Viruses

mailboxTWiM regularly receives listener email with corrections, comments, suggestions for show topics, requests for clarification, and additional information. A selection of these is archived on this page.

TWiM 34 Letters

Peter writes:

Dear TWiM Team

I see that some action is now being taken in America against the non-therapeutic use of antibiotics as livestock growth promoters:

http://www.nytimes.com/2012/04/12/us/antibiotics-for-livestock-will-require-prescription-fda-says.html?_r=1

http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm299802.htm

Having read the FDA Press Announcement I think that that the N.Y. Times article may be misleadingly optimistic, I feel that this is probably too little and too late.

The practise of using antibiotics as growth promoters was stopped in Sweden in 1986 the UK in 1988 and in Europe by 2005, without significant adverse effects on the meat industry.
As I see it the only reason this practise persists in America is the lobbying by the livestock industry against the scientific consensus.

Your views please doctors.

Peter

Article about how use of AGP's was phased out in the Danish pork industry:

http://www.thepigsite.com/articles/2/ai-genetics-reproduction/1735/danish-pork-industry-antibiotics-prohibited-as-growth-promoter-part-3

Antibiotic Growth Promoters in Agriculture: History and Mode of Action:

http://ps.fass.org/content/84/4/634.full.pdf

History of the Use of Antibiotic as Growth Promoters in European Poultry Feeds:

http://ps.fass.org/content/86/11/2466.full

Sergio writes:

I have a question for Michael Schmidt. While doing my research on R. solanacearum, I read an old paper where they mentioned that Pseudomonads were able to internalize copper and therefore detoxify a copper rich liquid medium, I have observed this myself with the R. solanacearum strain I was working with, but since Michael is the copper expert in TWIM, I would like to know if there is some more new information about this phenomenon. It is of my interest beyond my doctoral thesis because copper is one of the few fungicides allowed to be used in organic farming. Therefore, this phenomenon deserves more attention from organic farmers, I think.

Sergio

Ph.D. in Biocontrol Science Electronic Cigarette
Tokyo University of Agriculture and Technology
United Graduate School of Agricultural Science
Biocontrol Science Department

Instituto de Investigaciones Fármaco-Bioquímicas
Miraflores
La Paz, Bolivia

Sarah writes:

Dear TWiM-ologists,

You know how sometimes you run across a word or phrase which sounds like it's got a specific meaning that's really important to the context of whatever you're reading or hearing?

Well, I've been catching up with episodes 27-29 lately, and true to TWi form, the phrase "type III secretion" got the gears crankin'. The phrase sounded significant but I didn't remember learning about secretion mechanisms under this framework in undergrad 10 years ago. I did a little reading and wanted to share how fascinating these mechanisms are and how relevant they seem to be for many common human pathogens. Depending on the bug, the product, and the environment, these guys can deliver a variety of toxins into the extracellular environment, spit out antibiotics and other compounds, or deliver proteins or nucleic acid directly into target cells via injection or vesicles. What a spectacular array of intricate and elegant mechanisms - as Dr. Schmidt would say, "Remarkable!"

It's fitting that these podcasts are award-winning. They always nurture curiosity and prompt trains of thought into unexplored territory.

The discussion about TUNEL and apoptosis in episode 29 reminded me of a suggestion for pick of the week - A couple of music videos that Roche released in 2009 to promote some new lab tools to measure viability and cytotoxicity. They're more for tissue culture than microbiology, but hilarious nonetheless.

http://roche.cnpg.com/video/flatfiles/843/
http://roche.cnpg.com/video/flatfiles/771/
(in case the above links don't work: http://www.roche-applied-science.com/usa/celldeathtour/)

Stephen writes:

<http://ksjtracker.mit.edu/2012/05/16/twim-32-a-microbiology-chat-with-monolakian-arsenic-buster-rosie-on-scientific-error-sci-journos-and-a-submission-to-science/>

Horizontal transfer between blogs.

TWiM 31 Letters

Peter writes:

Dear TWiM Team

A fascinating article from New Scientist this week.

Standard medical teaching is that the foetus is sterile and that the microbiome only begins to develop post natal.

New research from Spain indicates that the microbiome starts to develop before birth:

http://www.newscientist.com/article/mg21428603.800-babies-are-born-dirty-with-a-gutful-of-bacteria.html?full=true

"Pilar Francino and her colleagues at the University of Valencia in Spain collected and froze the meconium of babies from 20 women. They removed the outer layers of each sample to rule out any bacteria picked up after birth, then looked for bacterial DNA.

The team not only identified bacteria in the babies' meconium - which before then was thought to be sterile - they found bacterial communities so developed that they seemed to fall into two categories. Around half of the samples appeared to be dominated by bacteria that produce lactic acid, such as lactobacillus, while the other half mostly contained a family of so-called enteric bacteria, such as Escherichia coli."

Peter writes:

Dear TWiM Team

There was an interesting article in the March Scientific American on long term effect on health that food poisoning can cause:

http://www.scientificamerican.com/article.cfm?id=food-poisonings-hidden-legacy#comments

New studies by scientists in several countries show that food poisoning rather than lasting just a few unpleasant days can in some cases cause life long problems.
Though this possibility has been known for some time the recent work indicates that this phenomenon is much more common than previously thought.

"A survey of 101,855 residents of Sweden who were made sick by food between 1997 and 2004 found Electronic Cigarette, for instance, that they had higher-than-normal rates of aortic aneurysms, ulcerative colitis and reactive arthritis."

"...several years after a 2005 outbreak of Salmonella in Spain, 65 percent of 248 victims said they had developed joint or muscle pain or stiffness, compared with 24 percent of a control group who were not affected by the outbreak."

Peter

PS I that the Scientific American journalist and author Maryn McKenna would be a good guest for TWiM or TWiV.

Nathen writes:

Hey thanks for the great podcast. TWiM is one of my new favourites. (I'm about to post a review on my blog.) I'm a little afraid to start listening to TWiP and TWiV--if I get hooked I'll never be able to keep up with all of them.

I just listened to your episode that included the paper on the autism microbiome study, and one of you said something about it being difficult to recruit controls for this kind of invasive procedure. It might make the statistics more complicated, but what about recruiting siblings of autistic kids as controls? The parents would be much more likely to be on board, as they have a vested interest in the progression of science on the problem of autism.

Thanks again,

Nathen

Steve writes:

Hello Vincent and cast of TWIM;

I have to say, even though I am a novice, I really enjoy your podcasts.

Because of the nerdy-ness and nature of this song, I thought I should pass it along. Happy St Patrick's Day! Enjoy!

http://www.youtube.com/watch?v=L6dzUOYTQtQ&feature=channel

TWiM 30 Letters

Megan writes:

I am a Clinical Microbiologist, and have really been enjoying the insights and discussion on TWIM and TWIV (and am hoping to get to TWIP soon). I have really found the information being presented helpful, and am wondering if any of the lectures from the hosting professors are available online. I have found some of Dr. Racaniello's lectures in the iTunes store, are any of Dr. Schaecter and Dr. Schmidt's lectures available online?

Thank you for any information, and thank you for the valuable resource you are providing with these podcasts.

Dallas writes:

Being a retreaded physics/physical chemical/thermodynamic type without any formal education in biology of any kind, I find your podcasts accessible -- even if somewhat hard to get my mind around.  Your are good about defining the jargon that exists in every field of science.  

I have spent 35 years working in aquaculture (the raising of aquatic animals) in systems whose real performance is controlled by the microbiologic ecology.  In my sub-field of recycle aquaculture, I partition this microbiological ecology into separate unit operations like biofilters, where the performance is a little more controllable/predictable, but still would have a metagenomics as complex or more complex than the human gut.  I have seen very few papers even attempt to get a handle on these complex system.  

In the practical microbiology department, I have developed a series of fluidized bed biofilters that are able to remove some hazardous materials from ground water down to non-detetable levels of < 1 ppb, well below the minimum substrate concentration for the bugs of about 20 ppb.  In particular MTBE , a water soluble gasoline additive, enters ground water from leaky underground storage tanks and people can taste it at 50 ppb.  In Calif. the political class went ballistic over this minor contamination problem and forced a multibillion dollar solution, which means that gasoline is 50¢/gal higher in Calif that the rest of the country.  The political class supported by the press was going on about how MTBE was non-biodegradable and the lawyers were making a fortune.  

My experience indicates that very few chemicals are non-biodegradable, if there is energy that a bug can obtain from degradation.  If that weren't true, we would be up to our eyeballs with all sorts of refractory organic chemicals.  

I heard that UC Davis and UC Riverside researchers has some very slow growing bacteria that seemed to metabolize the MTBE and they were digging up all sorts of leaky underground tanks in my area.  Knowing that these bugs had a 10+ day or so doubling time combined with a 10% or so yield, I knew that I had to setup a reactor that could maintain the bacteria while processing large volumes of liquid over very long time periods.  It took me 9 mo to get my first bioreactor running using seed from the universities, sewerage plants and every soil around a leaky tank I could find and a continuous feed of MTBE as the only energy source.  I ended up making some money growing kg amounts of these bacteria consortia semenax wiki attached to sand grains used to as seed to start up new bioreactors on new sites and went through many bbl of MTBE growing and feeding them.  We can go into a bioreactor at 2000 ppb and come out at < 1 ND with a 15 minute contract time.  

The trick of obtaining a continuous discharge concentration below the Smin (minimum substrate concentration for the bacteria to break even -- zero net growth) is to have plug flow on the liquid phase of the system and mixed flow on the biological phase.  You fatten up the bugs in the bottom at a concentration above Smin and they keep eating when they get moved to the top where the concentration is below Smin.   If the inlet concentration gets near Smin, we have to add MTBE to the input water to maintain a lower discharge concentration.  Try telling a regulator that you are going to add a pollutant to the water to get a lower discharge concentration and it blows their minds.

The concept of these fluidized bed bioreactors could be an interesting research tool for the dental bugs you have mentioned.  You could fluidize small grains of tooth enamel, where effectively every small grain is in free fall in the culture media all the time, and you could see what happens to the consortia as you change the feed composition -- coke vs pepsi vs apple juice vs mouth wash, etc.  

Continue the good work.  

Dallas

David writes:

Dear Professor,

I am a former molecular immunologist who now works as an attorney doing catastrophic birth injury defense.  I can't thank you enough for enriching my drives with TWIP, TWIV, TWIP and TWIM.

As you can imagine, one of the bugs which occupies a lot of my thoughts is GBS and its proclivity for vertical infections of fetuses.  I know that in a certain percentage of individuals are colonized and happily walk around with GBS never causing a problem.  What I would be really be interested in learning more about is what can make happy colonizers into pathogens.  My thought was that perhaps in fighting for territory a bacterium like GBS expresses virulence factors which, in some conditions, allows it to crowd out other flora.  Some sort of swarming like event gets it to spread out and it encounters the fetus.

I know this is likely a gross simplification- but if you have any ideas or suggestions for reading I would be in your debt.

Once again- many thanks for the hours of fun.

Nathan writes:

Hi TWiM-ers,
I have not listened to every episode of TWiM yet, so you may have answered these questions already. If you haven't, though, will you address these two?

What do you think you do differently in your non-professional lives because of what you know about microbiology?

Describe exactly what it takes to create selection pressure on microbes. I'm thinking about the mainstream conversation around microbe-specific antibacterials vs. alcohol-based sanitizers vs. regular soaps, but I'd like to know the general principles with which you approach that line of thought.

Thanks!

TWiM 3 Letters

Hubert writes:

Hello Professor,

I'm a Belgian student in veterinary medicine (I hope my English isn't too bad), and I'm very interested in microbiology. I have a few questions about the last episode of TWiM (and quite a lot about episodes of TWiV, but I'm still in the process of listening to all of the episodes first in order to be sure answers aren't already discussed) :

The first questions are about the Yersinia Pestis infection story : during the explanations about the life cycle of Yersinia, you talked about iron as the main limiting reagent in many infectious processes. Is it only because of the fact that it's not easily available in the host, or is iron a more important reagent than other trace elements like Zinc of Manganese? Also, are the requirements for such reagents the same in bacteria as semenax hoax in eukaryotic cells? I suppose not since there are already some variations among domestic animals, but in that case are the differences important?

The other question is about the microbiome. You talked about the NIH microbiome project and studies about bacterial microbiome. Is there a similar project about a viral microbiome going on?

Finally, could you make an episode about bacteriophages and their relations with bacteria, and phagotherapy?

Thanks a lot for all your podcasts and blogs, it's really informative and feeds my passion for microbes more and more. Keep up this great work!

PS : I plan to do a PhD in microbiology after I get my diploma, but I hesitate between bacteriology and virology, both are so fascinating. How did you choose your area of research, and do you have advices to choose between one or the other?

TWiM 29 Letters

Charlotte writes:

At the beginning of Twim #28 Michael articulated his love for math and around minute 12 his desire for "ground truthing" the number of times one touches their face. In response I offer the attached article from a colleague at UCB.

I really admired the candid and humble discussion at the end of the podcast about proper attribution of ideas.

With warm regards (-65 C in Berkeley),

Charlotte

Carol writes:

I don’t know how I dare to email you as you must be really busy but here goes.

My name is Carol and at 51 have just embarked on a teaching course, my brain cells, I possess a few, are overloaded.

My tutor wants me to use innovative (new) technology in my lesson and write a 4,000 word assignment plus portfolio on the use of such technologies.

In the real world, when I teach, often even basic computers or powered points are in short supply; anything fancier than that is NEVER available but as this is for an assignment we must pretend that we do have it.

I teach food safety and thought that a good way of introducing some tech would be to have a microscope in class but really he is talking does vigrx really work of interaction, podcasts, phone apps, live chat and possibly video clips.

I don’t need anything too techy as this is not biology A level, just food hygiene, therefore something to do with salmonella would be fantastic.

Are you aware of any links, materials, videos on this subject or any ideas on how I could use a microscope that would immediately be able to send what it sees to a computer?

Think of this as your charity work, helping someone less fortunate than yourself (me)

Many thanks and apologies for my forwardness

Alicia writes:

Hello,

I'm an undergraduate student and am currently working in Montreal on a co-op where we manipulate yeast to create either the best bread strains, booze strains, or biofuel strains. Because of this, I'm always reading up on new articles about biofuel. I was wondering if you had heard about this: http://www.sciencemag.org/content/335/6066/308.short
and what your opinions might be.

Thanks for making the hours fly by on the train and in the lab.

Best,

Alicia

Peter writes:

Dear TWiM Team I came across this New Scientist article on the general disregard for microbial life in conservation and the need for education to counteract negative perceptions of microbial life.

http://www.newscientist.com/article/mg21328546.800-lets-protect-earths-unseen-life.html

Your comments please.


Peter.

TWiM 28 Letters

Daniel writes:

I would like to point out that the idea of "Fitness Factors" was originally published by Brussow et al 2004 (Microbial Molec Biol Reviews68:560) and did not originate from Michael Schmidt as was suggested in your last podcast.

Here is the pdf
http://mmbr.asm.org/content/68/3/560.full.pdf

You may wish to scroll to page 565 in the pdf to validate this fact.

I think it is important to keep all forms of scientific information as accurate as possible and since your podcast is likely heard by students and perhaps lay-people who might not check the accuracy of claims as often as a scientist may, I bring this to your attention so that you can publicly set the record straight.

I listen to all three of your podcasts and find two of them of high distinction. TWIP in particular is excellent and TWIV  generally deserves an honorable mention. TWIM on the other hand is not so well developed for accuracy or claims of originality.

When I heard the "fitness factors" comments I immediately recalled this paper and its citation in many subsequent papers.

The way it was presented on the podcast made it sound as though is was your colleague's idea. Clearly this is not the case.

Sincerely,
Dr. Daniel J. Guerra
This email address is being protected from spambots. You need JavaScript enabled to view it.

Cam writes:
Dear Vincent and the team,

I am  third year Medical Student at the University of Cambridge currently doing a BA in parasitology, parasitism, immunology and  microbiology. I very recently discovered TWiP et al and am now harboring a full scale addiction from my girlfriend.

I have a number of questions and suggestions, which are relevant across the TWi platform.

I have just finished listening to TWiM 25. I found the discussion of magnetotactic bacteria fascinating, especially as I am also a technophile so the prospect of a bacteria powered smart phone blew me away! On the question of where to find soil inhabiting magnetotactic bacteria; perhaps industrial sites that produce large electromagnetic fields would be a good place to start. E.g. big electricity transformers, or power stations?

I was also interested by the discussion of TDR TB . I am currently writing my dissertation on human infection with Bovine TB (which is increasingly recognised as a misnomer). Mycobacterium bovis is generally intrinsically resistant to pyrazinamide, and often carries resistence to isoniazid (both first line human TB drugs). Given that there is no good way of differentiating M. bovis and M. tuberculosis infection without culture and PCR, I would suggest that M. bovis infection in humans has played an as yet unquantified role in the poor management of TB infection that has lead to the development of resistance. However, there is very little data on what proportion of TB infection can be ascribed to M. bovis infection, with reports ranging from 0%  (Brazil, Rocha Garcinia Cambogia Fruit Extract, 2011) to 21% (Tanzania, Kazwala 2001 in Lymphadenopathy patients). To compound this, it is suggested that there is a large degree of under-reporting of M. bovis because labs are not using pyruvate supplemented media to culture, preventing its growth. The aim of my dissertation is to identify antigens that could be used for differentiatial diagnosis in resource-poor setting (e.g. by card test) where the majority of M. bovis infection seems to be found.

Also in TWiM 25, Peter's letter discussed the role of the microbiome in mosquito attraction. Michael Schmidt replied that it was unfortunately smelly short chain fatty acids produced by bacteria that would likely be the repellent. However, in my Biology of Parasitism Class (taught by Dr Sheelagh Lloyd), we were taught that Anopheles gambiae are attracted to Limburger cheese, which contain Brevibacterium linens that produces short chain fatty acids in cheese, and is closely related to Brevibacterium epidermis on the skin. Similarly,Corynebacterium and Melessazia spp. on the skin also metabolize triglycerides to short chain carboxylic fatty acids that are attractive for A. gambiae. The other main attractants to mosquitoes (depending on the species) are carbon dioxide, lactic acid, acetone, 1-octen-3-ol and nonanal .

There are two specific questions that I have:

Whilst I recognise that the three TWi shows are increasingly showing more overlap, I wondered whether there was room for a 4th niche? It would be great if you could produce a podcast in the TWiP format that focuses on Immunology. Whether looking at the subject as a whole, or more specifically the interactions between infection and immunity rather than autoimmunity, cancer and pregnancy, I think this subject area would provide an essential underpinning to the wide and varied discussion found on your current podcasts. I look forward to hearing your thoughts on TWiII (This Week in Infectious Immunity).

Thank you again for the sustained propagation of scientific values through your podcast, and in particular, making parasites accessible and exciting! It is a good antidote for an unfortunately common attitude that restricts the unilluminated to a reaction of disgust and aversion, when in actuality the lives of these parasites demonstrate a beauty and elegance beyond the most highly choreographed ballet.

Yours expectantly,

Cam Stocks

Josh writes:

Hello Twimmers,

I have been slowly trying to catch up with TWIM from the beginning and my memory was jogged by one of the letters at the end of TWIM #13 suggesting a collaboration between TWIM and an astrophysics podcast.  I read an article in Popular Science recently about this "Extra-Terrestrial" Arsenic Bacterium  (http://www.popsci.com/science/article/2011-09/scientist-strange-land), and the article left me with more questions then answers.  It would be great to hear your thoughts on the matter, I would love to hear you guys talk about it in a future podcast.

Thanks so much!

Josh

TWiM 27 Letters

Bill writes:

I was fascinated by your conversation about government censorship of science (TWiM 24). To further criticize the government's move, I'd like to point out that the Soviet's bioweapons program has been leaked in bits and pieces over the years, yet we don't see terrorists able to recreate those projects. In fact, aspiring bioterrorists find themselves recruiting Soviet era scientists rather than doing it themselves, which suggests the information alone is not dangerous. Here are three examples:

1. Putting B. anthracis pXO1 and pXO2 plasmids into B. subtilis, a common flora
2. Splicing in myelin genes into viruses to induce MS in survivors
3. Creating chimeras between VEE and smallpox

Perhaps you could do a TWIM on biodefense?

Richard writes:

Hi Vincent and gang

Listening to the end of the last episode, you mention the possibility
of there being phage that pack magnetite, from magneto tactic
bacteria.

I think this is something that I could do, just for fun. I'm assuming
that the phage can be separated by filtration, then concentrated by
magnetic means, and the resulting material (if any), could then be
added to some of the bacteria. If phage are present then, a good
proportion of the bacteria should be killed, hopefully this provides
detection, since I lack anything but simple equipment.

I thought would ask, is this reasonable?

If so, can anyone suggest where I could get information on culture of
magneto tactic bacteria. Getting hold of some sounds easy enough, but
someone (sorry I don't recall who) said that growing them is not
trivial. Any info, or pointers to sources of information would be
appreciated.

Many thanks for the great group of podcasts. Keep up the good work!

Regards

Richard

P.S.

I have filled out the listener survey, but being in the UK, I'm not do penis enlargement pills work
sure how much that helps.

Trudy writes:

Dear TWiM doctors,

I am an enthusiastic Virologist who has recently become fascinated
with Immunology.  In addition, inspired by Vincent’s thirst for all
knowledge, I have started listening to TWiM in an effort to bridge the
vast gap in my knowledge and be less of a virus snob.  TWiP is next!

I just finished listening to TWiM episode 22, where you discussed
microbial infections encountered in the emergency room.  You talked
about how wiping out the normal gut flora with an antibiotic can
encourage the overgrowth of C. difficile, and how this can cause some
people to eventually have to lose their colon.  I was very shocked by
this information, especially when you mentioned that Clindamycin was a
common antibiotic that could cause this kind of imbalance in gut
flora.  Over the past few years I have used a Clindamycin foam to
treat a life-long acne problem.  While this treatment is topical, I am
aware that many topically administered drugs can have systemic
effects.  Could you please provide some insight into the possible long
term side effects of this drug?

Thank you so much!

Trudy

P.S. While you don’t do weekly picks on TWiM, I would like to
recommend The Ghost Map by Steven Johnson.  It is a highly captivating
account of the cholera epidemic in 19th century London.

http://www.amazon.com/Ghost-Map-Steven-Johnson/dp/1594489254


Emerson writes:
I saw this rather fanciful notion and thought I'd pass it along to you fine gentlemen.

http://gajitz.com/bio-engineered-bacteria-colors-poo-translates-your-health/

Howard writes:
After listening to the fascinating podcast (TWIM #26) on the possible involvement of microbes and autism, I ran across the following article  ( http://www.nutritionjrnl.com/article/S0899-9007(11)00261-9/abstract ) discussed in the Winter newsletter of the International Probiotics Association. The links between neurological and immunological issues grow more numerous.

Howard Cash, Ph.D.
Ganeden Biotech
Mayfield Heights. OH

TWiM 26 Letters

Peter writes:
Dear Twim team

An interesting paper on artificial selection of yeast giving rise to evolved  clusters. The clusters evolved to be larger, produce multicellular progeny, and even show differentiation of the cells within the cluster—all key characteristics of multicellular organisms. This took  just 2 weeks, or about 100 generations.

http://www.pnas.org/content/early/2012/01/10/1115323109.full.pdf+html

A nice time lapse video of clusters dividing:

http://the-scientist.com/2012/01/16/evolving-multicellularity/

While this is very interesting I would be wary of reading too much into it.  How do we know that single celled yeasts have not evolved from earlier multicellular forms? This could be an innate -  previously evolved trait that enables the yeast to develop to a multi celled form with relative ease.

Kimberley writes:

Great job with these podcasts. I really enjoyed the ones I’ve heard.

Someone asked if CEUs are available? What can you tell me about that?

Thank you,

Kimberley
Microbiology Section Leader
Morton Hospital

Peter writes:

Arsenic-based life
In late 2010, NASA researcher Felisa Wolfe-Simon and colleagues reportedly uncovered a species of bacteria in Mono Volume Pills Lake that not only survived in unusually high levels of arsenic and low levels of phosphorus, but also appeared to incorporate arsenic into its DNA backbone. However, critics were soon questioning the results, citing poor DNA extraction techniques and a supposedly phosphate-free growth medium which actually did contain phosphate. Science published 8 technical comments about the work in May, though the paper, which has been cited 26 times, has yet to be retracted.

It seems it was a bad year for publish and perish.

Thomas writes:

Greetings,

I am a graduate student at the University of Georgia, working on my MS is plant pathology.

At the moment I am working my way through TWiP, TWiV, and TWiM.

Do you all have any interest in starting a this week in mycology podcast? I realize that fungi and oomycetes are more interesting to plant pathologists than animal pathologists, but I think this is a fascinating and diverse subject.

Keep up the good work!

Tom
UGA Department of Plant Pathology

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