Final grades are in - we're done!

Final grades have been submitted, and at 5:00pm (40 minutes from now, as I write this), they will turn over to and become permanent.

This has been a great class, and you should all be proud of how you did. Hope you have a good summer! I'll be seeing many or most of you on Saturday for Graduation!

Cheers!

Jim Brown

Final grades and final grades

The Final exams have been graded and the scores posted on the Grades page. If you wish, you can pick them up in my office any time after noon on Thursday. These scores were a bit low, and so I added 10 points to each raw score - this "curved" score is what is posted in my gradebook and on the Grades page. I have not posted the key yet, because I have one last makeup exam to give on Thursday morning.

More importantly, I have also tabulated FINAL GRADES, and these are also posted on the Grades page. These were calculated based on the scale in the Syllabus (see the Grades page) after curving your total score by giving you a 1/5th rebate on all missed points; i.e. raw% + (100 - raw%)/5 = curved%.

PLEASE LET ME KNOW ASAP IF YOU FIND AN ERROR IN YOUR SCORES. I will post these scores Thurday, and they will become final at 5:00pm.

Lab writeup scores

The lab writeups have all been graded and the scores posted on the Grades page. I'll have these available for you to pick up at the end of the exam on Monday.

Term Project scores

The Term Projects have been graded and the scores posted on the Grades page. Most of you did a very nice job on your project - the average score was 84.4%, despite rigorous grading standards. I'll have these available for you to pick up at the end of the exam on Monday.

Reminder - Final Exam one week from Monday (May 4) at 8:00AM

All material from the Monday and Wednesday lectures since the second midterm will be covered in the exam. Material from the Discussion Sessions will not be covered in the exam! Exams will focus on new material, but students should also expect questions that require cumulative understanding and knowledge required to deal with this new material. The Final Exam will not be comprehensive.

The final exam will be worth 100 points (20% of your final grade). Plan on it taking about 1 hour to complete, although we have 3 hours scheduled. The format of the exam will be a mixture of multiple-choice, short answer, short answer, and essay questions.

I've posted a study guide on the page for today's study session.

Good luck!

If you are an online student, you should plan to take the exam with the other students. If this is not possible because of a final exam conflist, contact me ASAP so that we can arrange a time and date for you t otake the exam early.

Course feedback questionnaire

On Friday (tomorrow) I'll pass out the Course feedback questionnaire. I'll also have them available next week in class, and below is a link to the form as a pdf file you can download & print for yourself. You can turn these in right away, next week, or at the Final exam.

• Course feedback questionnaire

This questionnaire is designed to collect information from you for improving the course. Every non-trivial change I've ever made in this course has been based on data from these feedback forms. Nothing you write on this form can affect your grade. There is no place on the form for your name, and I won't be reviewing these until after final grades are turned in.

This Feedback questionnaire is not a replacement for ClassEval - you are still required by the university to fill out a class evaluation via the ClassEval web site.

Term project question

A common class question seems to be:

I'm having a little trouble with the tree analysis. I'm not sure what a "good" organism is to compare to my sequence. Once a tree is generated how do I tell that it's a good tree or not? I can see how the organism isrelated to others and if it's a strong relation, but not sure how to make further predictions or how to not make predictions.

An answer to this question might be:

In terms of whether or not the tree looks good overall or not, review the major phylogenetic groups & see if they look right - are Aquifex & Thermotoga the deepest branches? If you have more than one member of the same phylum, are they together? For example, are all of the proteobacteria, or at least the alpha, beta and gamma's together? Are the Sphingobacteria and Chlorobi together? Also, VERY long branches for one or two organisms is a bad sign.

About sequence choice on your final tree, let me give you an example. Let's say your organism comes out as an enteric (Enterobacteriaceae) in the Classifier. Then perhaps your closest matches in SeqMatch might be E.coli, some Shigellas, and a couple of Salmonellas. So you might choose the single closest match, and then one of each species in that same genus, and then one example from each of the other genera on the list. SO, you might have both "type" species of the genus Escherichia, then one Shigella and one Salmonella species. Then you might want to sprinkle in a few species of other enterics, familiar ones e.g. Klebsiella pneumoniae, Serratia marsescens, and Yersinia pestis. Then sprinkle in some representatives of the major branches of gamma proteobacteria; Chromatium okenii (Chromatiales), Legionella pneumophila (Legionellales), Pseudomonas aeruginosa (Pseudomonads), Vibrio cholerae (Vibrionales), for example. Then add a couple each of familiar alpha, beta, delta and epsilon proteobacteria. If your tree now looks too complicated (with all of your representative sequences from your first tree still included), then you might decide to winnow out some of the less interesting phyla representatives: maybe Chlorobium, Chlamydiae, Spriochaetes, Deinococcus.Thermus, this sort of thing. Look again - are there big holes in the tree? Crowded areas in parts of the tree far away from your organism(s)? (For example, if your sequence is closely related to E.coli, no need to include 18 different Gram-positives.)

The last question is about predictions. This is relatively straightforward. Identify the smallest group you can specifically assign your organism to - not species (rRNA analysis isn't this high-resolution), but genus, family class, order or phylum. What does the Classifier tell you about this? Then find out what properties are present in all or nearly all members of this group - since your organism is also a member of this group, you would predict that it would share these properties. For example, if your sequence seems to be a memebr of the cyanobacteria, you would predict that it would be able to carry out oxygenic photosynthesis and fix carbon using the Calvin cycle. On the other hand, other properties, that are not conservd within this group, you cannot predict for your organism with any confidence - in other words, these are the things you cannot predict about your organism. For example, if you have a member of the family Clostridium, you would predict it to be heterotrophic, but different genera & species in this group use different growth substrates, the particular growth substrates your organisms might use are probably not predictable. Be sure here to include the obvious - Gram + or -, cell shape, this sort of thing.

Final exam study guide

I've put together & posted a study guide for the final exam.

Uncoming due dates

• Any remaining lab wite-ups due this Friday - April 17th.
• Term projects due next Friday - April 24th
  

ClassEval

ClassEval, the University's online class evaluation system, will be open from 8 am on April 13 until 8 am on April 27 when finals begin. During this period, you will receive email message(s) asking you to evaluate each of your classes and labs (with a few exceptions) by going to a website and completing brief questionnaires.

Please go to ClassEval at: https://classeval.ncsu.edu/ . If you need help, you should email classeval@ncsu.edu .

PLEASE complete a questionnaire for this course. Reminders will be sent every few days to anyone who has not completed all of their class evaluations. You will stop receiving the reminders as soon as you have completed all of your class evaluations.

Reminder -This is the last week of lab!

This is the last week we'll be having labs. If you're in the Friday lab and have work to finish uo, you're welcome to come to either the Wednesday or Thursday lab to get your work done.

Also remember - any remaining lab write-ups are due April 17th

What do you want to talk about on Friday?

I forgot to have a poll in class today to determine what we're going to talk about on Friday, so if you could send me an email with your preference over the next 24 hours, I'll tabulate the results & let you know what it'll be. In order to keep things simple, let's choose between:

Paper	Votes so far:	The Winner
Bacterial symbionts of the deep-sea hyderthermal vent scaly snail	|||| ||
Pelagibacter ubique (a.k.a. SAR 11) - the most abundant creature on Earth	|||| |||| |

And, as usual, we can review anything from the recent lectures you wish.

Midterm Exams grades & scores posted

I've finished grading the exams, and posted the scores on the Grades page. I should be able to bring the graded exams to class on Monday for you to pick up.

• Key to midterm exam #2

The scores are a bit low, so I've added 10 points to each actual exam score. It is these "curved" scores that appear on the Grades page. This brings the average up to 79%.

If you're concerned about your class grade so far, I'd be happy to chat with you about it. Many of you are very close to the next grade up, and so have reason to hope you can bring it up. In addition, lab grades (both the write-ups and Term Project) are usually higher than the exam scores, and so present an opportunity to bring your grade up from where it is right now.

Last sequencing results in and posted

The results of the sequencing of the last batch of PCR proucts from lab are back. Most of them look good. Those that are weak or bad will be redone, but I don't hold out much hope for these, none of the previous weak reactions have improved when redone.

Note added 3/27/09 : The last of the redo's are in, and a couple of these are improvements. Look for the sequences with the "#2" tag.

So this means you can all start on the Term Project.

If you have more than one good sequence, you can use them all, or only use the one(s) you find most interesting. Consider donating one to a fellow student who doesn't have any good sequences.

If your best sequence is weak, go ahead with it. If you have weak sequences but also hve one or mosre good sequence(s), drop the weak one(s).

If you have NO useable sequences, you should ask one of your fellow students who has extras to donate one to you. Make sure you collect their microbiologiucal info, you'll need this for the Project as well.

What are students responsible for from the papers for each lecture?

From now on, each lecture will be primarily a discussion of 1 or 2, or 3, scientific papers. I will provide links to copies of these papers or each class. In past years, I have required students to read each paper, and be responsible for this material for exams. I don't think I was very successful with this requirement, and in any case because all of this material is now concentrated in a single block of lectures (from now until the end), I've decided not to require you to read these. You are, of course, responsible for the material we cover in class and in the notes, but not for material in these papers that we do not cover.

Sporocytophaga

I can't remember who it was, but someone showed me a slide from a single colony on Thursday or Friday with nice long spindled flexible rods (often laying side-by-side) and large cocci together - a beautiful textbook example of pleomorphism. I couldn't dredge up the name of the organism at the time, but it's Sporocytophaga. Here's a picture from "The Prokaryotes" (my main source of info for all things microbial):

The third batch of sequence data has arrived

The sequencing data from the PCR DNAs that you pruified & examined on the gels last week have arrived. You can look these up in the data folder (use the link below) by reaction number. I've also updated our results to date by reaction number.

• Sequencing data files
• PCR & sequencing results summary table

The gels from last week are also posted:

• Gel image page

Online students need to arrange for taking midterm exam #2

Online students:

As you know, the second midterm exam in MB 451 is scheduled for March 23rd. As usual, I ask you to come & take the exam with the non-online students at the usual class time (11:20) and place (2312 Williams) if this is possible. If this works for me, please let me know.

If this is not possible for you to take the exam with the other students, then we need to arrange an alternative date & time. You can see what my schedule is on my advising calendar at:

http://www.mbio.ncsu.edu/advising/

The time zones on this calendar in green or blue are available to take the exam. Times in yellow might be arranged, times in red/pink I won't be able to do. Don't worry about the blue time slots when I'll be meeting students for advising - I'll be in my office during this time & you can be taking the exam next door in my lab. Let me know by email when you can take the exam - Wednesday would be best, alternatively let's try to do Thursday. Friday is the last day. Plan on giving yourself at least an hour.

Notice that I've posted some study guidelines on the web site in the space or the Study session next Friday. These might be useful for you.

Lastly, it would be best if you could attend the next 2 Friday discussion sessions if you can. This Friday we'll be taking in detail about the Term Project, and next Friday we'll be talking about the exam. Of course there is online material for these, and there will be the audio recordings of these sessions, but think about coming in person if you can.

Lectures for next week posted - the last for the upcoming midterm exam

First batch of lab write-ups graded

Despite some delay caused by the birth of Bryan to TAs new child, the firtst batch of lab writeups have ben graded, and these will be available in class and lab this week to pick up. Scores for these have been posted on the Grades page.

Today's lecture notes repaired?

The apparent incompatibility of the web page from today with Internet Explorer has, I think, been repaired. If you still have each paragraph shown on a single line of a page WAY too wide, first try refreshing the page in your browser. If this doesn't work, please let me know by email.

The second batch of sequence data has arrived

The sequencing data from the PCR DNAs that you pruified & examined on the gels last week have arrived. There aren't very many of them, but they all came out with nice sequence. You can look these up in the data folder (use the link below) by reaction number. I've also updated our results to date by reaction number.

• Sequencing data files
• PCR & sequencing results summary table

The gels from last week are also posted:

• Gel image page

We'll use the Discussion seession on the Friday after Spring Break to talk about the Term Project.

The first batch of sequence data has arrived

The sequencing data from the PCR DNAs that you pruified & examined on the gels last week have arrived. Most look good, a small number are weak or bad, and these will be tried again in the next day or so. You can look these up in the data folder (use the link below) by reaction number. I've also tabulated our results to date by reaction number.

• Sequencing data files
• PCR & sequencing results summary table

Have a look at your data - the .pdf files are probably the place to start. How do they look?

We'll use the Discussion seession on the Friday after Spring Break to talk about the Term Project.

Discussion session next Friday canceled

Given that the following week is Spring Break, I don't see an informal Discussion session this Friday being a very high priority for most of you, and so I've decided to cancel it.

Those of you in the Friday lab will, of course, still need to come to lab next week. Sorry.

I've set aside the first Discussion Session after Spring Break (March 13th) to talk about the Term Project.

Lab gel images posted

I've posted the images of todays lab gels on a web page linked to the Data page of the Term Project. They look good - it looks like everyone had at least one PCR product!

• Gel image page

Midterm exams graded & scores posted

The midterm exams are graded and scores are posted. For your overall grades for the course, see (as usual) the Grades page. Drop me an email if you can't remember the PIN you requested for posting your scores.

• Key to midterm exam #1

The average on the exam was 81.3, the median score was 85, and the range was 54 to 100.

Those of you that are concerned about your score should keep in mind that each of the three exams in this course are very different, and many who don't do well on the first exam fare better on the other exams. This is also a warning to those of you who did well on this exam, because this is also true visa versa. You should also keep in mind that most students get overall better lab scores than exam scores. For example, the overall average exam score last year was 80%, whereas the overall lab score was almost 90%.

I will have the graded exams for you to pick up in class and lab next week, starting with class on Monday. You should review your scores and my grading, and get up with me ASAP if you have a question. If you think I've marked off for a good answer, be prepared to explain how your answer as written deserves a better score - do NOT whine or tell me what you meant to write.

Error on midterm exam - impossible branch lengths!

As most of you know, there was a problem with the "tree building" question on the exam. One of the numbers was not changed during a last-minute adjustement in the question, resulting in a tree in which no set of branch lengths could match exactly those given in the matrix. This error only affects this problem of branch lengths, it does not affect solving the tree structure.

As a result, the 7 points that went with these branch lengths (1 point for each length) will be given to all students, and only the process of solving the tree structure in this question will be graded, for 8 points.

Study session Monday at 2:30 in the teaching lab

We'll have an exam study session/workshop at 2:30pm on Monday (Feb 2nd) in the regular teaching lab space (GA 1522). The focus of this study session will be phylogenetic analysis: alignments, tree construction, and interpreting trees. All students are welcome.

Reminder - First Midterm Exam next Wednesday (Feb 4)

As you know, the first midterm exam is fast approaching - next Wednesday.

If you are an online student, we need to arrange a time and date for you to make up the exam.

The exam will cover all of the material in the notes to date (including Monday's lecture), and will be worth 100 points (20% of your final grade). Plan on it taking 1 hour to complete; some will finish much faster, some may need a little more time than this. The format of the exam will be a mixture of multiple-choice, short answer, short essay, and problem-solving questions. Expect an exam very similar in format to the recent Midterm #1 exams posted on the Exams page of the MB 451 web site.

Your best approach to studying for the exam might be to:

• study the notes,
• do the problem sets,
• go over the old exams, starting at the most recent and working your way backwards in time. Keep in mind that the material covered changes, and so you may see unfamiliar material, especially in the older exams.
• then go over the notes again

Good luck!

Updates of this weeks lectures posted

I've updated the posted lectures for this week. No difference in material, I've just asumed that we get further in Mondays lecture than originally planned, and spend more time of the subsequent materail than originally plnned. To have a look at these, go to the Lecture Page.

Lecture audio recordings

Thanks go to David Culver, who's been recording class lectures and is making these available for me to post for everyone. Links to these recordings are now included on the Lecture page, and at the top of any lecture that it's available for. Look for the icon that looks like a tape and microphone:

These are MP3 files, 30-40 Mbytes each.

Update : I'm doing these myself now, and plan to do all of the remaining lectures.

Opportunity for lab experience in microbial diversity

Dr. Levin in the Vet School has an opening for a student who wants to get some lab experience. They're woking on bacterial colonization of freshwater clams. If you're interested, contact Tony Szempruch at ajszempr@ncsu.edu.

Blue Cards

This is just a reminder that if you're planning to graduate this semester, you need to have your "Blue Card" in to Robert in the Microbiology office by Jan 30 at the very latest. Before you can do this, you will need to have meeting with your advisor, so plan ahead.

Results of the poll - what we'll be talking about today

The poll results for todays Discussion session are:

• 4 votes - Canine transmissible venereal tumor, a contageous cancer (4.9Mbyte PDF) (the paper, a 584Kbyte PDF)
• 4 votes - Detection of 400-year old Yersinia pestis DNA in human dental pulp
• 3 votes - Fossil evidence for past life on Mars? (This is an elderly paper)
• 3 votes - Molecular phylogenetic analysis of Bacillus in bees fossilized 23-40 million years ago in amber.
• 1 votes - The deep sea scaly snail and it's symbionts (1Mbyte PDF) (the paper, a 1Mbyte PDF)
  
• 1 vote - Pelagibacter ubique (SAR11); the smallest known free-living organism (2.2Mbyte PDF) (the paper, a 140Kbyte PDF)

As we have a tie for first place, I flipped a coin. The result is that we'll be talking about Canine transmisible venereal tumor.

Which of these papers would you like to discuss on Friday?

Since we're not going to start lab until next week, perhaps we should hold off on reviewing the basis of the lab isolations (planned for this Fridays Discussion Session), and instead talk about an interesting paper. So, let's take a poll - which of the following papers would you like to review & chat about?

• Fossil evidence for past life on Mars? (This is an elderly paper)
• Molecular phylogenetic analysis of Bacillus in bees fossilized 23-40 million years ago in amber.
• Detection of 400-year old Yersinia pestis DNA in human dental pulp
• The deep sea scaly snail and it's symbionts (1Mbyte PDF) (the paper, a 1Mbyte PDF)
  
• Pelagibacter ubique (SAR11); the smallest known free-living organism (2.2Mbyte PDF) (the paper, a 140Kbyte PDF)
• Canine transmissible venereal tumor, a contageous cancer (4.9Mbyte PDF) (the paper, a 584Kbyte PDF)
• Nanobacteria - tiny life or normal human biochemistry?

Send me an email with your vote by Thursday night - I'll tally up the votes and which ever paper has the most votes wins.

Yet another lecture room change - we'll be in Williams 2312

We were originally assigned to Daniels 216, then moved to Mann 323, but this room was already informally booked for another class, so we've been moved again, this time to Williams 2312.

First set of lectures posted

I've posted the first batch of lectures, covering the material for the first midterm exam. To have a look at these, go to the Lecture Page.

Lab schedule change

Although originally we had planned to start lab in the first week of classes, this has changed to the second week, Jan 14-16. For more info, go to the Lab Page.

Lecture room change - we'll be in Mann 323

Although originally assigned to Daniels 216, this room doesn't have any A/V equipment and so we've been moved to 323 Mann Hall.

Welcome to MB 451 - Microbial Diversity!