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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.
Dear Vincent, I have a fun question for your panel about Mars
I was watching NASA talk about how Mars' atmosphere was stripped away and was wondering about Mars bugs. Here are some fun (probable) facts I learned.
When life was starting on earth, 3.8 billion years ago, Mars had an atmosphere about the same size as earth and had liquid water in lakes and streams all over the surface. So Earth and Mars look a lot alike. At 3.5 billion years ago, Mars' dynamo cooled down and its magnetic field stopped. Then the high solar activity of the sun sent strong solar winds that stripped away Mars' atmosphere, and Mars turned into the icy desert we see today. The one place NASA would look for microbial life today is in Mars' aquifers. If they found some, they would like to know if the genetics are essentially different between Mars and Earth
So let's assume that there was some cross pollination between planets when both were watery, by asteroids throwing Mars and Earth rocks back and forth. My question is; would it be possible for Mars microbes and viruses to infect Mars colonists or would the genetics be too diverged after three or so billion years. Will Martians have to put up "Don't drink the water!" signs.
Here is another one of those articles I find a little strange but what do I know....
I guess it kind of makes sense but I would never have thought of this. I bet you already know about this, don't you?
The rains have returned to Seattle. Yippee!
I've been an avid listener off and on regular for many years since my undergraduate days! I started off learning about viruses from you and now love to listen for interesting tidbits on other microbes! I work in Mycoplasma pneumoniae and my graduate school has one of the largest mycoplasma research groups in the US!
I think you've discussed the synthetic genome cell before (a Mycoplasma species!), but I don't think that I've seen a full session about the smallest known self replicating prokaryotes! I'm a bit biased, but I know some wonderful researchers who would LOVE to do a podcast if there would be interest!
Keep on being awesome and thanks for making my bench time entertaining!
I've been listening to TWIM for the last few months during my more monotonous lab tasks and have learned so much more about microbiology in systems I'm not familiar with. I would have never thought to read some of the papers shared on the show. However, as a plant pathologist, I keep waiting for the day you put us on the map and bring one of us on! I've only been listening since TWIM #87, so maybe I missed it. If not, I know Michele lives about an hour southeast from a university with a pretty decent plant path department.
Though exposure to Aspergillus by immunocompetent people, generally is without drama, that's not true for penguins. Air quality is a big question in maintaining these birds in captivity.
If climate change brings an increase in Aspergillus spores to the arctic, this won't be good for penguins.
# # #
Air quality: Penguins as a group are highly susceptible to air-borne fungal infections. For this reason, the air quality in an indoor penguin exhibit should be optimal. Airflow, fresh air exchange, and filter capacity should be researched to provide the cleanest air possible. Aspergillus fumigatus spores range in size from 2.5–3 microns with other aspergillus species spores as large as 10 microns. In order to remove
these spores from the air, a filter should remove particles in that size range or smaller. If possible sources of aspergillus are external to the exhibit then consideration should be given to reducing fresh air intake and providing a high-quality filter on the incoming air line as well as in the recirculation line. If the possible sources of aspergillus are internal to the exhibit, then a high-quality filter in the recirculating system, a
high volume air change per hour, and increased fresh air exchange—as well as identifying and removing the aspergillus source within the exhibit—should be considered. Collection of regular air cultures in the exhibit as well as the air-handling system is a good practice in preventative maintenance. ...
Drs. Schaechter, Racaniello, Swanson, Schmidt, and Any Guests that I Might Have Missed:
In honor of a section that shows up on your show on occasion, I thought that I might send you an actual talmudic question that I posed and partially answered for another podcast a year or so ago:
Why were the Hebrews unable to take their leavening with them when they left Egypt under Moses’ leadership?
During the seven days of Passover (the comemortation of the Exodus), Jews are forbidden to eat chametz. Although often translated as "leavened bread” (the word seems to derive from a root for “sour”, indicating that it was a sourdough-type food), the word is probably better translated as “foods or drinks containing leaven” (Exodus 12:15) which includes beer (the production of beer and bread were intermingled in Ancient Egypt and, probably, most of the Ancient Middle East). Why bring this up on TWiM? because chametz is the result of se’or or microbial fermentation. What could be more appropriate than an actual talmudic question about microbiology?
Now, Exodus 12:15 provided the injunction against leaven - “For seven days you shall eat matzeh” (matzeh is unleavened bread, flour and water mixed and baked within 20 minutes, not enough time for yeast production to kick in) but not the reason. A reason was given in Exodus 13:8 - “And you shall explain to your son on that day, 'It is because of what the Lord did for me when I went free from Egypt.’.” - but, honestly, that isn’t much of a reason. Part of another reason was given in Exodus 12:34 where it stated that “they took their dough before it was leavened” and in 12:39 where it stated that "they baked matzeh of the dough, which they brought forth out of Egypt, for it was not leavened, since they were thrust out of Egypt and could not delay”. That, on its surface, might seem reasonable enough but any of us who have baked bread and / or know anything about bread microbiology know that there is something wrong about this whole situation. If they took their dough with them, then it already contained the se’or (“starter”). The bread might have collapse on them if they waited too long to cook it but they didn’t leave the se’or behind. That could only have happened had they only brought their grain or flour with them and mixed it with water while they were setting up camp and that is not what the text says.
And there is another complication. Exodus 12:39 implied that they couldn’t bring their leavening with them because they were “thrust out of Egypt and could not delay”. In other words, they didn’t have enough time. Yet the Hebrews had sufficient time to gather jewelry from the Eqyptians (Exodus 12:35-36), enough supplies to build the tabernacle and an altar (Exodus 36-38), and their livestock (Exodus 12:32, 38). They even had time to bring their kneading-boards (mish’eret) bound in the clothes on their shoulders (Exodus 12:34). We know that the Egyptians (and, therefore, and Hebrews living in Egypt) used two main types of starter: a baked yeast cake for storage and, basically, a sourdough starter for continuous use. As most people who have dealt with sourdough starters know, these starters, with their often unique tastes, were cherished family possessions being maintained like a family pet and passed down from generation to generation. They were also mobile. Many American prospectors in Alaska in late 19th / early 20th Century kept them as a cherished part of their minimal possessions in their camps. That means that, if the Hebrews had time to gather other possessions, then they had time to pack their se’or and bring it along. In fact, if they brought their dough along, then they were, technically, bringing their se’or.
So, that brings us back to the question of why leavened bread was forbidden during Passover. I propose that the reason was cultural rather than physical (i.e., a matter of time). The Hebrews that left Egypt were depicted as belonging to many tribes. Their journey through the Wilderness was a depiction of their unification into one overall tribe: the Jews. Se’orim (sourdough starters) were cultural heritage. Because they were handed down from generation to generation, they represented the past. Discarding the se’orim and eating matzeh for seven days until they could make more through wild capture was an act of discarding the past as various hebraic tribes and starting a new life as one larger jewish tribe. I suspect that the Rosh Hashanah ceremony of tashlikh - when one tosses bread crumbs into a body of water to cast away the sins of the previous year - is a similar act. Here too, the se’or and chametz serve as symbols of ones past but delving into the connection further is, I fear, a talmudic question for another time.
This might seem a strange excursion for the TWiM podcast but, when I started to piece it together, I found it to be another fascinating example of how microbiology can serve as a scaffold for understanding cultures long-since vanished from the Earth.
Thanks for the podcast,
I just finished listening to Chewates and Coconuts and was so elated to hear about the open access paper comparing the Soybean Oil, Beef Tallow, and Coconut Oil effects on fungal colonization. I am a biologist by education, but I also have quite the “Crunchy” side. If you have ever seen My Big Fat Greek Wedding you may recall that the father figure uses Windex to solve all of life’s problems, and that is me with Coconut Oil. I have several friends in different fields of science and they poke fun at my inFATuation (pun totally intended) with Coconut Oil and often demand scientific evidence for my claims. This is going to be a great addition to my arsenal along with your entertaining and informative podcast! If you ever have the time or desire you should devote an entire tsegment to Coconut Oil and all of its anti-microbial claims! Thank you for the segment and your weekly contributions to science.
Greetings Dr Racaniello and colleagues,
Thank you so much for your wonderful podcast. I am a high school biology teacher and I thoroughly enjoy your discussions of current articles and topics in microbiology. My background is in biochemistry, and your discussions are engaging and keep me thinking about the unseen microbial world that is all around us.
I am currently working on developing a curriculum where students will investigate the Microbiome of drosophila guts. I was fortunate enough to have a lab fellowship in an immunology lab at the University of Massachusetts medical school this past summer where I developed the fly dissection techniques and basic plating. As most of the Microbiome of Drosophia is comprised of Lactobacillus and acetobacter, I used MRS agar and ACE agar this summer but I found the ace agar difficult to work with and I think it will be challenging for my students (plus it contains cyclohexamide which I don't want to bring into my HS classroom). Could one of the panelists recommend some other potential media that I could consider for introducing these techniques to my students?
Again, thank you for the wonderful show and I look forward to future episodes.
Dear TWIM Team,
I have listened to TWIV for a while but just recently added TWIM to my repertoire, so forgive me if this has been addressed in earlier episodes.
Having a background in chemistry and biology with an eye toward human therapeutics (if only in part for funding purposes), I was a amused by the apparent surprise expressed by the hosts at a microbial secondary metabolite being used in human therapy (TWIM #112). I would argue that the majority of small molecule therapies (especially antibiotics and anti-cancers) to date are derived from microbial secondary metabolites, either directly or some having been chemically tweaked for enhanced stability and pharmacokinetic properties.
Chemists are getting better at rational design or the clunky approach of high-throughput screening of random chemical libraries to find new therapies, but 3.8 billion years of evolution has done a lot of work for us.
I found this review paper on the subject which is rather dated, but seems comprehensive and doesn't appear to be behind a paywall.
Always a joy to listen,
Hi Professors TWIM,
I am a recent convert to microbiology and I am preparing to take a medical microbiology course soon. In preparation, I have been reading several microbiology textbooks and getting a little frustrated. Every book starts with a long discussion of the marvels of the gram stain, but yet after a few hours of googling I still can't find the answer to one very simple question: are gram positives and gram negatives monophyletic? From my initial reading it seems that gram positives are a small monophyletic group, and that 'gram negatives' encompasses a massive group of bacteria so large as to be almost meaningless. Am I completely wrong? Do you know of good review papers that explain bacterial taxonomy? Right now I am left wondering if our obsession with the distinction between gram negative and positive is a relic of a pre genomic age. Or maybe I have no idea what I am talking about (likely). I would love to hear your take on this interesting question.
I love all three of your science podcasts, and I keep meaning to get to the vertical farm podcast soon. I have listened to almost every episode of the others though, and I loved them all.
The weather at Stanford right now (10 pm) is 17 °C, humidity 69%, dew point 12° with a cool breeze from the ocean. A lovely evening; although I really wish we would have some rain.
Thank you ask for the wonderful podcasts, they are all a fabulous service to the community and to the public. They are also wonderful good fun.
Thanks for your help,
So if I understand this correctly, this means that the cooling towers spray a mist of the bacteria (with or without amoeba) into the air and that "rains down" and contaminates the air around the building?
This really conflicts with how some sources are saying it has to do with showers http://abcnews.go.com/Health/wireStory/legionnaires-deaths-tied-spray-shower-faucet-33068564 since the cooling towers shouldnt feed into the showers at all.
Could you provide a clarification for me as to what is actually going on? I'm inclined to trust the cooling tower mist idea just because of the source but that's a lot of bacteria you'd need to have raining down...
Thank you for your lovely show. I started with Twiv after taking Dr Racaniello's online virology course, and have since moved to Twip and Twim, all very instructive and pleasant.
Yesterday my daily Twix dose consisted of TWIM 19. During that episode, there was some speculation whether syphilis had been brought to the Americas by Columbus after having surged recently in Europe, or whether he brought it back. I am passionate about history, and the conquest of the new continent has been a rather merciless and bloody one, especially in the 16th century. Viruses and bacteria certainly played a major role in the extinction of native Americans (in the broader sense) as well, although this biological weaponry was not intentional. So this debate caught my attention, as it would be one disease that might have been brought back to Europe as a sort of pyramid's curse.
Jo remarked that the paintings of Hieronymous Bosch often depicted noses affected by syphilis, and suggested that could be an argument that syphilis in Europe predated the discovery of the West Indies. However, Bosch died in 1516, with his birth estimated around 1456. His works are not dated. It is probable that his more exuberant works may have come at a later stage in his life - when he might not have needed to adhere so much to social conventions to sell his works, and after having grown artistically. If syphilis was indeed introduced from the Americas, the grotesque deformations the disease causes may have provided a ghastly inspiration for his marvelous works.
As the recording of TWIM 19 lies several years in the past, I wonder if new research has revealed more about the origins of syphilis, that is, whether it came from the Americas or the old Continent.
I want to thank you all for your continuing effort in making Twix possible. I am sure people around the world have grown accustomed to your voices and expressions, providing them insights, company and joy. I eagerly read STC now, although I must admit that I skip the talmudic questions as they are way beyond my knowledge level.
Sunny greetings from Nicaragua where it now 30 C at 6 PM,
How a fake typhus epidemic saved a Polish city from the Nazis
I just heard this podcast from "Disaster Podcast" that's mostly devoted to hospital sanitation. It sure raises my concern about going to a hospital for treatment. I think the emphasis was on Disaster Clean Up, so the speaker didn't didn't talk about the use of copper which would be a preventive measure, but certainly one you'd think they'd promote as a sideline. Thought the podcast might be of interest as one that connects the clinical with the research side of things.
I’m writing this email in response to episode 112. My first comment is regarding the talmudic question (which I can’t find on Small Things Considered for some reason), which generally concerned exceptions to rules in Biology. Vincent’s comment about how Taxonomy is difficult because naming conventions are based on what is currently known, reminded me of picornaviruses. When I took my first Virology class in graduate school, we learned that the name “picoRNA” is derived from Spanish, literally meaning “small RNA”. The name is based on the viral genome, which at the time was considered the smallest known RNA genome. However, since this group of viruses was named, other, much smaller RNA viruses have been discovered (such as Rous sarcoma virus, for example). Am I remembering this correctly, Vincent? Anyway, these thoughts can be further supplemented by listening to TWiV 357, which features a discussion about Taxonomy, and how imperfect this classification scheme can be. I just love how all the sciences complement each other. One can learn a lot by venturing outside one’s comfort zone!
Completely unrelated to this discussion, I would like to mention this recent article in Nature, which I found interesting.
While most antibiotics function by targeting bacterial DNA, RNA, cell wall, or protein synthesis, this potential antibiotic strategy targets a bacterial regulatory mechanism for synthesizing riboflavin. Apparently riboflavin facilitates several enzymatic reactions, which are essential for bacterial growth and reproduction. As I understand it, this is a previously unexplored strategy for development of new antibiotics. As our imminent antibiotic crisis terrifies me somewhat, I’m wondering if this something to be excited about.
Thanks again for all your entertaining and informative podcasts. They keep me thinking!
P.S. Having grown up in Romania, and having spent summers at my grandmother’s house in Transylvania, I have great memories of going mushroom picking with my grandmother, who was very knowledgeable about which ones were safe to eat and which ones weren’t. But you’re right, nobody in America seems to do this!
Mysterious fungus killing snakes in NY, at least 8 other states | wivb.com - http://wivb.com/2015/08/10/mysterious-fungus-killing-snakes-in-ny-at-least-8-other-states/
One for Elio, if he's not on to it already.
Amphibians, bats, and now snakes: have the fungi just declared war, or what?
All the best,
Thank you for your excellent discussion about graduate and postdoctoral education in TWiM 108. I enjoyed the conversation about career options for people with advanced training in microbiology. I earned my PhD in microbiology and did postdoctoral training before taking my current position as a research scientist at 3M Company. As a scientist doing research in industry, I don't think of my career path as "alternative", although I often hear that term used to describe non-tenure track careers for scientists. It would be a step in the right direction for advisors in graduate programs to start using the term "careers" instead of "alternative careers" when talking to students about options for the future. The use of the word "alternative" to describe non-tenure track career options seems to be particularly pervasive in academic departments specializing in the biological sciences. As biologists, let's start a movement to catch up to our colleagues in chemistry and physics departments where moving to non-tenure track positions after graduate school is a normal and valued option.
Many thanks for a great show. Listening to TWiM is a great way for me to stay current on a wide variety of topics in microbiology, which is not only fun but also part of my job.
I was so confused when I first heard you talking about this. It sounded so familiar I was sure you'd mentioned it before but it sounded like it was new to you. After a bit of thought I wondered if I'd heard of it during a class I took on Beowulf last spring. I checked the discussion board archive and there it was! Someone had linked to an article about it on newscientist.com. What a cool overlap between online communities! If you're still wondering, the language spoken in England back then is now either called Old English or Anglo-Saxon. Beowulf was written in that version of English and it's nearly unintelligible today unless you spend time learning the language. But there are still familiar words here and there. Chaucer wrote in Middle English which we English speakers can still understand somewhat without a whole lot of help. My favorite thing about Old English, really about pre-printing press English, is that there were dedicated letters for our "th" sounds. One was like a cross between lower case p and b which looked kind of like a mouth with a tongue sticking out. Which makes perfect sense.
Dear TWiM Hosts,
My Name is Wytamma, I am a honours student in microbiology studying in North-Eastern Australia where it feels like a pleasant 18C. FYI honours is a year of postgrad research that can bridge you into a PHD without completing a masters degree. Anyway, my question is about Taq polymerase. My girlfriend Anna is currently doing some TA cloning and I was surprised to hear that the Taq pol enzyme adds an adenine overhang to the ends of the PCR product making it perfect for this cloning method. I was wondering what biological significance this function has? I guess the the first step would be to insert a polymerase lacking this function into the bacteria and seeing what happens but I’m a little busy with my own project on ranavirus to take that on.
Thanks for the great podcasts,
All the best,
James Cook University
College of Public Health, Medical and Veterinary Sciences
[this is a property of many DNA polymerases, adding a single non-tempated nucleotide to the 3’-end of a blunt strand. Function unknown, as these polymerases copy circular DNA genomes. Perhaps it is a signal of DNA damage?]
Hi Twi Team,
Absolutely love your podcasts. I’m a public health specialist coming to the hard sciences late in life and enjoying it immensely. Thank you for all you do communicating the wonder of science.
That said… I think you blew it on the public good explanation in TWiM #111.
The reason public goods are fundamentally different than private goods is that unlike with private goods, the producer of the public good gains no advantage vis a vis his peers. If a Pseudomonas bacterium developed a mutation that allowed its siderophores to differentiate gallium from iron, that benefit would be diluted across the entire population of the colony. Everyone - including the mutant - would encounter the same environment filled with a majority of gallium-bound (and therefore toxic) siderophores. There would be no individual survival advantage to the individual that developed the mutation - thus no selection pressure.
Now if there was a mutation that allowed a cell to make use of the gallium as if it were iron in its cell processes, that would be a different story since that would be an individual advantage and would be selected for. But given the diversity of uses of iron in various metabolic pathways, the likelihood of an individual mutating to accept gallium in all the places where iron is currently used is essentially nonexistent.
So public vs. private does matter.
Keep up the amazing podcasts. My dog loves your show because he knows when I put on the headphones he’s going for a long walk!
I'm Peter, writing from Falmouth, UK (not to be confused with it's no-doubt sunnier namesake in MA). We're somewhere about 16˚C (that's about 61 in your currency), with showers, and autumn is starting to tell.
I'm just writing to comment on the evolution of resistance to public-goods based antimicrobials - the gallium storey in TWiM 111.
I'm going to first run with the assumption that there is a mutation somewhere in gene space that allows a siderophore to exclusively pick-up iron. Then the problem with public-goods (for the bacteria, that is), is that the individual bacterium that gets that mutation isn't necessarily the one that gets the fitness benefit from it: It's highly likely that the super-siderophore gets taken-up by a different bacterium, as the siderophore diffuses away from the bacteria that produced it, and then the fitness advantage is conferred on an individual who didn't have that mutation. I guess that the selective advantage for a super-siderophore will be higher in a more viscous media; one in which the siderophore remains spatially close to the bacterium that produced it.
I suppose most of the places we're going to be medically concerned about P. aeruginosa are going to be places with a bit of spatial structure, but still the fact remains that compared to a completely "privately operating" mechanism, a "public goods" based anti-microbial will be less prone to resistance, simply due to the "who gets the benefit of the mutation" idea, though it seems to me that resistance would none-the-less eventually evolve given sufficient time and selective pressure.
That's all, except I just want to say that I have a lot of love TWiM and TWiV and what you guys do; over the last 5 years of tuning-in you feel like familiar characters, the sort that I might regularly meet in the local pub and chat the night away with. And as a PhD student who never does enough reading I cannot say enough what an amazingly useful tool you guys are providing: multiple lifetimes-worth experience pouring over the latest, bleeding edge research with such wonderful insight. What an inspiration!
Cheers all, and here's looking forward to 112 and beyond!
I am writing to help clear up some confusion as to why resistance might be hard to evolve if public goods are targeted.
In episode #111, Elio talked about gallium intoxication of siderophores, and a proposal was put forth that since the siderophore is extracellular, it would be hard to evolve resistance to gallium.
Vincent said, it is the atomic mimicry of gallium and iron being so similar that is important: loss of gallium binding would almost certainly cause loss of binding to Iron.
Elio replied that both the extracellular nature and the mimicry are important, but why extracellular matters was perhaps not so clear.
I think the distinction is not extracellular vs. intracellular, but rather that the siderophore is a public good, that has impacts on a population of bacteria. In contrast, mutations that may produce an altered siderophore occur in individual bacteria.
What this means, is that mutant bacteria bacteria that produce a siderophore that distinguishes iron from gallium does not receive the full fitness benefit of that mutation. Instead, the whole population of surrounding bacteria will receive that benefit. In this manner, fitness advantages from a mutant are redistributed to a community, instead of benefiting only the mutant bacterium.
However, in my opinion, this is still not necessarily a satisfactory explanation as to why resistance would not develop. Even if the whole population receives the advantage from one individual, the mutant bacterium is among that benefited population and will receive some benefit. The counter argument would be that by spreading the fitness advantage among a population, the fitness advantage is so diluted that there is virtually no selective advantage conferred to the mutant bacterium. Personally, I think targeting public goods such as a siderophore may slow expansion of resistant alleles in a population, but not prevent them from occurring.
It's interesting to conjecture that diffusion properties of these "public goods" (to a large population or a relatively small population of bacteria) may impact the rate at which natural selection occurs.
Thanks for your great work, look forward to the next episode!
Postdoctoral Fellow Brigham and Women's Hospital
Dear Dr. Schaechter,
First off, I want to thank you for the effort you and your colleagues have invested in Small Things Considered and the podcast TWIM. Back when I had a longer commute to work, I listened more religiously than now, which is pretty much the only thing I regret about switching my job and reducing my commute. As a physicist, turned synthetic biologist, I really need an education in microbiology (that most of my peers got in graduate school), and TWIM is a great resource for people like me.
Now, a question: (I apologize if this topic has already been covered by you in a previous post or article.) Thermophilic organisms have DNA sequences that are higher in GC content in order to remain stable at higher temperatures. The enzymes and protein structures found in thermophiles are also significantly more thermostable. If you were to examine a conserved enzyme from psychrophile through the temperate zone and up to thermophile, what do you see in terms of its amino acid content? Are there certain amino acids that are correlated with thermodynamic stability of the protein (fold)? Do these amino acids correlate with higher GC codons? If so, do you believe that this was part of the driving force for the evolution of the genetic code? Namely, that a more thermostable codon should correspond to an amino acid that is more likely to contribute to a more thermostable folded protein. (This thought never occurred to me before, but I read the abstract of this paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403753/) and it seemed to imply this concept, which struck me as sensible, but I hadn't heard it before.)
Thanks, in advance, for any thoughts and for your time to help educate us all,
Christoph Weigel responds:
in principle, your ideas are fine. yes, GC-rich DNA has higher melting temps., GC-rich genomes - as e.g. streptomycetes - tend to have a bias towards G and C at the 3rd position of codons in their genes, and also more G and C in conserved transcription factor binding sites. however, there's a big caveat: one of the most thermophilic bugs we know today,
the archaeon pyrococcus furiosus (grows at 100°C, has a wikipedia entry), has a genomic GC-content of 40% (see here: http://www2.unil.ch/comparativegenometrics/AE009950.htm) that's 10 points less than e. coli. if i remember correctly, there is evidence that this bug employs histone-like proteins to keep its DNA double-stranded. and given it's low genomic GC-content it can't have this codon bias. i could/would go into more detail - if you want - but not before end of september as i'm on vacation right now, enjoying açores islands :)
then Noah responded:
Hi, and thank you for your quick response from your vacation. (Do not feel that you have to respond again before returning!)
I guess my question was not "do all microbes that live at higher temperatures also have higher GC-content genomes?" since that is easy to disprove, as you pointed out... Instead, I am wondering about the evolution of the genetic code and the transition from a RNA-world to a protein-world: At this moment in evolutionary history, was thermodynamic stability a driving force of the genetic code? I am assuming that an early RNA-only ancestor of modern life (all of which has protein enzymes, correct?) would very likely have needed ribozymes that were stable at its ambient temperature, and thus, higher in GC content. Also, we should be able to determine (using bioinformatics) if microorganisms that survive at higher temperatures have a consistent skew in the amino acid content of their proteins. For example, if these thermophiles had a disproportionate number of Gly (GGN), Ala (GCN), Pro (CCN), Arg (CGN), then you might be curious about whether thermodynamics were a factor. Looking a little more deeply, you could also ask whether individual transitions from similar amino acids (such as Lys to Arg) contribute to stable folds, since they are also more stable codons (e.g. a comparison between AAA and AGA).
I think it's probably clear that this will not account for everything, but just wondering whether anyone else had thought it may have been a factor. Are there any papers considered "seminal" in the field of the evolution of the genetic code?
Thanks again for your time! Cheers and enjoy the rest of the summer!
I was quite excited by your podcast on AMPs since I studied bacteriocin usage in bacterial vaginosis (BV) prophylaxis as part of masters. So in response, bacteriocins have been identified that inhibit BV-associated pathogens while having little impact on normal microflora in laboratory environments. There's been some promising research on bacteriocin usage but it's been most extensive in food research. Finally, a self plug for a recent publication: I just wrote a review on bacteriocins and their potential usage in conjunction with antibiotics which is currently in press in IJAA.
I love the podcast so much!
Have you seen this? Unbelievable!
It is 64F and "rainless" in Seattle.
Love the podcasts.
Love the podcasts, keep them coming! In response to Michele bringing up the NYC Legionella outbreak Vincent was trying to come up with Michigan-specific infections. Unfortunately, here in Southeast Michigan (mostly in Detroit) we seem to have created a breeding ground for infections with highly resistant organisms including CRE, VRSA, healthcare-associated Acinetobacter, and even a "small" outbreak of 5 cases of colistin-resistant, carbapenem-restistant Klebsiella. (http://aac.asm.org/content/55/2/593). Some have suggested this is due to the high prevalence of diabetes, end-stage renal disease, as well as high baseline rates of MRSA and VRE infections in the area. All of these factors increase the probability that a patient will at some point require vancomycin or a carbapenem to treat an infection. So apparently multidrug-resistant organisms are Michigan's microbial gifts to the world. Anyway, as a medical student I don't get a ton of time to enjoy our wonder summer weather (27°C today) so I'm going to go do that while it lasts.
Pages 41 to 45 of Popular Science magazine, Aug 2015 discusses the danger of our war on bacteria and viruses. They cite hospitals problems where 75000 people die of hospital acquired infections in spite of strong efforts to make things sterile. This war may be related to the rise of the superbug that is rendering our antibiotics useless. The space Station is probably a dangerous place because of the lack of normal microbes.
This article in the most recent issue of Scientific American (special issue with a picture of Einstein on the cover) reminded me of the points you raised during a recent episode of TWiM.
It has long been my opinion that the best advice to give to someone in school is to develop expertise in two complementary fields. In my case I was able to combine skills in shipboard engineering and maintenance with at least a modicum of understanding of computer technology. Similarly, I think that someone with a degree in microbiology who is fluent in Portuguese (the Brazilian variant) or Chinese would be in a strong position. A person with a degree in microbiology who went to law school and specialized in intellectual property law could probably retire at 40.
The attached article describes a need for a marriage between computer scientists and neuroscientists (and by extension with any of the biological sciences). That marriage sounds like a promising “combination” for a student — a major in microbiology and a minor in computer science, or vice versa.
I'm sorry, I may have missed something, but the mechanism behind an effective vaccine is still unclear to me, since infection with F. tularensis does not confer protection. How would a vaccine work?
Katy Bosio replies:
In general, any protection against tularemia is very dependent upon the dose of secondary infection, the route of secondary infection and (likely) the subspecies of infection. Following infections with virulent subspecies, the evidence suggests that there is some minimal "protection" against low dose secondary infection. In humans this would be manifested as a very sick person, ie you might want to die, that had a delayed development of symptoms or someone with slightly attenuated symptoms. However, if the dose is modest to high it's unlikely that the small memory response one generated in the primary infection will be effective. Moreover, infection via inhalation poses its own problems, since the bacteria thrive within the pulmonary environment while evading a suppressing inflammatory responses- a critical element if one wants to jump start adaptive immunity.
Finally, if one is infected with a type B strain (the less virulent, but still pretty nasty) there is some, but not optimal protection against infection with fully virulent type A.
All of this is supported by evidence from human trials using an attenuated vaccine strain (LVS). This vaccine (which is no longer licensed in the US) was generated from type B FT and offered pretty good protection against low to moderate cutaneous infections. It also engendered some protection (in one study around 50-60%) against low doses of aerosolized FT. However, it was very poor at protecting against moderate (around >1000) doses of FT delivered by aerosol. Also, retrospective studies have indicated that people needed yearly "boosters" of LVS to protect against pneumonic tularemia. This supports the observation that long lived immunity against pneumonic tularemia is difficult to achieve.
We can recapitulate most of these findings in our animal model. So, what do we do? My lab has generated some immunologic tools to really dissect how vaccines protect against low doses of FT as well as how virulent FT modulates the innate, and sequentially adaptive, immune responses. By identifying what the host needs to survive on a molecular and antigen specific level we will be able to design a vaccine and vaccination strategy that gets the better of this bug.
Hope that's helpful and glad to hear that people took an interest in this incredible bug.
Thought you would like to know that you have saved many lives in Houston -- when I listen to TWIM during my commute, I am not tempted to use my car as a weapon or a means to clean up the gene pool, I'm thinking too much.
I teach microbiology at a community college and use TWIM for ideas that I can use in class -- applications of the basic material we are covering, new information to update the textbook, etc. In a recent episode, you were talking about how important it is for students to do research to really understand science. We are incorporating that idea into several of our classes here: for the last two years I have had my General Micro students do research projects. The level of their questions has been amazing and their excitement is infectious (pun intended). Our biotech students also do research projects in some classes, but also take advantage of a "project lab" that is open to students to try out ideas -- it is equipped with equipment and some supplies for growing algae and bacteria, making biodiesel, prepping scanning EM samples, making microbial fuel cells, and testing samples for bioremediation. I am going to try to take this research approach to an introductory, non-majors class (I'm trying it with honors students first) by giving them choices of six different types of projects (bacterial pesticide degradation, DNA barcoding of algae in nutriceuticals ...) that have many different ways to go. They will get to work on projects that they "chose", so I hope the buy-in will be there. You will notice how many of these projects are based in microbiology -- great systems to use, little cost. Some of our projects are supported by NSF, others we just do because we can see the benefit for students. It was nice to hear that those of you at universities can see the benefit of what we are doing -- it may be easier for us to do because we can focus on teaching.
Thanks for all the mental stimulation,
Julie Harless, Ph.D.
Professor of Biology
Lone Star College Montgomery
Anaerobic region of the mouth:
The buccal cavity does have an anaerobic region, the gingivodental sulcus. That is why anaerobes are less likely to be found in aspiration pneumonias in edontulous patients: they have no gingivodental sulci. Proper brushing addresses the buccal and palatal/lingual aspects of these sulci, while flossing takes care of the mesial and distal aspects.
Keep up the great work. Gosh, the TWIx on Wolbachia controlling male/female moth ratios and the possibility of a phage vaccine was all incredibly fascinating. Best to all. You are changing lives.
I just went to my semi-annual dental appointment and I thought of a potentially interesting oral health monitor - the plaque biofilm that they scrape off your teeth during the cleaning. Brush immediately before the cleaning to remove the loose food bits then send the scraped-off plaque biofilm for sequence analysis. It wouldn't have to be deep-sequencing. It would only need to monitor the presence of, say, twenty common plaque microbes. Obviously, detection of dangerous pathogens would trigger a return visit but I am thinking that the plaque biofilm is probably a fairly stable and person-customized biome so any serious changes to the biome would trigger further dental investigation.
Do you folks have familiarity with dental plaques (or could you get a guest on)? What kind of sequencing testing might be effective and affordable for this kind of monitoring?
As always, I enjoy your show and my special thanks to Dr. Swanson for allowing a fan-boy to visit her back in April, I believe.
Hello Current TWiM Cohort,
I’ve enjoyed your recent additions of talmudic questions into show episodes. I was surprised one of your listeners wrote in saying, and I paraphrase, that using the word “talmudic” was introducing unprovable theology into the show and veering away from science.
Growing up and studying on the East Coast I came to understand “talmudic”, with a lowercase initial ’t' as an adjective. Its meaning being roughly “the study and making specific distinctions between things relevant only to experts”. Written with a capital ’T’ the word becomes a noun meaning study or interpretation of the Jewish Torah. The word “catholic/Catholic” is also an adjective or noun depending on the case of the initial ‘c’ in the word. Spoken word podcasts don’t differentiate case, and can be ambiguous.
In a recent episodes there was discussion about the human immune system, its “memory” and “loss of memory” by B (or was it T?) cells. This anthropomorphizing raises several interesting, and — dare I say — talmudic questions. They are:
1. How did the human immune system evolve to have different memory ability for different pathogens?
2. How does the immune system lose memories? Isn’t the ability to recognize and fight non-self pathogens a benefit?
3. Is there a beneficial function by “memory loss”, i.e. the immune system losing memory about some pathogens?
4. Is immune system “memory loss” a result of pathogens that have a near homology to the self’s own proteins?
5. What is the essence of the immune system’s memory - is it the structure and shape of a pathogen’s proteins?
6. If spoken or written fiction creates human memories, then is there a corollary in terms of the immunity system?
7. Can we fabricate different shape proteins to create immune system memories against real or imagined pathogens?
8. Is the cytokine storm analogous to the immune system using “dumb” bombs instead of “precision laser-guided” munitions?
9. Is there an immune system corollary to PTSD, i.e.does it suffer dysfunction resulting from memories of past activities?
I offer these up as talmudic — small t — questions for you TWiM Hosts and your listeners. If any of these questions have answers, please explain and strike them from the list.
The journey is the reward.
Heard this three part program from the Canadian Broadcasting Corp and thought it might be of interest:
Science Under Siege, P1 55 mins (165 mins total) - “Scientists around the world are increasingly restricted in what they can research, publish and say -- constrained by belief and ideology from all sides. What happens to societies which turn their backs on curiosity-driven research?” At the link find the title, “Science Under Siege, Part 1,” right-click “Media files ideas_20150603_33313.mp3” and select “Save Link As” from the pop-up menu. Do the same for P2 and P3 for their media files.
I've attached downsized versions of the files, but they may still be too big to get past my server's limits.
Jim, Smithfield, VA
Hello TWIMers from State College, Pennsylvania. As most residents would agree, summer is what earns this place the name Happy Valley, with plenty of warm weather, lots of festivals, and plenty of options for outdoor recreation. This summer we also have had more rain than we know what to do with (sorry Elio).
I was driving to my sister and brother-in-law’s cabin outside of Syracuse this 4th of July, and my inner nerd was more than happy to make this drive a total TWIM-binge. Let’s just say I listened to many, many episodes. I was on Route 13, making the climb out of Ithaca, NY with a beautiful view of Cayuga Lake on the left, listening to episode #105, when Michael made this ASM Division P Chair smile with his food microbiology discussion about E. coli and Salmonella contamination on fresh herbs. That giddiness was short lived though, as he wrapped up the story saying he learned growing up “the old adage that you should eat local and not global”, implying that the globally-sourced herbs from this study were the reason behind the levels of contamination. Luckily I was past Cayuga Lake by this time, as I may have driven off the cliff that leads to it otherwise.
There are several reasons to eat local, including to support your local economy and its hard working farmers, and to eat produce that is as fresh and tasty as possible. Unfortunately, the myth that local means safer perpetuates in the minds of many people. My colleague Dr. Catherine Cutter and her talented graduate student Joshua Scheinberg, for example, highlight several outbreaks from small vendors selling strawberries, bagged peas, and cashew cheese, as well as known hazardous foods that are mistaken to be safe because they are local, such as raw milk (1). Cathy and Josh have also shown that chickens purchased from Pennsylvania farmers markets have a much higher incidence of Salmonella and Campylobacter than store bought chickens (2). To food microbiologists, this is not terribly surprising in retrospect, as the big “factory farms” have armies of microbiologists developing strong pathogen control programs, and these companies strive to ensure that their products a
re refrigerated continuously from the plant to wherever they end up across the United States. Unfortunately, many in the press spun this paper as implying chicken from farmers markets isn’t safe, when the more accurate conclusion stated in the paper was that these vendors need proper training to minimize risks to the purchaser. The smaller clientele base, limited distribution area, and CDC estimates that only one in 30 foodborne illnesses caused by high profile organisms such as E. coli, Campylobacter, and Salmonella get reported (3), means that the larger food producers and distributors give epidemiologists more data points to confidently identify an outbreak. This is a better explanation for why most foodborne outbreaks covered by the press are linked to larger companies.
You also correctly stated that washing produce reduces pathogen load (but doesn’t eliminate it), and mention talks on this topic at the 2014 ASM. This advice should also have mentioned the presentation at this same meeting by Dr. Maria Brandl. Her group at the USDA, and others, showed that human pathogens are not terribly happy on the dry and nutrient-limited surfaces of a vegetable leaf, however damage by harvesting equipment, plant pathogens, or senescence can cause plant cells to release their banquet of nutrients, enhancing the growth of non-native bugs such as E. coli and Salmonella. Therefore, another recommendation is to be wary of older produce or that with obvious damage.
Thank you for what you folks do, keep up the outstanding work, and Michele, let me make a prediction for November 21, 2015. Penn State 35, Michigan 27.
Edward G. Dudley, Ph.D
Associate Professor of Food Microbiology
2 Scheinberg, J., S. Doores and C.N. Cutter. 2013. A microbiological comparison of poultry products obtained from farmers markets and supermarkets in Pennsylvania. J Food Safety 33:259–264.
3 Scallan, E., Hockstra, R. M., Angulo, F. J., Tauxe, R. V., Widdowson, M. Roy, S. L., Jones, J. L., and P. M. Griffin. 2011. Foodborne illness acquired in the United States – major pathogens. Emerg. Infect. Dis. 17: 7-15.
Nervous in San Diego writes:
Dear Professors of TWiM,
I was recently introduced to TWiM by a neighbor. For the last few weeks I have been listening to the backlog of TWiM podcasts, mainly while walking our dog. Regrettably, our dog is a lousy conversationalist. Listening to TWiM while walking is therefore a major improvement. As we walk, the dog investigates things I can not see, while I listen to you talk about them.
Because I have no background in microbiology I must deduce the meaning of the five, six and seven syllable words that you use so effortlessly from the clues provided by the occasional simpler words that surround them. I think it is fair to say that microbiology is the study of what can not be seen using words that can not be pronounced.
The other day our dog and I were listening to a TWiM podcast. (In truth, I was listening and she was otherwise occupied.) You were describing how some parasites modify the behavior of their hosts to the advantage of the parasites. Because I was nearing the end of our walk — and the podcast was not yet complete — I decided to take another lap around the block.
It suddenly occurred to me that TWiM was modifying my behavior. My decision to extend my walk seemed substantively the same as the behavior of a grasshopper afflicted with Summit Disease. As I continued thinking about this phenomenon, I surreptitiously checked my mouth for evidence of frothing, while resisting the urge to climb a telephone pole.
Fearing the worst, my first thought was to rip off my earphones to rid myself of the TWiM infection. But, before taking such a drastic step I decided to solicit your expert advice.
Questions: If listening to TWiM is capable of causing me to walk further, is it possible that you are also inducing behavior changes that I have not yet recognized? Will I soon start craving pickles or become addicted to reality TV? Would it be safer for me to restrict my future podcast listening to Car Talk? I await your response with some trepidation.
Nervous in San Diego
P.S. The weather here seldom changes, but I’ll leave it to my neighbor Elio to provide the details.
Hello, This Week in Microbiology,
First of all, your podcast is amazing, it made my microbiology preparation much easier in university and got me curious about many things.
Now, I've listened to the battle for iron podcast and one thing that I couldn't find on Google got me interested. What is the exact etymology of 'ocelloid'. It was mentioned the word has something with "eye" inside of it and I had to look it up but nothing really came up. Do you by any chance have any idea where it might have come up from?
Thank you in advance,
keep being awesome!
Best wishes from Bulgaria.
In response to the letter from Mark:
Besides West Nile and other mosquito-borne illnesses, fungal diseases leap to mind. Dry soil becomes dust that can be inhaled. Coccidioidomycosis (aka Valley Fever) is probably most relevant to California. There is an open access systematic review available from Plos Currents that may be of interest.
Alice I. Sato, MD PhD
Pediatric Infectious Disease
Albany Medical Center
PLoS Curr. 2013 Jun 5;5. pii: ecurrents.dis.7a2cee9e980f91ad7697b570bcc4b004. doi: 10.1371/currents.dis.7a2cee9e980f91ad7697b570bcc4b004.
[Mark had asked: How do drought conditions change public health risks? CA is now experiencing higher incidence of West Nile virus infections (TWiV listeners will recall Prof Despommier has explained mechanisms coupled to drought and mosquito habitats several times). Should other risks be expected? Or shifting between risks?]
For your interest in listening to physics, there is a podcast called The Titanium Physicists Podcast. They use a conversational format similar to what you use. They have a panel of experts and a guest who is not a physicist but who is accomplished in some other area. BTW I recommended the twix group to him when he was looking for a biology podcasts.
Love the 4 podcasts you people do.
Hello TWIM overlords,
I have been listening to this podcast since it first came out in 2011. Now I am an incoming senior at UC Berkeley majoring in Microbial Biology. It was your podcast that helped me decide what to study. I would also like to say hi to the graduate student that captured fruit flies with wine; perhaps we have already met.
It's summer for me, and I have been re-listening the podcast. Everything is glorious, but what caught my attention is TWiM #48: It's all about direction with Jo Handelsman. This was released in 2013 and it talked about the deficiency in science educated workers in the bachelors level. I was hoping in working in a startup or in industry for a year or two before I went to grad school for a phD, but should I bother at all? I don't plan on going to academia, and I don't know what to do about further education. My grades are not the best but I'm a student researcher in a lab up in the hill and I enjoy research. I have a lot of autonomy in what I can do and I'm afraid I'll never regain that sense of freedom without a phD -- at the same time, I don't want to get lost in constant paperwork. Berkeley has a lot of academics so I don't know what it's like in industry. I do enjoy it when you guys bring it up in the podcast.
This podcast was the fodder to keep me going through bad semesters. At first, they all seemed fascinating and quite confusing. Now I understand more, but more importantly, I'm questioning the paper and thinking about what the data means. I still have a long way to go, and in a way, I feel like I have learned nothing because there is always so much. I would like to thank all the hosts of TWiM for being part of my high school and college experience. I still have a year left in college but I should have thanked you three years ago when I first got accepted.
Kathy Spindler writes:
In the late 1970s, when there were a couple of years of droughts in California, the complete saying was, "If it's yellow, let it mellow. If it's brown, flush it down." And a very memorable billboard I saw in the Central Valley showed someone in the shower with the caption, "Sing shorter songs."
I enjoyed crossing over to TWiM 104 to hear the measles story covered!
Hi Vincent et al,
I was just listening to your TWiM 41 interview with the HealthMap man, and called it up, to have a look. There were a couple of red dots, not far from me--one a mystery illness making an EasyJet plane turn back home--and the other, this shocking news about the, endangered, Saiga, antelope. It does not seem that long since I was watching wildlife programmes that featured migrations of, seemingly, limitless numbers of these animals: now we hear that they are being wiped out with extraordinary speed, by what is thought to be a bacterial infection.
It seems to be happening almost impossibly fast. Perhaps the team would like to look into it for your podcast.
All the best,
Weather still rather grey and windy (But I don't get out, as I'm housebound with ME, and can only stay upright for a few minutes at a time.).
[also see Zimmer article: http://www.nytimes.com/2015/06/02/science/saiga-antelope-mystery-disease-die-off.html?_r=0]
Loved your SNP. In addition to washing produce, only reverse your stomach's HCl when necessary. (Also, the STEC dose is lower than Salmonella.)
Wink Weinberg (Atlanta)
Greetings from sunny Seattle! Where its 21 degrees C with clear skies.
Because you asked...Here are my 2 cents on the whole handwashing situation that has been discussed over the past few episodes.
My solution would be to change building codes to require shared sinks for men/women that are located outside the actual bathroom.
This would ensure compliance because it would allow for policing without violating any privacy issues. It could be especially effective in a restaurant setting where a manager could simply discipline employees they watch leave the restroom without making the required stop at the handwashing station located outside.
Additionally, some peer pressure and social stigma would be enough to guilt people into not skipping the handwashing station. Behavior might change if poor hygiene is on display for everyone to see.
Thanks for the great podcasts! I am a fanatic Twiv/Twim fan and listen to the podcast on my 1 hour commute to my job in a manufacturing lab @ a biotech company.
Long time listener, first time email-er.
Greetings podcast team,
I'm a long-time listener to TWIM and TWIV and if I had a longer commute I would get TWIP in the mix too. Only so many hours in the week!
I am a research tech in Portland Oregon, where our dry mild winter has given way to a gorgeous dry mild spring. Currently 57F and sunny. 2015 to date has been bad for farmers (and skiers) but pleasant otherwise.
I wanted to commend you all for taking on papers and questions outside of your specific areas of expertise, because the conversation that ensues lets us listen in on how you think about science questions.
If you had all the answers at your fingertips it would be highly accurate but of less interest and utility for me at least.
I wanted to weigh in on the mandatory handwashing sign question because I think it is a Trojan horse. Libertarian politicians and letter writers claim they want to see freedom of choice for consumers so free markets can make everyone's lives better but the handwashing argument is a pretty clear tell regarding their true intentions.
Since handwashing is the slightest of inconveniences to the restaurant worker and has no downside for the consumer, it's hard to believe that they are truly driven by their desire to be able to buy a meal at a restaurant where the employees have not washed their hands.
I am convinced until I see some persuasive arguments to the contrary that each time you hear about this free market handwashing topic the real motivation of the person putting this idea out in the culture is to normalize the idea that government in general and regulation in particular is bad, and they really care about their favorite business interest believed to be oppressed by Washington, not oppressed cooks who'd rather have dirty hands.
What I'm really curious is how the independent certification would work. Why are third party monitors watching us wash up better than a government mandated sign? If the government was keeping an eye on us in the bathroom they'd be marching in the streets!
Hello again - I just listened to the Red Queens discussion about iron battles on TWIM 103. Regarding your interest in other occurrences of this phenomenon there is a paper by Roy Jensen et al at http://www.ncbi.nlm.nih.gov/pubmed/?term=24616884 where he discusses in detail the battle for tryptophan between Chlamydia and their mammalian hosts.