the gel with the wells is positioned towards the negative electrode. The end without wells (towards which the DNA fragments will migrate) is positioned towards the positive electrode.

How do DNA fragments move through the gel?

Once the gel is in the box, each of the DNA samples we want to examine (for instance, each PCR reaction or each restriction-digested plasmid) is carefully transferred into one of the wells. One well is reserved for a DNA ladder, a standard reference that contains DNA fragments of known lengths. Commercial DNA ladders come in different size ranges, so we would want to pick one with good "coverage" of the size range of our expected fragments.

Next, the power to the gel box is turned on, and current begins to flow through the gel. The DNA molecules have a negative charge because of the phosphate groups in their sugar-phosphate backbone, so they start moving through the matrix of the gel towards the positive pole. When the power is turned on and current is passing through the gel, the gel is said to be running. 

[What voltage is used to run a gel?]

$80$80-$120 \text{ V}$120, space, V

DNA samples are loaded into wells at negative electrode end of gel.

Power is turned on and DNA fragments migrate through gel (towards the positive electrode).

After the gel has run, the fragments are separated by size. The largest fragments are near the top of the gel (negative electrode, where they began), and the smallest fragments are near the bottom (positive electrode).

Based on similar diagram in Reece et al.$^2$start superscript, 2, end superscript

As the gel runs, shorter pieces of DNA will travel through the pores of the gel matrix faster than longer ones. After the gel has run for awhile, the shortest pieces of DNA will be close to the positive end of the gel, while the longest pieces of DNA will remain near the wells. Very short pieces of DNA may have run right off the end of the gel if we left it on for too long (something I've most definitely been guilty of!).

Visualizing the DNA fragments

Once the fragments have been separated, we can examine the gel and see what sizes of bands are found on it. When a gel is stained with a DNA-binding dye and placed under UV light, the DNA fragments will glow, allowing us to see the DNA present at different locations along the length of the gel.

The bp next to each number in the ladder indicates how many base pairslong the DNA fragment is.

A well-defined “line” of DNA on a gel is called a band. Each band contains a large number of DNA fragments of the same size that have all traveled as a group to the same position. A single DNA fragment (or even a small group of DNA fragments) would not be visible by itself on a gel.

By comparing the bands in a sample to the DNA ladder, we can determine their approximate sizes. For instance, the bright band on the gel above is roughly $700$700 base pairs (bp) in size.

Check your understanding

Leftmost lane: ladder with 3000 bp, 1500 bp, and 500 bp bands marked on it.

Lane 1: 5000 bp band.

Lane 2: 100 bp band.

Lane 3: 1500 bp and 2000 bp bands.

Lane 4: 500 bp band.

Four lanes are numbered on the gel above. (A lane is a corridor through which DNA passes as it leaves a well.)

Which lane matches each description below?

	$1$1	$2$2	$3$3	$4$4
This lane contains the longest DNA fragment.
This lane contains the shortest DNA fragment.
This lane contains a $1500$1500 base pair (bp) DNA fragment.