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TWiM 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.
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.
S Dave of Fresno.
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
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.
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?
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!
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?"
Sydney, Australia (12°C and dark)
P.S. Welcome to Australia Vincent!
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.
How long can food sit on a counter?
The conventional wisdom is that Thanksgiving dinner leftovers must be refrigerated within two hours. For example:
True or False?
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.
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,
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,
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,
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)
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.
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.
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,
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?
Rick, DSc (Computer Science)
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
Varun C N
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,
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?
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]
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
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.
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.
Particle Data Group review of cosmic ray propagation:
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).
I can only say WOW…
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.
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.
Don Kingsley Jr. MD
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
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.
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
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.
Hi TWIM, TWIV and TWIP Argonauts,
Your three wonderful podcasts are the nutrient media for growing my scientific knowledge. I have been downloading them from ITunes for a couple of years, and although as a mere amateur I sometimes struggle to keep up with the content, I've never listened to a single one that did not teach me something significant that I can understand. The work load to keep up is heavy, but I've never fallen behind more than a few weeks (well, I"m a couple months behind on TWIP). I even listen to them for an hour or so at night before I fall asleep, and the mellifluous guidance of Dr. Racaniello helps me knit up the ravelled sleeve.
This morning while on the treadmill at the gym, I listened to another, very different kind of science podcast: the UK Guardian's This Week In Science, for June 20, 2014:http://www.theguardian.com/science/audio/2014/jun/20/science-weekly-podcast-longitude-prize-2014. It was entirely devoted to a very interesting discussion of the six possible challenges for the 2014 UK Longitude Prize (celebrating 300 years since the original prize for the invention of the chronometer to determine longitude at sea), including one that was based on the rise of worldwide antimicrobial resistance, so familiar to your listeners. The public was asked to vote to select one of the six possible challenges for the 10,000,000 pound sterling prize, and yesterday the result was announced. The voters picked the challenge to create a cheap, accurate, rapid and easy-to-use point of care test kit for bacterial infections.
I was particularly interested in the discussion between the UK's Chief Medical Officer Dame Sally Davies and Dr. Emily Grossman, educator, broadcaster and expert in molecular biology. It seems that finding a cheap, quick and easy way for GP's and other medical practitioners in out of the way places, like desert communities, is needed to enable them to on the site determine whether an illness is viral or bacterial. This would allow them to stop treating with antibiotics, which continuous and increasing use, of course contributes to the resistance problem. I understand there has been some recent progress in developing a better laboratory test for this purpose, but the quick, cheap, easy black box is still elusive.
I thought you might be interested in this, and maybe some of your listeners, too. I should think there may be a potential winner of the prize among them. So far as I know, competition is not limited to UK persons, and I think there is going to be a five year period allowed for entry and submission of a solution. I hadn't been aware of this prize, and it seems a great way to encourage and stimulate discovery and innovation outside of the academic and corporate institutions.
Thank you again for the great work all of you do to make the world a little more scientifically literate.
The weather in Sausalito, just north of the Golden Gate Bridge, at 3:00 p.m. is typical for our summers: Wind from the west, gusting at 20 knots; clear, with fog ready to roll in over the hills behind us; temperature in the seventies Fahrenheit; barometer 29.92; humidity 55%. In one word, spectacular.
"One of the mentees of my former graduate student"
UNC Wilmington NC)
Mentor - protege.
A separate distinctive colour should be reserved for surgical scrubs. No entry or exit from restricted areas wearing scrubs should be permitted. Each area requiring scrubs should use a distinctive colour and enforce the same policy. No distinctive coloured scrubs should be permitted in areas that do not require them.
This needs to be enforced through federal regulations. Many horsespittles will be reluctant to annoy their surgeons, the geese that lay so many of the golden eggs for them.
Dear pH-balanced hosts:
It was 22 C in the air, but more importantly the pH was 10 under my feet.(*) I was at the shore of Mono Lake wondering why thermophile acidophile extremophiles get all the publicity. See TWiV 195 "They did it in the hot tub", for example.
What sort of microbes live in cool to cold alkaline lakes?
I know algae grows there, because that is the larval diet of the alkali flies that breed in huge numbers. Unfortunately I was too early for peak fly season.
* According to published figures. I didn't measure, and when I last measured pH of a lake I don't recall the equipment going to 10.
vr: https://microbewiki.kenyon.edu/index.php/Alkaline_Lake lists microbes found in such lakes
I'm biased towards single-topic discussions because they provide hooks, and are easier to file and retrieve from a blog that is now a living encyclopedia book with the amazing and imaginative tile of "Podcast Encyclopedia." I've stuffed a few TWIV, TWIM and TWIP's into titles that pointed at a key topic, then let listeners discover the related material. All of your episodes, including UrbanAg, are astounding non-fiction, with too many hooks to use as a title and because of that I leave them out.... Probably just lazy.
My solution is to suggest single-topic podcasts; easy to say, of course.
Just thought I'd make the pitch for single-mindedness in case anyone wants to suggest another approach.
Also wanted to ask about all the presentations at each ASM conference and how some have better attendance. Does high attendance suggest importance? If so, is there a way to list or get the topics (links, refs) for each? Might be useful notes for a podcast.
9k people. Must be a madhouse. What a challenge for a robotics class: create a group of drones you could disperse for simultaneous attendance at all the presentations you want to cover...
PS I just wrote and asked about popularity of talks at the conference, but it looks like you can see that from the live archive, so disregard that... However, none of them can be downloaded, so I wrote the ASM contact and put a vote in for making things downloadable.
I listened with interest to your discussion of the ASM annual meeting.
As a food microbiologist I feel compelled to point out that an expert panel recommends not-rewashing bagged salad (http://ucce.ucdavis.edu/files/datastore/234-851.pdf). Of course as microbiologists you may be better than the general public about cross-contamination in the kitchen ;)
If you ever want to chat with a food microbiologist on the podcast I'm available. I co-host a microbial food safety podcast here: foodsafetytalk.com.
I also have a strong ASM connection. I've been an editor for Applied and Environmental Microbiology for almost 10 years and I was elected a AAM fellow this year, although I had to leave the annual meeting before the induction ceremony because I'm also the President of the International Association for Food Protection and we had a board meeting that week.
Donald W. Schaffner, Ph.D.
Distinguished Professor and Extension Specialist
Food Science Building, Room 207
Rutgers, The State University of New Jersey
65 Dudley Road
New Brunswick, NJ 08901-8520
Hello TWiM team,
It was great seeing some of you at ASM last week in Boston either in passing between sessions or at the live TWiV episode. I have a few questions about the ASM meeting:
What was something that you all took away from ASM that was particularly interesting, inspiring, or changed your views about a topic?
Second, from episode 78 (a bacterium grows in Brooklyn). There was discussion at some point about the hypoxic environment of the hemolymph impacting the growth of the fungus. That raises a question: I thought that the hemolymph was the ‘blood’ equivalent for insects and I presumed it would be oxygen rich. That made me think about oxygen utilization by bacteria in an animal’s blood stream: blood in animals is oxygen rich, but is mostly bound by hemoglobin. Are bacteria that end up going septic able to utilize that oxygen bound by hemoglobin or must they be able to survive in a ‘hypoxic’ state?
I can’t remember talking about this in my bacteriology classes and my notes and a quick search around the web didn’t turn up a clear answer.
As always, it is a pleasure to listen and learn from all of the TWiX podcasts.
Washington State University
Washington/Idaho/Utah Regional Program
College of Veterinary Medicine
Class of 2016
Dear recently evolved hosts:
It is 28 degrees C in Grand Junction, Colorado.
At episode 75 time 1:18:10 Vincent suggests that icky stuff that came
out of us probably can't hurt us because it was already in us.
Coincidentally, one of my oldest memories is watching a baby trying to
eat the contents of its diaper and asking my father what happened if
you did that. I suggest listening to an interesting podcast called
"This Week In Parasitism" where the hosts describe parasite life
cycles that depend on recycling waste.
I have two comments on episode 74 time 8:00-10:00.
1. I was confused by the discussion of which species have
endosymbionts. I don't think you were using a consistent definition.
Both cows and humans depend on symbiotic gut bacteria. Those bacteria
like their hosts, but remain potentially free living forms. They are
not obligate symbionts. (Is facultative symbiont a proper term?) In
contrast, mitochondria are obligate endosymbionts.
2. Youth as a species is not an excuse for not having symbionts or
other characteristics. Each of us, human, insect, or microbe,
belongs to a billion year old lineage, but not a billion year old
species. Individual insect species are of comparable age to humans as
a species. We could (and almost certainly did) inherit gut bacteria
from our ancestors, the same way extant termite species inherited
their bacteria from extinct ancestors.
I mention termites because coevolution of termites and their symbiotic
bacteria has been studied and parallel phylogenies reconstructed. I
am far away from my book collection but I recall this was explained in
_Evolution of the Insects_ by David Grimaldi and Michael Engel, which
is worth a read in any case.
Greetings Micro Monarchs:
Here in Vancouver, it is a wonderful spring afternoon; partially cloudy and 16 C.
I know Dr. R is a bit sensitive about sensationalizing science to scare the public but I must respond with a listener pick , based on the horror scenario of TWIM #78's fatal insect fungus sprouting out of human heads.
My pick is the audio play FUNGUS AMOUNG US by Steve Nubie & narrated by the supremely sinister sounding actor, Malcolm McDowell, and available at audible.com
This gem is right on target, mixing a mad scientist with bad science for some good clean fungus.
Still waiting for the first episode of TWIF.
Dear microbial incubators,
It is 40 C in Death Valley and I confess to writing from here in an attempt to win the weather report. I am listening to TWiM during a long road trip. Understanding takes some effort but I haven't crashed yet.
Regarding recent discussion of supplementing antibiotics with bacteria: Is it possible to engineer strains of E. coli and other gut bacteria that are resistant to standard antibiotics? Then ones microflora could survive antibiotics. The resistance would have to be a kind that is rare in the wild but that hospitals are accustomed to dealing with. This would reduce the consequences of trading resistance genes with pathogens.
Follow-up on TWiM #81:
Friends, please forgive brevity of pleasantry; sleep is overdue (internet Player FM re-podcast excellent soporific).
Fear presumptuous correction of trivia you already know, but, re: stress and arterial plaques, some points. Stress is not just perceptual/emotive response to psychological irritants like commuting. The popular usage has been misleading us. It is bodily response to stressors including many non-psychological events, including physical exercise. Therefore, sudden BP changes in even "moderate" exercise, at least when not begun with modulated warmup, is a stressor to arteries and their plaques. Regular exercise benefits longevity in many documented ways, but burst of exercise can also rupture (burst) plaque deposits (as well as initiating arterial damage for initiation of plaque site), releasing gruel into circulation and setting off the big trouble as it clogs the smaller vessels. (With bad luck, even well modulated exercise might do it.)
Arterial plaques, Vinnie, unless my ignorance has overtaken me, are distinctly macroscopic. You can definitely see them. Resident bacteria and biofilms are fascinating news to ignorant self, certainly microscopic, and must have distinct role in plaque derived sudden circulatory injuries. The whole topic sounds thrillingly promising.
So maybe Vince doesn't need a driver, and Michelle had better watch out how she exercises. And we should all hope for fortunate expression of our genes. And for magical cold iron transport, or whatever.
PS Re: pre-, proto-, or prokaryotes vis a vis eukaryotes -- awhile back, in a perverse moment, I skimmed an interview with a Bible literal believer who is biology professor (Dept. Chair? !) at Regency or Liberty University (who can keep em straight), arguing for a 6000 y/o earth and denying evolution "dogma", which he illustrated by nonsense about pro-evolution bias being built into modern bio by sly usages of language such as "pro" and "eu". Since "pro" means "before," he said, the bias is a built in acceptance that they came before "true" cells, thus adding years to the story of life and denying the Biblical true age of life, the earth, and everything, including the evolution of species in any meaningful way..
I betcha the pre and proto discussion mentioned by the letter writer has some place in this teapot tempestuousness. I'd guess "protokaryotes" protects against the suggestion that those cells may have temporal precedence, but are merely simpler versions of the fully formed thing. Or something.
On which note, as long as PhD candidates aren't misled about jobs, the more educated the better. Staff scientist is one good idea. So is Forest Ranger. So is RN. So is high school teacher, or teaching college. Etc. Besides, faculty need students.
As always thanks for the podcasts.
Weather jumping between 20 / 30 (celsius, depending if I'm in San Francisco or Palo Alto).
Very quick idea / question. Do you think there could be a link between hypoferremia (anemia) and defence against bacteria in relation to it being a conserved trait in humans?
Rick writes (re:zombie plants): Interesting that you focused more on the behavior of the zombie more than that of the vampire.
My question is: what is the mechanism providing the awareness that you would assume would be necessary to comprehend the behavior of the creature being influenced or zombificated.
Does the virus have a telescope to see what's going on at our human scale of existence?
Another great show. Thanks.
An interesting study regarding the development of the microbiome of infants - would be a fascinating discussion, I think, following your discussions of evidence for bacterial species in brain and urine.
Might be a good pair with the lung data.
I believe that you missed the most important question in this episode. Can the N-formylated peptides that were found to induce pain in some bacterial infections be used in cooking? I smell a whole host of potential patents in the spicy foods marketplace.
Thanks, as always, for the show.
Hi TWiM hosts,
I have been a long time listener to TWIM, TWIP and TWIV, but have never written to TWIM before.
I really enjoyed your episode Twim #79, in particular the story about using Listeria as an immunotherapy for Cancer. I am not very familiar with Listeria and my knowledge of the immune system is limited to what I have heard on TWIV and Vincent's Coursera course so this story prompted me for clarification on a few points.
1. If you can use the surface antigen from the tumor to stimulate an immune response against the tumors why don't the tumors themselves already stimulate the required immune response. If the immune system isn't responding to the antigen on the tumor why would it respond to the antigen secreted by the listeria, does the antigen have to be in the cytosol of a cell to be detected?
2. If the listeria has a mutated internalin which won't allow it to attach and get into cells, how is it getting into the cytosol to stimulate the immune response or is it just secreting the antigen in the extra-cellular space? Or is it only picked up and eaten by macrophages?
3. If the the listeria is using these Actin rockets to propel itself from cell to cell, how does it get out of the existing cell, does the actin propel it through the membrane to it just breaks through the both the current cell and the destination cells membrane, or does it use the actin to get to the cell membrane and then use the internalin to get out of the cell and get into the next cell?
Thanks for your amazing efforts on the best science podcasts on the internet, keep up the great work.
TWiM & TWiV team,
Keep up the excellent work! I am an electronics engineer who has never studied biological sciences, but now in my 50's, I find your podcasts fascinating. I listen to episodes while working out - a good combination of mental & physical exercise ... thank you!
If you haven't already, please read this article in Scientific American, Dec 2013:
What I found interesting:
(1) Fungi have much larger genomes than bacteria or viruses, and this combined with sexual reproduction, gives them a larger arsenal for rapid adaptation.
(2) In the wild, the biggest predators for this fungus are amoebas, therefore it has developed protection mechanisms. If fungus ends up in humans, marcophages look very much like amoebas, and the fungus hitches a ride inside the macrophage, protected from the immune system until it can replicate and do damage.
Maybe you can do a show on virulent fungi? TWiF? Elio should be interested …
Here's an article which describes a TB drug that can be tweaked to target multiple disease-causing bacteria, and also ward off resistance by targeting multiple pathways in organisms.
[here is the paper: http://www.ncbi.nlm.nih.gov/pubmed/24568559]
I have a suggestion for a slightly out-of-the-way article that would be interesting to hear you analyze. I may be wrong but this article seems a little "primitive" and almost designed to continue an "alien origin" scenario. Despite that, this appears to be a genuine phenomenon in need of some specificity.
Personally, I'd love to learn that it is a stratospheric life form that got swept down to earth but I suspect that it is much more likely to be an oceanic life form swept up by a typhoon.
"Morphological and Molecular Analysis Calls for a Reappraisal of the Red Rain Cells of Kerala", Rajkumar Ganagappa, Mark J. Burchell, Stuart I Hogg, Current Microbiology (2014) 68: 192-198.
Regarding episode 72, I have to confess that it was one of those episodes that went, mostly, right over my head. Fortunately, I was saved by a listener's question regarding using beer as a vaccine medium against yeast infections. At least I know a little about beer.
First of all, I don't have any set answers for your querent. I do have some information that might help set the stage.
Yeasts are indeed used in the production of beer but comparing the basic beer yeast (Saccharomyces) with an infectious yeast like, say, Candida is lot like comparing the stomping power of the hyrax versus an elephant. They may be related but they're different beasts. That said, it might be possible and even practical to infect a beer wort with infectious yeasts and have them proliferate. If you could figure out some way to engineer a non-infectious version of that yeast, then I suppose that it might be possible to prime the immune system against infectious strains of that yeast. My guess is that the process is a lot tricker than with, say, polio or people would already be doing it. In addition, it would likely change the taste of the beer which might or might not be a good thing. Fermentation with non-Saccharomyces yeasts is being studied and does have some beneficial properties.
Then there is the question of actually getting the non-infectious infectious yeast or some significant immune-response-inducing part of it into the final product. If you lysed the yeasts and the appropriate vaccinating portions were soluble and smaller than the filter size, then that could work if you didn't denature it with the heating process first.
There might, however, be a simpler way. Europeans and Americans prefer their beer clear and non-yeasty so they heat it up and filter it. There is, however, a class of ancient beers called opaque or sour beers. These are simple beers which are not filtered (hence both yeasty and carbohydraty - a full meal at lunch time). They are also produced by the combined actions of yeasts and lactic acid bacteria (hence the sourness). For the most part, these beer are living beers, made in the home, and drunk within a day or two. They are best-known in Africa.
If the non-infectious infectious yeast could be supplied in a dormant state able to withstand, for instance, the hot african sun, (perhaps in a spray-dried sugar-yeast mix) then the yeast could be added to this sour beer, proliferate, and be drunk live to induce the immune response. Any taste differences would be much less noticeable in this product and it would fit in well and easily with the daily food consumption of some areas of the world.
Of course, if you could get it into a dormant state in sugar, then it might just be easier to distribute it in lollipops.
Interesting idea that probably won't work but it does lead to some interesting possibilities for integrating other medicinal microbes into diets.
Heard you mention that you had a competitor by the name of Goggles Optional, so being obsessive about science, I looked them up and tried listening to a few of their podcasts. It's reminiscent of TWIS and no real competition to your in depth science podcasting! Actually, it's a bit aggravating.
Hi, I have some comments regarding your dislike of some choice of words in the microbiology and molecular fields. This discussion should be able to fit both twiv and twim.
First you say that the term prokaryote is wrong, but i think the meaning that it has widely attached to the word is wrong. Usually people think of the word to mean without nucleus, and usually we think of these organisms coming before the eukaryotes (that is another discussion altogether) but i don't find this is correct.
there are two stems pre- and pro- , both of them can be meant to mean before, but in a different way. pre- would mean to me something that happens before the appearance of anything, so cells that appeared before eukaryotes would be prekaryotes. Now, prokaryote would mean to me protokaryote, which people may have chosen to shorten to prokaryote. This fits best with the description of these organisms, since they have a nucleiod or protonucleus, some sort of organization that is not quite a nucleus but it is there. so I think prokaryote fits best if it is explained right.
The other is your dislike to the expression "a protein is expressed in the X", you say that we shouldn't say this but instead the protein is translated and that a only a gene can be expressed, and i think this is wrong as well. A gene is transcribed, a protein is translated. What i mean by wrong is that the word expressed according to (http://dictionary.reference.com/browse/express) can signify to manifest. Following this, a gene is expressed when the DNA is copied and the specific bases of the gene are put together, an mRNA is expressed when the gene is transcribed by RNAPol, and a protein can be expressed when it is translated and when it has reached its final destination.
One other comment is how we are thought about bacteria. It is regarding the fact that bacteria are thought of archaic life forms, and while the first lifeforms might have resembled more single celled organisms, both the lineage that gave rise to humans is as old as that of bacteria since we should have the same primordial ancestor, unless there were independent primordial life forms formations. Everyone should be taught that any extant organism is as "modern" as any since all organisms have to adapt to the changing and current environment. So we can say that current bacteria are the best expression of their lineage, and not that being unicellular organisms they chose to not continue to innovate biologically.
A latest topic of discussion has been the state of science, and it occurred to me that while most people in science say that cutting down the number of PhDs and restructuring, it seems contradictory the fact that there are very active programs of highschoolers and minorities into science with the excuse that we need more scientists, what are your thoughts on this?
Thanks for your discussions, I'm always looking forward for each episode of the Twimvps and also urban agriculture.
Dear TWIM hosts,
I enjoyed episode 76, "Genetic biopixels and a pathogenic sweet tooth". I really enjoyed hearing about the course that Dr. Schaechter teaches and in particular the work his students did in developing the biosensor. I would like to recommend a couple of papers that a classmate in my differential equations class told me about. They can be found at Biomed Central and are open source which is great. The first is "Solving a Hamiltonian Path Problem with a bacterial computer", Jordan Baumgardner et al, J Biol. Engineering 2009, 3:11. The second was also published in the same journal, "Engineering bacteria to solve the Burnt Pancake Problem", Karmella A. Haynes et al, J. Biol. Engineering 2008,2:8.
A Hamiltonian Path Problem involves finding a route in a directed graph that starts at a node ( the beginning node) and visits all of the nodes in the graph exactly one time. Companies like FedEx solve these kinds of problems daily in determining the most economical and efficient routes for their delivery persons. Solutions to these types of problems are very complex and computationally intensive. The authors used E. coli that contained a Hin/hixC recombination system from S. typhimurium to randomly shuffle DNA segments as the computing system. They represented nodes in the graph as linked halves of two different genes encoding red or green fluorescent proteins. The bacterial populations displayed phenotypes that reflected random ordering of the edges of the graph. A Hamiltonian path was reported by fluorescing both red and green, resulting in yellow colonies. The Burnt Pancake Problem involves sorting a stack of distinct objects into proper order and orientation using the minimum number of manipulations. This paper describes a proof-of-concept of "in vivo" computation. volunteer
I enjoy so much listening to all of the TWIV, TWIM and TWIP podcasts. Since I've been working on my math degree I don't really have anyone to talk biology, biochemistry, etc with and I miss it. I'm down to the last 2 course before I'm finished, "Real Analysis" and "Probability". I'm hoping that I can find a lab to volunteer to help out in and I've been looking but so far no one has been too keen on having a 70 year old guy hanging out in the lab. Oh well, I have had been able to take some interesting breadth classes and just finished BIoInformatics. It was a trip to actually do sequence analysis and construct heat maps and run blasts! Anyone working on a machine to reverse aging I'm a willing volunteer.
Weather in Orange CA this week has been hot and dry. Today was 98 F, 37 C, 4% humidity, dew point 4 F, winds 20 - 30 mph. We have more of the same predicted for tomorrow and into the weekend. To windy to sail, to hot to just lay around at the beach, and with the winds the surf sucks. So good time to hole up inside in the air-conditioning and enjoy some episodes of TWIM.
Dr. Robert Kelley (Bob)
Dear TWiM team,
I am currently studying for my Biology degree second year exams in the UK and have listened to my first TWiM podcast today. Id like to quickly thank you as the zombie plant topic made perfect outside reading for my plant exam in a few days! I’m about to tackle the paper now.
I will continue listening for more interesting topics!
Thanks so much,
I'm giving a final exam right now, then flying out to Boston for ASMCUE/ASM. Maybe I will see some of you there!
I adore this concept of parasites/pathogens/symbionts altering the behavior of their hosts. Sounds like you all do, too!
Elio had some interesting ideas about viruses and behavior.
I know that folks are short on time, but the SF writer David Brin has an old story about this, called "The Giving Plague." It's online here:
Here you have a virus that causes altruistic behavior! It reminds me of the story (I'm sure it's not true) about the fellow who survives rabies. After he recovers, he is asked why he tried to bite people. He thinks for a moment and replies "It seemed like a good idea at the time."
Even though the virology may make you wince (I love SF, but the authors sometimes...well...play a little fast and loose with the actual world of science), I think you and your readers might enjoy Dave Brin's story.
I will be teaching a freshman writing course on symbioses and parasitism this Fall at my small liberal arts college, and you can rest assured I will be discussing this and related issues with them (including TWiP!). Happy for any suggestions or assistance out there!
As always, I so enjoy listening to your podcasts.
Mark O. Martin, Ph.D.
Department of Biology
University of Puget Sound
Dear Drs. Racaniello, Schaecter and Schmidt,
Thanks for the great episode on swabbing the environment around hospitals to check for prevalence of antibiotic resistant microbes. The idea of resistance spreading out from health care facilities seems very intuitive after hearing about it but I'd never thought of this before. It got me thinking about the number of other livestock farmers I know who have a family member that works in health care as well as helping on the farm. Could this be leading to increases in antibiotic resistant organisms in livestock or obviously vice versa?
I also found the practice of using antibiograms interesting. I had not known how doctors make decisions on which first course antibiotics to use. I will have to ask my veterinarian friends if there is an antibiogram equivalent in animal medicine.
Thanks again for another great episode and also for the TWIV bump for our AgSciToday podcast. It was much appreciated by Steph and I. Hope that nice late spring early summer weather has rolled in where you all are and that you have a few chances to get out and enjoy it. It's a balmy 18 C here in MN and finally not raining for once although it did just rain 1.25" the other day so we were due some decent weather. I'll also add a planting progress report despite that not being a typical feature on the show - we have around 60% of our hay fields seeded, 0% of our corn and 0% of our pasture ground interseeded. Usually those numbers would all be around 100% at this time. It's been another wet spring to say the least.