Thank you for managing yourselves last Friday and maximizing learning during the jigsaw activity.
Some reminders on the Creative Output/Infographic activity:
Please write your answers to questions (by group) and paste a copy of your posters in the gdoc so your classmates can refer to it easily.
If your poster did not address all the necessary guide questions, please revise it and resubmit. Either through the gdoc or through my email: email@example.com. You cannot earn credit for a poster that your classmates cannot use. I discussed some of the gaps/issues with you last meeting and gave some samples of posters from previous batches that did discuss these issues.
Please accomplish these ASAP. We hope that your classmates can still use the information you can share to review for the Bio2 Perio on Tuesday.
Perio (Tuesday, May 8th) Coverage and links (Animations and other resources may be found here):
Search for the Genetic Material (including virus life cycles: lytic v. lysogenic) (presentation, worksheet from Sir Felipe)
Central Dogma (replication, transcription and RNA processing in eukaryotes, translation) (presentation, worksheet)
To fulfill the notebook requirement, you may submit the completely-accomplished 5 worksheets (please staple together or put in a folder) together with or IN LIEU OF your notebooks at SHB109 after the exam on Tuesday.
Letter to a member of the community about Human Impact
Address the letter to a specific person in the community (e.g. Campus Director, EAPWM Head, Agriculture teacher, etc.)
Introduce yourselves briefly and state your purpose (e.g. students of Bio3C learning about…, recommending a site for a proposed MRF, etc.)
State important considerations for the proposed site and how information on this can be obtained (e.g. soil should be moist and fertile and this can be measured through the use of soil test kits, etc.)
Describe your chosen site, include a map/picture
State what you have found out about the site based on interviews/field surveys conducted (e.g. according to a Lumad resource person: …., our survey on biodiversity revealed the presence of…, etc.). You may include a photograph.
State your recommendations about the site, how it is constructed, and how we can monitor its effects on humans and organisms in its surroundings.
List your names.
Send or share with me: firstname.lastname@example.org by the end of the period.
Letter will be rated according to
Purpose – clearly and well-stated
Considerations – comprehensive and practical
Site description – well-described
Data presented – properly-attributed, related to the considerations and recommendations
Recommendations – clear and actionable
Structure and style –proper salutations and closing, correct grammar and proper degree of formality is observed
Your groupmates will also rate you according to your contributions to the activity.
Summative paper is due on April 27, 2018, Friday.
We will have a short trip to the Quezon City Hall Model Waste Management Facility at UP Diliman on May 3, 2018 (Thursday), during lab period (7:30-10:30). Please download the Parent Consent Form here.
Read through the introduction to phylogenetic trees found here.
Use MEGA to create phylogenetic trees from molecular data (instructions are for MEGA 4, so we will have to find equivalents for MEGA 7
Appendix 1—The MEGA_4U Step-By-Step Guide
Like many other scientists, biologists have to rely on computers to solve various problems. One type of problem that requires the assistance of a computer is comparing proteins from different species. In the lab that you are about to do, you will learn to use some newly developed software that professional biologists use on a daily basis to compare proteins.
How to Retrieve Sequences over the Internet Using MEGA 4
Open MEGA 4
From the “Alignment” menu at the top of the MEGA 4 window, select “Open Saved Alignment Session.”
In the pop-up window, locate and open the file named “Project_MEGA_4.”
The Alignment Explorer window will open. Minimize this window for now and go back to the main MEGA window.
From the “Alignment” menu at the top of the MEGA 4 window, select “Query Databanks.”
The NCBI Entrez webpage will automatically open in a separate window.
Next to the “Search” prompt, select “Protein” near the top of the list.
Next to the “for” prompt, type “PAXNEB Pan Troglodytes” and click “Go” (btw, PAXNEB is a gene that controls eye development).
You will be taken to a flat file for the protein sequence.
Find the source organism for this protein sequence and record it on your sheet. It will be listed near the top of the flat file next to the word source.
Scroll down to the bottom of this file and you will see a 424 amino acid sequence (note: each letter represents a different amino acid).
To add this sequence to your alignment, click the “Add to Alignment” button at the top of the window as shown here.
A popup window should confirm that the sequence was added successfully.
Next, you will use the protein sequence you just obtained to find similar protein sequences by performing a BLAST search.
Go to the top of the flat file and next to “Format” click “FASTA” as shown to the right.
The displayed sequence will begin with a header that starts with a “>” symbol and includes the name and accession number.
Highlight the sequence including the header and then copy it (Ctrl C).
Click the back arrow twice (or until you get back to the NCBI Entrez webpage).
From the left side of the Entrez webpage, select “BLAST” (under “Related Resources”).
Just below “Basic BLAST” select “protein blast.”
Now paste (Ctrl V) your sequence into the window just below “Enter Query Sequence.”
Click the blue “BLAST” button.
It may take several moments, but eventually a list of results will appear.
Note: A window may pop up with an error message. Click “OK.” This will not cause any problems, but may pop up frequently.
Scroll down to the box titled “Descriptions.” Try to find PAXNEB genes from one other animal you find interesting. Follow the steps above to add the sequence to the list.
Tip: Use the find function to locate these organisms faster. You can do this by hitting the Ctrl + f keys at the same time and typing part of the organism’s scientific name into the box that pops up.
Click on the accession number (in blue in the leftmost column) and you will be taken to a flat file for the sequence.
Scroll down to the bottom of the report and observe the protein sequence. Add this sequence to the Alignment Explorer by clicking the “Add to Alignment” button at the top of the screen. A box will pop up to let you know the sequence was successfully added. Click “OK.” Once you have added all the sequences you want, you may close the NCBI Sequence Viewer window.
Aligning Selected Sequences Using the Alignment Explorer
In the Alignment Explorer window, select “Save Session” from the Data menu and name your file.
From the Edit menu, select “Select All.” All of the sequences will be highlighted in blue.
From the Alignment menu, select “Align by ClustalW.”
Under Pairwise Alignment in the Clustal Parameters window, change the gap opening penalty from 10 to 35 and the gap extension penalty from 0.1 to 0.75. (Side note: Gap penalties are used to prevent ClustalW from inserting an excessive number of gaps into the alignment it produces. The quantities used here are based on many previous studies of protein alignments and are sufficient to achieve this goal).
Under Multiple Alignment, change the gap opening penalty from 10 to 15 and the gap extension penalty from 0.2 to 0.3.
Click “OK” and MEGA 4 will align the sequences you selected using the ClustalW alignment algorithm (alignment places highly similar, conserved regions in vertical columns by inserting gaps between and around them. Note: the gaps show up as hyphens).
In the Alignment Explorer, select any random letter or dash in the display window. This will cause all other amino acids in the alignment to adopt colors that reflect their biochemical properties.
Scroll through the alignment and note how strongly similar (conserved) regions have been placed into vertical alignment (the gaps were inserted to account for length differences among the sequences).
Sometimes, regions at the beginning or end of the alignment will be poorly aligned because the sequences were too dissimilar in length. We should crop off these poorly aligned regions on the ends of the alignment before moving on.
To remove these areas, first go to the far left side of the alignment.
Look for a small gray box on the top of the first column in the alignment and select it.
Now scroll to the right until you encounter a large conserved block, which will look like several columns with few gaps in them.
Find the leftmost column in this block. Now hold down the shift key and select the little gray box above the column just to the left of this place.
This will select all of the amino acids in the not-so-well aligned region from the beginning up to this point.
From the Edit menu, select “Delete” and Poof! They are gone.
Repeat this procedure for both ends of the alignment, if needed (you will need to select and scroll starting from the opposite end to do this).
Now it is time to export the trimmed, aligned sequences as a MEGA file (with a “.meg” extension). From the Data menu, select “Export Alignment→MEGA Format” and name the file. You will also be prompted to name your input data.
You are now finished with the Alignment Explorer and may close it.
When you close the Alignment Explorer, you will be asked if you would like to open the saved MEGA file. Select “Yes.”
Investigating the Aligned Data with the Sequence Data Explorer
When the MEGA file is opened, a new window will also be opened. This is the Sequence Data Explorer window; we will use it to examine the aligned data.
The data in the Sequence Data Explorer is shown in black and white. To change it to a color-coded format, select “Color Cells” from the Display menu.
You will notice that there are amino acids, in the single letter code, running along the top row of the Sequence Data Explorer; these amino acids are known as the reference sequence.
Below this each cell will contain: (1) a “•” for a match to the reference sequence; (2) a letter, when an amino acid does not match the reference sequence; or (3) a “-” wherever a gap has been inserted.
What we have done up to this point is to make an alignment of PaxNEB genes from many different animals.
Did you notice how some animals have PaxNEB genes that are more similar and others have PaxNEB genes that have more differences? This information will be used to do the next step….
Inferring a Phylogenetic Tree Using the Main MEGA 4 Window
Now go to the main MEGA 4 window.
From the Phylogeny menu, select “Construct Phylogeny→Maximum Parsimony (MP)….”
In the new window that opens, click on the tab that says “Test of phylogeny.”
Select “Bootstrap” and accept the default number of replicates (which should be 500), then click on the red check mark.
Now select the button on the bottom of the Analysis Preferences box that says “Compute” and has a green check mark on it.
In a few moments, you will have an inferred phylogeny based on your aligned data set. This tree shape implies the fewest overall amino acid substitutions for your aligned protein sequences.
Root your tree by clicking on the rooting button (shown to the right) on the top of the left hand toolbar under the arrow and then clicking on the branch leading to the sea anemone. The sea anemone should now be at the bottom of the tree.
You can save a picture of the tree as follows: In the Tree Explorer, from the Image Menu, select “Save as TIFF file.”
Import this file into the shared doc and label where each of the following characteristics first appears on the tree.
Characteristics: body hair, amniotic egg, forelimbs and hindlimbs, hinged jaw, large brain, mammary gland, opposable thumb, left–right symmetry, placenta, muscles, nipples, and vertebrae.
Complete the Pair SW on Point Mutations. Make sure you understand the concepts because this will be included in your LT on Thursday/Friday. You may raise your hands for clarifications or to ask questions.
You may use the following images to help you:
Pass your papers to Ma’am Dawn when complete and get the second worksheet.
Complete the worksheet on Gene Expression. This is not included in the Long Test and will be discussed briefly next week. Check for understanding by answering the quizzes that follow the animations (when available).
Load the following links in separate tabs before answering:
Accomplish the following activities during the designated library period.
Log in to edmodo and check your tentative grades for the third quarter.
Complete Pair Worksheet 1 on the Search for the Genetic Material, link: http://www.dnai.org/timeline/. We will discuss this in class during the first meeting next week.
Your photocopy persons will be distributing Pair Worksheet 2 on DNA replication, transcription and translation within the day. Please complete this by pair. Pay special attention to the items assigned to your class number because you will be asked to show what you know in a creative manner (similar to the enzyme activity). This will be presented in class starting the second meeting of next week.
Graviton, please bring your Biology books tomorrow (3/2/16, Wed) (at least 1 per pair) so you can accomplish the second worksheet during the time allotted for Biology.