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TWiM 100 Letters

Matt Daugherty writes:

I just listened to the latest TWiM. Thanks for covering our horizontal gene transfer paper! It was great to hear you all talk about it and give your thoughts.

With regards to the selective pressure for retention of the Dae’s in genomes once the extremely unlikely horizontal gene transfer event happened, I’m not sure we will ever know the bacteria that drove that. For instance, in ticks and mites, it was likely an ancient pathogen of that ancestral chelicerate over 400 million years ago. Borrelia is a current bacteria in one lineage of ticks, but is not in other mite and tick species (to my knowledge), so while the Dae2 gene works against Borrelia in the deer tick, we have to infer that it also works against several other bacteria in these critters. Finding out what those bacteria are and how inhibition of their growth would have driven retention of Dae’s is, of course, an active area of study now that we know these antibacterial genes exist in these species.

Hope all is well there.

Best regards,

Matt Daugherty

Geoffrey writes:

Perhaps it has already been brought up but, in your discussion of the shipworm / bacterial symbiosis, you didn't mention a, to me, rather remarkable point: This symbiosis involves anaerobic bacteria on the gills, the very point of maximum oxygen saturation (I presume) in the shipworm's body! I would have to suspect that the symbiotic trade-off, at least in part, would have to involve enzymes for shelter from oxygen.

Jesse writes:

Dear Wonder TWiMs,

I just listened to your discussion of nitrogen fixation on TWiM 94 and greatly enjoyed it! My current research is on Azotobacter vinelandii and its nitrogenases, so nitrogen fixation is close to my heart (and mind) right now. I hadn't heard about these algal symbioses before though.

A couple things I would add, for general interest:

Nitrogenase as an enzyme is good for reducing N2, but it can also reduce a lot of other similar-shaped molecules! Acetylene (C2H2) is one, commonly used in assays for nitrogenase activity, but the enzyme (at least, some forms of it) (and in vitro at least) can also act on carbon monoxide, cyanide, and even carbon dioxide, reducing them to mainly hydrocarbons. So this could be an ancient link between carbon and nitrogen cycles. A hypothesis, anyway.

Despite the toxicity of oxygen, Azotobacter is an obligate aerobe, with very high rates of respiration observed. It's been thought that this high respiration rate is part of what protects the nitrogenase from oxygen (reduce quickly O2 to H2O before it can react with the enzyme). My reading so far suggests this is controversial though.

Thanks for all the good discussions,
Jesse

 

 

TWiM 98 Letters

 

Patrick writes:

Hi Vincent,

I thought you and the rest of the TWiM/TWiP folks would be interested in the following paper: Transferred interbacterial antagonism genes augment eukaryotic innate immune function, published online in Nature this week. Matt Daugherty (Malik Lab) who you know, co-authored the paper with Seemay Chou (Mougous Lab). We've had a lot of fun following this story in the lab. I think it's a beautiful example of interdisciplinary approaches coming together to uncover a very cool bit of biology.

Happy Holidays to the entire TWi-fecta,
Patrick

Dave writes:

Dear Mr. Pres., Pres alum, and Pres to be,

Elio said Cretaceous referring to four hundred million years ago and Michael agreed. I thought, wait! That's when Jurassic Park was set (Cretaceous), ie in the last era of the dinosaurs (exclusive of birds), from one hundred some to sixty six million years ago. You guys were talking about how ancient must be the tenuous association of the tiny cyanobacterium with the tiny algal bit in getting fixed nitrogen into the eukaryote.
Four hundred million years ago was just at the end of the Devonian and beginning of the Carboniferous. I had to look that up.

Perhaps you meant the era starting with a "C" which was not the Cretaceous.
Looking forward to contemplating my metabolibiome under the influence of my Microbiome and my virome, enjoying my insomniac listening again,
I remain faithfully yours,

Dave
Fresno

Robin writes:
For those unacquainted with the Armed Forces, about the email question on food safety:

Page 65
3-501.19 (B)

http://www.med.navy.mil/directives/Pub/5010-1.pdf

Nick writes:

Hello all, Thank you for for the wonderful and insightful podcast. I am a somewhat regular listener as I work in viticulture and spend my spring summer and fall scouting vineyards advising grape growers on integrated pest management in Northern California. It was brought to my attention by my girlfriend and dentist that new born children are born with sterile mouths. I am curious as to why this is the case? Could it be that some newborns have colonies of bacteria that are passed on from the mother?

Thanks for your thoughts on this question. Happy New Year!

Just found an interesting paper suggesting the microbiome of the placenta...

http://www.ncbi.nlm.nih.gov/pubmed/24848255

Bethany writes:

Greetings. I have just finished episode 77, so I am slowly catching up. I wanted to say that while I am a layperson as an elementary school teacher and hobbyist fermenter, I enjoy learning about microbiology and find the topics fascinating on the show. One of the anthropological aspects of food that I find fascinating is and other foods where saliva has started fermentation although I would hesitate to try this myself.

http://en.wikipedia.org/wiki/Chicha

I wonder how much this kind of thing impacts the diversity or monotony of the indigenous population's salivary flora.

Overall, I just wanted to say thanks for a good show and I look forward to getting caught up soon.

Bethany, Austin Tx

A question from TWiV (Caroline)

Are virus infections more likely to be species specific than bacterial infections? It seems to me they would be since viruses rely so much on the specialized relationship with cells for "survival".

David writes:

Hi guys. Sorry for such lag in response. Re: number of rats in NY -- I'm uncertain. Heard a couple million recently. However, I felt obligated to share an anecdote. Popular Canadian life scientist David Suzuki in interview with Bill Moyers a few years ago stated, sharing an air of astonishment and awe, that planet earth now has more humans than it has rats. This is noteworthy, of course, because rats are so much smaller, eat so opportunistically, and reproduce so florescently, that you'd kind of think there'd be more of them than of us, overall. There must once have been. That was his impression, anyhow, and I was willing to buy in. It sort of left an impression of the massive quality of earth's infestation with H sapiens at this point. Just think.

Next time, I've decided to share with you the story of the remarkable biofilm I've been able to cultivate in my, at this stage, really dramatically bachelorized toilet. I'm obligated to be embarrassed, and unequipped to analyze it, but it really seems pretty astonishing. I hope to spell it out for you in a message to follow, as long as you assure me of some modesty in revealing the attribution.

One time, I may tell you about the bioluminescent, presumably fungal, growth observed in my compost heap while turning the thing in the dark of the less hot night a while back.

No more rain here. Cool weather, finally, but no exceptional freeze, and probably warmer average. No rain and some sunshine cooks ozone and nitrogen oxides, irritating the lungs of many worse than in most places. We have particulates too, of course, which are pleasantly washed away for a day or two by some rain. Do expect not very pleasant.

Gratefully,
Dave
Fresno
PS heaps of praise on your communications works. - d

 

TWiM 97 Letters

Dennis writes:
hi Doc,

A paper just published in nature:

http://www.nature.com/nature/journal/vaop/ncurrent/pdf/nature14098.pdf

reports an effective antibiotic against world class killer bacteria including tuberculosis, MRSA and C. diff. Is it too early for a TWIM on this? Would be interested in so many aspects including whether anyone has found the bacterium responsible and what the chip does for "in vivo situ" detection in the dirt where the "unculivatable" bacteria live.

Was 21C this afternoon and sunny although a cooling trend is forecast.

Wow, what a wonderful world it can be,

Dennis

Dennis writes:

Hi Dr. Vincent and the TWIMtastics,

Thanks so much for your V101 course! In lecture 5 and the slide on estimated speeds of viruses through the cytoplasm, I was struck by the difference between the velocity of the bacteria Listeria Monocytogenes (LM) with its Actin tails in cytoplasm versus these more sedate diffusion times. Given gene sharing, I wonder why more bacteria haven't been discovered using that mechanism. I learned of LM from Michele's discussion of Dr. Portnoy's Listeria work in TWIM #79. It is so fascinating and possibly world health changing. Perhaps Dr. Portnoy could be invited to do a TWIM. There are at least two helpful youtube videos:

The first is 16 seconds long and shows LM racing around a cell and creating protuberances in order to be phagocytosed by an adjacent cell. It's a favorite of mine and is called "Listeria monocytogenes" by Jun S:

https://www.youtube.com/watch?v=sF4BeU60yT8

The other is a 43 minute presentation by Dr. Portnoy describing some of his work called "Listeria: From Food Poisoning to Cancer Immunotherapy":

https://www.youtube.com/watch?v=aY_zdk5dYA0

Michele might have already posted one or both of these.

Thanks so much. You have set an example to which all podcasters should strive and a model that many would do well to adopt. Oh, 14 degrees C here and light rain which we really need. Hoping the Northeast can dig out from it's record snowfall!

Dennis

Dave writes:

Re: the letter which was under discussion when I came into TWIM just now, in the last few minutes of the episode:

The sensitive science fiction author Clifford D. Simak published a story fifty-some years ago, about a peaceful society and how it happened that they could be that way. Every so many generations they would go ask ceremonial questions of the omniscient computer, after carrying on life as usual for a goodly time.

First question was, "What is the purpose of the universe?" Answer: "The universe has no purpose. It just is."

Second question was, "What is the meaning of life?" Answer: "Life has no meaning. It is an accident on the face of the universe."

After that everybody could go home, go to the rocking chairs on the porch and resume shucking the peas while telling each other entertaining stories about life, the universe, and everything. Certainly nothing to fight about, given sustainable resources.

Unseasonably hot October in Fresno. No rain.

Regards,
Dave

PS Now that the show's over today on Science360 internet radio, I'm gonna have to go get the podcast for myself. I'm lazy, and prefer to have a DJ bring it to me, while I'm shucking the peas. d

he added later:

Y'know, I think the two questions make more sense the other way around. I got it backwards.

1) Meaning: Life is an accident.
2) Purpose: The universe just is.
Think so?
Dave

Jim writes:

In light of the discussion about C. elegans in TWIM 89 have any of you seen the OpenWorm? I just ran across it. Jim, Smithfield, VA

Steve writes:

Hi Vincent,

As a mostly bed-bound sick person, I really must thank you and all your team at TWiX for helping me to keep my sanity with your wonderfully absorbing and entertaining podcasts. With your frequent asides into seemingly almost any subject under the Sun and out into the depths of the Universe‎, distant past, present and, speculated, future, you keep my mind as active as it could be, and it helps me feel a part of the real World, away from the confines of my room. I'm even beginning to form a mental map of the USA, its wildlife, and even weather, which is something I've always felt I needed to study more.

I loved the idea of the 'nitrochondrion', and will need a few more listens through to take it all in, but I think I ought to ask you and Elio to clarify at least a couple of 'conversational typos', for the benefit of other listeners:

I'm sure that many people will have written to you about the assertion that the *Cretaceous* (Carboniferous) Period was 400mya; but some may not notice the conflation of water fern and duckweed. Elio did say, correctly, that Azolla was a fern, but this was after he already said it was duckweed. He clearly knows it isn't, but the listeners may not all appreciate that.

Azolla is a serious invasive alien plant in UK wetland habitats, and can quickly choke out almost everything else when it gets into ponds where there is nothing that can control it or compete with it. Even the duckweeds that might, otherwise, cover the whole surface of ponds, can be deprived of the open water that they need and be replaced with an almost hummocky surface of piled up water fern. It can be quite a dismaying sight to go to visit a pond from one's memory, and then see, as one approaches, where it used to be, the tell tale red of the hummocky surface of water fern that has obliterated it.

I don't know if anyone has yet come up with a safe and practical control method. I used to get a bit concerned when eutrophication had enabled the duckweeds to cover the whole water surface, but this Azolla, is orders of magnitude worse.

These slips and 'typos' are inevitable with such ‎a wide ranging and unscripted format. In a way, they are the 'deliberate' 'Where's Wally's' that encourage us to keep listening carefully.

May they, and you all, long continue.

Best wishes for the New Year,

Kind regards,

Steve
Luton
England
(Wet and windy with a high of 3C)

TWiM 94 Letters

Kieran writes:

Dear Vincent,

I have just finished listening to TWiM 92 and it was very interesting, as always. It is a pleasure to listen to all of you discuss these fascinating topics.

At the end of this episode, you talk about probiotics because it was a question from a listener, basically asking about the efficacy of these. I would very much like to hear a probiotic themed episode as my research/thesis area is in some way related to the probiotic/prebiotic area.

Two big names that come to mind are Todd Klaenhammer (North Caroline State University) and Willem de Vos (Wageningen University, Netherlands). Both are well known in the area of lactic acid bacteria research (which for obvious reasons is very intertwined with the probiotic research area).

Anyway, just thought I'd mention these names and thank you and your co-hosts again for the great work that you do, for making microbiology so accessible to everyone, and for teaching me about the great diversity that exists beyond my own thesis area! Keep up the good work!

Kind regards,

Kieran

(P.S. I also liked Elios' Small Things Considered snippets idea...)

Kieran
Ph.D. Candidate

Department of Biological Sciences
Cork Institute of Technology
Cork, IE

Adam writes:

My understanding is that each of the two existing Polio vaccines (OPV, and IPV) each have their own issues which might prevent them successfully eradicating Polio.

To summarize the issues:

• Because OPV replicates in the GI tract, it can mutate and revert to the wild-type (pathogenic) strain.
• IPV is delivered by IM injection. It protects against paralysis, but does not sufficiently inoculate the gut. As a result, people vaccinated with IPV can still be infected with, and shed wild-type Polio.

You have had many great discussions about these issues and many debates about whether either vaccine could be used to eradicate Polio. Theoretically immunizing with OPV would come very close to complete eradication, but would be stymied by the rare revertants. While there seems to be great uncertainty whether either vaccine could do the job, it does leave open another possibility.

Shouldn't polio eradication be possible if both vaccines are given to everyone?

If IPV was given first, and then a few months later OPV was given to every individual, that would seem to solve the problem. IPV would prevent paralysis, and a subsequent vaccination with OPV would provide gut immunity.

In this scenario there would still be rare cases of people mutating OPV into the wild-type virus, but those people would not be at risk of paralysis because out side of the GI tract they would be protected by their prior IPV immunization.

Eventually no one would be at risk of paralysis because of IPV, and no one would be able to carry or shed the virus because of OPV. At that point immunization could cease.

There are of course plenty of logistical issues with doing this. It would substantially increase the cost of immunization, and makes the job of distributing the vaccine regimen even more challenging, especially in areas embroiled in conflict. This means economic and political issues may prevent this approach from being successful, but hopefully it would solve the theoretical issue with either vaccine being used individually.

I apologize if you have already discussed this possibility. I try to catch everything but occasionally I'm forced to focus on what I am actually doing while I listen.

Thanks!


Ken writes:

I had an interesting thought today while reading about problems with antibiotic usage. I am hoping some sort of answer is provided so that you can tell me I am a nut job or this is an interesting idea or somewhere in between please.

There is certainly a lot of study as to what comprises the microbiome. This has lead to ideas of weight control, mood moderation, and other health stasis attributes.

One thing that has always bothered me has been looking for the "safe" microbes, and not necessarily the balance. My thought was could people that have side affects from antibiotics actually identify a risk factor for items such as c-diff or even some cancers? The idea being that if a persons "balance" at an earlier date has a "normal" population ratio that increases the risk of the afflictions later in life.

This could be something to allow for earlier screening or modify future treatments for other ailments in the future. It seems like this idea is wide open?

Obviously the idea shares some aspect of using flatulence as a marker as well. Maybe a gas spectrometer measurement could provide a quick and easier route for treatment. Of course that seems a lot more varied with a lot more problems than idea of antibiotic side effects. The latter seems like a simple piece of medical history that could be readily studied.

Harold writes:

Vincent & Friends

Long time TWIV listener. Used to listen to TWIM when is was on the TWIT network.

Temp in cube 78.8 F. Its always bright and fluorescent in the cube farm.

As a lifelong high BMI obese person I am always looking for research on obesity treatments.

Saw this study and wanted your comments

http://www.cell.com/cell/abstract/S0092-8674%2814%2901241-0

Can transplanting the gut microbes of low BMI people into high BMI people lead to weight loss?

Will this be a new angle for weight loss scams?

What kind of diseases could you transmit using gut microbe transplants?

Thanks

 

TWiM 93 Letters

David writes:

Why not eat locusts? Assuming you can find any fuel to cook em, and apart from deficiency illnesses, I've always wondered why people didn't hunker down and harvest them for emergency food. Did original peoples endure swarms by eating them? Did Euro food aversions prevent eating in the midst of plenty? Are swarming locusts full of noxious alkaloids which render them distasteful or toxic? Am I full of it?

What am I overlooking? End of message.

Fondly,
Dave
Fresno. Weather sunny, meaning increased ozone smog, and warmer than normal. Dry, except for teasing.

Did locust swarms function as sort of restorative wildfires? Did they leave behind a refreshing load of nitrogen and phosphate on somewhat depleted soil, preparing for a rich regrowth of the plants as they sprouted in the following season, feeding on up the food chain?

Did they serve as a somewhat restorative protein feast for creatures, such as humans, who may have spent some years on relatively protein poor diets of corn and squash?
Did microsporidia play some cryptic role in the dynamics of any of this? Did they result in animal/human disease or adaptation?

Do you wish I'd think of all my inspirations before I sent the first letter, and wish I'd send them from the same address? Sorry. Asleep at the time of composition and gmail arousal.

Good morning,
Dave
Fresno

Shubham writes:

Hello,

In TWIM #92, you club India with Pakistan, Afghanistan and Nigeria when talking about countries which still have cases of Polio. Please note that
The strategies for polio eradication work when they are fully implemented. This is clearly demonstrated by India’s success in stopping polio in January 2011, in arguably the most technically-challenging place, and polio-free certification of the entire South-East Asia Region of the World Health Organization occurred in March 2014.
My source is WHO's website (http://www.who.int/mediacentre/factsheets/fs114/en/)

I wish you were kindly more considerate when talking about countries you don't know enough about :-) Just because a country is poor now does not mean it takes its citizens' health any less seriously. My intention is not to offend, but rather to inform. I am offended though, being an Indian citizen and having relatives who have worked so hard to help make India polio-free.

I really hope you would correct yourself in the next podcast.

Thanks.

Warmest Regards,
Shubham

 

TWiM 92 Letters

Dave writes:

Laurene Mascola's distinctive voice and laugh has won my heart this month. I found that when TWiM came up for the third time in my playlist the last couple weeks, I kept listening just for a fix. She should be a star.

I'm glad you had a good reason for featuring her, and that she had a good reason for being with you. Great discussion, too.

Thanks.

S Dave of Fresno.

Ron writes:

Sorry if this question is so elementary it is boring, but are the terms “autotroph” and “prototroph” synonyms? I read somewhere that, early on, the two terms were used synonymously. Unfortunately, that reading did not go on to describe any differences in the two terms as they are used today. I understand that prototrophs can make all their necessary organic molecules themselves, and therefore do not need organic molecules in their environment. Do autotrophs only make their own food? Are there autotrophs that must take certain other organic molecules in from the environment, ex. Amino acids or vitamins?

Thanks for your time

Ron C. Michaelis, PhD
Division of Life Sciences
Department of Genetics
Rutgers University

Juan writes:

Hi Twimsters, I'd like to make a follow up comment about Dr Swanson's comment that it doesn't matter what kind of bacteria are in any environment, but solely what sorts of metabolic pathways are there. I have heard this argument before, but i consider it not to be completely true because if that was the case then we would not have such diversity. I believe that this diversity, regardless of the repetition of metabolic pathways, is because each bacterium has a specific program which will be executed on specific conditions (diet, health,etc) depending on the bacterium. So we want to know what bacteria are in there, which pathways do they have, and under which conditions they are invoked.

Regards

Judi writes:

Hi all--

I have several friends who take capsules of probiotic bacteria - lactobacillus, acidophilous and the star (apparently) bifido​.

I have asked them, and I asked them to ask their doctors and nutritionists, but no one answers my two major questions about these probiotics...

1) What do these bacteria do in your gut?

2) How do they get to the gut if you are taking them in gelatin capsules. Don't they die in the stomach acids?


Thanks ---

Loyal TWI X3 listener from the start.

(I used to be a high school science teacher, but I have retired and now spend time gardening and volunteering with little kids to teach science - it's a blast but they ask hard questions!)

San diego - 71 degree F (22 degrees C) light breeze (6MPH), sunny, 63% relative humidity - yes, just another day in paradise. I know - you don't do weather on TWIM but I wanted to brag!

Thanks for all you do!

 

TWiM 91 Letters


Jacob writes:
Hello hosts of TWiM and TWiV,
I'm sending this to both podcasts because I'm interested in hearing what all of you have to say (I figure that I'm going to catch Dickson on TWiV, but if not feel free to ask him on TWiP).

I saw this question on Reddit today and thought I would put it to you all as well:
" If you could convince the entire human population of one thing, what would it be?"
http://www.reddit.com/r/AskReddit/comments/2ajcs7/if_you_could_convince_the_entire_human_population/

Thanks,
Jacob
Sydney, Australia (12°C and dark)
P.S. Welcome to Australia Vincent!

Jennie writes:

I've realized with all of the learning that I do on digital media that I don't always do the best job of writing notes - as I used to in the margins of books for example. This relates to your inspiring podcast since it is a major means for me as an RN to understand our relationship with microbes. I know that at this point you are barely started with the process of TWIM transcription. But, just for the sake of daydreaming, what would be a best case scenario of your audio --- backed up by an interactive transcript? When I think about the best possible learning tools that grow and change with the learner - I would like to see 2 things. First - a generic "important points at a glance" that shows up whenever you take a peek at what you've heard - you have a start with that but its not complete. Second - I wonder if there is a way to have a "reader/listener"s notes on that piece --- again that show up "at a glance" on a transcript or marked to listen to again on audio. Often the epiphanies of TWIM are hidden in offhand comments. Then I have to ask myself much later ----Dang - which TWIM was that in? By the way, I've been listening from the VERY beginning and listen to whole trifecta regularly --- TWIM, TWIV & TWIP

My tech savvy husband showed me the old school client that he uses - Thunderbird - and we installed Quick Notes on this email-client-without-the-email. We were able to write a note on the Prochlorococcus - and the note was stable on completely deleting the RSS for TWIM & reinstating it. BUT - I'm still at the whim of continuously aging / changing tech that can disappear - and my notes along with it. I want my notes to grow with me as I go through life as an adult learner - AND attach to the original document interactively. If anyone has any ideas on capturing the elusive audio epiphany as an enduring note --- let me know.

Thanks Jennie

Bradley writes:
How long can food sit on a counter?

The conventional wisdom is that Thanksgiving dinner leftovers must be refrigerated within two hours. For example:
http://abcnews.go.com/Health/Wellness/thanksgiving-leftover-turkey-fridge-stat/story?id=15018550

True or False?

--bKS

Justin writes:

Has there been any work to show the changes in the microbiome when someone takes a multivitamin (also I do recognize that all multivitamins are not created equally). I want to use this knowledge to assist me in picking my supplements more intelligently. Thank you so much for everything you do on the podcasts. If you just want to respond with sending me an article that would be perfectly fine by me.

Jesse writes:
My department recently invited Dr. Susan Erdman from MIT (http://erdmanlab.us) to speak, and I thought she would make a very interesting guest for TWiM. She spent a good chunk of her day chatting with graduate students here, including stuff about how gut microbes might influence food cravings, which reminded me of your discussion in ep 86; part of her research is on microbial effects on host hormones.

Just a suggestion,
Jesse

TWiM 89 Letters

Peter writes:

Dear Michele,

Prof. Szybalski might have been referring to a truck with a wood gas generator

Apparently they are still in use north of the border from where I live. (see http://en.wikipedia.org/wiki/Wood_gas).

 

Best Regards from Incheon,

 

Peter

 

Adam writes:

 

Hi, TWIM crew,

 

Often while reading articles or Micro textbooks, I see something along the lines of "bacterium X ferments sugar Y."  Could you please provide more detail into what this terminology is actually referring to?  Based upon my limited knowledge, I was under the impression that many different sugars eventually make their way through glycolysis and oxidative phosphorylation, which is different than a fermentation pathway.  I hope this email is clear and you can see the reason for my confusion.

 

Thank you for all you do!

 

All the best,

 

Adam

Reading, PA

 

Robin writes:

 

Why eukaryotes have bigger genomes

 

TWIM 81 "Cold Iron" email re: Cryptococcus genome larger than protozoa

The ingestion of an aerobic bacterium (= mitochondrion) by a Archean formed the eukaryote. The eukaryote mitochondrion has shrunk its genome to that whose ongoing activity is necessary for its metabolic function in the supportive cytosolic milieu; the rest has been shed with some intermittently needed sequences ceded to the nucleus. Thus the multiple mitochondria can support the maintenance and function of a helluva lot more nuclear DNA.

 

Is complex life a freak accident? (24 Jan 2012)

http://youtu.be/aCpq3ixgfnE

 

Scott writes:

 

G'Day Team TWIM,

 

Regarding TWIM 77 where you guys spoke of bacteria stimulating sensory neurons to induce pain sensation and by doing so decreased the local immune response, I was wondering how various pain killers would effect this mechanism?

Thanks for all the great podcasts, and hope there's many more to come.

 

Regards, Scott. Perth, Western Australia.

 

Samantha writes:

 

Hello,

 

I listen to your podcasts a lot. You always ask people to email in.

 

So, I have a really cheeky question - I figure it's worth an ask:

 

I'm an undergrad' biomedical science student in the UK, but I love microbiology. I'm currently writing my dissertation on "whether or not Phage Therapy is an appropriate avenue to pursue in the war again antibiotic resistance, specifically in staphylococcus aureus" (working title). I decided to look at phage therapy after listening to one of your podcasts.

 

If you are ever looking for a topic to review papers on, would you consider papers on phage therapy specifically against staph. A?

I've learned so much from listening to your podcasts. I would love to hear what you find and say about the above topic.

 

Regards

 

Samantha

 

Bob writes:

 

Hi Twim Folk -

 

I was listening to TWIM 77 tonight on the topic of S. aureus, mouse models, and pain. You discussed the parallels between the response to the microbe-generated agents with respect to triggering a response in the neural cells and the similar response to capsaicin, as well as the result of that response reducing inflammation. This made me think about the topical capsaicin products that are used for pain relief, and if their effect may come from a similar response.

 

I am working my way backward through the TWIM episodes and am thoroughly enjoying them. I’m a software engineer by training and profession, but have been working with biologists on a NIH bioinformatics project at Argonne National Laboratory for the last eleven years or so, and have been able to mostly keep up with your excellent explanations of the science.

 

Thanks for your great work,

 

Bob

 

Rick writes:

 

Dear Dr. Racaniello and Associates,

 

I so enjoy TWIM, TWIV and TWIP. Thank you for providing such stimulating podcasts. You are a national, no global treasure and your contributions to both lay and scientific understanding will prove to be a lasting legacy. 

 

I read this news clip about an interesting use of carbon nanotubes to stimulate T-cell growth. Please comment on where this new direction might lead. Are there any other breakthroughs in the programming and use of cytotoxic T-Cells to combat cancer you might wish to highlight?

 

Thank you!

 

Rick, DSc (Computer Science)

 

http://www.rdmag.com/news/2014/08/immune-cells-get-cancer-fighting-boost-nanomaterials?et_cid=4099951&et_rid=527188906&location=top

 

TWiM 87 Letters

Varun writes:

Greetings TWiM Profz,

As a person constantly associated with Clinical microbiology, I have seen the resistance grow up one by one. I couldn't agree more about the problem of using carbapenems, owing to MBL. In my personal experience, carbapenems have become almost "of no use". In last couple of months I have also begun seeing resistance to some last resorts, inc Tigecycline. And a couple of days ago, I have also seen a clear case of Colistin resistance. Tigecycline and colistin resistance is now well documented in literature, hence I'm not surprised. Your thoughts?

Clearly we are desperately in need of new battle options. One of the papers that I happened to have read recently in connection is Collateral sensitivity. I believe it is a TWiM able topic, at least a worthy discussion.

Use of Collateral Sensitivity Networks to Design Drug Cycling Protocols That Avoid Resistance Development. http://stm.sciencemag.org/content/5/204/204ra132.abstract

Thanks for everything that you do
TWiX Fan,

Varun C N

Dave writes:

Hi y'all! Haven't flirted with 40° recently, but San Joaquin Valley real humidity is higher than theoretical due to decorative and crop tree respiration, I think, despite severe drought. Air quality the worst, and better than it used to be. Ground level ozone cooks right up on still, sunny days, not to mention particulates with a breeze. So much for pleasantries I previously skipped.

Email writer on episode of Aug. 14 called attention to scrubs in hospitals, and cross contamination. My limited experience leads me to think those thoughts delightful, and heartily endorse it. Also, if a big place, imagine some of the hues!

Mostly moved to propose hypothesis re: the increase of scrubs worn promiscuously between hospital areas, but also in and out and home. Lack of locker rooms and time were mentioned, and deserve mention. Also, however, I believe many workers who are not surgeons have to buy and launder their own these days (the old binsfull tend to walk off, one by one, adding to facility cost). Why mess up street clothes, then?
Eh! I digressed from hypothesis. In current social environment, a certain pride in glorious, elevated status role in medical facility impels some of these garment decisions. I'm specially important, it hints, and busier than you. It extends easily to lab techs and nursing assistants. When observed in MDs specifically, however, it grabs the identity more simply than the longer white lab coat, and becomes a source of silent pride. This is concomitant with decline of physician/surgeon's role as social dignitary and repository of wisdom. Rather, dignity having been generally deflated (thank gawd) in recent culture, physicians/surgeons have become tradesmen. They also are finally no longer humiliated by mere lowly student status. They also really do have special skills and earnings to signify.

They are thus deflated by their own identity search, at base. They have abandoned role of interested, knowledgeable advisor, and slipped into that of mechanic or technologist of uncertain trustworthiness. This sociological trend has been proceeding for several decades.

Scrubs of identifiable hues, anyway, are a brilliant suggestion. So are locker rooms, and time in to-the-minute productivity demands to ceremonialize their use. They seem like a consciousness-raising device as well. Bottom line, the casual cross contamination is reminiscent of 19th century practice. It deserves attention.
Sorry. I shouldn't listen in middle of night, and submit to urge to share by writing.

All the best,
Dave


John writes:
Dear amphitropical podcasters,

In TWiM 84 Melanie Thomson said she needing to come up with an allergy test for maggots before letting them eat people. Do the FDA and IRBs impose similar requirements in America? Does approval of maggots for use in America make it easier to get approval in other countries?

John

P.S. I have attached a photo of three _Lucilia sericata_, the fly licensed for use in the USA, eating a dead slug.

[vr: maggot therapy http://en.wikipedia.org/wiki/Maggot_therapy]

Michael writes:

Hello All,

Thank you for all you do, I love to listen to all your podcasts as I am at the bench, I am a Medical Laboratory Scientist (new terminology for Medical Technologist).

In TWiM 85, when Michael described the Modified Hodge Test (MHT) near 53:30, he made two mistakes.

1) It was described that the lawn was of an E. coli that was resistant to carbapenems. That is not correct, it is actually sensitive to the carbapemens, and we do a streak of QC orgs and clinical isolates from the carbapenem disk (Meropenem or Ertapenem) out to the edge of the plate. If the isolate has certain carbapemenases, it does diffuse like Michael said, and allows the E. coli to grow closer to the disk.

2) Michael stated in essence that the MHT will detect MBLs. That is not correct. It detects KPC type carbapemases well in Enterobacteriaceae, but according to CLSI (Clinical Laboratory Standards Institute), it is only 11% sensitive for the New-Delhi metallo-β-lactamase.

I also attached a recent paper from JCM on a possible way to detect carbapemases using LC-MS/MS in about 75 minutes.

Please keep up all the good work, I just finished my first Master’s course, heading towards a degree in biotechnology, I decided to continue on with school largely because of your podcasts (I started listening to TWiV in 2009), but only part time because I believe there is a lot to learn in a clinical micro lab.

Michael, MLS (ASCP)CM
http://jcm.asm.org/content/52/7/2500

 

 

TWiM 86 Letters

 

Suzanne writes (re Aphids):

The best way to get rid of aphids in the garden (the ants in my yard love to herd them onto my okra) is a sharp stream of water from the hose. Aphids wash right off! They don't tend to come back right away, either.

John writes:

While discussing the Siberian doomsday virus (TWiM 74 at 50:00) Michael wonders how the virus survived cosmic rays.

The only charged cosmic ray particles that can penetrate 30 meters of rock or ice are muons. Protons and electrons are absorbed.

I estimate half of muons get through, resulting in a dose of about 1 mSv per year.

Over 30,000 years the virus accumulates a dose around 30 Sv.

It takes 1,000 Sv or more to inactivate a virus. This value is similar for RNA, small DNA, and large DNA viruses. See reference below. So 30 Sv should just make the virus angry and ready to go on a rampage. Or maybe I'm thinking of the Incredible Hulk.

Radiation is even less effective on viruses in ice. The virus irradiation paper says so, and I had independently predicted the effect because most DNA damage is caused indirectly by hydroxyl radicals, which are less mobile in ice.

I look forward to papers about 300,000 year old viruses.

John

References:

Particle Data Group review of cosmic ray propagation:
http://pdg.lbl.gov/2011/reviews/rpp2011-rev-cosmic-rays.pdf

A 1971 paper titled "Inactivation of Thirty Viruses by Gamma Radiation" gives a dose threshold around .4 Mrad, which is similar to 4,000 Sv (gamma rays and muons both convert 1 rad = 1 rem = .01 Sv).
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC377377/

I can only say WOW…

Geoffrey writes:

Doctors:

What a funny coincidence. I heard a letter of mine read in episode 78 then, two letters later, you read Matt's letter. The coincidence is that I asked almost exactly Matt's question to my allergist not 2 months before you read it on your podcast. My doctor didn't think that nasal mucosal colonization was a "thing" so a transplant was unlikely to have any real effect. I don't think that he noticed my vulcan-like raised eyebrow at that answer and we went on with the visit. I will be sending him a link to the letter and the episode of the podcast. If he decides to test an off-label use of mucosal biota on me, then I'll try to let you know how it works. Thanks for reading "both" my letters and thanks for the encouragement.

Don writes:

While reading "small things considered" it was mentioned that chloroform was used to sterilize the soil in an experiment on exoenzymes. From behind the "paywall" I was unable to find vapor concentrations, but wondered if this could be used in the treatment of sepsis. Chloroform was used as a general anesthetic, but with some cardiotoxicity. Is there any data on using chloroform to treat sepsis in lab animals? I suppose there would be some concern about massive demise of the bacteria triggering a cytokine storm, like t[he Herzheimer reaction when siphylis was first treated with penicillin.

Your podcasts are wonderful and do so much to foster scientific literacy.

Thanks again

Don Kingsley Jr. MD

Robin writes:

Tuberculosis

Pott's disease is tuberculosis of the spine causing vertebral body collapse and kyphosis.

Kyphosis is "curved", convexity backwards, as in the Hebrew "kefufa" referring to non-terminal forms of the letters
כנפ&צ

Anyone making a decision for respiratory isolation for tuberculosis should have been trained at least once to competence in the performance of a Ziehl-Nielsen stain. While a negative result does not change a clinical decision to commence respiratory isolation, a positive result instantly makes a whopping difference in the clinical picture.

There are things every physician should have learned to do, including a manual CBC in a Wintrobe haemocytometer, a spun haematocrit, a Wright's stain, a silver stallion sigmoidoscopy, a lumbar puncture, endotracheal intubation, etc. These are as basic as learning to ride a bicycle is for most people.

Surprisingly, most hospital labs do not even have the reagents for the Ziehl-Nielsen stain at hand. They should have single-use aliquots of the reagents in a freezer, so that even if the technician cannot do the stain, the physician caring for the patient should do it.

Oxygen dissociates from haemoglobin at various partial pressures. Foetal haemoglobin holds on to oxygen more avidly than in the adult because it has a lot less oxygen around. Deep sea fish haemoglobin is a champion in this regard.

Rebekah writes:

Hello TWiM team,

I am a Medical Laboratory Scientist and I work in Microbiology at a small Hospital in Michigan. I also teach Cilinical/Diagnostic Microbiology at a community college to future Medical Laboratory Technicians (which is the associate degree level of hospital laboratory bench technicians). I am already thinking of ways to incorporate some of your discussions on Microbiology for my students. I will especially recommend episode 52 which can show the students how far they really can take their careers.

I have been listening to TWiM since June 2014 and have just completed episode 66. I have fairly long drive to work and I also am in the habit of listening to books and pod casts while I am working alone on weekends; which is how I have gotten so far.

As I was listening to episode 66’s discussion of C. diff I really had to laugh at how you found the wording “forms to the shape of the container” so funny! That is the exact criteria we use here at the hospital to determine whether or not a stool sample is suitable for C. diff testing. When I got to work I found the episode online and had my coworker listen this part of the discussion. We both thought the TWiM Team would really get a kick out of this too: If there is a stool sample that a tech is unsure whether it is diarrhea or not a stick test is performed. A wooden applicator stick is put it into the stool about ¾ of an inch. The container is tilted 45 degrees. If the applicator stick falls at an angle greater than or equal to 90 degrees than the stool sample is suitable for testing. This is the way it is stated in our procedure manual! It is hard to imagine, but we get a variety of stool samples and sometimes it is hard to determine if testing should be performed, which is why the criteria is defined in this way. I can’t wait to hear you have a good laugh at the expense of our stick test.

Keep up the good work. I love listening to this pod cast. Once I get caught up on TWiM I am going to start TWiP, and then TWiV. I am saving Virology for last because it has the most episodes and it is the subject I know the least about, but I am looking forward to knowing more. Thank you again for all the hard work and effort that goes in the creating these pod casts they are truly a benefit to the scientific community and the general population.

Rebekah MLS (ASCP)CM

Trudy writes:

Dear TWiMmers,

I just ran across this commentary in Nature and thought you might find it of interest since many of your discussions involve the microbiome/microbiota.

http://www.nature.com/news/microbiology-microbiome-science-needs-a-healthy-dose-of-scepticism-1.15730?WT.ec_id=NATURE-20140821

Kind Regards,

Trudy

 

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