Monthly Archives: October 2013

Week 9: Shouldering the load

Saturday was a big sports day.  We had work and visitor distractions, but I did manage to watch most of the Aggie game and the end of the Stanford-Oregon State game after the wild ending of the World Series game 3.

Vanderbilt at A&M started at 11:20AM. The big question going into yesterday was whether Johnny Manziel would be able to play after hurting his shoulder last week against Auburn.  He had been seen in a sling and had been reported to be throwing left-handed in practice (presumably goofing off). The fear was that without Johnny Football, A&M would not be able to ourscore Vandy, who had just beaten Georgia. Vanderbilt was without their starting QB, but the freshman who would start had played well vs. the Dawgs and the much-maligned Aggie defense was predicted to give up lots of points. As it turned out, Manziel did play, and the D had its best game of the year, allowing both backup QBs to get reps and lead TD scoring drives.

The game felt closer than the 56-24 final score. A&M jumped out to a 28-0 lead by early in the second quarter, but then went turnover on downs, interception, fumble, fumble, fumble on possessions spanning halftime. Before the intermission, Vandy scored 17 unanswered points and would get the ball first in the second half.  At this point many TAMU fans were getting nervous. Fortunately for the Ags, on first play from scrimmage, Vandy QB Patton Robinette threw a pick-6 to safety Howard Matthews.  This meant that the Aggie D and the Vandy offense each got 7 points out of the Commodores 8 second-half possessions.  A&M doubled their total sacks for the year by adding 7.

Between the end of the TAMU game and the Stanford game, there were a bunch of other interesting things that I mostly didn’t watch while working on the grant and on the previous post about peptidoglycan.

  • Va Tech lost to Duke
  • Undefeated Texas Tech lost to OU
  • Undefeated Missouri lost in OT to S. Carolina

I did catch the end of game 2 of the World Series. Wow!

peptidoglycan transpeptidase diversity and nomenclature

A couple of weeks ago the Biochemistry Graduate Association Gyanu Lamichhane to give a seminar on his work on peptidoglycan transpeptidases.  In his very nice talk Lamichane told the story of how a search for transposon mutants with virulence phenotypes led him to work on an unexpected peptidoglycan transpeptidase. Lamichhane’s talk prompted me to look at what is needed to represent peptidoglycan transpeptidases in the Gene Ontology. This post is my notes so far on figuring out what is needed.

Some background is in order to explain why this enzyme was unexpected. Peptidoglycan makes up the bacterial cell wall. Because it’s not found in eukaryotes (e.g. humans), and it’s needed to keep bacterial cells from exploding, peptidoglycan synthesis has long been the target of clinically important antibiotics.  In the textbook version of peptidoglycan, an intermediate precursor is constructed where a pentapeptide is built up on a UDP-MurNac. This MurNac-pentapeptide is linked to a UDP-GlcNac to make a disaccharide with an attached pentapeptide.  This is transferred to a carrier, flipped to the outer surface of the inner membrane, and polymerized into the growing peptidoglycan. Crosslinks catalyzed by peptidoglycan transpeptidases create a polypeptide orthogonal to the polysaccharides.

In many organisms, including E. coli and M. tuberculosis, the unit can be written as:

GlcNac-MurNac-(L-Ala1-D-iso-Glu2-m-DAP3-D-Ala4-D-Ala5)

in others, including Enterococci, it’s

GlcNac-MurNac-(L-Ala1-D-iso-Glu2-L-Lys3-D-Ala4-D-Ala5)

20131026-224803.jpgm-DAP is meso-Diaminopimelic acid, also known as D, L-Diaminopimelic acid is made in a few different ways, but is an intermediate in both peptidoglycan and lysine biosynthesis. Lysine is made by decarboxylating the D end of mDAP. The L end is what gets incorporated into peptidoglycan.

The textbook version of peptidoglycan has crosslinks made by a transpeptidation reaction where the D end of mDAP (the acceptor) replaces the terminal D-ala on another pentapeptide.  This could be called a 4-3 D,D transpeptidation reaction with the D-Ala from the 5 position being the leaving group.

Lamichhane’s transpeptidase links two m-DAPs at the 3 positions directly together, with the side chain of one attacking the backbone of the other, with the release of D-Ala-D-Ala.  The donor is the L end of the mDAP, so I think this is why I’d call it a 3-3 L,D transpeptidation.  The nomenclature here is related to, but not identical to, what I’m seeing in the papers, where they talk about 4-3 and 3-3 crosslinks and D,D and L,D transpeptidases.

The reason we need names that are more specific than L,D and D, D is that it gets more complicated. In E. coli, in addition to the D,D 4-3 transpeptidases there are five L,D transpeptidases. Two make direct 3,3 links like Lamichane’s enzyme from TB. Three others use the ε NH2 of the C-terminal Lysine of Lpp (aka Braun’s lipoprotein) as the acceptor, resulting in attachment of Lpp to the peptidoglycan.

Meanwhile, in Enterococcus, what I wrote is oversimplified L-Lys replaces m-DAP at the 3 position, but sometimes the Lysine is modified to form things like (N ε-D-Asx)-L-Lys in E. faecium.  And this just scratches the surface of chemical diversity in bacterial peptidoglycan.

  1. Gupta, R, Lavollay, M, Mainardi, JL, Arthur, M, Bishai, WR, Lamichhane, G et al.. The Mycobacterium tuberculosis protein LdtMt2 is a nonclassical transpeptidase required for virulence and resistance to amoxicillin. Nat. Med. 2010;16 (4):466-9. doi: 10.1038/nm.2120. PubMed PMID:20305661 PubMed Central PMC2851841.
  2. Magnet, S, Dubost, L, Marie, A, Arthur, M, Gutmann, L. Identification of the L,D-transpeptidases for peptidoglycan cross-linking in Escherichia coli. J. Bacteriol. 2008;190 (13):4782-5. doi: 10.1128/JB.00025-08. PubMed PMID:18456808 PubMed Central PMC2446776.
  3. Magnet, S, Bellais, S, Dubost, L, Fourgeaud, M, Mainardi, JL, Petit-Frère, S et al.. Identification of the L,D-transpeptidases responsible for attachment of the Braun lipoprotein to Escherichia coli peptidoglycan. J. Bacteriol. 2007;189 (10):3927-31. doi: 10.1128/JB.00084-07. PubMed PMID:17369299 PubMed Central PMC1913343.
  4. Mainardi, JL, Morel, V, Fourgeaud, M, Cremniter, J, Blanot, D, Legrand, R et al.. Balance between two transpeptidation mechanisms determines the expression of beta-lactam resistance in Enterococcus faecium. J. Biol. Chem. 2002;277 (39):35801-7. doi: 10.1074/jbc.M204319200. PubMed PMID:12077139 .
  5. Wehrmann, A, Phillipp, B, Sahm, H, Eggeling, L. Different modes of diaminopimelate synthesis and their role in cell wall integrity: a study with Corynebacterium glutamicum. J. Bacteriol. 1998;180 (12):3159-65. . PubMed PMID:9620966 PubMed Central PMC107817.
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Imagine a boot stamping on your ideas forever

Via Daring Fireball, author Charlie Stross writes about his hatred of Microsoft word.  I don’t know enough to evaluate the technical arguments about design and file formats, including the comments left by a commenter “globetrotter” who self-identifies as a MS program manager for early versions of Word. But the empirical experience of Word is sufficient to share Stross’ loathing for it, shared by the majority of his commenters.  I just about choked when I read globetrotter’s comment:

In Word you can open a 200,000 page document, and make 20 quick edits and save without it taking most of the afternoon.

Really? Now it may be true that Word can handle a 200K page plain text document better than competitors.  But if this 200K page document contains any embedded textboxes, figures, or tables that are the reason to use Word vs a plain text editor, it’s likely to crash horribly.  I’ve suspected for years that Word has a calendar function that crashes more frequently as grant deadlines approach.

Even when it doesn’t crash, I hate the way Word (and Office) change your text to “correct” it. Word and Powerpoint are responsible for a generation of biologists misusing the abbreviated forms of the binomial species names; I’ve lost count of the times I’ve seen E. coli rendered as E. Coli. And things like this comment are all too familiar:

 One of the things the Tech Ed supplied us was a monthly Q&A column. Going over his copy, I noticed that he’d eschewed the usual “Q” and “A” prefixes in favour of “Q” and “R”. “Question and Response, I guess… OK, bit quirky, bit individual, leave it in”. The second question and answer were also given as a pair of paragraphs beginning “Q” and “R”; the third question and answer, however, came as a pair of paragraphs beginning “S” and “T”.

At this point I saw what was going on, and changed the “R” prefix to an “A”.Word changed it back, right before my eyes. It happened several times before I got the changes to stick, even after I’d told it not to format the paragraphs as numbered lists.

Editing a multiple choice test in Word can be a real adventure.  Then there are things like mysteriously unselectable formatting elements, and unusably dense track changes markup.

So I hate Word too.  So why do we use it?  First some minor quibbles:

Was Word first?

Stross writes:

Steve Jobs approached Bill Gates to write applications for the new Macintosh system in 1984, and Bill agreed. One of his first jobs was to organize the first true WYSIWYG word processor for a personal computer — Microsoft Word for Macintosh.

Xerox Bravo was first, but the Alto never made it to the market. Similarly, the WYSIWYG in the Xerox Star and Apple Lisa could arguably be discounted. But if we use the original Mac as the personal computer where WYSIWYG Word first appeared, both MacWrite and WriteNow (originally for the NeXT) were available before the first version of Word for the Mac. I wrote my PhD dissertation in WriteNow before Word was available. Perhaps Stross is saying Microsoft promised the first WYSIWYG for a personal computer, but was late to deliver it.

TeX and scientific writing

 

Not all commenters agree, but you see this kind of thing in discussions of Word suckitude

I know that for scientific publications, latex is the rule (a friend of mine does a lot of mathematic translations).

LaTex is the rule in some fields, but not others. NSF’s survey of doctoral scientists from 2008 (pdf) shows that 164,000/651,200 employed PhD scientists and engineers were in the life sciences.  Biologists use Word. The NIH grant templates are in word. Our journals accept Word files. Our journals even link to downloadable Word files as supplemental data (ugh).  But if my Facebook friends around grant time are representative, there are plenty of other biologists who hate Word.

If we hate it, why do we use Word?

To some extent, it’s for the same reason everyone else does: because everyone else does. The ability to edit Word documents is assumed when you are collaborating with others.  Collaboration with people who didn’t want to use Google Docs is why I did my most recent upgrade to Word; there were docx files that my older version could no longer convert. If you’re not collaborating with others who demand the ability to work in Word, the journals and granting agencies take pdfs these days, so you can switch to anything that can generate pdfs. Not that long ago, journals and granting agencies expected hardcopy, so you could do your word processing in anything that could print.  Several colleagues and I clung to WriteNow  for a long time.

For biologists like me, I think grants drove people to use Word more than publications.  After all, for publications, we still submit things in dull double-spaced text without inline figures and tables. The publisher has the fancy stuff to do the layout. But for the grants we used to print and now submit as pdfs, there is no other publisher/design house to handle the layout. And as much as we as scientists may try to value substance over style, all other things being equal, a grant that is easier on the eyes gets the edge.  Inline figures and tables for a grant are even more important now that page limits have been reduced at NIH. And even if a campus had their own service to do layout on our grants, we probably wouldn’t use it because it wouldn’t let us use every last available procrastinated minute before the application had to be sent.

But we can make inline figures and tables with a variety of software packages we hate much less than Word.  As a Mac user, why don’t I use Pages, for example? Some of it is the collaboration issue described above. But the other is summarized in one word:

Endnote

Scholarly writing means citing sources and at least in my part of the life sciences, EndNote is the de facto standard, and uses academic discounts similar to those Microsoft uses to keep people from switching.  There are alternatives to EndNote, but as far as I can tell, plugins to support EndNote-style Cite while you write functionality are relatively new. The expectation that collaborators will be able to share EndNote libraries reinforces the  disincentives to change.

Could Word lose its dominance in science writing?

Of course. I’m old enough to remember paying typists to do manuscripts and grants. That’s not coming back, but it means I also lived through the days when people advocated training all students to use WordStar, and I remember the competitive market for plastic sheets that sat over your keyboard with the Wordstar key bindings.  Perhaps WordStar’s dominance then was not as great as Word’s is now, but there is space for competitors, based on limitations of Word. I already use a combination of Google Docs and Word, where Word is used to tweak the final version, put in references, and so on.  Reference managers that work with Google Docs are starting to show up.  As I write this, Apple is preparing an announcement about iWork on iCloud.

Cardinal and Badgers win, Ags can’t pull another one out of the fire

Stanford fell out of the top 10 after losing at Utah last week, while UCLA stayed unbeaten by throttling Cal. Thus, the Bruins came into Stanford stadium as the higher ranked team. But they left with a loss and the Cardinal are likely to pass the UCLAns when tomorrows rankings come out. The game was on at the same time as the Ags, so I only saw bits of it.  A&M and Auburn went to halftime in time for me to switch and see this amazing TD catch, however.  Stanford ended up beating UCLA 24-17 with defense and power running.

Wisconsin handled Illinois easily in a game not broadcast here.

Texas A&M started the day at #7 despite having a defense near the bottom of the country. The Ags had given up 30 or more points to four of six previous opponents, and the two who failed to hit 30 were Sam Houston (28) and SMU (13).  A&M had destroyed Auburn last year, when the D was not as bad, but the Tigers got rid of Gene Chizik and brought back Gus Malzahn as their head coach. It was difficult to gauge how good Auburn would be based on their 5-1 record, as most of their wins were vs. weak teams.  But red flags were that they had beaten the Ole Miss team that the Ags barely escaped last week, and that they had not been blown out by LSU.  Auburn came to Kyle leading the SEC in rushing.

As has become customary, the Ags took the early lead by scoring on the opening drive. Auburn answered and then got the ball back on a Manziel INT that was deflected off the hands of tight end Nehemiah Hicks.  The Tigers moved the ball but the Ags forced them to settle for a field goal and a lead that lasted for all of two plays when Manziel hit Mike Evans for the second of his 4 TDs on the day.  A&M failed to capitalize on a fumble when Johnny threw his second pick of the day, trying to force the ball into coverage after escaping a sack on a classic Johnny football scramble. Auburn drove 96 yards for their second lead of the game.

Both defenses got multiple stops in the second quarter, but the Ags were able to tie things up at 17.  Then the Tigers made a tactical error after a Drew Kaser punt pinned them at their own 1 with 1:04 to go in the half. Instead of running Auburn threw on first and third downs, missing an open receiver the first time, and hitting WR Sammy Coates in the hands on the second throw.  Fortunately for the Ags, Coates dropped the ball and the Tigers had to punt from deep in their own territory. The Ags got the ball on the Auburn 42 with 36 seconds to get a score. It didn’t take that long. 1 play, Manziel to Evans for TD #3.  Ags up 24-17 at halftime.

At this point the Aggie faithful were concerned about the D, but felt like we had the service advantage going into the half. When the D got a stop on the opening possession of the second half, I expected A&M to put together a drive and open a larger margin. Instead the Ags went 3 and out.  Auburn drove and scored (24-24). A&M answered (31-24). Late in the 3rd quarter the Ags got another stop and it looked like the good guys would get some breathing room as the Ags drove down to the Auburn 5 as the quarter ended.

The Auburn D had been getting more pressure on Manziel than most opponents. A&M countered that by calling more running plays from passing formations, causing the rush to slow down for fear of being beaten by Johnny’s elusive running. For the past season and a half, Manziel has been able to avoid getting hurt on these runs.  Now, at the start of the 4th quarter, after a false start made it 2nd and goal from the 10, Manziel was landed hard on his right shoulder or elbow at the end of a run to the 2 and had to leave the game with an injury.  Backup QB Matt Joekel was not able to connect with Hicks on the 3rd down play and the Ags settled for a FG and a 10 pt lead (34-24).

From this point on, the Aggie D was completely unable to stop Auburn’s offense. The Tigers scored on drives of 75, 69, and 75 yards. After the first Auburn TD of the final quarter, Manziel was still being treated and Joekel was not able to move the team.  This allowed Auburn to take the lead at 38-34.  Manziel came back in and drove the Ags to a TD to retake the lead at 41-38.  Auburn answered to score their final TD and make it 45-41 with 1:19 to go.

At this point, it looked like  Johnny would get another “Heisman moment” game-winning drive. He took the Ags from their own 35 to the Auburn 18 with 43 seconds left.  A throw to a doble-covered Mike Evans in the endzone was incomplete – a few inches eithe way and it could have been either the game-winning connection or a game-ending INT. On second down Auburn’s Dee Ford sacked Manziel. On third down, Johnny scrambled around the left side but was brought down by Kris Frost with what Aggie fans everywhere thought was a horse-collar tackle for a personal foul and an automatic first down. No call. Fourth and 13 from the 21.  I still thought the Ags would pull out the thriller.  But instead, the protection broke down and as Good Bull Hunting’s Hypno-Toad wrote afterward:

Oh, somewhere in this favored land the sun is shining bright;
The band is playing somewhere, and somewhere hearts are light,
And somewhere men are laughing, and the smiles never lack;
But there is no joy in Aggieland – mighty Johnny took a sack.

ball game.

Ags were not the only upset victims this weekend.

Ags survive Ole Miss

While the last couple of weeks have had some games where the top teams survived upsets, week 7 of the 2013 season saw ranked teams fall.  As Lou Holtz pointed out on College Gameday Final, fans forget that this is also the time for midterms. Between road trips and exams and being college-age kids, looking flat in mid October should not be surprising.  It’s also a time when the effects of injuries build up.

Mizzou’s upset win over Georgia was the best of the early games yesterday.  When A&M and Mizzou joined the SEC last year, the conventional wisdom was that the Tigers would do better in the short run. Instead, Mizzou had a 5-7 year with conference wins only over bottom-dwelling Kentucky and Tennessee, two teams that changed coaches in the offseason. We all know how A&M outperformed expectations in 2012.  Mizzou’s 5-0 start came with the caveat that their opposition has not been particularly strong, and Georgia, despite being decimated by injuries, was favored at home. After stalling on their first two drives and letting the Dawgs draw first blood, the Tigers outscored Georgia 28-3 in the first half.  Georgia mounted a comeback in the second half, getting as close as 28-26.  When Missouri QB James Franklin was knocked out of the game with a season-ending shoulder separation, it looked like Georgia would be able to pull off the comeback.  Instead, a 40-yard double pass opened the margin to 8 pts. Interestingly, Ga had the play covered, but the Mizzou receiver just outjumped the defender for the TD.  With more than 9 minutes to go, Georgia still wasn’t out of it, but an Aaron Murray INT led to the final Missouri TD. Losing Franklin means that it will be hard for Mizzou to stay unbeaten before they host the Ags on Nov 30.  Georgia fans are left to wonder what might have been had they been at full strength.

The other early game of note was the Red River Shootout, where Oklahoma was favored to add to the miseries of Texas fans for yet another year. Instead, the Sooners laid a major egg, getting blown out by the Longhorns. The game was not as close as the 36-20 final score. While the Sooners were missing some key players on defense, the main cause of their loss was offensive futility.  The Oklahoma offense produced 2 FG and 1 TD, the latter from a short field following a tu fumble. OU had 12 possessions for the game. Of these, 3 went for 50 yards or more, resulting in 2 FG and a turnover on downs late in the game. The other 9 were the TD, 2 INTs and 6 punts, and included 4 drives that netted zero or negative yards ( -17, -7, -4, and 0). It appears that Blake “the Belldozer” Bell finished with a QBR of 4.2 (12/26 for 133 yards and 2 picks) and his longest run was 4 yards. This Sooner offense is a shocking shadow of their high-scoring editions of the Stoops era.

For Texas, the question is whether this is the turnaround that starts a run to the B12(base 8) championship and a BCS bowl? Or will things go back to underperforming as the season continues.  Texas is tied for the conference lead at 3-0. The good news for the sips is that nobody in the conference looks that great. Baylor’s high flying offense looked beatable vs. KState. They get OK State and Tech at home.

We mostly watched Aggie Michael Wacha’s pitching duel with Clayton Kershaw while the mid-afternoon games were on, so I only saw a little of Wisconsin’s win over NorthwesternLSU beating Florida, Clemson surviving BC etc.  In fact, I only checked the Baylor and Clemson games when they were on upset alert, but by the time I tuned in, they both retook the lead.

The Aggies had a 7:30 Central kickoff at Ole Miss, and that game turned into a wild one.  The A&M D has been so problematic that most were predicting the Ags would win a shootout, and while it turned out that way, the start of the game was pretty different.  A&M got off to its usual fast start and it looked like the Ags would get a comfortable margin when the Rebels oddly went for it on 4th down and 1 from their own 46 on their very first possession.  The Ags held, but missed FG after Manziel went out with a knee strain.  Ole Miss took over and drove for the tying score.  Johnny F returned to lead the Ags to an answering TD drive of 75 yards in 5 plays, capped by a spectacular 18 yard run by Trey Williams.

The Rebels cut the lead to 14-10 by halftime, but it looked like the Ags would take control again after the opening Miss. drive was a 3 and out, followed by a 9 play 67 yard drive to take a 21-10 A&M lead.  But that was the high point of the 3rd quarter for the Ags. Ole Miss used a mix of their two QBs to cut the lead to 21-17, and then, when it looked like the Ags would keep the Rebs at arms length, Manziel threw a pick in the endzone to kill an otherwise good-looking drive.  Bo Wallace threw an INT to give the Ags another shot at the endzone, but A&M could only get a FG from Josh Lambo. That made it 24-17 about a minute into the final quarter.

A short kickoff and a good return set up Ole Miss to tie the game at 24. A Manziel fumble on the second play of the Ags next possession set up the Rebels to take their first lead at 31-24.  The two teams traded scores to make it 38-31 Rebels.  Facing 4th and 7 from the Miss 45, Manziel found his receivers all covered and ran up the middle for 13 yards for a first down. A collision late in the run left Ole Miss LB Serderius Bryant needing a gurney to get off the field.  Fortunately, the news today suggests that he will be OK. When play resumed, Manziel hit Mike Evans for a 26 yard gain to the Ole Miss 6, adding to Evans’ highlight reel as he hurdled a defender on the way.  Manziel’s 6 yard TD run was vintage Johnny Football: starting right, reversing his field and beating the defenders to the corner.

At this point, the questions were whether either team would get a stop and who would have the ball last.  Starting on their own 25 with 3:07 to go, Ole Miss went 3 and out on 3 incompletions, with the last two being near catches for the needed first down. When the Rebels punted, everyone watching expected Johnny Football to use the last 2:33 to ice the win, and the Ags delivered. Josh Lambo hit the game winning FG with 0:04 seconds left

With Georgia and Stanford losing, the Ags #7 in both polls.  Defensive worries mean that maintaining or improving that position could be difficult. But regardless of polls, the thing to take from this season is the entertainment value of watching Johnny Manziel and the A&M offense.  He may not win a second Heisman, but in my maroon-tinted view he’s had the most spectacular performances so far.

Down goes Stanford

Last week I was at the GO consortium meeting in Bar Harbor, so I didn’t watch much football.  Since it was a bye week for the Badgers and the Aggies, only Stanford was in action of the teams I follow closely.  The Cardinal had a narrow escape in Seattle against the Washington Huskies which I was able to watch in my hotel room.

Today, the Cardinal weren’t as fortunate in Provo, falling to the Utah Utes. Utah looked like the stronger team from the middle of the first half, and I switched to watching the A&M Ole Miss game while watching the scoreboard updates.  I flipped back after Stanford cut it to 6 and began their final drive.  The Cardinal moved from their own 12 down to the Utah 6, where they faced 3rd and 2 with about a minute left and one timeout remaining.  I expected them to run the ball twice if needed, and score the go-ahead TD leaving Utah with no time to counter. Instead, Coach David Shaw inexplicably called two passes, which fell incomplete. Ball game. Ugh.

More after the Ags game is over.