Monthly Archives: November 2014

Thanksgiving dinner

We decided to be antisocial this year and are doing Thanksgiving at home. Since there are only three of us, a whole bird is too much, so I went for a Sous Vide turkey breast with some sides to be determined.

Classic Cranberry-Orange Relish

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before -pecans

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after

The first thing I’m going to make is the cranberry relish, so the flavors can mature while other things are going on.  This is also the most ridiculously easy recipe of the day: mix cranberries, unpeeled orange pieces, and sugar in the food processor and blast it to the appropriate texture. After doing this, Debby reminded me that we add nuts sometimes, so we added pecans

  • I bag cranberries
  • 1 orange cut into pieces
  • 1/2 cup sugar (less than the traditional recipe, which calls for 3/4-1 c)
  • 1 cup pecans

Processed, transferred to a stainless bowl and into the fridge.

Sous-vide turkey breast

After we decided yesterday to be antisocial, Debby went out and looked for a small turkey. She bought a turkey breast by mistake: the label said “Fresh young turkey” but the tag showed that it was a bone-in breast. So I went with a Serious Eats recipe for Sous Vide Turkey breast.

Prep:

IMG_1236.JPGStarted with a 6.13 lb bone-in turkey breast from HEB.

  • IMG_1239.JPGFirst you remove the skin.  Turkey skin is harder to just rip off the flesh than chicken skin, but with some coaxing with a knife I got it all off and set it aside.
  • The recipe at Serious Eats talks about using a boning knife, which we don’t own, to debone the breast. When getting boneless breast filets off of a chicken, my friend Tad Simons showed me many decades ago to use the wings as handles to pull the breast meat off the ribcage. There aren’t any wings on the bone-in breast we bought, so I used a combination of fingers and a chef’s knife to get the breast filets off the carcass. The top picture shows the nice side of the filets. The other side is a lot messier, and I also ended up with chunks of meat that I cut off the carcass. I set these aside  to cook separately.
  • To get a more or less cylindrical piece of breast meat, you put season the inner surfaces with salt and pepper, align them head to tail, and then tie it up with twine. This got transferred to a 1 gal ziploc bag and put away for later.
  • I browned the carcass a bit and made stock. I omitted carrots, onions, and celery for now so I could give some scraps to the very attentive audience:

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Sous vide

IMG_1245.JPGMoved the bag to a 145F water bath at 2:10. Actually the water bath was set to 145F at 2:10. Put the extra meat in a smaller bag and added it to the water bath later (4:30). This is how the turkey breast looked when it was pulled and sliced at about 6PM

 Turkey skin

Detail from Michaelangelo’s Last Judgement

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before

Cut parchment to fit a rimmed baking sheet and spread the skin onto it. Doing that reminded me of Michaelangelo’s Last Judgement.

Turned the oven to 400F. Covered the skin with a second piece of parchment and then a second matching cookie sheet.

Looked at it about 20 minutes later. I think I should have been more aggressive about removing the blobs of fat attached to the skin. There was a bunch of rendered turkey fat in the lower pan… poured this off to use for the gravy.

I put the skin back uncovered after pouring off the fat.  The skin comes out like a crackling. I liked it, but it’s different from the well-roasted skin on a whole bird.

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after

Gravy

Sautee’d a mirepoix of celery and onions (discovering on the way that we are out of carrots). Added the turkey stock from above with a bay leaf and a dash of soy. Meanwhile, used the turkey fat and some butter to make a roux by browning some flour. Strained the stock and then added it to the roux to make gravy.

Roasted purple sweet potatoes with yellow bell peppers

IMG_1240.JPG IMG_1241.JPGI had impulsively bought some Stokes Purple Sweet Potatoes at HEB, and the Ags are playing LSU tonight. So I decided to adapt this recipe to use purple potatoes and red peppers.

  • Preheat oven to 450
  • Peel and cut potatoes into chunks. These were smaller than the regular sweet potatoes, so I used  smaller chunks
  • Add strips of yellow bell pepper
  • Toss with cumin, red pepper flakes, a few cloves of minced garlic, and olive oil.
  • Transfer to a baking dish, add a some water

I think the idea is to get the water to do some initial steaming and then have the dry heat roast the potatoes and peppers. Got this into the oven at 2:40.  I figure I can reheat this later if necessary after making the dressing.

After 30 minutes, the sweet potatoes were nowhere near done and the liquid was not evaporated; if anything more had rendered from the veggies. Transferred to a cake pan to spread them out more and put it back in. Out about 15 minutes later and transferred back.

The dish tastes good, but the bright purple color is muted by the cumin and/or the cooking.

Corn bread dressing.

IMG_1243.JPGBased on scanning various recipes (plan ahead? Ha!), I think this will need 350F for about an hour. Using premade cornbread stuffing, I’m going to add:

  • Celery, onions. Sauteed and moved to a bowl
  • Mushrooms, Sage. Sliced mushrooms and cut the sage leaves as sort of a chiffonade. Sauteed in butter and added to the bowl
  • Granny smith apples. Chopped two into chunks
  • Tossed with cornbread stuffing from the bag. Added some thyme.

Some recipes call for adding eggs. Others don’t. So I tried both ways on two different aliquots. Into a 350F oven at 3:50 PM. Out at 3:45 to allow room for the  turkey skin. Should have been earlier and I should have used more stock. Ended up adding more afterward, so the experiment to see whether eggs matter was uninterpretable.

 Final result

IMG_1246.JPGThis is the third time I’ve done some kind of sous vide poultry, and while it was good, it’s still more like poached turkey than roasted turkey… which makes sense given how the meat is in a bag of its own juices by the end of the cooking time. With red meats the final sear and the fact that conventional braises are at higher temperatures obscures the difference, but with poultry and fish I think it’s more apparent. Some of the difference has to be the lack how the meat bastes itself with that fat that rendered from the skin.

As long as you are OK with that, Sous Vide for the turkey does have two big advantages:

  • Flexibility in the cook time. I ended up leaving the meat in the water bath longer than planned when Debby and her father took the dog for a pre-dinner walk.
  • Oven space. Instead of tying up the oven for several hours, the turkey only needed about half an hour for the crispy skin.

Hope everyone had a great Thanksgiving meal, whatever you had.

 

 

Analogy-creep in hyping science

Via Instapundit by way of Popular Mechanics, I just saw this press release from UW-Madison hyping a new paper studying the host-virus interactome between humans and influenza.

In a comprehensive new study published today in the journal Cell Host and Microbe, the University of Wisconsin-Madison’s Yoshihiro Kawaoka and a team of researchers have set the stage for an entirely different approach. They have revealed methods for thwarting the hijackers by shutting down the cellular machinery they need, like cutting the fuel line on a bank robber’s getaway car.

When this got translated by Popular Mechanics we get the headline

Potential New Flu Treatment Would Starve the Virus, Limiting Resistance

which is the text blogged by Instapundit. This caught my eye because “starve the virus” is an odd claim since a virus is only metabolically active in the host, and the metabolites it uses are generally things the host needs too. From what I can tell from the abstract (apparently we don’t get on-campus Cell Host and Microbe here), the study is a large scale interactome to identify host proteins that coimmunoprecipitate with influenza proteins. Some of these were validated as affecting virus growth in culture by doing siRNA knockdowns. I’m not sure whether they then showed that known drug inhibitors also affected virus growth.

Here’s my guess about what happened:

  • The researcher told a UW PR person that the study catalogs host proteins that might be needed by influenza to propagate itself, and points out that resistance to drugs that target the host can’t easily arise in the virus.
  • The UW PR person tries to come up with something that is not part of a bank robber and comes up with a getaway car.
  • Continuing the analogy, the UW writer picks an essential part in the getaway car: the fuel line.
  • The Popular Mechanics headline writer saw “fuel” and thought the study was about reducing fuel for the virus
  • We get the headline suggesting that the study is about starving viruses.

Of course, if the virus is a bank robber, the host cell is not the getaway car; it’s the bank. Inhibiting virus infection with drugs that target host proteins is not like cutting the fuel line in the getaway car; it’s more like preventing bank robberies by killing bank tellers.  And it’s not just killing the tellers in the bank that’s being robbed, it’s killing all the tellers in all the banks in the community, whether they are being robbed or not.  Maybe that’s a reasonable strategy if the tellers are really nonessential in an age of ATMs. But that analogy is a lot less attractive.

The abstract mentions two potential “targets”, GBF1 and JAK1. I’m not sure how promising those are in terms of being therapeutic targets, based on the phenotypes of mouse knockouts.

Learning Artemis

For editing genome annotations, many of my colleagues use Artemis while others use Apollo. For my own use, I’ve usually just made scripts that generate GFF and visualized that in Gbrowse, Jbrowse, or IGV. For the genomics class I co-teach, we’ve had students edit GFF in a text editor (emacs!) and display it in IGV. But this year we shifted to doing more stuff that we used to do on the command line to our local teaching Galaxy, so after many years of avoiding them, I need to quickly get up to speed with Artemis and/or Apollo (in the long run, we’re going to use WebApollo, but that isn’t happening before the next homework assignment). Desktop Apollo stopped development and it’s not clear what the status of Artemis is, so this learning exercise may not be that useful.

To teach the kinds of things that MAKER does as a complete workflow, we are showing students how to take pieces of ab initio and data-driven evidence and assemble by hand the kind of evidence stack that MAKER automates. This means that we want to start with an undecorated fasta file of our artificial genome and load a bunch of gff, gtf, and bam files.

Everything below was done on a MacBook Air running OSX 10.9 (Mavericks).

Loading a fasta file

It seems like there are a couple of ways to do this. I was able to load my fasta file using either File > Read an entry or by invoking a project manager (which only seems to be available from the File menu if nothing else is opened). I initially opened a copy of my fasta file from a directory I had used with IGV, but found that this caused saves to fail because there was also a fasta index file present. Copying the file into my artemis working directory, I was able to open and save. This is what the viewer looks like.

ArtemisScreenSnapz001

 

The top line of the viewer shows a selector for feature sets, aka “Entries” in Artemis’ jargon. Below the entry bar (which can be hidden), the viewer shows an overview and a detailed view. Scroll bars on the right allow you to adjust the zoom of each; you can make the lower panel more of an overview than the top if you want. Double clicking on either panel jumps the other to the area you are viewing. A variety of graph options for things like GC content are available and open as additional panels. As you zoom out, Artemis shows stop codons in all 6 reading frames. As you zoom in, you get amino acid and DNA sequences.

Layers of annotations are “Entries”, so I can load additional files in different formats or create them using Artemis’ built-in tools. For example, Create > Mark Open Reading Frames gives this:ArtemisScreenSnapz002Several things have changed.

  • We have a new entry “ORFS_100+” (I used the default lower limit of 100 aa for ORF calling) on the entries bar.
  • The panels are now decorated with aqua blocks showing CDS features
  • The bottom panel shows a textual list of CDS features

More tracks/entries

I loaded a couple more entries as gff files:

  • Augustus gene prediction
  • Blastx parsed with a bioperl script I wrote

 

To get this view I tried some additional options from the Display menu. I tried Display > Show One Line Per Entry View. This is Display > Feature Stack View. These two create another panel above the overview genome panel.

ArtemisScreenSnapz004

 

There are some nice things about the display, but other parts are kind of a mess:

  • I like how the coding exons are linked across different reading frames
  • The parent-child feature relationships seem to be incomplete. CDS features are linked within a transcript, but parts of the same gene feature are displayed separately, and are stacked onto each other in a way that is hard to see.

Create a new set of annotations

Create > New Entry adds an entry to the entry bar called “no_name”. Yes, really. There’s no field to name the entry when you create it. You have to use Entries > Set Name of Entry and pick the no_name entry before you can rename it.

Features can be copied from the evidence entry sets to your custom entry and then edited. But I think I haven’t found the right way to copy a feature set (e.g. gene, transcript, introns, cds etc.) together.

That’s where I am so far… more later, perhaps.

More info

Artemis manual (ftp/pdf)

Artemis tutorials:

 

 

Wendy Davis never had a chance, but she was a terrible candidate

When Wendy Davis lost to Greg Abbott last Tuesday, it was not surprising. But what would have been surprising looking at her campaign from the perspective of her initial rise to fame was the scale of the loss. But by election day I had seen the train wreck develop here in Texas based on how bad the Davis campaign was. Today, Ross Douthat in the NY Times reflected from the outside and made a devastating comparison

The Christine O’Donnell thing really did happen more or less by accident, because she happened to be in the right place at the right time to catch an anti-establishment wave and win a primary in which she was supposed to be a protest candidate. Whereas the Davis experiment was intentionally designed: She was treated to fawning press coverage, lavished with funding, had the primary field mostly cleared for her, and was touted repeatedly as part of an actual party strategy for competing in a conservative-leaning state. Of course she had a much more impressive resume than O’Donnell, with less witchcraft and real political experience, and in that sense she made a more credible candidate overall. (Though, ahem, O’Donnell actually outperformed Davis at the polls in the end …)

Ouch.

Remarkably, the morning after, longtime Texas Monthly political writer Paul Burka wrote

Davis didn’t run a bad race. She raised a lot of money and she chipped away at Abbott’s weaknesses with some effectiveness.

The Texas Tribune’s Jay Root disagrees.

Davis probably never had a modicum of a chance to win the Texas governor’s race. The 2014 election turned out to be another wave election that cost Democrats the U.S. Senate, governor’s races in heavily Democratic states and competitive legislative races across the land, including here.

But for more than a year, Democrats were crowing that with a well-funded turnout operation, Davis was the kind of candidate who could at least move the needle for the bedraggled party, which hadn’t won a statewide election since 1994. In one sense they were correct: She moved the needle, all right — backward.

Root talks about how Davis failed to utilize her inspiring personal story

When the curtain came down on Team Davis, the campaign had not aired a single English-language TV ad focusing on the Fort Worth senator’s up-from-the-trailer-park narrative once seen as her campaign’s thematic foundation. In the final days, Davis couldn’t afford to effectively air such an ad, despite her campaign’s own claims of raising almost $40 million, a top official acknowledged.

We probably don’t watch as much TV in the prime advertising slots as most prospective voters, and I time shift past commercials when I can. I did see some of the gubernatorial ads when I couldn’t avoid them during live events like sports, and I saw some of the online coverage in blogs and social media. I didn’t watch any of the debates, but I glanced at some of the news stories about them. My perspective on the race is thus pretty limited, but I suspect that it’s not that different from what an average Texas likely voter actually saw.

So, within that window, Wendy Davis started as someone who was pro-choice and against regulation of abortions at 20 weeks or later. She then told me that she was:

Really? I mean, Ted Nugent is a loon, but his groupie history and Abbott’s defense of sex toy laws as AG never seemed like things that are priorities for Texas. And while Root says Davis didn’t have the resources to run positive ads, the Kirby Vacuum salesman ad was one that I saw a lot more than anything else from Davis.

Setting aside problems with the up from the trailer park narrative, and the general problem of trying to base your narrative on overcoming adversity when running against the guy in a wheelchair, Davis never established a positive agenda that I could detect. There were lots of things that Davis could have used on the negative side against Abbott, but it seems to me that a smarter campaign would have realized that for average voters, Greg Abbott is still a nonentity. The place to attack Abbott was not for anything specific about Abbott himself: it was as a continuation of the bad parts of one-party rule and the continuation of Rick Perry’s time as Gov. I would have gone after:

  • dysfunction in the lege that meant that initiatives tapping the Rainy Day Fund were needed to deal with funding for basic things like roads and water over the past few elections
  • cronyism and its effects on things like CPRIT and the Texas Enterprise Fund.
  • the ways in which Perry’s appointments and The TPPF agenda have been hurting higher ed in Texas. Ted Nugent is a loon, but perhaps it would have been better to point out the looniness of Wallace Hall.  Despite the dislike for us pointy-headed pinko academics, I think that between sports and economics, even some conservative Texans are uncomfortable with where Perry’s Regents have been taking the UT and TAMU systems. The defenestration of Bill Powers was recent news.

Davis was perhaps never the best candidate to make these points. But she was the anointed candidate and while I agree that she was doomed from day 1, moving the needle forward required showing that there was more to her than pink sneakers and abortion celebrity.  Instead, she showed us that there was less.

Ebola transmission

I did some reading on this topic a week ago, and this has been sitting in my drafts for about a week.

In the last post I noted that NEJM recently stated

Health care professionals treating patients with this illness have learned that transmission arises from contact with bodily fluids of a person who is symptomatic — that is, has a fever, vomiting, diarrhea, and malaise. We have very strong reason to believe that transmission occurs when the viral load in bodily fluids is high, on the order of millions of virions per microliter.

The question of whether patients are contagious before they become symptomatic has come up in debates about whether quarantine is appropriate or hysteria. The judge’s decision in the case of Mayhew v. Hickox, where a returning MSF nurse contested Maine’s State Dept of Health and Human Services quarantine request repeats this. Citing an expert from the states equivalent of the CDC, the judge wrote:

Individuals infected with Ebola Virus Disease who are not showing symptoms are not yet infectious.

But others are not as sure:

Moreover, said some public health specialists, there is no proof that a person infected — but who lacks symptoms — could not spread the virus to others.

“It’s really unclear,” said Michael Osterholm, a public health scientist at the University of Minnesota who recently served on the U.S. government’s National Science Advisory Board for Biosecurity. “None of us know.”

[Dr. Philip K] Russell, who oversaw the Army’s research on Ebola, said he found the epidemiological data unconvincing

What is the actual data? Not being an epidemiologist nor a virologist, I’m not already familiar with the literature, and I am likely to miss things and not fully understand the field-specific issues and language. But I think I can at least get a superficial sense of what’s out there, and what questions I would want to ask a real expert. Bottom line: the expert opinion that only the symptomatic are significantly contagious looks pretty good to me.

The first thing I noticed was that the literature on transmission of Ebola includes lots of computer modeling and that like most other fields, the citations for facts that are regarded as well established are often to reviews that cite other reviews. In some cases papers cite things like the CDC website, where the information lacks references. But this 1999 review seemed like a pretty good introduction and starting point. Authors CJ Peters and JW Peters from the CDC summarize the history of Ebola outbreaks, and point out the difficulty of reconstructing what happened in many of the early cases. Baron, McCormick and Zubeir looked at the spread of Ebola in a 1979 outbreak in the southern Sudan.

Every case,except that of the index patient,could be traced to a human source of infection…
Details of exposure to infection were not available for 2 secondary cases; the other 27 were associated with physical contact. Of these, 24 had provided nursing care to other patients in the family; for the remaining 3 patients (including the 2 children) the history indicated that the physical contact had been less intimate.

More importantly, the large numbers of family members who did not get Ebola suggested that the virus is not easily transmitted without direct contact with bodily fluids. Antibodies in asymptomatic family members (who had contact) suggested infactions that never turned into symptomatic cases. There were no cases where these were the source of another infection. But the numbers were relatively small.

In January of 1995, a charcoal worker who probably got Ebola from a natural reservoir was admitted to the Kikwit General Hospital. Retrospective analysis showed that he infected his family in the area of Kikwit, and some of the secondary and tertiary patients went to the Kikwit II Maternity Hospital over the following months. The official index patient of the outbreak was a 36 year old male who worked in the Kikwit II Maternity Hospital as a lab tech. The lab tech presented fever and intestinal symptoms that led to surgery for a suspected perforated bowel.

He underwent laparotomy at Kikwit General Hospital for a suspected perforated bowel after protracted fever. Postoperative abdominal distention increased, and an abdominal puncture revealed bloody peritoneal fluid. The patient underwent a new laparotomy, which showed massive intraabdominal hemorrhage. Three days later, on 14 April 1995, the patient died.

By that time, medical personnel who had cared for the index patient were getting sick. Only then was a viral hemorrhagic fever suspected. CDC confirmed that it was Ebola on May 10 after getting samples from Zaire the day before. Even before the confirmation, the government had declared an epidemic. By the end of the Kikwit outbreak, 316 people were known to have gotten Ebola, and 285 deaths were attributed to Ebola. This provided another opportunity to look at who gets Ebola and who doesn’t during an outbreak.

Dowell et al looked at risk factors for transmission of Ebola within families in the Kikwit outbreak. The results are overall in agreement with what was seen in Sudan.

The exposure that was most strongly predictive of risk for secondary transmission was direct physical contact with an ill family member, either at home in the early phase of illness or during the hospitalization. Of 95 family members who had such contact, 28 became infected, whereas none of 78 family members who did not touch an infected person during the period of clinical illness were infected (RR, undefined; P < .001). Nevertheless, the 78 family members who did not report direct physical contact with an ill person during the clinical phase of illness participated in a variety of activities that would have exposed them to fomite or airborne routes of spread. During the incubation period, all 78 shared meals with their ill family member, 26 reported direct physical contact, 15 shared their bedroom, and 6 shared their bed. In the early phase of illness, 62 slept in the same house and 42 shared meals. During the late phase of illness, 24 visited the hospital and 18 spoke with their ill family member.

Of the 316 patients, the majority had a known source of exposure, but 55 were initially unexplained. Roels et al went back and reexamined the available epidemiological information for 44 of these 55 (8 couldn’t be found and 3 refused to participate).

The probable source of exposure was identified for 32 (73%) of the 44 patients. Seventeen had visited an ill friend or relative with symptoms suggestive of EHF, 9 had been admitted to a health center in the 3 weeks preceding onset of EHF symptoms, and 6 had both risk factors. Of the 23 who had visited an ill friend or relative with symptoms suggestive of EHF, 4 (17%) resided in the same household as the ill patient and were their caregivers, 14 reported touching the ill patient, and 5 visited without touching the patient.

This leaves 12 people unaccounted for, and these 12 are sometimes cited as a problem for the conventional wisdom.

we identified an exposure source for 32 of 44 patients for whom no source was originally reported. Of the 12 patients who did not have an identified exposure source, no sociologic, occupational, or dietary risk factors for illness were found. Direct person-to-person contact was the likely mode of transmission for most EHF cases during this outbreak. However, our findings suggest that other EHF transmission modes cannot be excluded and may account for infection in those individuals for whom no previously recognized mode of transmission could be documented.

Although the alternative transmission cannot be formally eliminated, it is important to note that the 12 should also not be taken as proof of alternative transmission. In fact, none of them were actually confirmed as even having Ebola based on culturing the virus (See Table 3). There are also questions of the ability of the researchers to really reconstruct the contacts for each of these 12 people.

In the recent outbreak there are cases of health care workers who have contracted Ebola despite precautions. This could mean that there is a route of transmission that bypasses the protective protocols… or the simpler explanation is that errors in following the protocols led to transmission by the accepted route of direct contact with virus-laden bodily fluids. The Spanish nurse who has now recovered says she doesn’t know how she got it, but earlier reports talk about contact with gloves as she removed protective gear. For at least one of the nurses from Dallas, there are reports that she contacted Thomas Duncan in the ER without protective gear, before it was recognized that he was an Ebola patient.