Viruses

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

TWiM 8 Letters

Catherine writes:

Hi Everyone,

I first found TWiP, which led me to TWiV which led me here (Hey Vincent- get on Dickson for more TWiP episodes!). I love all three shows. I work as a research technician at a medical/veterinary entomology lab, and spend several hours of my day counting and identifying mosquitoes caught in traps in rice paddies (when I'm not sitting in a makeshift african hut...) Your podcasts have saved my sanity on multiple occasions! While I work closely with vectors of many of the parasites/pathogens you discuss, it is great to learn about the mechanisms of infection and disease, a subject which I feel I am slightly lacking in.

I just finished reading a couple books about the history and discovery of prions, and while I am not sure they can be classified as microbes, I would love to hear a show on the subject. I've become slightly obsessed! Keep up the great podcasting - I have several thousand more mosquitoes to go!

Catherine

Robin writes:

Look forward to all the TWi* discussions. Last months TWiM on Salmonella, with its reference to Typhoid Fever, reminded me of Bertolucci's twenty year old film masterpiece, The Sheltering Sky in which Port played by John Malkovich contracts Typhoid.

The story written by Paul Bowles, is interesting by itself in that Bowles lives in Tangiers - - where the story plays out - - and for his friendship with William Burroughs.  Debra Winger is magnificent as Kit,  Malkovich's wife. At the end of the film the viewer struggles with moral issues and whether or not Kit lost her sanity. Reading the book doesn't help.

The photography and the acting are superb. The progression of the Typhoid Fever in Port is accurately portrayed.  The source of Port's infection is only hinted at. As one of the World's great films, the film was grossly underrated by film reviewers. Nevertheless, most people with a scientific background will appreciate the film and likely give it the highest ratings.

Robin M.D.

TWiM 79 Letters

Matthew writes:

Dear Doctors,

After listening to the second portion of TWiM 78, talking about the presence of gram-negative nosocomials around Brooklyn, I noticed a several people wearing scrubs while at lunch near a hospital in Houston, TX. Then a thought occured to me; disease! Disease everywhere! Might part of the problem, if these microbes are moving out from the hospital, be that they're carried from a day's worn clothes? I realize I'm asking to speculate, but think this might be a good consideration for hospital policy. Houston is currently 27 C at a low 50% humidity.

Matthew Folts

P.S. I finished my sandwich. It was a pastrami ruben.

Jim writes:
Hi Folks,

"Ideas" with Paul Kennedy on the Canadian Broadcast Corp site recently ran a 54 min program about invasive species that included a short reference to rock snot. At the link find the title, "Bioinvasion: Attack of the Alien Species!," right-click (here or there) "Download Bioinvasion: Attack of the Alien Species!" to download it. I thought it, along with Prof Schmidt's comment about furry teeth, are a good intro to any program for kids about bio-films.

Jim
Smithfield, VA

Peter writes:

You have spoken before on TWiM about the potential risks of triclosan-resistant pathogens developing through its over use.

A recent open-access article from the the University of Michigan, published in mBio, looks like it may be worth a mention. The researchers conducted a study that examined the nasal passages of healthy adults, 41% of those sampled had traces of triclosan in their nasal secretions and the presence of triclosan in the secretions also correlated positively with nasal colonization by Staphylococcus aureus.

When grown in the presence of triclosan, Staphylococcus aureus was was found to be better able to attach to human proteins.

Additional experiments found that that rats exposed to triclosan were also more susceptible to nasal colonization by Staphylococcus aureus.

http://mbio.asm.org/content/5/2/e01015-13

 

TWiM 78 Letters

Del writes: (re: episode 77)

I was looking forward to this discussion, after hearing you hint about it in a previous podcast. As a practicing ID doc, I have been fascinated by the difference in pain induced by cellulitis from presumed or proven Staph or Strep infections. I see some patients whose pain resolves in a day or so after antibiotics, and some fewer patients who have a much more protracted course of pain, with tenderness to minimal touch or change in position. I have suspected that different isolates produce different toxins to explain these clinical differences, as my clinical judgement and experience argues that patient personality differences or 'pain thresholds' are simply not enough explanation for the variation I see. It also seems to "be there, or not be there," more distinctly than a simple continuum would explain. I am grateful for the basic science work being done in the field at present, and for your discussion.

Thanks to you all for the work you put into this podcast. I am learning every week, and finding connections in areas I would have never before considered.

All the best,

Del.

Del DeHart MD FACP

Associate Professor of Medicine

Michigan State University

 

 

Geoffrey writes:

 

Good Doctors:

     I realize that this is a bit behind the times but I have two questions related to beta-lactamase (hope I got that right) form episode 6 - "Antibacterial Therapy with Bacteriophage".

1) We all know that the proliferation of bacterial resistance to antibiotics has a direct influence on infection recovery in humans and animals. What I'm pretty sure most people forget is that most antibiotics began their "careers" as part of microbial defense systems. Are you folks aware of any studies looking at the effects of increasing antibiotic resistance in environmental microbiomes? I would think that this human-induced change has got to be skewing microbial populations and interactions. Indeed, I'm having trouble even imagining what the impacts on the microbial and, therefore macrobial world might be.

2) During your discussion of beta-lactamase gene development in the environment, I thought of a possible counter that might help us continue to use beta-lactam antibiotics a little longer. Are you aware of any groups who are researching anti-beta-lactamase drugs that could be added to antibiotics allowing the beta-lactams to retain some effectiveness against resistant microbes? If someone developed a low-toxicity drug that had a significantly higher and, one would like, non-reversible affinity for beta-lactamase than beta-lactam. then one could, presumably, administer it along with beta-lactam and it would inactivate the beta-lactamase while leaving the beta-lactam free to do it's work. Such a system probably wouldn't be effective within a microbe but it should be effective for running interference at cell membranes.

                                Thanks for the interesting shows,

                                Geoffrey

 

Robin writes:

 

Consolidation

Dr. Schmidt's viral illness would be quite serious if there was consolidation as was asserted.

Consolidation refers to the gross characteristics of the lung when it turns from fluffy and pliant into solid as the air spaces become filled with cellular and proteinaceous exudates in pneumonias. Bad enough with bacteria and the antibiotic resistance problem; if it is a viral pneumonia, the treatment modalities are mostly supportive care.

 

Matt writes:

 

hello,

It's been found that nasal carriage of Staphylococcus aureus is associated with increased risk of infection due to dispersal of SA from the nose while breathing and by nose-picking and not washing your hands. Some individuals are colonized with SA and are more prone to infection. Now there's a lot of research on how best to decolonize the nose of SA, because it survives antibiotics and quickly recolonizes the body. Mupirocin is typically used, but results are not good and resistance is likely. Seems to me that the aim of decolonization is stupid, since it is impossible to kill every last cell in and on the body, and even if you could there's plenty more in an individual's environment (which can survive for months on surfaces) to recolonize them anyway. Surely a better aim is to find out why some people do not become colonized and reproduce whatever they have in colonized people. Presumably, there's something about uncolonized peoples' immune systems and/or microbiomes which makes it hard for SA to become a problem. Maybe it's like the problems some people have with gut bacteria, where gut bacteria (shit) transplants have been shown to be effective. Maybe similar transplants of bacteria from the skin and/or nose of uncolonized individuals would be as effective for SA depopulation? It's a revolting idea, but no more disgusting than a poo-transplant!

 

Matthew writes:

 

Professor Racaniello

Didn't recognize "Speak friend and enter!" and "NIN" ?!? What kind of barbarians do you invite on this show?!

Just kidding. TWIM # 73 was another amazing and wonderful podcast. I am only a geologist, so I can sometimes only vaguely hum along with yours, Michele's, and Michael's biochemistry arias. Nonetheless, TWIM is one of my favorite podcasts. When I listen on my walking commute from my home to my office in Seattle, I arrive smarter!. And grateful. I am always grateful after listening. Thank you!

 

TWiM 77 Letters

Francois writes:

Hello Twim team,

After reading the Pasteur lecture.
It seems that the idea of using the Pseudomonas aer, "coal & septicemia" came from a demonstration that the "bactericidie" in the blood from animal with anthrax ("sang charbonneux") was the only origin of the disease.
It was a point of contention in the fight against the last supporters of the spontaneous generation.

When use the "sang charbonneux" from death animals collected at a rendering facility was shown to kill rabbit, but without the presence of the bactericidie in the rabbit blood.
Pasteur was able to demonstrate that was due to contamination of the corps blood between the time of death & the collection, by the "virions" causing "septicemie". And that's was causing the destruction of the "coal virulence" (virulence charbonneuse). For him it was of therapeutic interest, but it seems he has never used it on human (only on guineapigs).

He has developed instead the vaccination against anthrax by selection of an attenuated variant.

By the way fun coincidence with Michael remarque to Elio about the LON & E coli turning to snakes.

In the same lecture Pasteur also observed that outside of the blood in septicemia killed guinea pigs, the bactericidies form long snake like filament "creeping, sinuous, and separating the blood cells as a snake separate the grass in the bushes".

Best regards.

Velma writes:

Speleosalutations, TWIMologists!

I have never been as excited about a podcast as I was when I saw the title of the latest episode of TWIM (#51, Cave science with Hazel Barton), and it definitely did not disappoint! I listened to it twice right away. I'm trying to specialize in metagenomics, and I love caves and caving. If someone had asked me to design my dream TWIM, it would have been exactly like this. I had actually thought about suggesting the antibiotic resistance in cave microbes -paper for discussion, but I didn't think anyone else would find it interesting - probably because I come from a country with no proper caves, where you only get blank stares when you mention caving. Thank you so much for this episode!

I also have a question. Dr. Barton mentioned they have tried to do 454 sequencing, but apparently they haven't published anything about that yet? Do any of you know of any sequencing-based cave microbiome papers, particularly about "normal" karst caves? I've been unable to find anything on my own.

Thank you once more for the most awesome podcast episode ever,
Velma
(your subway-driving fan from Finland)

[I asked Hazel. She wrote:]

Yeah, unfortunately we've done a ton, but the papers aren't done.

Here's some good references though:

Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave. Ortiz et al, ISME J, 2013 (1-14).
Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism. Tetu et al, ISME J, 2013(7), 1227-1236

Hazel

Pete writes:

Hi,

One of the other podcasts I listen to is CBC Radios' Quirks and Quarks. I find it always interesting, and often profound.

The segment I was just blown away by was this one: http://www.cbc.ca/quirks/2014/03/15/2014-03-15-1/.

It put together many of the keywords I have heard from your podcasts, and added a new one- "host-defence peptides".

It even made me consider what are "biofilms", a term I have heard you use but never thought significant.

So. as something different, would you consider reviewing this radio segment as you do a paper? You could bring into the discussion regular papers that are relevant, too.

And, a final question, what ARE biofilms and what are their significance?

Thanks for doing what you do (even though I understand 25% of it).

Cheers,
Pete
(Sydney, Australia),

Gian writes:

Dear Dr. Racaniello,

In your latest TWIM (#72?), I heard you wonder out loud why a virus such as polio managed just fine without virulence whereas one such as norovirus seemed to relish it.

Might the answer have something to do with the work of Dr. Graham Rook at University College, London? His Old Friends hypothesis (a re-formulated hygiene hypothesis) distinguishes between microbes that inhabited hunter-gatherer hominids before we lived in cities (like hepatitis A and H/ pylori, which protect against allergies/asthma/autoimmune diseases) and those more recently evolved to infect humans living in sufficient population densities to support epidemics (like measles, which does NOT protect against a/a/a).

Maybe virulence evolved as an adaptation to crowds?

Just a thought,
Gian

P.S. My mother's family has the name Ianiello, which means--maybe 500 years ago or so--our families may have known each other. Just another thought.

TWiM 76 Letters

Geoffrey writes:

Doctors:

I just got around to listening to episode 12 “Photothermal Nanoblades and Genome Engineering”. Your comment that it would need to be scaled up before it was practical for some of you to use intrigued me. I did a quick Google search and I didn’t see any recent articles addressing scaling up the process though I’m sure that there are groups working on it. In my own amateur fashion, I’d like to suggest an approach to such a process.

I believe that technology applying microfluidic flow cells to single cell streaming is reasonably well-developed currently and improving all the time. If you installed the insertion capillary tube into a microfluidic flow cell and added a photo-sensitive trigger to the capillary tube, then it should be fairly practical to mass insert bubbles of materials into cells fed through the flow cell and collected on the other side. Although flow cells would, most likely be tailored to particular cell sizes, it might be possible to make the insertion point slightly generic (i.e., slightly larger) by using laser forceps to automatically direct and immobilize the cells during insertion.

The main restriction would likely be finding a cell culture that would support the microbe in question with sufficiently low viscosity so as to flow through the cell with ease while prevented undesirable cellular effects (such as clumping or lysing) while the cells are waiting to inject. High cell density at the input reservoir could probably be achieved by centrifuging the initial culture then micro-diluting up the resulting pellet.

Although this may not prove to be the most efficient way to mass-process cells, I do see another potential advantage in using a microflow cell. With additional solvent input channels before and after the insertion point it might be possible to chemically manipulate the cell’s immediate environment for periods of milliseconds to seconds in such a way as to make them momentarily more amenable to insertion without long-term consequences to cell survival. Such manipulations would be easy to study, cell species by species in these flow cells until a manual of cells and optimum manipulation conditions could be generated.

Anyway, thanks again for the fascinating look at research that I don’t get a chance to look at very closely often (or understand).


Geoffrey

Tarwin writes:

Hi,
25c in Palo Alto, California.

I think humans (us) are so enthralled by the idea and stories of symbiosis because we see it as unusual. Even though our world is full of symbionts, life relies on symbiosis, we are blind to it most of the time until extraordinary examples are pointed out to us. These make great examples of the "precision", depth and complexity of evolution and of life.

It's easiest to make a headline in our mind when we see "small" examples of tightly woven systems than to keep the whole ecosystem of metabolism in our minds.

Thanks as always for the amazing education and entrainment,

Tarwin - Developer / Designer


Jacob writes:

Hi all,
Just wanted to make a point about organelles vs symbionts.
You suggested that the difference might be that if all cells in the organism have it then it is an organelle; however not all plant cells have chloroplasts.
http://www.ask.com/question/do-all-plant-cells-have-chloroplasts
Might the difference be just how high up the taxonomic tree the symbiosis goes?
Thanks,
Jacob.
Sydney, Australia.

Marion writes:

TWIM 74, about 26 minutes in.
the difference between enbosymbionts and organelles is:
1. WHEN it happened and
2. how much it increased fitness.

the endosymbioses that resulted in mitochondria and chloroplasts happened many billion years ago and apparently conferred selective advantage to recipients cells (future eukaryotes) over nonrecipients (future prokaryotes). we only have to wait a few billion years to see if the same is true for the endosymbionts discussed.


Bernadeta writes:

Dear Twim team,
Thank you for all the great episodes; I'm loving every single one of them!

I'm very pleased to hear more discussions on fungi-related subjects, being from Lithuania myself, I wait every year for the mushroom season, so that I could go and collect them. We even have national competitions for who can collect the largest number of mushrooms or find the biggest variety of them :)

On the mushroomy note, I would like to draw your attention on a recent paper describing the first fully sequenced genome of arbuscular mycorrhizal fungus, I think it's worth discussing.
"Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis" http://www.pnas.org/content/110/50/20117.full .


The second paper that caught my eye, was describes how S. aureus "intentionally" induces pain through neurone stimulation, in order to suppress immune system's response to the infection. I think it very much makes one think about systemic control of the immune system and, as ever, the unexpected ways that bacteria have evolved to evade it.

"Bacteria activate sensory neurons that modulate pain and inflammation"http://www.nature.com/nature/journal/v501/n7465/full/nature12479.html

Best wishes,
Bernadeta

 

TWiM 75 Letters

 

Timothy writes:

Hello TWiMsters! I recently discovered the trifecta that is the TWi series, and now I can’t get enough of your discussions of all things micro. For graduate students like myself, keeping up with the scientific literature can all too easily become just a means for cramming information into our brains that we feel we “should” know. Not only do your shows keep my mind stimulated and expose me to scientific papers that I might not otherwise read, but the informal and enthusiastic nature of the programs are just the slap in the face I need to crawl out from under the stack of papers, and remind me that I actually love to learn about science and to think about the various implications that a particular finding or result might have. After listening to your conversational discussion format and your fantastic insights that tie together the biology of the organism (or virus – are viruses organisms?) with the environment, host, experimental techniques etc., I am finding new clarity in the way that I think about scientific problems and evaluate scientific papers. I can’t commend you enough for what you do. Formal presentations of scientific findings are a dime a dozen - listening to world-class scientists “chat” amongst themselves about current topics in microbiology is an invaluable resource that few people really ever get a chance to do, until now. THANK YOU!

On a scientific note, I was recently listening to TWIM #43 and your discussion on the stable formation of caveolae in in E. coli. It was mentioned that it had previously been thought that stable caveolae formation in eukaryotic cells requires cholesterol, to which Michael replied that “there is [no cholesterol] in our friends the bacteria”. Although this was and is true in the context of E. coli and the paper’s findings, I think it is worth pointing out that there are several described examples of free cholesterol and cholesterol-containing glycolipids in bacterial outer membranes – namely in Helicobacter, Mycoplasma, Ehrlichia, Anaplasma, Brachyspira, and Borrelia species. In Borrelia burgdorferi, cholesterol containing compounds have been shown to form organized lipid rafts both in culture and in animal-derived organisms, with physical properties similar to that in eukaryotic membranes. A recent paper published in PLOS Pathogens in January of 2013 utilized fluorescent and radiolabeled cholesterol to demonstrate that B. burgdorferi extracts cholesterol from the plasma membrane of eukaryotic cells, and that prokaryotic cholesterol-glycolipids can be transferred to epithelial cell membranes through both a contact dependent mechanism (using direct attachment) and a contact independent method (through released outer membrane vesicles). I highly recommend looking in to this story (maybe as a TWIM topic?), as it provides a shift in the thinking about lipid rafts, expanding their biological relevance to prokaryotes, and could have implications for the evolution of the eukaryotic cell membrane structure. Additionally, transfer of antigenic lipids from bacteria to host cells could play a role in pathogenesis - having multiple consequences for the host immune response and potentially contributing to heightened inflammation, and perhaps even direct targeting of the cells themselves by immune effectors. I’ve provided the citations and Pubmed links to a few papers on the B. burgdorferi story below, but also recommend digging into the story for H. pylori.

I’ve rambled enough for now, I should run – I’ve got to get to iTunes to write a good review or two…

LaRocca TJ, Crowley JT, Cusack BJ, Pathak P, Benach J, et al. (2010) Cholesterol lipids of Borrelia burgdorferi form lipid rafts and are required for the bactericidal activity of a complement-independent antibody. Cell Host Microbe 8: 331–342.http://www.ncbi.nlm.nih.gov/pubmed/20951967/

Crowley JT, Toledo AM, LaRocca TJ, Coleman JL, London E, et al. (2013) Lipid Exchange between Borrelia burgdorferi and Host Cells. PLoS Pathog 9(1): e1003109. http://www.ncbi.nlm.nih.gov/pubmed/23326230

--------------------------------------------

Timothy Casselli
PhD Candidate
Department of Veterinary Microbiology and Pathology
Washington State University

“The truth is incontrovertible. Malice may attack it, ignorance may deride it, but in the end, there it is.”
- Winston Churchill

Alicia writes:

Hello,

During TWiM#46 it was discussed that spores are able to sense peptidoglycan that has been shed by other bacteria. I would like to know, are the spores able to differentiate between the peptidoglycan that is shed by growing bacterial neighbours and the peptidoglycan lost during lysis.

Thank you,

Alicia Zigay
University of Victoria, BC, Canada

Jon Dworkin answers:

Excellent question! If this any indication, your listeners are really paying attention!

Spores are able to differentiate between peptidoglycan fragments generated from growth and those generated by lysis since these processes in fact produce different PG fragments. Those resulting from lysis are thought to be produced largely by lytic transglycosylases which generate PG fragments containing an anhydro (non-reducing) end, whereas fragments produced in growth do not contain this group. In collaboration with Shariar Mobashey, an excellent PG chemist at Notre Dame, we demonstrated that synthetic muropeptides containing an anhydro group do not stimulate growth but synthetic muropeptides that lack this group are able to stimulate spore germination. Thus, spores can differentiate between cells in the milieu that are lysing versus those that are growing.

Bill writes:

Finally, I can send an intelligent comment (re: TWiM #51) ...

WOW!

bill mackintosh

Frank writes:

Dear esteemed doctors,

I am sincere in this appellation as one of your many listeners who depend upon your unbiased fact finding and enlightening delivery to both educate and debunk with the latest information.

You have often remarked on the contradiction of the numerous pathogenic bacteria in common public areas while you as individuals do not feel endangered. In commenting on a letter read on TWIM 72 you mentioned the "cloud" of toilet-originating microbes created with every flush, yet a lack of evidence of resulting disease. It comes up also in regular mentions of door knobs, railings, phones and other public conveniences. Often this is attributed to the protection provided by a healthy immune system.

My question is whether the mechanism of microbial balance achieved in the human microbiome should be applied to understanding the forces at work in these external environments. Might our Linus-like microbial cloud function like the often mischaracterized schmutzdecke which purifies much of our drinking water?

Analyzing the potential health affects of environmental microbes apart from the greater human and environmental microbiomes seems a bit like analyzing the path of stars orbiting the earth. Am I wrong to assume that the microbial community of the toilet, room air, hands, nose and mouth have a significant impact on the danger from most of the individual microbes within those communities?

It's 252 degrees absolute, (or minus cold aught six on the Retrograde scale) this morning in sunny Connecticut.

A sincere thanks to you all for your dedication to TWIX. The world is listening to you more intently every day, and better for it.

Best Regards,

Frank

 

TWiM 74 Letters

Katja writes:

Thank you for the great podcast! You've explained our story very well and it was funny to listen to it. I didn't know that "Speak friend and enter" is from lord of the rings! I just wanted to explain the name CYCLOPS because this was a question mark in the podcast. This is a link to Yano et al. 2008 where they describe the cyclops mutant phenotype in fig. 1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629324/ In the WT the fluorescently labeled rhizobia enter the root by the formation of an infection thread. In the cyclops mutant, the root hair curls around the bacteria but further infection is impaired. And because this looks like an eye of an cyclops, the mutant derived its name from :-)


Laurel writes:


Hello all! I am a graduate student at UNC Chapel Hill in the Microbiology & Immunolgy department, and since my lab is mainly focused on the immunology section of that I try to supplement my microbial knowledge with information gleaned from other sources like your podcasts (Though I am a particular fan of parasites and TWiP). And as you can probably tell from this comment being so behind, I am never caught up with the podcasts, though I listen to them regardless.


You all mentioned that perhaps due to the high salt levels and temperature of the lake the haloarchaea from TWiM 68 act very similarly to when you perform a transformation in their extremely high gene transfer rate. Wouldn't it be fairly easy to test this theory since the authors demonstrated that they grow at many different temperatures? You could follow growth at room temperature and examine if comparable gene transfer takes place. I just wondered if any had considered looking into that to determine if that is the case. Thanks!


-Laurel


Geoffrey writes:


Doctors:

While your show has been a real eye-opener for me in so many ways, much of my interest in the microbial world remains in the areas of endo- and ectophytic microbes, soil microbial ecology, and food / energy / raw materials fermentation. You speak frequently (and, I have noticed, rather lovingly) of exploratory deep genome sequencing just to try to find out what’s in the environment. Though a little more narrowly focused, that is exactly the kind of research that I am reading about frequently in my areas of interest. What is the microbiome of a Withania leaf?, miso?, apong (wine / beer from moldy rice)?, hydrogen-bubbling mud?, and other topics of that nature.

I won’t pretend to understand all the techniques that are being used to genetically identify the microbes in these environments but it is of interest to note that much of what we thought we knew due to culture techniques isn’t particularly accurate. Culture techniques often skew results towards easily culturable microbes which can greatly distort our reconstruction of microbial communities (especially reconstructions of microbial succession) and completely misses the contributions of NCO’s (Non-Culturable Organisms). Recent techniques involving direct analysis of DNA present has greatly expanded out knowledge of these communities but different techniques often produce different results. We are still expanding and improving these techniques and, more importantly, learning how to apply them so that they complement each other’s strength and weaknesses and give us unprecedentedly clear views of microbial communities.

With all that introduction done, I now present my question. I assume that deep genomic diving involves many of the same techniques used in the shallower explorations mentioned above and viruses definitely provide a deep and wide pool of NCO’s. Would you be able to discuss some of the major DNA / RNA detection techniques used in this field in terms of their strengths and weaknesses and how different researchers are overlapping their use to build robustness into their studies of microbiome and virome?

Thanks for the great podcast,

Geoffrey


Alice writes:


First, thanks to Vincent et al for the wonderful podcast series (all 3). I am a fellow in pediatric infectious diseases (a fellow is the MD-equivalent of a post-doc for subspecialty training). Your podcasts are thought provoking and timely and always intellectually stimulating - so thank you.


In return, the temperature here in Cleveland Heights is currently 15oF, winds west at 7mph, humidity 72% and I'm really tired of winter.


Regarding TWiM #72: your discussion of this paper coincided with my caring for a patient with a surgical procedure known as a ureterosigmoidostomy, in which the ureters are implanted into the distal colon when the bladder is not present or can't be used for some reason (e.g. congenital malformation). In the process of caring for this person, I learned that there is a significantly increased risk of cancer developing in the bowel (see references below). After this surgery, the urine drains into the bowel and greatly changes the chemistry and flora present. Examination of the microbiota and/or metabolome of these patients may turn out to be quite interesting.


Thanks for making me think differently about our relationship to micro-organisms every day.


Alice Sato, MD PhD


1. Eur Urol. 2011 Nov;60(5):1081-6. doi: 10.1016/j.eururo.2011.07.006. Epub 2011 Jul
14.

Tumor growth in urinary diversion: a multicenter analysis.

Kälble T, Hofmann I, Riedmiller H, Vergho D.


2. BJU Int. 2010 Mar;105(6):860-3. doi: 10.1111/j.1464-410X.2009.08811.x. Epub 2009
Aug 13.

Long-term outcome of ureterosigmoidostomy: an analysis of patients with >10 years
of follow-up.

Tollefson MK, Elliott DS, Zincke H, Frank I.


3. Acta Chir Belg. 2009 Jul-Aug;109(4):531-3.

Complications associated with ureterosigmoidostomy--colon carcinoma and ascendens
infection resulting in nephrectomy: a case report.

Turedi S, Incealtin O, Hos G.


4. J Urol. 1990 Sep;144(3):607-10.

Current status of tumor of the bowel following ureterosigmoidostomy: a review.

Husmann DA, Spence HM.


Clark writes:


I was wondering if you all had seen this recent paper on detection of oral bacterial DNA in synovial fluid. Given that one of the frequent hosts teaches dentists I would be especially interested in his comments about the relationship of periodontal bacteria in other diseases. I think it’d make a very interesting discussion for non-microbiologists like myself. (My background is physics)


A doctor friend of mine created an rss feed on the topic so it seems like there’s been a lot of work done on this.


http://www.ncbi.nlm.nih.gov/pubmed/23534379?dopt=Abstract&utm_medium=App.net&utm_source=PourOver

 

 

TWiM 73 Letters

Mark writes:

Hello Team TWiM,

I’ve followed with interest your coverage of Michael’s research into use of copper to fight hospital infection. Of all the interesting papers covered in 2013, I think the one most actionable is episode 55, The Copper Room. His research, described in that and prior shows, addresses an under-reported aspect of our health care system. Hospital acquired infections are a serious matter of which I am especially mindful as I prepare for surgery later this month. Kudos to Professor Michael Schmidt for proving how a relatively simple change of hospital materials can have a huge impact on improving patient health and outcomes.

Let me share some news, and ask follow-up questions.

Monday, 1/6/14, at the Consumer Electronics Show, Corning Inc introduced a new line of “Gorilla Glass” that it claims is the "World’s First Antimicrobial Cover Glass”. Links with information:

— press release: http://www.corning.com/CMS/Overview.aspx?id=60899

— video releases: http://www.youtube.com/watch?v=egU8GLD7MG8&feature=youtu.be

Corning is positioning the product for touch-based mobile devices to combat bacteriological growth and spread of disease. We have all have seen phones whose surfaces are, in plain speech, gross, disgusting and covered with layers of schmutz. TWiM listeners would call such objects “fomites” to use a polite, abstracted, and neutral term.


Here come my questions ….

1. Corning highlights the use of “ionic silver” as the antimicrobial agent in its new glass. Silver, Ag, is in the same column and one row below copper, Cu, in the Periodic Table. Below silver is gold, Au. Do I recall my chemistry correctly in that each has the same number of valence electrons? If this is true, can Michael or other hosts compare-and-contrast how Cu/Ag/Au vary in effectivity killing bacteria? Besides economics, is any of those metals a preferred choice for bacterial killing agent? Why, or why not? Is the preference related to their increasing conductiveness as you descend rows in the Periodic Table?

This question is truly cutting edge… I call your attention to

2. Would you describe in more detail the mechanism by which copper’s valence electrons kills bacteria?

3. What impact does copper have on neutralizing viruses and their ability to spread? I use “neutralizing” because you can’t kill a non-living virus. Do you agree with this phrasing?

Wishing all of you the best in 2014.


Mark


PS - the weather. Here in the San Francisco Bay Area the weather these past few days was mostly sunny, with highs in the mid-60’s and lows in the mid-40’s. This east coast refugee empathizes with easterners like TWiM’s Michiganders, Carolinians, Jerseyites, or his brother out on Long Island who have been experiencing extreme cold with daily highs in the low-teens. Only Elio’s San Diego has better weather as I write this.

CN writes:

Greetings Vincent and Team,

On the foremost, thank you for your excellent educast. Your podcasts has helped me generate and understand a lot of ideas which i would have never accomplished had it not been for your podcast. I have just joined, Dept of Neuro-Microbiology, NIMHANS, Bangalore, India as a PhD scholar. Maybe i can consider it a TWiX bump.

The issue of Health Care associated infection has come up, multiple times in your podcast. I have a query in connection with the same.

Hospital environment harbors microbes usually of MDR type. The ones commonly involved in Nosocomial infections are often environment and antibiotic resistant types. There is a very limited scope of competition from harmless and less robust environmental flora. I'm curious if we could (theoretically at least) introduce environmental flora into hospital regularly, which would then reduce hospital acquired infections. Just a wandering thought.

I always have wondered why doesn’t TWiM have Pick of the week. Keep up your excellent work. Never ever stop TWiX.

A yet another TWiX Podcast fan.

Mark writes:

Hi Vincent, Elio, Michael and friends,

Firstly, thanks for the show. It regularly blows my mind, and keeps me very engaged during the otherwise cold and rainy walks into work. Keeping up with each episode has very much broadened my mind to microbiological topics that I wouldn’t have come across otherwise, which has in turn enriched my own thinking and work.

In the fascinating TWiM 68 ‘The Fungus Among Us,’ Elio questioned the existence of uninhabited aqueous environments. I know of two naturally occurring habitats on the earth that are most probably functionally sterile (that is, supporting no active growth). These are Discovery Basin in the deep Mediterranean and Don Juan Pond in the McMurdo Dry Valleys, Antarctica. Both of these are extremely concentrated brines, where the main salt is not NaCl, but MgCl2 (in the case of Discovery Basin) and CaCl2 (in Don Juan). Previous studies report DNA sequences from Discovery basin, but the current thought is that these originate from organisms that live above the seawater/brine interface and have simply sunk into it. mRNA has not been successfully recovered, suggesting that there is no active life. Exactly what property of the brine precludes life is not fully understood; it could be either the dramatically low water activity (availability of free water) or the chaotropic, disruptive effect MgCl2 has on biological macromolecules. Check out this paper which discusses support for a chaotropic barrier to life:
http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01212.x/full

Don Juan is a particularly fascinating place, as it never freezes over despite experiencing temperatures down to -40oC. There is much less published biological data on this environment (none with molecular tools), but it is more chaotropic and more concentrated than Discovery brine, and most microbiologists who work with Dry Valleys lakes consider it a sterile environment. These environments are particularly interesting because of the current paradigm (in astrobiology) of liquid water being the holy grail for habitability, and yet even on the earth there are (albeit rare) examples of aqueous environments that may fundamentally preclude life.

On a different note, I thought you might all enjoy this paper exploring some of the novelties of haloarchaeal genome replication:http://www.nature.com/nature/journal/v503/n7477/abs/nature12650.html

I was reminded of it by your discussion of horizontal gene transfer in the archaea. It’s a really nice study and highlights how different and interesting these organisms are when compared to bacteria or eukaryotes. The authors hint toward some profound evolutionary implications in the discussion.

Apologies for the ramblings, and thanks again for all the inspiring discussions.

Best wishes,

Mark

--
Mark Fox-Powell
UK Centre for Astrobiology
School of Physics and Astronomy
The University of Edinburgh
Edinburgh

Bradley writes:

If you can find the backstory to this, it would be an interesting TWiM:

"Passenger with possible TB infection pulled from plane"

http://edition.cnn.com/2013/12/02/health/tuberculosis-us-airways/

--bks


Nathen writes:

Hello TWIM-ers,
A friend of mine just posted this question on tumblr and I thought you all would be the perfect people to address it:

Question of the day: A strain of Flavobacterium (KI72) evolved the capacity to digest nylon, obviously in recent history. Fine and well. How long will it be until one of the cariogenic bacteria species evolves the ability to digest dental resin? After all, we are putting a lot of it on their dinner table.

Original Article: http://recursivemuffin.tumblr.com/post/68921313389

Darcie writes:

Hi, great podcast. I just wanted to let you all know that stool taking "the shape of the container" isn't a British-ism. I work in the Micro department of a hospital/reference lab and we use this criteria on a daily basis when testing for C Diff. Specimens that are too formed must be rejected for testing, and we've had many discussions about what makes a stool formed or not; the criteria "takes the shape of the container" has turned out to be the best way to decide if we will reject a specimen or not.

Jesper writes:

Dear Magiis of the Microbes,

In the news here in Sweden there are unfortunately many reports about the spread of C Difficile, and we've had a few deaths as well. Remembering Michaels research about copper surfacing as a means to reduce harmful microbes in hospital settings, it may be of interest to learn that a study has been conducted here to show that using Chlorine and a detailed cleaning protocol reduced infections by 50%. I have not found the publication, but here is (in Swedish) the protocol recommended: http://www.lj.se/infopage.jsf?childId=16504&nodeId=31555. Essentially they swipe all surfaces with Chlorine.

Here is another article about the research in a Swedish medical Journal: http://www.lakartidningen.se/Klinik-och-vetenskap/Vardutveckling/2014/01/Lomskt-och-omfattande-utbrott-av-Clostridium-difficile/

I do not want to make the impression it was unknown that chlorine is effective as an antibacterial. CDC knew this (http://www.cdc.gov/hicpac/disinfection_sterilization/3_2contaminateddevices.html)

Thank you all for a very interesting pod cast!

--Jesper
Software Engineer

 

 

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