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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 45 Letters

Elitza writes:

Dear TWiM Team,

I just finished listening to the TWiM 35 on LPS in Vibrio (among other topics). Dr. Elio Schaechter mentioned a field in Microbiology that I think is of great interest to the scientific community and should definitely be covered in a podcast. The topic is: Outer Membrane Biogenesis in Gram-negative bacteria. For decades people have been hypothesizing and trying to find an evolutionary link that would answer the following questions: how did a second membrane in bacteria come about and was the last universal common ancestor (LUCA) a single or double-membraned organism. These questions are extremely difficult to address and rely heavily on bioinformatics and phylogenetic analysis.

I'm the first author of the paper that I'm suggesting here as a resource for a potential podcast. I've read extensive amounts of scientific literature before the paper was finalized and published in Cell to realize that currently, there are no favored hypotheses and the very few hypotheses that exist are highly controversial. In our paper we structurally characterize (using electron cryo-tomography) the process of endospore formation. The process is typically thought of as exclusive to Gram-positive bacteria members of the phylum Firmicutes, however, we imaged a Gram-negative organism (Acetonema longum) that is also able to sporulate! Through our structural studies, phylogenetic profiling and biochemical analysis we showed that A. longum possesses a true outer membrane. Not only that, after sporulation, the spore is surrounded by two membranes both of which originated from the inner membrane of the mother cell. Upon outgrowth, the second membrane of the spore becomes the outer membrane of the bacterium and therefore is remodeled from and inner into and outer membrane. These are fascinating new results that may provide us with a missing link between Gram-positive and Gram-negative bacteria and give insights into how an outer membrane may have evolved.

Here are a couple of links to the paper I'm suggesting and a commentary by Dr. W. Vollmer on this work:

http://www.ncbi.nlm.nih.gov/pubmed/21884938

http://www.ncbi.nlm.nih.gov/pubmed/22173345

Thanks!

 

Fabio writes:

Dear Prof. Schmidt, I listened the podcast in Microbiology that you recently contributed together with Vincent Racaniello, Joseph John and Elio Schaechter. You made a very nice summary and commentary of the International Symposium on Staphylococci held last August in Lyon.

Furthermore, I would like to thank you for all your nice words about the symposium that we organized and on our recent opinion paper titled “Inferring reasons for the failure of S. aureus vaccines in clinical trials” and published in Frontiers Cell. Inf. Microbio.

Best wishes,

Fabio

Fabio Bagnoli, PhD

Project Leader

Novartis Vaccines & Diagnostics


Alice writes:

Hey TWIM-MERs -- this is from a wildlife rehab newsletter, thought you might be interested:

MRSA in Wildlife

One of the most notorious and hard-to-treat bacteria in humans has been found in wildlife, according to a new study in the Journal of Wildlife Diseases. Researchers isolated methicillin-resistant Staphylococcus aureus (MRSA) in two rabbits and a shorebird. Wild animals may act as an environmental reservoir for the disease from which humans could get infected.

Molecular typing of the isolates showed that the shorebird carried a hospital-associated strain of MRSA, while the rabbits had community-associated strains. The rabbits' MRSA also was resistant to tetracycline, which is common in farm animals.

Perhaps most troubling of all was that one of the pigeons carried a Staphylococcus bacterium that, while still sensitive to methicillin, was resistant to the antibiotic vancomycin. "Vancomycin is used as a last resort in MRSA infections," says study co-author Shylo Wardyn, “and vancomycin-resistant staph strains are rare in humans.” Abstract: http://www.jwildlifedis.org/content/48/4/1069.abstractlink

Peter writes:

Happy Halloween greetings Twim Team.

For a slightly microbiology themed Halloween costume I constructed a Plague Doctor mask.

You can see its construction on the instructables site:

http://www.instructables.com/id/Plague-doctor-mask-for-Halloween-1/


Michael writes:

Hello, TWiM!

News Article: http://www.guardian.co.uk/environment/2012/oct/15/pacific-iron-fertilisation-geoengineering

Comment:  I feel like this issue is quite broad and interesting and was hoping that ocean geoengineering might be worth discussing.  It's my understanding that scientists are wary of such approaches, to say the least, but this event seems to demonstrate a certain necessity for the international community to come to terms with geoengineering and sort out strategies and methods.  As a layman, I'd be very interested in what you guys have to say!

Quick excerpt from the beginning of the article:

"A controversial American businessman dumped around 100 tonnes of iron sulphate into the Pacific Ocean as part of a geoengineering scheme off the west coast of Canada in July, a Guardian investigation can reveal.

...

Satellite images appear to confirm the claim by Californian Russ George that the iron has spawned an artificial plankton bloom as large as 10,000 square kilometres. The intention is for the plankton to absorb carbon dioxide and then sink to the ocean bed – a geoengineering technique known as ocean fertilisation that he hopes will net lucrative carbon credits.

George is the former chief executive of Planktos Inc, whose previous failed efforts to conduct large-scale commercial dumps near the Galapagos and Canary Islands led to his vessels being barred from ports by the Spanish and Ecuadorean governments. The US Environmental Protection Agency warned him that flying a US flag for his Galapagos project would violate US laws, and his activities are credited in part to the passing of international moratoria at the United Nations limiting ocean fertilisation experiments

Scientists are debating whether iron fertilisation can lock carbon into the deep ocean over the long term, and have raised concerns that it can irreparably harm ocean ecosystems, produce toxic tides and lifeless waters, and worsen ocean acidification and global warming."

Thank you for the great podcasts,

Michael

 

Øystein writes:

Dear TWiMmians,

I just found the latest edition of Clinical Microbiology and Infection and read about a concept that is new to me: culturomics.

Maybe you'll be as intrigued as me by this concept. It contrasts well wil all the high-throughput-genomics hype these days. It might be a good article to put on the show (some day?).

Here are the links, I am happy to forward pdf's of the articles to you if needed.

Culturomics: a new approach to study the human microbiome

http://onlinelibrary.wiley.com/doi/10.1111/1469-0691.12032/abstract

and

Microbial culturomics: paradigm shift in the human gut microbiome study

http://onlinelibrary.wiley.com/doi/10.1111/1469-0691.12023/abstract

And again, thank you for three great show to walk, commute, run, bike and do housework to:)

All the best,

Øystein

Registrar in clinical microbiology

Vestfold municipal hospital, Tønsberg

Norway

TWiM 44 Letters

Jeff writes:

Hi All - I am getting to the part of my Micro class where I have students analyze antibiograms and noticed a blog pointing to the attached paper. Forgive me if this topic (antibiogram data changing as a function of when samples are taken from a patient) has already been covered or commented on, but just in case, take a look. I particulary enjoy data tables showing "time to unreliability" and boy, things sure change fast in the ICU! I would be interested to hear a program about the "ecology of antibiotic resistance" in hospitals/clinics. I can think of reasons why resistance might vary depending on location within a hospital, but not being a clinical person I have no idea what the real reasons are. Forgive me if this too has been already featured.... teaching 5 classes and then coming home two young children keeps me chronically behind.

Love the program, thank you so much!

Here is the link - I don't know if it is copyright protected or not....

http://www.ccih.med.br/m/aluno/mod/biblioteca_virtual/revistas_2012/ICHE/Junho/0589.pdf

Jeff
Georgia Perimeter College

Katie writes:

Dear TWIM Doctors,

Thank you so much for your wonderful podcast.  I enjoy the entire TWI series, and I am thrilled that I finally have something to contribute!

In TWIM #43, a really interesting paper on bacterial caveolae was discussed. While this was amazing work, I do have to point out that being chock full of membrane vesicles is not unheard of in bacteria.  The photosynthetic purple nonsulfur bacteria (PNSB) Rhodobacter sphaeroides forms membrane vesicles in the cytoplasm to house its photosynthetic apparatus.  I have attached a paper with EM images (see Fig. 2 of the Adams and Hunter paper) showing how full these bacteria are with vesicles.  Beautiful studies by investigators such as Dr. Neil Hunter are beginning to uncover how these vesicles are formed, but there is still a lot that is not understood including what happens to these vesicles during division.  Another PNSB, Rhodopseudomonas palustris doesn’t form vesicles, but it does form lamellar membranes in the cytoplasm. If you look at the EM images in the second paper I attached, you can see that they have just a splash of cytoplasm. Considering how crowded the bacterial cytoplasm is already, it is really amazing!

Keep up the great work, and I look forward to the next podcast.

Cheers,
Katie

[she sent:
http://www.sciencedirect.com/science/article/pii/S0005272812001703

http://www.ncbi.nlm.nih.gov/pubmed/6343353 ]

Ayush writes:

Hello TWiM team,

I enjoy listening to you all every week. I apologize that my comment here is about not-so-recent TWiM (#30) about Burkholderia pseudomallei.  Some of you may know that that Melioidosis was perhaps described (Tapanuli fever) as a bioterror agent by Sir Arthur Conan Doyle in 'The Dying Detective'.  In this story, Sherlock Holmes was sent an unknown bacterium in mail to get him killed. Here is a paper describing Holmes' encounter with the bioweapon.

Please keep up the great work. I would strongly recommend TWiM as a must-listen for every microbiologist.

Alice writes:

Soil bacteria as source of drug resistance genes - does this have implications for nosocomial infection via contamination followed by gene swapping?

Glenn writes:

TWim podcast #11

I am wondering about the comment that was mentioned about the cutting board being the most dangerous tool in the kitchen. What is the best way to clean the cutting board? Also if one was to only use quick frozen chicken and cook it without pre-thawing. Will this keep one from acquiring the transfer of microbes from chickens to human by touch. I am assuming that by cooking all meats it kills all microbes.

Thanks,

Glenn

Glenn writes:

first I am really enjoying listening to TWiM and as a non-scientist you make the information about the micro world understandable. My question is related to TWiM podcast #16. I have several health issues that require me to take ibuprofen for pain and inflammation. How much concern should I have about the depletion of change in my gut and its ability to function properly.

thank you,

Glenn

TWiM 43 Letters

Jake writes:

Hello Vincent,
I've been listening to your TWiM podcast now for a few weeks as I am a student at SDSU taking a microbial genetics class with stanley maloy.  It be be another few months until I've caught up to the current episodes.  I saw this recent article on phage use in cleaning up achne and thought you'd like to hear about it.

http://www.genengnews.com/gen-news-highlights/zapping-zits-with-viruses/81247383/

cheers
Jake

Franco writes:

The article by Frits R. Mooi et al. linked on the episode “The sound of whooping cough” is contradicted by a study published on the current issue of EID: Schmidtke AJ, Boney KO, Martin SW, Skoff TH, Tondella ML, Tatti KM. Population diversity among Bordetella pertussis isolates, United States, 1935–2009. Emerg Infect Dis  Volume 18, Number 8—August 2012 http://dx.doi.org/10.3201/eid1808.120082.

I would greatly appreciate a comment on this point.

Best regards
Dr. Franco Giovanetti
www.aslcn2.it
http://medicinadeiviaggi.blogspot.it


John writes:

Dear TWIMmers,

I just finished listening to TWIM #39 (yes, I'm behind) and I had a question about the paper Michael reviewed.  Let me spell out how I understood the discussion, and then maybe you can tell me if I've misunderstood something, or if my question even makes sense.

Michael was talking about the question of how mutations arise and are selected for in nature.  The idea supported by Darwin (though long before anyone knew about DNA) was that mutations were in some sense driven by stress, right?  And then, there was this famous experiment which showed that mutants were present in the population before selection pressure was applied--a bunch of microbes were put on a plate with some antibiotic, and a small fraction of them were mutants that had resistance genes.  In this case, there was no pressure on the microbes to adapt the the antibiotic until they were put in a situation where they died unless they had the resistance genes.  Is this right so far?

Then, there was a second experiment, which used less powerful selection--the microbes were put on a plate where the only source of carbon was lactose, which the normal population of these microbes couldn't use for carbon.  And at first, these didn't grow much, but over time, even in an environment where the normal microbes couldn't grow Buy Viagra at all and so selection shouldn't have been able to bring anything new about, some microbes arose that could grow under these conditions.  Again, have I understood the basic idea?

Now, this is where I got a little confused.  From Michael's explanation, what I got was the idea that a bacterial cell can mutate in place even when it's not dividing.  That is, even in these bacteria that were sitting there unable to divide because they couldn't get any carbon from their environment, mutations could arise over time, and this led to a population of microbes that started out without the ability to grow with no carbon sources other than lactose, and then a few mutations arose that allowed some growth.  Is this right?  Is this kind of mutation important in eukaryotic cells, say in cancer or cellular senescence?

An alternative seems to be that the bacteria started out with a huge diversity of mutations already present, many of which gave them some small ability to get carbon from the lactose.  Then, over time, it seems like those would do all the dividing, and you'd get something like classic selection, with the bacteria that could reproduce faster leaving more copies of themselves which themselves could mutate to get better at reproducing.  Was there something observable in the experiment that ruled this out?

Anyway, thanks for answering my amateur questions.  I'm a computer scientist with no biology background, so I apologize if I'm making some dumb mistakes somewhere.

I wanted to also point out a really fun quote I ran across awhile back.  It's in a very old book (_Mutual Aid: A Factor in Evolution_ by Petr Kropotkin)--I think it was published in 1902.  It was a kind of argument against social Darwinism from a Russian naturalist and anarchist, combining observations on history and nature both.

> Mutual aid is met with even amidst the lowest animals, and we must be prepared to learn some day, from the students of microscopical pond-life, facts of unconscious mutual support, even from the life of micro-organisms.

Reading this, the words "biofilms" and "quorum sensing" popped immediately into my head.  Along with all the other kinds of mutualism between microbes.

Thanks again for your wonderful podcasts,

--John

TWiM 42 Letters

Sarah writes:

Hi Twimologists!

I just found this wonderfully instructive paper on concepts of bacterial ecology that are relevant to the antimicrobial resistance problem (doi: 10.1086/340245,link). The author mentioned the existence of genes conferring resistance to metallic ions like copper, which reminded me of the discussion about copper surfaces from TWiM episode 1. I hate to ask because it involves chemistry which we ALL took ages ago, but could you comment on this? (Dr. Maloy?)

A lot of papers about copper resistance in bacteria came out before Y2K, such as the above paper's reference # 47. But this paper just talks about metabolism of ionic copper, which is different than metallic or solid state copper (if I remember right). However, a 2004 paper (link) in BMC Microbiology suggests that metallic copper releases copper ions which are transferred into bacterial cells when a bacterial suspension is incubated in a copper vessel.

So, is it futile to celebrate the antimicrobial properties of copper surfaces, or is metallic copper reliably antibacterial by brute force, able to overcome any resistance gene that lets bacteria metabolize copper ions?

Thanks!
Sarah, BS, BSN, RN, Infection Preventionist

Peter writes:

I am not sure if the BBC programme Horizon is available in America but I found  the recent edition on combating antibiotic resistant bacteria was very interesting.
Of particular note were the interviews with Dr David Harper of AmpliPhi BioSciences in England on the development of bacteriophages to fight bacterial infections and Professor Viagra 100mg Bonnie  Bassler of Princeton University who is investigating  using antagonists to bacterial quorum sensing compounds to moderate their pathological effects.

http://www.ampliphibio.com/index.php/about/about_us

http://molbio.princeton.edu/faculty/molbio-faculty/31-bassler

I think that these scientists would make good guests for TWiM.

Behzad writes:

It is always a delight hear Vincent chairing these informal and incredibly informative podcast discussions of microbiology.  The world should be eternally grateful for what he is achieving and making so accessible both through smart phone streaming and on the web.  He engages his panelists enthusiastically as they discuss a wide range of topics important to understanding the diversity of microbes and their to understanding infection, ecology and even climate!

Hearing Elio is particularly rewarding as he is, dare I say, even more articulate than Vincent as he explains his topics clearly in terms that non-experts can understand and, importantly, puts these into historical context.

I do hope that this message is communicated to the shows sponsor, ASM.

Keep up the great work!

Steve writes:

Hi,
Of course, I immensely enjoy the podcasts. Thanks for making front-line science so accessible and informative. This is something America, society needs -- a more intimate, clear-eyed look at science and scientists in action.

Are there transcripts available for the TWIM podcasts? If not, is this something planned or in process? If not, I would help transcribe and index the text to the audio/video files.

Regards,

Steve

Abhinav writes:

Why do only a few bacteria out of billions act as endophytes by entering tissues of plants?

TWiM 39 Letters

Merry writes:

Writing the sprint event for the Microbial Olympics published recently by Nature Reviews Microbiology was surely my most fun writing assignment ever! The idea for this feature article originated with Dr. Andrew Jermy, Senior Editor at NRM in London back when the city was just starting to hum with preparations for the summer Olympics. He invited Forest Rohwer and myself to cover one of the events. Fortunately he offered us the sprint, which was a perfect opportunity for my favorite entrants, the phage, to win. He also enticed me by clearly stating his intent, that this was to be a fun piece for the reader (and the authors alike). Because my name happens to be first on the article, rumors have been going around that this was my idea. Actually, this was but the latest of a series of innovative features he has put together. I look forward to the next one.

Merry Youle

James writes:

Hello twim,

I just wanted to write to you guys and say thanks for highlighting our nature reviews article (Microbial Olympics). I'm glad our approach of writing a pieces that could be appreciated by experts and laypersons alike was successful and as its my first outing into the publication world I'm thrilled it has received such positive feedback! Thanks again!

Sincerely

James Gurney

Jim writes:

Another wonderful TWIM.  
Jo Handlesman's credentials are more impressive by the week.  

Will apologize for my low brow humor in the letter you read.

Taking a dump is used to say having a bowel movement. Hence "dump data" would be data derived from the study of bowel movements.
73

Stanley writes:

So, maybe it was because I was irritated from sitting in a traffic jam in LA, or maybe (like Elio) I was just being an old curmudgeon. As I was parked on the freeway listening to TWiM and looking forward to accelerating through Elio and Michaels autobahn through the recent General Meeting of the American Society of Microbiology, their comments made me feel stuck in an intellectual roadblock.

Elio made a good point that when a field gets started it begins with a lot of ideas, then goes through a period of accumulating a lot of data, before finally maturing into a robust blend of ideas, data, and broad insights that lead to interesting, testable predictions. But research on the microbiome is not just stuck in the boring burial in data phase. The field began with learning about a small number of cases to learn "who is there" and trying to guess from the sequences "what are they doing", work that was important to build the foundation of microbiome studies. And, it is true that there is a lot of that still going on in labs around the world. But the research has also progressed to other broader questions like how does the microbiome change after treatment with antibiotics and how long does it take to recover, how does diet influence the microbiome, is a person's microbiome stable or does it change over time, do certain microbes in the microbiome seem to protect against particular diseases -- questions that both make us think about the role of microbes in our health and illness, and data that leads to testable predictions that can lead to new therapeutics and treatments. For example, probiotics have been around for a long time, but we didn't understand how they work (and in some cases didn't even have good evidence that the really do work). Likewise for age old treatments like fecal transplants.

In short, this is a very exciting time for the microbiome and, if you're willing to listen and think, a fun time to be in the audience learning about the new Generic Viagra discoveries. If you'd like to hear from some of the people who spoke at the ASM as well as some perspectives on the future of this work, check out the ASM Life interviews from the General Meeting (http://www.microbeworld.org/index.php?option=com_content&view=article&id=1204).

Thanks for the cerebral distraction from the bumper in front of me. --> Stanley


Joe writes:
I wanted to follow up to an email the I sent to you all a while ago about evolution and entropy and my sense of paradox  regarding the ever increasing complexity of biologic systems and their concentration of energy in spite of the overriding  natural continual dispersal of energy captured in the idea of Entropy.

Let me first say that one of my gifts as  a scientist and engineer is an ability (and willingness) to ask fuzzy questions about bigger concepts at the boundaries of my knowledge looking for unexpected insights. Usually these questions are not quite so fuzzy that I mistake 2 for 3 as in the laws of thermodynamics, I guess I just like Gibbs Free Energy more than Entropy! That effort to identify what we don't know that we don't know is what has always excited me about science, the chance to think an entirely new thought that reveals something new about nature. How cool is that!

I appreciated that Michael and the rest of the crew tried to tackle the question in the spirit that it was offered and his answer essentially pointing out that nature arrives at complexity through massively large numbers of trial was useful after I thought about if for a while. Yet I must say that it still did not quite get at the core of my question. I was surprised by the email responses to my question that you later read. Particularly by the person who all but accused me of being an evil Creationist! I will just say that since it is not an issue that I care about I suspect the assertion says more about his world view than my own. The phrase "evolution driven by random chance" has never seemed to capture the awesome  sense of inevitability and thoroughness that I see in evolution. To me that phrase seems equivalent to calling it "magic".

Since then, I have come across a much more complete answer to what underlies this drive to complexity in Ray Kurzweil's book The Singularity Is Near, which I recommend as an interesting read whether you agree with his thesis or not. On page 85, he references research done by Stephen Wolfram on Cellular Automatons. This is a mathematical study that describes how complex non repetitive patterns can be generated from digital systems with a few very simple rules. In particular there is a category called class 4 automata that appear to characterize the evolution of biological systems. I have picked up  Wolfram's book A New Kind of Science and even though I am but a few pages in, it appears to be a very promising brain stretcher. Assuming I don't injure my back lifting it, I will let you know if it addresses my questions about the underlying drivers in evolution.

In closing let me say that I appreciate all the great work you all are doing in all 3 podcasts. I value the dialog, spontaneity  and asides and believe that you all capture the emotional enthusiasm that make science such a great life's work.

Joe
EH&S Manager

Peter writes:

Greetings TWiM team

I saw these instructions on instructables.com for culturing bioluminescent bacteria from fresh sea fish and thought they may be of interest.

http://www.instructables.com/id/Bioluminescent-Bacterial-Lightbulb-Water-Polluti/?ALLSTEPS

For those not familiar with it Instructables is a very eclectic DIY site where people can publish instructions for various projects they have done.

TWiM 38 Letters

Jim writes:

As usual I loved TWiM #37. Jo Handlesman adds a lot imho.

I think Michael Schmidt meant "dump data" instead "data dump."  Apologizes to Alan Dove.

Look forward to the up coming bioinformatics guest.

Thanks a million

Tim writes:

Dear TWiMeisters,

I'm quite behind in TWiM, TWiP and TWiV, because of my exams, which is a poor excuse, I know! Anyway I just listened to TWiM #22 with Dr. Sacchetti, and thought I'd write in with my appreciation. As an RN student, I love it when your podcasts are specifically pertinent to my area of interest. In this case, hospital-acquired infections and the most common infections in emergency departments.

This was one of the most fascinating episodes yet. I was wondering though if you'd consider doing something on infection-control in a surgical setting? That is, if you had any papers on the effectiveness of surgical attire in preventing spread of infection to the patient, and/or protecting the surgical staff from the patient. Particularly, I'd be interested in hearing which microbes are most commonly found on the Online Blackjack skin or in the hair of surgical staff. I wonder if surgical infections would be similar to those in emergency departments, or if the percentages would be slightly different.

Admittedly, such an episode would probably not be of interest to many, and the literature may not even be out there. My main purpose for this email was simply to express my appreciation for everything that you do. Keep it up! Much respect to every one of you.

Regards,
Tim (Melbourne, Australia)

Alicia writes:

Hello,

I was listening to TWiM a few weeks back and, if I remember correctly, it was mentioned that it would be interesting to find someone that could discuss spirochetes with you.

I would like to recommend one of my professors, Dr. Caroline Cameron. She is Canada's Research Chair in Molecular Pathogenesis and teaches at the University of Victoria. I have spoken with her and if you have any future papers concerning spirochetes (especially Treponema pallidum subsp. pallidum or Leptospira) she would be interested in participating.

I hope you will do an episode!

Best,

Alicia

TWiM 37 Letters

Pat writes:

Hi Vincent,

I'm a regular TWIM listener and Assistant Professor at the University of Michigan in the Department of Microbiology & Immunology (I enjoyed your visit last semester).  I was also heavily involved in much of the data analysis for the Human Microbiome Project.  As I was unable to attend the ASM General Meeting, I cringed when you and your co-hosts described the human microbiome talks at ASM as being glorified data dumps (TWIM #36).  This is most unfortunate!  I was wondering whether you might be willing to have a guest, say…  me to help get the general microbiologists through the weeds.  As a former postdoc in Jo Handelsman's lab, I can tell you that I am very interested in making computational concepts more engaging and feel that we have an important job as scientists to view our research mission as part of our teaching mission.  Anyway, if you're ever interested, please know that you have a standing offer from a  microbial ecologist / bioinformaticist to help your listeners get excited about this amazing topic.

Sincerely,
Pat Schloss
--
Department of Microbiology & Immunology
University of Michigan

Mark writes:

Hello, Vincent, Michael, and Elio (and the other contributors!):  I want to thank you so much for these podcasts.  I have been having to sit around in traction for a pinched nerve a couple of times a week, and listening to TWiM enriches my mind while I feel like a science fiction character!  Better than watching television, in any case.

I really appreciate the interactions and information that are presented in all of your podcasts, but the comments on the ASM General Meeting (which I had attended, too),in TWiM 36 resonated.  The new "card" format for the posters was indeed wonderful for forgetful people like myself, and I have to agree strongly with Vincent's comment (and Elio's quite gentle criticism) of systems biology:  things are getting so complicated that few people can be generalists. I used to worry about "eukaryocentricity" in biology, but clearly I need to start worrying about "colicentricy."  I too thought that third slide at the opening session was a backgrounder for Salmonella phase variation---but decided I must not be "getting it," since the speaker was so clearly brilliant and engaged.  So a solid background becomes vital, even for MacArthur Genius Grant Online Casino winners, as our field sprints (it no longer marches!) forward!

One final thing.  I will be trying to introduce my undergraduates to TWiM in my Fall microbiology course.  The podcasts give an engaging and current "feel" for microbiology (I was going to say the "ferment" of microbiology, but I restrained myself).  While my students might not want to listen for an hour, we do discuss journal articles...and I intend to assign some of the ones you have been covering, with the relevant TWiM assigned as "background listening."  Extra credit points often focus attention like a laser, I find.

Best wishes to all, and thanks for what you do.  Hope to see some discussion of microbial endocrinology at some point?

-Mark Martin

P.S.  The human microbiome descriptions are indeed hard to follow!  I half-expect to see advertisements for entero-Harmony, the dating service that matches people based on their enterotypes.  Hmm.  What about antibiotics then?  Best wishes, MM

Spyros writes:

Hi

I heard you read my email on the last TWIM and I was super excited. Really excited.  And it looks like from the comments on the panel it's something you guys would like to pursue.  Please let me know when or if you guys get the time.

I am up to the ICAAC podcast, but i have listened ahead to the most recent ones obviously.  The podcast keeps talking about probiotics and the benefits, and I'm truly interested in them.

however I'd like to point out a recent MedWatch release and here is the link

http://www.fda.gov/Safety/Recalls/ucm311050.htm?source=govdelivery

this isn't the kind of pharmaceutical I manufacture but it's interesting nonetheless to me, and this is an example of what happens when things go very wrong in my industry, a lot of folks can get hurt, each unit is going into a person and I treat each one like a person.

Also I hope you guys mention what's going on in Cambodia, I saw 65 illnesses on CNN and no cause for it right now.  Of course that may have changed, I have had a horrendous day of travel and have been out of touch with the news, but the new can't do as good a job as you guys can discussing this latest issue.

Again thanks, look forward to hearing future podcasts and hearing from you guys.

TWiM 36 Letters

Todd writes:

Just a quick note to say how much I enjoy TWiM, and in particular, how much I enjoyed episode 32 featuring Rosie Redfield. I don't know how you find time to do this, but I'm glad you do. Keep up the great work.

BTW, I was also fortunate enough to attend the SGM meeting in Dublin in March. I enjoyed hearing you talk about the use of new media, as well as the rest of the meeting. I was also impressed at the weather they arranged for us! I entered Dublin into my phone's weather app several weeks before the meeting, and haven't yet removed it. I haven't seen a single week with weather as nice as ours before the meeting or since.

Spyros writes:

Hi

My name is Spyros and I'm a manager of a Biological Quality lab in a pharmaceutical plant.  I'm in the process of listening to all your podcasts and I really like it.  I have a Microbiology degree (Bachelors) from the University of Illinois at Urbana-Champaign, so I don't have the education of a lot of your friends / guests, but what I may be able to bring to the show a different perspective. I remember in one of the first ones, a lab tech from industry called in and asked some general questions.

I don't know if this has been brought up or were looking from someone from industry to speak on topics of pharmaceutical manufacturing and controlling flora in the environment,  monitoring we do, what we monitor, what we monitor for and general career advice.

I probably will have to work with my company's public affairs division and probably legal around what I can / can't say but I will only do that if you would be interested in having me on the show.  I don't know the exact time commitment but I will arrange to meet it if possible.  I live in free online casino bounuses North Carolina, and I know one of you regular contributors is in South Carolina, so, you would have the Carolina's covered!

I'm only on episode 6 so if you have this covered I understand.  Keep on going really enjoy the topics.

Thanks

Sarah writes:

Hi Vincent and guests,

I have been an avid listener of the TWIM/V/P podcasts for just over a year now; they help pass the time during long animal surgery hours, even longer stereology sessions, as well as during my rollerblade home from work in Los Angeles... yes I know it's dangerous to wear headphones and rollerblade in a city where people care more about the scratches on their car than a pedestrian's broken bones if a collision occurs, but hey we all have to take risks for science right?

My question is a little delayed in terms of timing; it was sparked from the January 26th podcast looking at a possible role for microbes in the onset of autism. It was mentioned in the beginning anatomy lesson that the appendix may have a role in priming the gut microbiome. I know there has been at least one study that has shown a correlation between appendectomy and an increase in heart disease in humans, and I also found a paper linking germ-free mice with an increase in atherosclerotic plaque formation. I'm curious if you or your colleagues have any postulates regarding which particular group/groups of bacteria in the appendix may be the "keystone genus" within the community- knocking them out will potentiate the results found in the germ-free mice in terms of plaque formation or other early markers of heart disease. I guess if you were going to look more closely into causal links between appendix, gut microbiota and heart disease, where would you start and why?

I hope that question made sense and thanks again for the hours of entertainment...enjoy the Spring weather!

Kindly,
Sarah

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

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