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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 59 Letters

Oscar writes:

This is the greatest TWiM ever. (#58)

I've always been interested in evolutionary complexity and for the last seven years or so I've been unable to think of evolution in terms of traditional survival of the fittest on an individual level--at first it just seemed too simple. But through these years of rumination on the subject often provoked by a science story in the news (or on a science-ey show (radio-lab, I'm looking at you--I love you but I'm looking at you)) that approaches evolution through the perspective of survivability of the individual as opposed to survivability of a complex ecosystem of interactive life-ey things and then failing to see obvious conclusions because of this narrow view, I'm nearly unable to conceive of the idea of an 'individual' organism having any meaningful impact on (even short term) evolution.

This episode of TWiM starts with Elio giving a very masterful explanation of the paper: Underground Mycelial Networks Carry Warning Signals to Plants. His gentle and thorough description makes me long for an opportunity to attend a lecture class with him. He is truly a masterful lecturer with managed digressions that are interesting and make it clear that he is processing the information further as he speaks making the reality of hearing a brain (or brain-biome) at the top of its performance and with such great depth of knowledge really tangible and exciting.

Of course the content of that paper is also remarkable and Vincent and Michael do spectacular jobs of interjecting and referring to relevant information as well as questioning things where it's due. The dynamic in this episode is really great.

Then to top it off the second paper about the Brain Microbiome is as amazing as the first paper. During the discussion of this paper one can really feel the excitement and disbelief from the trio as they consider the implications of how this can change our understanding of the brain. I'd like to add that I wasn't at all surprised by the fact that our brain has it's own microbiome (I actually was a little surprised that it wasn't a foregone conclusion).

This episode was truly enlightening and highly entertaining. I was so riveted to the entire thing--I felt like that's what witnessing the moon-landing for the first time must have been like--it's real discovery and really cool.

So thanks TWiM guys and keep up the work. I don't care if you don't produce an episode every week, just get them out occasionally because this is important stuff that people need to know.

Finally: I'd just like to throw this out there: I'm at the point now where when I seriously think of how things evolve, all pieces of a system have to be taken into an account. It's easiest for me to grok if I consider a physical space and all of the life and non-life inside it and then also to consider a significant time-period that must include thousands if not millions of generations of changes and co-dependencies that have developed and curated. I know life has evolved to evolve (I can give a number of examples of that) and I know life has evolved to evolve to evolve (I even have a couple of that) the next level isn't easy to see but I guarantee it's there and it probably recurrses an innumerable amount of times in ways that are both simple and complex and we just have yet to understand.

I'll leave you with this: Despite the appearance of randomness guiding the evolution of the beaks on Darwin's finches I promise that the beaks of those finches have evolved to have high-rates of randomization and likely even environmental influences that either magnify or reduce the amount of randomness that's displayed--after all, evolving a trait that helps them evolve will increase survivability and that's the meaning of life.

Thanks for the great TWiM!

Oscar Prill
Technology Director
Lionsgate Academy


Mark writes:

Hi Vincent et al
I have been listening to TWiM for several weeks after moving to a new job that requires me to undertake a one-hour drive to work. I enjoy the show very much: in fact, I enjoy it so much that I am thinking of setting up a similar podcast this side of the Atlantic.

But this is not the reason I am writing.

I listened to your discussion of the brain microbiome this week. And, even though I note the question mark in your title after the term "brain microbiome", I think you were not skeptical enough.

OK, I admit that the paper presents an internally consistent story. But they don't report trying to grow the bacteria. And, rather than one organism, they would have us believe there is a kitchen sink's worth of microbes in these brains. Remember when we look at most sterile samples, we assume that a mixed growth equals contamination! And alpha-proteobacteria are common contaminants of water supplies, even in the International Space Station! http://www.ncbi.nlm.nih.gov/pubmed/16364606

But more generally, as Carl Sagan put it, extraordinary claims require extraordinary evidence! And IMHO the evidence presented here is not compelling enough to overturn over a century of microbiology and histopathology. If these bacteria are really there, would we not have seen them already? If we look at precedents, we could be looking at the next Helicobacter pylori and these authors are going to be Nobel laureates. But I think a more plausible precedent is XMRV or arsenic life, both of which turned out to be nonsense. Go take a look at Ioniddis' paper "Why most published research findings are false" http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124

Only time and attempts at independent replication will tell what is going on here. But I am prepared to wager that in ten years time this paper will have been discredited or forgotten.

Keep up the good work!

Cheers

Mark
Professor Mark Pallen
Professor of Microbial Genomics and
Head of the Division of Microbiology and Infection
Warwick Medical School
University of Warwick

http://blogs.warwick.ac.uk/microbialunderground/

Robin writes:

TWiM #58: The brain microbiome

The brain microbiome would have been outright heresy in the latter 1960s when I had medical microbiology in med school. Today's facts are stranger than the wildest imaginable fiction of a bygone era.

Both papers go to show the enormously complex interconnectedness of all things.

The idea of signals transmitted through a network of mycorrhiza suggests a slow intelligence with signals acting over hours or days instead of milliseconds as is the case with neurones. An awareness associated with such an intelligence would have little commonality with what is familiar to us. Even though chemical inputs equivalent to smell and taste, mechanical inputs equivalent to hearing and touch, and light inputs equivalent to vision could affect such a system, they would be so different that it may be impossible to form a concept of such awareness.

It is to be noted that in Eastern traditions, awareness is consciousness with content; appropriately organised complex configurations of matter and energy will manifest awareness just as non-magnetic pieces of iron in a magnetic field will manifest magnetism.

Methyl salicylate is present in large quantities in oil of wintergreen: even a teaspoon if ingested can cause severe salicylate toxicity. Aspirin is acetylsalicylic acid. It is less irritating and less toxic than methyl salicylate. The intrinsic stickiness of blood platelets depends on platelet cyclooxygenase, which is inactivated by acetylation by acetylsalicylic acid. A single tablet of aspirin will inactivate the platelet cyclooxygenase in all the platelets. It also affects the other blood cells, but unlike platelets, they regenerate their cyclooxygenase. Platelets have to be replaced by newly formed platelets. Since platelets have a lifespan of seven days, a tablet of aspirin is good for two to three days.

Eli writes:

Hi Vincent et al!

I was listening to the TWIM episode #55: In the copper room, about bringing down hospital infections.

You mentioned two things as being the main problem. The first one was high occupancy rate.

Quote from the episode:

"The second and this is probably the most important reason, is that you can't tell that things are dirty - from a microbial perspective. And we don't routinely survey the area to ask what is the microbial load"

I am thinking, what if the bacterias could somehow be made visible. It would be real cool if material could be engineered to change color to show if there is a high level of bacterias and other pathogens, to alert that a surface needs to be cleaned. It doesn't necessarily need to be visible to the naked eye, but just if some special lights got shined on it. I have no idea if it will be possible, I just liked the thought.

As you say, the main problem about hospital infections, is that the problem is invisible. And if things are invisible to our eyes, it is harder to shine mental light on it, because we don't directly get reminded about it on a daily basis. Hereby my wish for "bug luminol" is passed on.

Joe writes:

Hi guys

I really enjoyed the discussion of PULs on the most recent episode of TWIM. I had a minor correction with respect to the discussion of the connection between diet and IBD. During the discussion, one of you talked about a progression from ulcerative colitis to Crohn’s disease. In fact – these diseases, although categorized as inflammatory bowel diseases, have fairly different (albeit poorly understood) etiologies. UC is generally restricted to the colon while CD can be localized anywhere between the mouth and anus. Also, IBD patients generally have one or the other – but not both. They don’t really progress from one to the other in any individual patient.

Keep up the great discussions of the wonderful world of bacteria and human health.

Cheers,

Joe
----------------------------------------------------------------------------
Joseph McPhee Ph.D.
Michael G. DeGroote Post-Doctoral Fellow
Coombes Laboratory
McMaster University, Department of Biochemistry and Biomedical Sciences

Dave writes:

Most interesting talks on copper in disease transmission reduction environments. How about silver?

I possess several pairs of army socks (literally), a percentage of the fibers (3%? 12%?) woven into which are microcoated (or embedded, or something) with silver. The purpose is suppression of undesirable (potentially mission-defeating) microbes.

I believe they are effective. I believe there is some literature on the efficacy of silver, and rationale for its selection over copper. I think I've seen some ventures at explaining the mechanism, but I don't have the stuff in my head and can't go looking. Worth observing that they seem to enable wearing socks for more than one day without getting stinky.

Interesting aside: I went looking for army socks after hearing an ER doc describe managing the pain of 36 hours on his feet by wearing wool army socks. His belief was that the wool provided a sufficient secondary cushion to dampen the impact of walking all day on concrete floors (which have no give, relative to asphalt or whatever). My feet have plagued me with easily acquired aching, so I went looking. The socks, combined with placebo action, seemed to provide noteworthy reduction of discomfort. As to heat objections, which seem culturally common among us, he reported year-round use without problem. I found them entirely comfortable, probably downright insulating, when worn in Fresno summers under boots, and certainly no worse than conventional or lightweight socks, so I ratify his year-round prescription, since they're pleasantly warm in winter too. (pause for breath) Not itchy either, in this formulation, to the contrary of old complaints about wool.

Anyway, recently I went to the military/police gear store for more socks. I was disappointed not to find the familiar thick wool, but did decide to try the new blends. Some were thinner wool blends, and others blend cotton with synthetics such as lycra, I guess. I sprung for some, and was so pleased with the (quite inexpensive, relative to Walmart work socks) performance of the silver blended ones that I went back for more. This model is near knee-high, so has the benefits (for those to whom it matters) of compression as well, potentially reducing edema and whatnot.

Anyway, whatever. Much enjoy the show(s), encountered on internet radio Science360 (which you might mention sometime). Hope you find the bit on silver vs. copper interesting. Maybe it suggests a further look along the table of elements.

dave

Tim writes:

Michael Schmidt's enthusiasm and passion for all science is always wonderful to listen to. Hearing him discuss his own work was even more of a treat. Congrats to him and his collaborators on their great work telling a fantastic and relevant story!

- Tim

Bernadeta writes:

Dear TwiM podcasters,

Thanks for another great episode! Each TwiM/P/V episode you do brings me so much inspiration and I wait impatiently for another one to come. Usually, though after each episode I have more questions than answers, which I think is great because that what science is based on, like Feynman said: science is expanding frontier of ignorance the more we know the more there is to answer.

Regarding the last episode, I always find these phage-bacteria arms races very fascinating; they are a perfect example of how evolution can work in short period of time.

On last episode it was mentioned that CRISPR/Cas system takes up DNA randomly irrespectively of whether that would come from a "helpful" or a "bad" phage. If the process is random then would it also take up DNA that was acquired through transformation or transduction?

Can Cas somehow distinguish if it's a phage DNA or not?
Is it maybe specific for some kind of base modification like hydroxymethylcytosine that are found often in phage DNA, or does DNA sequence has to be of certain size, or maybe the DNA has to be either linear or circular (but if circular then why the phage induced resistance islands do not get accidentally incorporated into the CRISPR locus)?

Can one do a BLAST search to find if the spacer sequences in CRISPR locus are exclusively from phages or sequences from other sources are also present? I know that it would probably be of no use to incorporate random sequences into the system but then I presume that there has to be a mechanisms for distinguishing where the DNA comes from?

Regards,
Bernadeta

Andy Camilli writes:

As far as we know, the capture system is random. The phage CRISPR/Cas even occasionally captures a piece of its own genome, which is a big mistake, because it will then degrade its own DNA! What we find in these instances, is that points mutations have arisen, either in the spacer or in the target in the phage genome, that abrogate hybridization of the crRNA and thus degradation is prevented. Presumably, these mutations are selected for rather quickly.

-Dr. Camilli

Charlotte writes:

Re: ASM Discussion - I wonder how much journal's biases against publishing negative results contributes to misconduct.

Peter writes:

Hi TWiM team
I hope you were able to see the Google tribute to Julius Richard Petri:

http://www.independent.co.uk/life-style/gadgets-and-tech/news/google-doodle-celebrates-julius-richard-petri--the-scientist-credited-with-inventing-the-petri-dish-8638084.html

Not sure about the streaking technique shown in the doodle though.

Jim writes:

Dr R:

This is old on uTube, but new to me. Can I suggest it as a listener's pick. Surely a similar dance be created from all the fields your podcasts represent!

I heard about the dance from class 129 by Dr. Gerald Cizadlo. His engaging manner is somewhat like yours and just this year he began offering an online version of this class, Bio 3020.

Regards,

Jim
Smithfield, VA


Jim writes:

Hi Y'all,

Dr Schmidt, on TWIM 35, after the 2012 ASM conference, you mentioned use of the Quartzy networking cards at many poster sessions. Did you see the cards used this year, were they more prevalent (3,300 used last year), and were poster sessions as plentiful as last year? Have the cards stimulated any competitors?

Thanks.

Jim Vandiver
Smithfield, VA

PS: TWIM 56 at the ASM was awesome, just awesome! It's like listening in on a discussion between Einstein, Edison and Feynman.


Peter writes:

Dear TWiM team
I see that the Oregon Senate approved a bill establishing brewer's yeast, Saccharomyces cerevisiae as Oregon's official state microbe.
http://www.oregonlive.com/politics/index.ssf/2013/05/oregon_could_be_first_in_natio.html

I can understand the popularity of brewers yeast, what other microbes do you think could be chosen as official state microbes?

I think food and drink related microbes would be favoured by most people so various species of Lactobacillus may be popular.

On that subject I see that there is a paper on microbiological profiles of ŞALGAM, the Turkish lactic acid fermented turnip and black carrot drink:
http://onlinelibrary.wiley.com/doi/10.1111/j.1745-4557.2012.00447.x/abstract

It is a popular drink in Turkey but rather an acquired taste for those unfamiliar with it.

Regards


Jacob writes:

Hi all,
My Dad sent me this article after I sent him a link to your episode on biospeleology.
It's about biofilm sheets in underwater caves under the Australian desert that glitter in the torchlight due to calcite crystals that are formed in the biofilm.
http://www.australiangeographic.com.au/journal/ancient-sparkling-algae-found-in-underwater-cave.htm


Jim writes:

Hi,

Here's a link to a Maker site that discusses how to do a 3D print of your brain.

Jim
Smithfield, VA

TWiM 58 Letters

Daniel writes:

Dear Vincent and his fellow TWIMsters,

Hello, my name is Daniel, I am a first year graduate student at Michigan State. I would like to thank you all for making a great podcast. I recently caught up to the most current episodes by having my own TWIM marathon during my 6 hour drive home to Wisconsin over the holiday break.

I'm not sure where to begin explaining how much I value this podcast. As someone who cares for outreach, education, research and in general having a good time with science, you folks are first rate. This series has been accessible all the way through for grandparents to grad students. When things maybe get a little to verbose you have done well to bring it back down. But you also make it just intriguing enough to hold the attention of the grad student in me. I have even been known to actually follow along in the articles. :) And of course I have had a great time learning and exercising my mind while listening in. You guys went even further to impress me with the discussion of Jo Handelsman's research last time, it gave me lots to think about for the future. Please keep up the great show!

I also wanted to share a paper with you all that I thought about after listening to TWIM #47: Resistance On the Surface. Michael said something that made me remember it during his discussion of the paper in reguard to conjugation. He said, "It's having sex wicked fast!", and you guys went on to exclaim about how fast conjugation was happening.

In this Science paper by Babic et al. in 2008 they are using a very beautifully designed experiment to visualize DNA transfer by conjugation, and it agrees... wicked fast! I suggest the supplemental videos. The experiment involves a recipient strain that is Dam- or defective for DNA methylation by Dam methylase, and which has a SecA-YFP fusion . (Note by MGS--- it is not SecA...it is SeqA ) SecA being (correct me if I'm wrong) the protein that keeps replication from occurring when hemi-methylated DNA is present in the cell. Effectively keeping multiple rounds of replication from occurring at once since newly replicated DNA has not yet had the time to be methylated on the new strand.

The result of this recipient cell is no DNA methylation, or SecA-YFP binding and diffuse fluorescence. The donor cell, however, has Dam methylase and will donate methylated DNA during conjugation. When this happens, the donor DNA will become hemi-methylated upon replication allowing SecA-YFP to bind and show a localized fluorescence to that DNA. This means we can watch it happen at a single cell level! They do show a rather surprisingly fast transfer of DNA, as well as make other neat conclusions in the paper which include the use of a red fluorescent gene on the donor DNA to measure expression of conjugated DNA, but the e-mail is long enough already. It's not a bad read, and I hope my explanation was TWIMable enough.

Thank you for providing a wonderful supplement to my microbiology education, and Happy New Year,

-Daniel

Here is the link to the article.

http://www.sciencemag.org/content/319/5869/1533.accessible-long


Robert writes:

I am listening to eps 49 and heard the mention of biodynamic vineyards. Biodynamic farming is similar to organic farming, with the addition of such things as burying dung in the horn of a bull and sprinkling magical powders around the farm. Take a look, it's quite entertaining total nonsense.


Clark writes: [this email was read on TWiM #56 but not published]

I'm slowly getting caught up with TWIM after Christmas and just listened to episode 43. I came away very confused and I hope you can clarify something for me.

I understood that the major problem with using phages for disease was due to FDA regulation. However when speaking about acne you suggested that there were ways for the FDA to approve them as a type of drug treatment. If this is the case, then why on earth aren't they being used to treat anti-biotic resistant TB or other such diseases?

If you could do a show on the interplay between the FDA, government regulation and commercial use of phages to control disease I'd be quite excited. I confess I get confused when hearing about the problem of antibiotic resistance on the one hand and phages on the other.

Todd writes:

it's true

http://www.mentalfloss.com/article/30380/why-some-civil-war-soldiers-glowed-dark

(also, I love your podcast, and in the future when I write a longer letter I'll explain more why I love the podcast)

Erik writes:

Long time listener, 2nd time emailer. ID doc. Mostly i treat HIV patients and hospital acquired infections. You've talked a lot about copper as an antimicrobial and that ancient civilizations might have used it to reduce war wound infections. I'm not aware of it's use in modern wound care. However silver based products are used a lot in wound care and on catheters, etc. I would be interested in understanding the antimicrobial properties of silver, and in why copper is not used topically if it is so effective at killing bacteria. Thanks.

Jim writes:

Hi all,
Thought Michael Schmidt might like this reference. It is to a Canadian podcast called Quirks and Quarks.
The reference is: http://www.cbc.ca/quirks/episode/2013/01/19/january-19-2013/index.html#3

In this episode, they discuss a paper by Jayne Danska talking about diabetes in nonobese mice. The outcome of diabetes can be changed by changing the microbiome in young mice. It reminded me of Michael' s thinking on how the microbiome might come into play in the future.
I found it very interesting after hearing the TWIM episode.

The paper appeared in Science.

Best Wishes,
Jim

Justin writes:
Hello to the TWIM team and guest(s) I have written to TWIV but this is my first letter to TWIM. I was recently watching a documentary about
how beer was the driving force behind beginning agriculture and numerous other massive human accomplishments and the documentary
mentioned skeletons from 500 BCE containing tetracycline. My first reaction to this was where is my computer I have to find this article.
Well I did find that the orgiginal discovery in the late 1980's was meant with extreme skeptacism (not surprisingly) but then I also found
an article from 2010 with more data to back up the claim. Now, I am not one to interpret Mass Spec data very well but would love to hear
what the TWIM team thinks of this. Here is a link I found to the article in the American Journal of Physical Anthropology http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21340/full

Thanks to all for the wonderful podcast,

Justin

Robin writes:
Alaric the Great

One would expect that Italians would be familiar with Alaric the Great.

Alaric I (Gothic: Alareiks; 370 – 410) was the King of the Visigoths from 395–410. Alaric is most famous for his sack of Rome in 410, which marked a decisive event in the decline of the Roman Empire.

http://en.m.wikipedia.org/wiki/Alaric_I

TWiM 57 Letters

Wink writes:

Great HAI work! I'm not through it yet. I want to question, though, whether fomites are really important in influenza transmission. I don't think so.
Wink Weinberg (ID)

[flu can transmit by fomites in guinea pigs: http://jid.oxfordjournals.org/content/199/6/858.full ]

Bernadeta writes:

I'm a second year microbiology undergraduate and I very much enjoy all of your podcasts; they are a great pleasure to listen and I wait for the new ones every week.

Since the last episode was all about copper I would thought it would be appropriate to point out this paper published in Nature in 1984- "Why whip egg whites in copper bowls?".
Who would have thought that a paper about copper bowls and cooking could've been published in Nature :)
http://www.nature.com/nature/journal/v308/n5960/abs/308667a0.html


I also think that this paper could be shortly discussed one one of the podcast: traditional mutational study but seems quite perspective- what do you think?
"Identification of Salmonella Pathogenicity Island-2 Type III Secretion System Effectors Involved in Intramacrophage Replication of S. enterica Serovar Typhimurium: Implications for Rational Vaccine Design"
http://mbio.asm.org/content/4/2/e00065-13

Thanks again for your podcasts and keep them coming!
Kind regards,
Bernadeta

Frank writes:

Bravo Michael!

I formerly developed a oxygen radical (not ozone) surgical instrument sterilizer so have dealt with the difficulties of disinfection and HSAs. Successfully sold to Stryker Instruments.

You mention the problem of economically obtaining copper hardware due to the pervasive use of plastic. If you think about our common household plumbing fixtures, it is clear that plastic can be plated with many metals and shipped around the world by air.

Plastic plumbing fixtures are typically plated with electroless copper followed by nickel then chromium. Air shipment is not an issue so your former plating vendor simply did not have the technique/knowledge to give you a sturdy uncontaminated injection molded part. I was involved on the development of many of these processes in the 70s. Rhom & Haas is still a major supplier of plating solutions and methods.

Similarly, any metal part can be easily plated in whole or in part with copper or copper alloys by the OEM. A quick swipe with ammonia will remove finger oils which could allow bacterial film growth and will expose fresh copper surface.

Despite all this antimicrobial furor, I look forward to the "omic" studies identifying how many HSAs are from the environment vs. the patient. Microbiome studies seem to be showing that microbial diversity balance rather than eradication is often the key mechanism of maintaining health.

Thanks to all you TWIV, TWIP & TWIMmers for creating and maintaining one of the most educational, accessible and plain old FUN scientific forums ever!

Best Regards,

Frank

Jim writes:

I was amazed to see note 13 in the caption for this article out of Apr/May 2013 AARP magazine about use of copper alloys on frequently touched surfaces. Copy of that page attached as a PDF.

Jim
Smithfield, VA


He sent https://docs.google.com/file/d/1zTSj5KGk9ADlamy_IWG6N8IWT4s_b75d-y-QJ47e4QpDk5mBzXIpdpTPdE6x/edit?usp=sharing

Lori writes:

I love your show, especially the recent episode about the use of copper in hospitals.

I am a nursing student at University of Nevada, Las Vegas and I am always cleaning patient bed rails and call lights. Patient hands are not the only thing that comes in contact with bed rails. The rail is also frequently used by nurses to temporarily hang pieces of tape while inserting an IV or changing a dressing. The tape, with all its germs attached, is removed from the bed rail and taped onto the patient's skin in close proximity to an open wound.

A future study might include the pathogens transmitted by stethescopes. People are pretty good about washing their hands, but I never see anyone cleaning their stethescope. It is my very unscientific, empiric observation that the stethescope is one of the biggest fomites in any hospital. I have seen copper writing pens for sale, but I am not aware of anyone who makes a copper coated stethescope.

Another possible fomite is employee badges, they come in contact with our patients when we lean over them (I stuff mine in my pocket so it does not contact the patient.)

TWiM 55 Letters

Jennie writes:


Hello TWIM friends!


Jennie here - a long time fan of TWIV, then TWIP and of course happily learning from your great TWIM podcasts.


Thanks to Michael Schmidt's fascinating discussions - including those regarding copper and microbes - which have really got me thinking. (Copper's natural anti-microbial activity can lower nosocomial infections by decreasing pathogens on hospital surfaces. To plagiarize Mr. Schmidt's own site at the Department of Microbiology and Immunology at the Medical University of South Carolina: "The 4th leading cause of death in the United States, behind heart disease, cancer and stroke, is Hospital Acquired Infections (HAI) where approximately five percent of the patients admitted to US hospitals will acquire an infection.  Very little is known of what fraction of these infections result from a microbial contribution obtained from objects present in the built environment."


It appears that copper does have a contribution to make - and I can imagine that there will be some formidable costs in changing surfaces from plastic & alloy & steel to copper.

To decrease costs of switching to copper surfaces for commonly touched fomites (microbe carrying objects) like IV poles and steel hospital infant bassinet units - you're talking to an OB nurse here - I began to think about a 6th or 7th grade experiment we did in school when I was a youngster with copper plating.


With that in mind - I did a quick search for a video on copper plating on Youtube and found this video - which just gives you a peek at how easy it can be to copper plate existing metal surfaces. I'm wondering if this could potentially be a cost saving application for some institutions. Will it be necessary for institutions to re-purchase when perhaps they could resurface?


http://www.youtube.com/watch?v=Co1LwPWfRHM


Of course, I hope that you realize how very much your team has done and is doing to increase our understanding of the tiny denizens without and within us. What an adventure!


Special thanks to you Vincent for sparking greater excitement and transparency in science. Thanks to Jo Handelsman - soil microbes are so vital and so unknown - thanks for the recent apple orchard soil discussion and for her deeply appreciated advocacy for women - Yay! Of course Elio Schecter and Stanley Maloy - fantastic!


Yours with warmest regards

Jennie BSN RN


“In the world through which I travel, I am endlessly creating myself.”

Frantz Fanon

TWiM 54 Letters

Jacob writes:

Hi all,

Saw this media release from the Australian Institute of Marine Science about researchers isolating a combination of probiotic bacteria to assist in the prevention of Vibrio infections of spiny lobsters in aquaculture and thought of TWiM.

Keep up the good work,
Jacob.


12 December 2012
Winning combination of bacteria found to combat deadly marine pathogen
Research conducted at the Australian Institute of Marine Science (AIMS) has delivered promising results in combating Vibrio owensii - a bacterium that is responsible for mass mortalities of cultured ornate spiny lobster larvae.
The high commercial value of the ornate spiny lobster (Panulirus ornatus) means it has the potential to be an important product of the Australian aquaculture industry. However, nutritional deficits and bacterial disease during the long larval phase of the species makes captive rearing difficult.
Scientists from AIMS and the University of New England (UNE) have been able to isolate a large number of bacterial cultures – or probiotic candidates – from wild lobster larvae and their natural prey items, and from the lobster aquaculture system at AIMS in Townsville. After successive tests, they found that a combination of two probiotic bacteria, referred to as PP05 and PP107, provided the most effective protection against the pathogen Vibrio owensii, enhancing survival of the larvae by as much as 80 per cent.
AIMS Research Scientist, Dr Lone Høj, who led the project, said “Our work has uncovered a winning combination of “good” bacteria that appear to dramatically improve larval survival. In a further study we looked at how and why these two bacteria were so effective when working together against Vibrio owensii.”
UNE PhD student Evan Goulden said “This research highlights the value of identifying biocontrol agents that are able to intercept the infection cycle of a serious aquaculture pathogen, as such the study represents a milestone in proving the value of using probiotic mixes to prevent microbial diseases.”
“Disease management is critical in food production systems and this is particularly true for seafood produced in aquaculture systems. The development of alternatives to the antibiotics currently used in such systems is becoming a national priority in countries around the world” says AIMS Principal Research Scientist, Dr Mike Hall.
‘Identification of an Antagonistic Probiotic Combination Protecting Ornate Spiny Lobster (Panulirus ornatus) Larvae against Vibrio owensii Infection’ is published in PLOS One: http://dx.plos.org/10.1371/journal.pone.0039667
‘Probiont niche specialization contributes to additive protection against Vibrio owensii in spiny lobster larvae’ is published in Environmental Microbiology Reports:http://onlinelibrary.wiley.com/doi/10.1111/1758-2229.12007/abstract
The authors are Evan Goulden (AIMS/UNE), Mike Hall (AIMS), Lily Pereg (UNE), Brett Baillie (AIMS), and Lone Høj (AIMS).
Media contacts:
Dr Lone Høj, Research Scientist, (07) 4753 4364; 0408 716 094; This email address is being protected from spambots. You need JavaScript enabled to view it.
Dr Evan Goulden, Research Assistant, University of New England,0439 446 204, This email address is being protected from spambots. You need JavaScript enabled to view it.
Dr Lily Pereg, Senior Lecturer, University of New England, (02) 67732708, 0427063057, This email address is being protected from spambots. You need JavaScript enabled to view it.
Wendy Ellery, AIMS Media Liaison, (07) 4753 4409, 0418 729 265, This email address is being protected from spambots. You need JavaScript enabled to view it.


Trudy writes:

Dear TWiM team,

Since the topic of patent law came up on episode 48 I wanted to add my two cents. Six months ago, I switched to a career in patent law after 12 years as a bench Virologist. I have found this job to be very challenging and rewarding, and I'm currently experiencing a rather steep learning curve. However, the reason I'm writing is because I did want to mention that one does not have to be a lawyer, or even plan to go to law school to practice patent law. Many firms are willing to hire PhDs with no prior experience in patent law as science advisors or patent agents and train them on the job. The reason they're willing to do that, is because of their extensive background in science, which is imperative in this particular legal field. In our firm, all of our six science advisors have PhDs, and three of our five attorneys do as well. Although learning the law is pretty difficult, in my opinion, it is much easier to learn the law on the job than it would be to learn the science, and I have tremendous respect for the two attorneys in our firm who do telephone directory ireland reverse phone lookup not have PhDs, because they seem to be so well versed in the science as well. I recently asked one of our partners (who has a PhD) how much of what he learned in law school he has actually applied to this particular job, and he said “zero”! On the other hand, attorneys do make a lot more money, and there are certain things that they can do that a patent agent can't do, but my point is that a PhD is more than enough to have a rewarding career in patent law. Personally, I have absolutely no desire to go to law school!

Thanks again for continuing to provide so many different stimulating and thought-provoking topics.

Kind Regards,
Trudy.

Jim writes:

Esteemed Sages:

Post-Sandy seems an appropriate time for a TWIM devoted to mold since the storm generated many opportunities to deal with it? I'm also battling it in my ventilation ducts to the extent that we replaced all the supply lines beneath the house and some of the returns in the attic, and installed an electrostatic filter upstream from a HEPA-type filter, plus a UV light by the heating/cooling coils. Over the years I've inspected the ductwork for integrity and cleanliness and just didn't think we had conditions that allowed mold growth until we found 7 of 23 supply lines each of which that looked inside like they were spray-painted with black primer over a good many feet. Meanwhile outside we've been unable to prevent black mildew from growing in playing-card patches on treated wood coated with mildewicide-infused stain and exposed to sunlight about eight hours a day.

I bought five mold collection kits containing petri dishes and growth medium just before detecting the seven register lines. At first they seemed a good idea to apply now and perhaps in the spring or summer, but then I found this site with considerable mold information that seems reputable. My interpretation of what the site says is that conditions and materials contributing to mold must be removed to fix problem. While removing bad ductwork helps I don't think it corrects the condition problem(s). The site says sprays and chemicals don't work! And sampling with my kits followed by lab work to identify mold types won't tell if harmful mold is at levels requiring action. In addition, unless you use laboratory grade filtration, it won't reduce the presence of mold to livable levels, and UV radiation is only good directly under the light, not particulates flying by. Electrostatic filters apparently only remove a small amount of mold-related material as do good filters, but not all and probably not enough for sensitive people, plus they work best if the ventilation fan runs continuously. Much harmful mold material is too heavy to get sucked into any ventilation system, anyway, and is only removed by vacuuming often, mopping and washing fabrics. Finally, only an expensive, trained environmental specialist can do a good evaluation, prescribe corrective action and determine if that action has been effective. This site shows we have just one such specialist in my state,Virginia, about 300 miles away.

Do you folks agree our best approach would be to napalm the house and replace it with a stainless steel cube, or wear environmental protection suits, or move to who-knows-where....? Of course the guys doing all the ventilation work used no respiration protection, but then they were all in their 20's and 30's versus our 70's.

So what's going on with mold nowadays, anyway? Is there more of it? I've no problem understanding why you need to remove wet and moldy plasterboard and carpeting, but have seen home shows where mildew-stained woodwork behind the wallboard is sprayed with something which they implied would fix the problem. You're the only really reliable source of complete and competent knowledge on the topic, so many of your listeners should appreciate your comments.

Regards,

Jim
Smithfield, VA

Don writes:

When do we get to hear the results of Michael's experiments and interventions with copper and microbes?. The suspense is killing me, or did I miss it? Please continue your marvelous podcasts.

TWiM 49 Letters

Robin writes:

The matriarch of a hunter-gatherer band might prefer males to be assigned to specialised training in hunting skills. So the subconscious bias probably goes back a couple of million years to the early days of Homo before sapiens.

Chip writes:


Saw this paper in my inbox this morning and thought It might be a good fun discussion paper on an upcoming TWiM episode!

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0035507

Enjoy.

Meimei writes:

Dear Dr Racaniello,

I do not have the talent for a M.D-Ph.D. at Columbia, but I am madonna pokies definitely a huge fan:)

It's striking how and where the interaction of antibody and bacterium occurs (TWIM #48)! Learned a lot from listening to your interpretation of the paper. Many Thanks!
Just have a question about one antibody and one bacterium. Is it commonly considered more than one antibody molecule per bacterium?

Many Thanks, again!
Meimei

P.S. Can this finding extent to the interaction between virus (e.g. HIV) and neutralizing antibody? It might be we just look at the wrong place for all those years!


TWiM 48 Letters

Sierra writes:

Hello Racaniello et al.,

I am a plant pathologist for a vegetable seed company in Washington state.  I listen to TWIM, TWIP and TWIV podcast while I read extensive disease resistance screens.  I started out studying microbiology as an undergrad and discovered plant pathology that allows me to study microbes and plants together.  Listening to these podcasts keeps my mind engaged while looking at thousands of potentially disease baby plants.  I really appreciate what you all do to put together such intellectually stimulating topics.

If I may suggest a topic as well.  Iron sequestration and uptake in bacteria is very fascinating and affects many aspects of bacterial life.  I may be biased as I worked on iron uptake during my Ph.D. I have listened to many of the TWIM podcasts and iron pops up in discussion now and then.  It would be nice to listen to a discussion of this topic from your perspective.

Keep up the good work,

Sierra

Eric writes:

Dear Twim:

Episode 2 had a career inquiry from a listener.  The listener was considering additional graduate work Pokies, but was not sure which way to go or whether to invest the required time and energy in an MBA or Ph.D.

May I suggest intellectual property as a career path?  Most patent attorneys are former "lab rats."  Patent attorneys enjoy a good salary and interaction with some very intelligent and interesting people.  Though considerable work is required, intellectual property can be a very rewarding career.

Best regards,

Eric

Patent Attorney

Flagstaff, AZ

Ori writes:

Hello all!!

Quick follow-up from Twim 47. 

It seems that many bacteria have means to take up foreign DNA and integrate it Into their own chromosomes. This definitely can provide a selective advantage depending on the nucleic acids being taken up. On the other hand, transferring your own DNA to another cell seems to be quite unselfish. For example, if I had some form of an antibiotic resistance gene, why would I give it away to others that would, in the end, compete with me for nutrients? In essence, what is the selective advantage for giving away nucleic acids?

Thanks a lot and have a happy holiday!

TWiM 47 Letters

Maureen writes:

I love all your series (TWIM,TWIV, and TWIP) and learn immensely from them. I am a Clinical Research Nurse and work at NIH in the National Institute of Allergy and Infectious Disease (NIAID) unit that houses the KPCR  patients that you may have recently read about.

http://www.washingtonpost.com/national/health-science/superbug-stalked-nih-hospital-last-year-killing-six/2012/08/22/5be18b1a-ec66-11e1-9ddc-340d5efb1e9c_story.html

I'd like to hear a discussion about this isolate as you educate everyone so thoroughly. Our hospital has worked diligently to track and eliminate this organism from our hospital and we've just about succeeded but I'd still like to be better informed about KPCR. Thanks.

http://stm.sciencemag.org/content/4/148/148ra116.full

P.S. Please Please Please start a TWIB!! We work with so much that I still need to be educated about various bacteria.

Thanks immensely for all the education you give us.

Jim writes:

Hi Vincent and Friends,

Thank you very much for the informative and often imaginative discussions that take place in TWiM. It's a real pleasure to listen to such a quality, fun, easily accessible (and free!) source of microbial material. I'm sure you are often thanked for taking the effort to put it out there, but I wanted to add my voice. As a cell and molecular biology student it offers some wonderful connections and points of interest to my education.

My question relates to a recently published book by Trudy M. Wassenaar that I have been reading, titled "Bacteria: The Benign, the Bad, and the Beautiful." Has anyone read this book, and if so what are their thoughts on it? I would recommend it to those with a broad interest, or who need an introduction, like students such Pokies as myself. It offers an incredibly interesting and diverse description of bacteria and is easy to understand. I actually picked it up because it was recommended by the google+ "Microbiology" account (https://plus.google.com/u/0/109102265263486263584/posts).

Thanks again, and warm regards.

Steve writes:

TWiM Audio File with Interactive Transcription

Here is a link to a partial, video I created from the TWiM 06 audio file: http://www.youtube.com/watch?v=JtOXD_X6g_w. I created a video file from the audio file so that I could use the YouTube captioning tool to import an interactive transcript -- minutes five (5) through twelve (12). I created the time-coded transcript using an online tool called Subtitle-Horse, (http://subtitle-horse.com).

If you click the interactive transcript button on the button-bar (Like, Dislike, Add to, etc) just below the video player, you can see how the transcript works. The transcript is indexed, time coded to the audio.

Potential Benefit of Interactive Transcription

The time-coded transcript text could be parsed and placed in a database for easy query. Then all included audio/video files are text searchable and associated to the segment of the source audio/video clip.

Collaborative Transcription

On TWiV a number of people have completed or are working on transcripts. In my experience, transcription is a time intensive process. To lighten individual time commitment, it would be nice to get several people to work collaboratively to transcribe one TWiV audio/video. Although far from perfect, the subtitle-horse online transcription tool could be used for this.

Volunteer to Help Transcribe

As a first step, if interested, I’d be interested in coordinating a collaborative transcription of a TWiV session with one to three others.

TWiM 46 Letters

Jeff writes:

Hello TWIMers -  In TWIM 26  I heard the listener email asking if you would consider offering continuing education credit for your podcasts, and you understandably cited the work that would you need to do (such as writing learning objectives, tests etc) as a real barrier to that.  I was wondering if you would consider "contracting" that kind of work out to some of your listeners; being a teacher of a microbiology class at a community college, I spend a large amount of time coming up with learning objectives, tests etc  anyhow, and it would help me to generate fresh material for my students from your podcasts.  I wouldn't be surprised if there were others in your listening base who might feel the same.  This still would add work for you, so I understand if its a no-go.

In a separate vein: quite a while ago I was doing dishes and listening to a TWIM.  As I was using a sponge to wipe off the counter a ridiculous question popped into my head (as opposed to my toe, I guess): are there strains of bacteria that can provide a protective commensal role on environmental surfaces?  A counter top is nothing like a biological surface, as only the latter should have organic material to eat on it, but still, is there any evidence in any situation that something like this happens?  Please read  the following sentence with extra emphasis: I am not fishing for an excuse to get out of doing the dishes, and I regularly boil our kitchen sponges and use bleach to Pokies clean the counters.

Keep up the great work!

Velma writes:

Dear TWIM-team,

Greetings from a longtime listener and fan of all three TWI-podcasts. I'm a biotechnology Masters student at the University of Helsinki, Finland, but I earn my living as a part-time driver in the world's most northern metro. Your podcasts help me pass the dull hours at work so that I feel like I'm doing something to advance my studies as well.

I've been thinking of writing for quite a while. Now that I'm finally doing it, I have a rather general suggestion and a link. The suggestion is, I'd like to hear more about the archaea - maybe even an entire episode dedicated to them. They seem like such a mystery. At least at my home university, they're almost always just mentioned as an aside, while the bacteria get all the attention. The one time they were actually discussed on a course, I learned that they are not just extremophiles, but actually all around us, just like bacteria. This made the fact that there are no pathogenic archeae seem even more curious to me.

As for the link, it's for the Earth Microbiome Project: http://www.earthmicrobiome.org/

I just ran across it today, and don't remember this project being mentioned on TWIM before. I think the idea is awesome, not to mention really ambitious, maybe even overly so. What do you think, is creating even a rough map of the microbiome of our entire planet an attainable goal? And would it be a useful resource for research?

Thanks for the inspiring and informative podcasts,

Velma

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

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