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.

[pmid-refs key=’peptidoglycan transpeptidases’ limit=10]

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 Northwestern, LSU 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.

College football 2013 – week 5

Stanford and A&M won, while the Badgers fell in Columbus to favored Ohio State. Overlapping game times meant that I didn’t watch all of any game. In fact, I confess that I missed parts of the Ags opening drive to stick with the end of Georgia’s win over LSU.

LSU at Georgia was clearly the game of the day, with the outcome in doubt all the way to the end. Between them, the two teams had 3 turnovers and 4 punts over the whole game. By the second half, it seemed that neither defense could stop the other offense. When LSU scored to take a 41-37 lead with 4:14 to do, it was clear that they’d left too much time on the clock. That score came when Georgia mysteriously decided to rush only 3 on a 3rd and 22, allowing LSU to keep the drive alive with a 25 yard completions. When Georgia scored to go back on top 44-41, I thought perhaps they’d left too much time for LSU to answer.

LSU had the most effective defense against A&M last year, and it will be interesting to see how the teams stack up when the Ags go into Death Valley on Nov 23. The inability of the LSU D to sack Aaron Murray should bolster the hopes of A&M fans that Johnny Manziel’s second game against the Bayou Bengals will be more effective than last year’s performance in Kyle Field. It also might have been not so close without the SEC refs decision to ignore some pretty clear pass interference calls against both defenses.  In my view, LSU benefited from these more than Georgia. The Dawgs also played most of the game without Todd Gurley, who got hurt in the first half.

The Ags took the opening kickoff in Fayetteville while the Tigers and Bulldogs were finishing up in Athens.  A&M prevailed 45-33, but Arkansas stayed close enough to force Manziel to play the whole game and to cause Aggie fans to continue to bemoan the state of our defense, which gave up big plays on the ground and through the air to the Razorbacks.  The Ags did get a pick 6 early in the second half and another INT at the end.  Arkansas was not able to wrest the lead from the Ags despite having the ball down 4 to start the second half, and on several other possessions.  But Arkansas put up 483 yards on the Ags and were 5/12 on 3rd down.  On offense, the Ags were almost perfectly balanced, gaining 261 and 262 passing and rushing, respectively.  This statistical balance came on a mix of very unbalanced possessions, however, as A&M took what the defense was giving them.

The closeness of the TAMU game meant that I only watched bits of the first half of Wisconsin at  Ohio State.  By the time the Ags had sealed the win, Stanford vs. Washington State had started. I watched the end of the Badgers vs. the Buckeyes.  The loss had the feeling of a game where Ohio State was hanging on for dear life but the Badgers ran out of time.  Wisconsin’s offensive limitations let down a Badger D that played pretty well at times.  For example, after the Buckeyes were stuffed on 4th and 1 from the 38 in the middle of the 3rd quarter, it seemed like an opportunity to get back in the game. But the Badgers followed that defensive stand with : sack, INT.  By this time the Buckeyes had shown that the vaunted Wisconsin run game was not going to work. Ohio State took the ball from the Badger 32 to the end zone for their final score.

The Badgers Jarred Abbrederis had a remarkable 10 catches for 207 yards and a TD in the loss. This might have been even more remarkable than Mike Evans performance against Alabama, because Evans has a better QB and A&M has better receivers to spread the coverage.  By contrast, Wisconsin’s other receivers are not that good, and there were several key drops that killed comeback drives.

Stanford handled Mike Leach’s rebuilding Washington State Cougars pretty easily. Final score 55-17.

Other notable results

  • Oklahoma State fell in the first upset of the day to West Virginia.
  • OU beat Notre Dame in South Bend. Tommy Rees threw 3 picks.
  • Bama shut out Ole Miss
  • Arizona State tied Oregon for scoring the most points (62) vs USC ever.  Sun Devils win 62-41

iPlant

Spent Thursday and Friday at an iPlant workshop I helped set up at Prairie View as part of a genomics education project I’m doing with Gloria Regisford in the PVAMU Biology Dept.  iPlant just got renewed by NSF and will be expanding their scope beyond plants.  The focus of the workshop was the DNA subway set of workflows that are used for teaching, and we did a mix of computer exercises and wet lab work where we amplified some DNA from plant samples to send for barcode sequencing.  I had heard about some of the barcode projects, including Sushigate, but I hadn’t looked at the urbanbarcoding site from CSHL that aggregates these kinds of projects.  I’ve been advocating incorporating more things like this into our undergraduate curriculum.

But the things that will probably affect my own teaching and research were:

  • Atmosphere, the soon to be openstack-based cloud system being done in collaboration with TACC and
  • Plans to integrate the iPlant middleware with Galaxy.

No surprises, but some drama, on this weekend in college football

Yesterday was generally viewed as a less than exciting weekend for college football matchups. A few teams flirted with upsets, but the only top 25 team to lose was Arizona State, who played #5 Stanford. The Ags, Cardinal, and Badgers all won convincingly. A&M and Stanford were on at the same time, so I mostly watched the Aggies and Johnny Football while switching to the Stanford game during commercial breaks. It turned out to be well-timed. There were at least two Stanford TDs that happened moments after clicking over.

Earlier, the Badgers looked strong in demolishing Purdue. Wisconsin shook off their perplexing loss last week to Arizona State and showed off yet another set of exceptional running backs, now that Monte Ball is gone. James White and Melvin Gordon each had 16 carries for 145 and 147 yards respectively.  Gordon scored 3 TDs to White’s one.  Despite the dominating performance on Saturday, Wisconsin’s passing game may not be strong enough to prevent better opponents from packing the box and daring the Badgers to beat them through the air. Next week in Columbus will be a test for new coach Gary Anderson.

Johnny Manziel was pulled from the game after only a half+1 series of the Aggies win over SMU.  That was long enough to get 244 yards passing and 102 yards rushing, with 1 passing TD and 2 running TDs.  Manziel also threw another pick that went off a receiver’s hands. Several of Johnny Football’s runs were of the “how did he do that?” variety.  More than once he just changed directions in ways that made SMU defenders look foolish.  Causes of concern: Center Mike Matthews had several penalties and one bizarre bad snap. Kicker Taylor Bertolet was replaced by walk-on Josh Lambo after a return of Bertolet’s extra point woes from last season. The Ags wound up missing 3 XPs in a row, as Lambo’s first attempt was spoiled by a bad hold.

The struggling defense had a much better game. SMU is no Alabama, but the Aggie D also looked better than it had against Rice and SHSU.  A combination of personnel moves (e.g. a new Middle Linebacker and DeShazor Everett moving from CB to S) and experience seems to be helping. The Ags batted down several Garrett Gilbert passes, and forced 2 fumbles and an INT. One fumble was returned for a score.  Still, the Ags gave up a lot of yards and as DC Snyder said in the post-game presser

We get the quarterback and bounced off… was watching the end of the LSU game. When they hit a quarterback, they don’t go anywhere; they go down.

It will be interesting to see if progress continues as the Ags hit the road for the first time this season at Arkansas.

Former Badgers coach Bret Bielema can’t be happy with what happened in the Pigs game at Rutgers.  The Razorbacks were up 24-7 in the third quarter… and ended up losing 28-24. After going up 24-7, Arkansas possessions reconstructed from the play by play record:

  • 3 plays 9 yards, punt
  • 3 plays 8 yards, punt returned for a TD (24-14)
  • 5 plays, 22 yards, punt from their own 47

4th quarter

  • 3 plays 8 yards, punt (Rutgers scores on their possession 24-21)
  • 5 plays 14 yards, punt (Rutgers scores on their possession 24-28)
  • Now trailing, Arkansas starts at their own 18. They get to their own 45. Sack, loss, incomplete, punt on 4th and 24 (Rutgers runs out the final 2:48)

Coach Bielema may need to get his wife off of Twitter.

Ranked teams that had moments of dread:

  • Georgia was tied with N. Texas after the Mean Green blocked a punt for a TD in the third quarter.  The Dawgs put their fans at ease by scoring 24 unanswered points.
  • Michigan trailed winless UConn going into the final quarter before rallying to win by a FG.  This was the second week in a row where Michigan dropped in the polls after a win.  The Wolverines were #17 in the preseason AP, rose to #11 by virtue of beating Notre Dame, fell to #15 last week, and are now down to #18.

Virginia Tech is unranked, but played well enough against Alabama to be thought of as a pretty good team.  Marshall had several chances to pull the upset in Blacksburg but couldn’t close the deal.  Marshall led most of the game after taking the lead in the second quarter. On VT’s 4th quarter drive to tie the score, the Hokies had to convert two 4th downs. The touchdown came on a 4th down pass that was deflected by a Marshall defender.  On the next drive, Marshall got to the VT 34 but lost 5 yards before taking a shot at the end zone that was intercepted.  On that play a) they only needed to get in FG range and b) the receiver was open but the pass was late.  Having failed to pull off the upset in regulation, the two teams played 3 OTs, with VT ultimately benefiting from a very dubious non-call of pass interference where the defender seemed to commit two fouls on the same play from the replay.  Even then, Marshall had a chance to win on a FG in the first OT. The kick was blocked.

 

Not all wins and losses are the same

It can be argued that a win is a win and a loss is a loss, and from the point of view of calculating standings it doesn’t matter how you win or lose.  But the aesthetics are not the same, and the loss at the Alamo or at Thermopylae are remembered very differently than the losses at Little Big Horn or Salamis.  Saturday’s College Football had a mix of good and bad wins and losses. The teams I root for went 1-2 this week, with Stanford beating Army early, the Aggies falling to Alabama, and Wisconsin getting burnt in the desert by Arizona State.

Army was a 30-pt underdog to the Cardinal, but their option gave Stanford some trouble in the first half. Stanford pulled away in the second half. This was a neutral win: expected and solid.

The game of the day was #1 Alabama coming here to College Station to face #6 Texas A&M.  I had no idea what would happen going into today; I could imagine blowouts in either direction or a close game. There were too many unknowns about whether Alabama’s defensive experts had solved Kevin Sumlin and Johnny Manziel’s version of the Air Raid, and whether the Tide’s offense and Ags defense were as bad as they seemed in the first games.  The good news for the Ags: the A&M offense is better than last year’s. This was expected, despite losing several key players from last year and replacing offensive coordinator Kliff Kingsbury, who left to become the head coach at Texas Tech. The Ags were deep last year, and despite his overhyped off-field issues, Johnny Manziel was expected to have a better grasp of reading defenses and mastering the options in the Sumlin offense. Johnny Football and the offense scored 42 points on the Crimson Tide on 628 total yards.  It could have been more, but two interceptions and a questionable offensive pass interference call on Mike Evans stopped three drives.  Manziel had 464 yards from 28/39 passing  with 5 tds and 2 ints and 98 yards rushing.  Mike Evans had 7 catches for 279 yards, including a late 95 yard catch and run that set a record for Kyle field.  All of this would have been impressive against anyone, but against Alabama it’s truly remarkable.

Unfortunately, the bad news was that the A&M D has not found its stride. The past couple of years we’ve had an outstanding pass rusher, first in Von Miller and last year in DaMontre Moore. As noted last week, there were many other important seniors on Mark Snyder’s defensive squad. Their replacements haven’t stepped up yet, and despite getting back several suspended starters, the A&M defense had trouble stopping Alabama after their third possession.

That said, this was a good loss in the sense that it was close, entertaining and was a valiant effort by A&M that left the impression that the teams on balance were near equals. If Manziel and/or Evans are up for postseason awards, this game provided plenty for the highlight reels.

By contrast, Wisconsin’s loss to the Sun Devils was one of the many varieties of bad losses.  The two teams traded errors and scores until the middle of the third quarter, when Wisconsin’s defense started to wilt in the heat and ASU’s receivers stopped dropping catchable balls. Arizona State took the lead for good with 11:40 left in the game and made it an 8 point lead at 8:50 to go. Nevertheless, a fake punt led to a Wisconsin TD that cut the lead to 2 after a failed 2-pt conversion, and a 51 yard pass play set up the Badgers for what should have been the winning FG.  But after getting down to the ASU 13, Wisconsin inexplicably tried to position the ball for the FG try with only 18 seconds left and no timeouts.  The clock ran out without the Wisconsin FG unit even seeing the field.  Wow.

Texas and Nebraska exemplified a different kind of bad loss.  Both were blown out at home after leading at halftime, 23-17 and 21-10 respectively. Ole Miss beat Texas 44-23, while UCLA beat Nebraska 41-21.  These were the kinds of losses that put coaches on the hot seat.

For an example of a bad win, see Michigan holding on against 37-pt underdog Akron.  Akron took the lead several times in this game, the last time being at 4:20 to go. Michigan scored with 2:49 left, but as one Michigan fan posted at MgoBlog

Saddest question ever, “did they leave too much time for Akron?”

In fact, Akron drove down the field but could not convert on 4th and 3 from the Michigan 4.