Viruses

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

TWiM 65 Letters

Alexandra writes:

Dear TWIM-ers,

When I began listening to TWIV almost a year ago, I had just switched majors from philosophy to biology. I am now writing to you good people at TWIM at the end of my first undergraduate summer research gig, where I have had quite a bit of fun (and frustration) mucking about with wetland bacteria. As I've been reading about all these different Bacilli, though, I've been wondering about species identification among bacteria, and about what it even means to classify bacteria as belonging to different species.

As far as I understand, most of the current work on species identification and the evolutionary history of bacteria relies on comparing the genomes of bacteria, looking for differences and similarities in highly conserved regions and in the presence or absence of accessory genes. My adviser told me that one shorthand for distinguishing between a "strain" and a species is whether or not the genomes of the two bacteria are more than 95% related to one another. This seems like a fairly arbitrary figure to me!

Then, too, some species are very closely related but lead significantly different lives, in different environments. I have had the pleasure of getting to know Bacillus mycoides this summer, but I don't think I would have been able to handle this little bug if it behaved much like its more famous and dangerous relative, Bacillus anthracis. It seems to me that any species classification must take "lifestyle" - metabolism, behavior, environment - into account.

So how do all of you microbiologists think about this notion of "species" - how do you distinguish between a genus, a species, and a strain? Is it primarily down to differences in the genome, or do you care mostly about those differences which lead to substantially different ways of living?

Thanks so much for reading!

Your faithful listener,

Alexandra

Peter writes:

Dear TWiM team I thought that this was worth a mention.

The fungus Chalara fraxinea causes Ash Dieback disease and is killing many ash trees in Britain and Europe, losses in Denmark are believed to be 60% to 90% of all ash trees.

Dr Dan MacLean, of the John Innes Centre in Norwich came up with the idea of crowd-sourcing the analysis of the fungal genome and the genomes of susceptible and resistant trees through a facebook game:
https://www.facebook.com/fraxinusgame

The hope is that the detailed analysis will give clues to the origins of the disease, and help identify fungus resistant ash trees to grow in the future.
Top gamers may have their names published in scientific articles for their role in helping analyse the genetic information. Results of the project will be made available on the crowd-sourcing website OpenAshDieBack.

More on Ash Dieback:
http://www.theguardian.com/environment/2013/aug/13/ash-dieback-facebook-fraxinus-game

http://www.forestry.gov.uk/chalara

http://www.woodlandtrust.org.uk/en/about-us/faqs/your-woods/Pages/ash-dieback.aspx

Andres writes:

Hi TWIM Team,
I love listening to all your shows TWIV, TWIP and TWIM on Stitcher Radio. Thank you very much for the many hours of entertainment and learning.

On TWIM #61 it was mentioned that the body needs gut bacteria to make vitamin K and B. If you have not had a show on these bacteria I would like to suggest that these would make a good show topic.

Keep up the great work!

Thank you,
Andy
Fremont, CA

John writes:

Dear TWIMmers,

In TWIM #61, you talked about a species of insect with a symbiotic bacteria (which itself had a symbiont), and which also had a lot of bacterial genes that had been taken up into the insect's DNA. My understanding was that bacterial DNA and eukaryotic DNA have some differences that make it hard to move between the two. Do those differences cause a problem for movement of genes between insects and bacteria? If so, is there any indication of what has to happen for the gene transfer to work, and how common that is?

At the risk of slipping into TWIV territory, it seems like these endosymbionts would provide a lot of opportunity for infection of the host cell with bacteriophage. Are there examples of phage infecting eukaryotic cells?

Thanks for answering my amateur questions, and for your wonderful podcasts.

--John

David writes:

In TWiM 60 during the email segment, there was a discussion about preservation of DNA in amber. Irregardless of Michael Crichton's book Jurassic Park, written in 1990, DNA preserved in amber has not panned out. Amber, which preserves in great detail the outer structure of insects, rarely preserves any internal material. Essentially, organisms in amber are casts. In addition, amber is porous to air, and air is corrosive to DNA. Searches for DNA in amber have not found much. Early 90's claims of DNA found in amber have been disputed. Vincent may recall my email answered on TWiV episode (I don't remember which one) about viruses trapped in amber. The article was behind a paywall so I was not able to read it, but I'm pretty sure no DNA was recovered.

FYI, DNA from bone has had more success. A recent announcement was made that DNA was recovered from a 700,000 year old frozen horse bone. So ancient DNA recovery is still possible, just not from amber.

See this You tube video by a paleontologist discussing DNA from amber.
http://www.youtube.com/watch?v=anceTKEIOXg


Christyne writes:

Dear Vincent and fellow TWiMmers,

I really love your podcast. My son told me about them, and I have worked my way through the shows. I have been learning SO much.

I recently read that children with folic acid deficiency may have a higher incidence of regressive autism, and it got me wondering about the microbiome and nutrition. I heard Michael and maybe Jo? mention that the microbiome supplies 5-10% of your calories, and I found review articles that include references for that, but I haven't found a good review of micronutrients the microbiome supplies, like the b-vitamins. Would you consider having a TWiM on the microbiome and the nutrition it supplies? Since children with autism often have problematic microbiomes, could it be that they aren't getting the right vitamins at the right times for their brain development? Can the body "ask" the microbiome for more vitamins when it needs them through signaling? Could the microbiome supply much larger amounts of vitamins than we realize? Perhaps there are micronutrients that we don't know of yet because our microbiota supply them instead of our food?

I am interested in the vitamins because of my own story. (You could leave this part out if you want to). I used to be a bioengineer working in microscopy, gene arrays and bioinformatics, but I suddenly got sick with a disabling mitochondrial disease in my mid forties. I could run a mile without thinking about it, then a year later I couldn't sit up for 30 minutes, then a year after that I was going into heart failure. I started taking very large amounts of riboflavin and my heart, which had become enlarged, shrunk back to normal size and started working just fine! Unfortunately my other muscles didn't respond so well, but I'm still alive 5 years later, which wouldn't be the case without the riboflavin. Some of my friends on my mito and FOD (fatty acid oxidation disorder) support groups are also helped a lot by particular vitamins, and it makes me wonder why did it change? I was doing fine for 45 years then suddenly I need a bunch of riboflavin to survive. I'm starting to suspect the microbiome. I like how you think about it as another organ.
Thanks for your great work! Chris

There were various review articles in pubmed related to the microbiome harvesting energy and obesity and diabetes
e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601187/

The folate deficiency in children/autism papers are sort of patchwork, but here is a sampling
http://www.ncbi.nlm.nih.gov/pubmed/?term=folic+acid+deficiency+autism

p.s. I love Elio's voice

(p.s.s. my genetic defects are normally mild ones in nuclear genes affecting fatty acid oxidation and complex 1 of the respiratory chain, so the odd inheritance and aging effects on mitochondrial dna disorders don't really apply to me)

Joe writes:

Dear TWiM folk,

Hi from Denver and ICAAC.

I'm delighted that you are finally devoting the time and attention to the most important microbiology of all--yeast fermentations.

Your letter last week from Mark on yeast inoculations reflects a very modern North American perspective on winemaking. Inoculations with clonal yeast strains are of course quite modern--wine was made for millenia without inoculation.

Many of the finest wines of France, Vincent, are fermented with their indigenous yeasts. A complex microbiome produces a more complex metabolome, unsurprisingly, giving wines of distinct complexity and subtlety of flavor. One man's complexity may of course be another's excess funk in some cases, taste is always paramount.

It is also true that choices in the vineyard may influence the success of native ferments--heavy spraying with fungicides, for instance, surely selects yeast populations. But so does weather during the harvest, tying the wine more closely to its vintage. The requirement of highly alcohol-tolerant yeast to finish the fermentations of high-sugar grapes reflects some climate change, but it also reflects a recent cultural preference in California for riper (and to my taste simpler) fruit flavors that come with grapes left on the vine later in the summer to eliminate "green" flavors and coincidentally raise sugar contents.

I hope I have the chance to wave from the audience at a live TWiM or TWiV this week, and I hope you will continue to give alcoholic fermentation the attention they surely deserve.

Best,

Joe

TWiM 64 Letters

Tim writes:

Vincent and friends,

While driving around a field cutting hay lost in my science podcast playlist the episode of TWIM #61 came up and I had to listen intently as salmonella typhimurium came up as this is a common enteric issue in agriculture. When you mentioned the work around salmonella came up with to outwit lipocalin and the idea people could in many millennia possibly evolve a second antisiderophore to combat it a thought occurred to me. Is modern medicine slowing our rate of evolution by reducing selection pressure for more fit individuals? This is not an argument for withholding medical treatments to improve the human race or something silly like that b/c obviously everyone has more important skills than the ability to fight off an enteric disease but was an interesting thought that hadn't really occurred to me before. Just wondering what you all thought of this.

Also thanks for the TWIP mention of our farm. I'll let you know if there's a TWIP bump like there is for TWIV ; )

If you decide to do an agriculture themed podcast like you and Dickson mentioned I'll be sure to listen to every episode as your opinions on agriculture are always well thought out and enjoyable to hear b/c it's interesting to see the views of very intelligent people that aren't directly in the field. Have a great day I need to get back to putting this hay down while the suns shining.

Tim Zweber
Zweber Farms
www.zweberfarms.com

Sent from mobile device w/ a small keypad, forgive brevity and typos ; )

Click to listen to this episode of TWiM (64) Live in Denver from ICAAC 2013.

TWiM 63 Letters

Hugh writes:

Hi Vincent,

I really enjoyed hearing about Carl Woese in TWiM #50. You mentioned the controversy surrounding of Woese's 1977 discovery of Archea as a third domain of life, as it contradicted entrenched scientific beliefs. Although Archea soon found its way into general scientific thinking, his work brings up another fundamental idea that is still controversial today. It relates to the word 'prokaryote.' Norm Pace, one of Woese's former students, is a strong believer that we need to stop using this word. I think he makes extremely compelling arguments about the harm this word does to basic biological understanding, and thought this could be an interesting discussion point on TWiM. Here are the the titles of two papers by Norm Pace that discuss this issue. They're both geared towards a general audience: Problems with "procaryote" (Journal of Bacteriology, 2009); Time for a Change (Nature, 2006).

I recently discovered TWiM and TWiV and am now an avid listener, mostly while cooking dinner and washing dishes, which always seems like deja vu after a long day of experiments and washing glasswear at the lab. Thank you for making that process infinitely more enjoyable. Writing from Seattle, WA,

Hugh

[we had a brief discussion of this on an early TWiM; Elio if I recall does not mind the term]

Megan writes:

Hi TWIM team,

Could you do a TWIM about the archea and viruses that infect them? It is a fascinating area that doesn't get as much attention as bacteria.


Thanks,

Megan

Jim writes:

Just another update on the hand-washing issue. This link discusses the article, which costs $10 to see at the journal.

Regards,

Jim
Smithfield, VA


Mark writes:

Hello Vincent, Michael, Elio --

I enjoy TWiM, and have listened since episode #1. Keep up the good work and keep going. Out of TWiV, TWiP, and TWiM, I discuss episodes of TWiM with my wife the most!

I am writing, belatedly, to correct some inaccuracies in episode 49 "Grape-like Clusters". These are:

1. Someone, VR?, commented that French wines were the best. This is not FACT, but a matter of taste. The Latin expression "De gustibus non est disputandum" applies.

2. Michael speculated that natural yeast was used to ferment wine. This is a common belief and is mostly wrong. There is a vigorous industry dedicated to selling commercial yeasts to winemakers. A small number of boutique wineries are experimenting with using natural yeast -- these are a minority, and the quality of their results is highly variable.

I am an amateur wine maker of 17 years. See the attached image of a macro bin containing 0.5 ton of Cabernet Franc grapes from 2012. Note the white, powder-like color on the grapes -- this is natural yeast that grows in the vineyard. Note also the stems with missing grapes -- as harvest occurs the growers typically take weekly samples to measure sugar content.

In wine making, after the crush (in which a machine separate the stems from the grape berries, and in which the berries are lightly crushed) potassium metabisulfite is added to the must (the residual grapes & juice) to kill natural yeasts and inhibit fermentation. Typically 24 hours later the must is inoculated with a yeast starter and nutrients. The image of nubile virgins stamping barefoot on grapes to make wine is, sadly, a myth.


Our winemaking group purchases yeast from a company which supplies commercial wineries, Gusmer Enterprises. Attached is their 2012 catalog. Its front and back covers commemorate scientists whose discoveries were key to wine making -- Pasteur, Leeuwenhoek, Riley, or Dewar.


There are subterranean links to virology. Vincent can speak to physicist-turned-virologist Max Delbruck and his seminal work. Did you know that his uncle, also named Max -- http://en.wikipedia.org/wiki/Max_Delbrück_(chemist) -- developed a yeast, Torulaspora delbrueckii, that will live in high alcohol levels? These yeasts are especially important in California because our climate products grapes with very high sugar levels which, through fermentation, produces high alcohol levels.

3. The paper that Michael presented provided a quantitative framework to characterize and measure the differences between grapes grown in different blocks on the research vineyard. As winemakers we see a qualitative difference in each barrel of wine. Rule of thumb: half a ton of grapes = 1 barrel = 24-25 cases of wine. It is too labor intensive to produce and label at such levels, thus wine from each barrel is blended which averages out the different tastes of each barrel.


I have TWO recommendations for listener-picks-of-the-week:

-- to learn about how a Californian coup d'etat established their wines as equals to French wine makers, watch the movie "Bottle Shock" which combines fact and Hollywood sensuality; watch the trailer here: http://www.youtube.com/watch?v=DYs0kblXToA

-- to read more about the entire process of making wines from growing grapes, figuring out when to harvest them, and fermentation I recommend the book "From Vines to Wines" http://www.amazon.com/From-Vines-Wines-Complete-Growing/dp/1580171052


In closing,

in vino veritas

Mark

PS - feel free to use the grape image. The catalog image is technically copyrighted, though I doubt Gusmer would care if you want post it.

grapes: https://docs.google.com/file/d/0B8dwAT4VdQdjRHlIdlFjdVJndVU/edit?usp=sharing

catalog: https://docs.google.com/file/d/0B8dwAT4VdQdjN3RUMHZqcjFjSmM/edit?usp=sharing

TWiM 62 Letters

Robert writes:
In TWIM #60 @1:06:23 Michael Schmidt suggests that glucose for fermentation from biomass is a necessary step in production of fuel ethanol. Fuel ethanol and other low molecular weight compounds can also be produced by autotrophic anaerobic fermentation of syngas. Syngas is a mixture of carbon monoxide, carbon dioxide, and hydrogen produced by pyroclastic treatment of a wide variety of organic material including ligno-cellulose, recycled tires, sewage sludge, and natural gas or methane. These reactions have been studied for many years and are being commercialized by Coskata. www.coskata.com.
Never underestimate the ability of microbes to scrounge a living from nearly any environment with water and energy available.

Tim writes:

I am a Canadian, here in the USA attending graduate school. Occasionally I hear hints in Michael Schmidt's language that he might be a fellow Canuck (words like "university" and "zed", and of course his impeccable class and intelligence). Michael, thinking back I'm not sure you've revealed anything about your past prior to your days in Indiana (at least not in the TWiMs I've listened to - I'm still working through them). If this is on purpose I respect that decision (I don't mean to pry into personal lives) - I was just curious.

Happy TWiMing!

- Tim

Juan writes:

Hi, i'm currently a Bioinformatics and Genomics Phd student at Penn State with a masters in Computer science and statistics. I'm currently working in antibiotic resistance in bacteria. I'm almost up to par with twim and i'm very grateful for your insightful discussions and the time you put in teaching everyone. This has been a great foundation for my microbiological knowledge. Keep up the good work.

I recently had the good luck to meet Dr Jo Handelsman during a distinguished talk here in my department.

I'm also a listener of twiv and twip, but not as often as twim.

Anonymous writes:

Last year, I started teaching microbiology for students interested in health-related fields. I caught up on all past TWiM episodes to help prepare me for teaching. I have learned so much from the podcasts, and so much what I already knew has been reinforced! In particular, the recent mention of conjugation experiments brought back happy memories, since I worked on a self-mobilizing pathogenicity plasmid for years. Listening to TWiM has an added benefit, since my students think I'm much smarter than I really am. :-)
I'm from another country and a few days ago, I was talking to a colleague (also from another country), and we discussed our shock when we first came to the US and found that everyone who works in health care can simply go home in their work clothes. In fact, they almost seem to wear their scrubs as a badge of honor (Do you see my scrubs? I do really, really important work!). It is my impression that many cases of nosocomial infections are associated with health care staff (consider that renovating an entire building wasn't enough to get rid of Klebsiella, which was probably brought back in on the first day of re-opening by the staff). The staff carry these bacteria, fungi, and viruses in their noses, on their skin, hands, and clothes around with them. They leave work, stop to buy groceries on their way home, pick kids up from daycare/school, and take their clothes home and wash them with the rest of their household laundry.....
In a number of other countries, health care personnel have to change in designated rooms at the facility. Their uniforms have their names sewn in, or embroidered on, stay behind at the end of the day, and are properly washed by the facility itself. Personnel can (and sometimes are required to) showers before they change into their regular clothes and leave the facility.
Maybe I'm missing some crucial piece of the puzzle, but it seems like a relatively inexpensive and effective way to limit spread of antibiotic resistant bacteria to the general community. It may also have a positive outcome on the spread within the health care setting. I would appreciate it, if anyone on the podcast could comment on this.

Tim writes:

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

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

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

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

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


Jennie writes:

Jennie Williams (RN) here - I've just seen something from Medscape that I thought you'd be delighted to know. An offering of clinical guidance on a successful recipe for Fecal Transplantation (bio-transplantation) for C difficile. Historical background on Fecal Microbiota Transplantation and a picture of success beyond C Dif to inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), idiopathic constipation as well. Fecal Transfer appears to work for C Dif that relapses as well.

Aside from fairly direct fecal transfers - this synthetic poo is described:
Elaine O. Petrof, MD, assistant professor, Department of Medicine, Infectious Diseases, Kingston General Hospital, Queen's University, Ontario, Canada, and colleagues created the human synthetic stool mixture by culturing the stool microbial diversity of a healthy 41-year-old woman and brewing a mixture of 33 different intestinal bacteria isolates in pure culture. They named the synthetic stool mixture RePOOPulate.

The bacterial mixture was infused into the colon of 2 patients in their 70s, both of whom were infected with a hypervirulent strain of C difficile, ribotype 078, and who had failed at least 3 courses of antibiotic therapy.

Both patients returned to normal bowel patterns in 2 or 3 days and remained symptom-free for 6 months. At that time, rRNA sequences representing the RePOOPulate mixture made up 25% of the gut bacterial population.

This link should get you to the right place.
http://www.medscape.com/viewarticle/779307

Thank you once again for making the world safe for microbiota Vince and friends!

Yours with warmest regards
Jennie

TWiM 61 Letters

Nate writes:

Hi my name is Nate. I am a senior in high school aspiring to become a microbiologist. I heard about this podcast through a class I took on biotechnology and have been listening for about 2 months. I really enjoy it and the other two shows even if I don't quite understand everything you talk about, but I grasp most things. So a few weeks ago I attended a biotechnology summer academy for high school students where we study one certain topic for three weeks with a professor at the college it was at. My subject was about the microbes that make up the stromatolites in the Great Salt Lake and why it's important that we understand it. I learned that they are made of Cyanobacteria and certain types of archea. The Cyanobacteria don't really make sense because they don't have a very high salinity tolerance, especially as high as the GSL which is 33% at parts of the lake. But yet they are there. I also learned that the rock is formed by the waste of the microbes which is calcium carbonate. These rocks have the potential to help with global warming. I'm not saying that I agree with the idea of global warming or not, but it is happening a little bit. So that brings up the question, Can we harvest and "grow" these rocks in a lab until they are big enough to put into the wild to "catch" some of the carbon dioxide in the atmosphere? I would like to hear your input on this subject as I didn't have a lot of time at the academy to study it. Thanks

[I asked Hazel Barton, here is her reply]

Actually this is a pretty good question and a number of folks have thought
about microbial CO2 sequestration in just this way.

Many of the carbonate rock deposits (limestone) from about 360+ million
years ago were formed during high periods of CO2, and we believe the CO2
was sequestered as rock by microbial activity. It dropped the atmospheric
CO2 levels and preserved it in a form that is obviously stable over
geologic time scales.

The problem we have today is the ion. To precipitate CO2 as carbonate,
you need a divalent ion. In the ancient oceans, there was plenty of
calcium around, so it was deposited as calcium carbonate (limestone).
Unfortunately, that easy source of calcium has been exhausted, so the
problem comes in generating the ion for the carbonate to precipitate. It
takes quite a bit of energy to do synthetically, so there's no net loss of
greenhouse gases. If someone could come up with a handy ion, generated
from a more passive process (such as decomposition in garbage), then we
could certainly sequester CO2 this way.

A good PhD project!

The stromatolite question is quite a bit more complicated and has to do
with the saturation index of carbonates in seawater when the CO2 levels
drop (from photosynthesis) - I can elaborate on that more if you need, but
the ion is still problematic.

Hazel


Jim writes:

Hi guys,

This Google Plus community knocks off socks when just skimming through the photos/captions! Don't want anyone to overlook it.

Jim
Smithfield, VA

Robert writes:

In TWIM #60 @1:06:23 Michael Schmidt suggests that glucose for fermentation from biomass is a necessary step in production of fuel ethanol. Fuel ethanol and other low molecular weight compounds can also be produced by autotrophic anaerobic fermentation of syngas. Syngas is a mixture of carbon monoxide, carbon dioxide, and hydrogen produced by pyroclastic treatment of a wide variety of organic material including ligno-cellulose, recycled tires, sewage sludge, and natural gas or methane. These reactions have been studied for many years and are being commercialized by Coskata. www.coskata.com.

Never underestimate the ability of microbes to scrounge a living from nearly any environment with water and energy available.


Jesse writes:

Hello TWiM team! Thank you for the hours of entertainment and education you provide. I have a somewhat morbid question for you that's fairly random--I forget what inspired it exactly--but it has been bugging me: normally when an animal dies, it decays, but what happens if that animal is totally free from all microbes? So, what happens if a germ-free mouse dies in a sterile environment and no one disposes of it for a while? Does it decay somehow, or just dry out maybe?

Thanks again for all you do,
Jesse

TWiM 60 Letters

Kelly writes:

I’m reeling from this episode!! The symbiosis, the web of life, the energies, chemicals, organisms of
evolutionary progression shaping our world naturally and by human intervention with unknown consequences, then you all tie it to the brain microbiome alterations affecting behavior! Yes!!!
A recent quote from a researcher says soon we’ll call our immune system the bacterial interaction system!
Yes! The microbes rule our world and us. God is bug. Oh the heresy!
This is what we see with inflammation therapy…bugs rule even if you can’t culture them with Koch’s postulates.
I have a Talmudic question:
If most alphaproteobacteria are phototrophic, and the brain doesn’t get sunshine, does vitamin D endocrine system dysregulation have an effect on their population in the brain?

Vitamin D hormone transcribes the AMPs to balance our bugs. https://chronicillnessrecovery.org/images/stories/How_Vitamin_D_Metabolism_Affects_Autoimmune_and_Inflammatory_Diseases2.pdf
Why we use olmesartan to correct vitamin D dysregulation.
Angiotensin and Systems Thinking: Wrapping Your Mind Around the Big Picture
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603174/

thank you!!
Kelly

[the following email was sent to TWiP but I think TWiM listeners will like it]

Joe writes:

Vince and Dickson,

Here is a follow up on your biofuels question. To make fuels from crops succeed we need a biotech breakthrough that I really thought someone would have done already. Basically we need a bug that eats cellulose and converts it back to sugar so you can ferment it. Personally, I think there is a Nobel Prize in it for the group that creates an e. coli strain that converts cellulose to sugars. Once you have that, then you can feed the farm animals the corn and run your tractor on the corn stalks! Or you could use hay or grass clips or wood chips or waste paper, whatever is available cheaply. Until we get that bug, ethanol from corn will just be a niche technology.

People will keep pushing to use corn crops or other high sugar crops to make fuel, but the economics are not good and the lost opportunity costs are too high. Look how the modest current efforts in the USA have pushed up food prices and still required government subsidies to be competitive. No doubt there is a listener out there with lots of arguments for how great ethanol from corn is but I don't see anything like the margin needed to make it a viable market changing crude oil substitute.

I will show my age and tell you that as a senior chemical engineering design project in 1980 at Purdue, we looked at how to convert crop waste materials (like corn stalks) into fuel and it wasn't pretty. The only real way to break down the cellulose was to grind it up and treat it with hot fuming sulfuric acid in big reactors. Fuming sulfuric is 98% concentrated acid that is saturated with sulfur trioxide gas, brute force chemistry for sure! As I remember, you could get pretty good conversion of the cellulose, but the ugly part was separating the good stuff from all the waste acid and the non reactive lignin. Once you got all the acid out of the good stuff, then you still had to ferment the sugars. It is not surprising that you don't see anybody running this process to make fuel! We need a biotech solution to break down the cellulose without all the mess. I think folks were looking at the microbes in termites' stomachs as a place to start., but I have not heard of any progress on this in several years.

I will add that biofuels are not the only option for our fuel supply. For the past 100 years, we have had repeated dramatic reports that we are about to run out of oil and yet it never seems to happen! I remember a particularly detailed one in Scientific American about 10-15 years ago with beautiful graphs and everything. Each time the trumpets of doom sound, some smart engineer or geologist comes up with a new way to extract more oil. I don't see any reason why this trend will suddenly stop this time, we still have lots of tar sands, deep oil, and shale oil that have not been touched. Please note that I am not expressing a political view on the social correctness of these options just the technical aspects. Even more impressive are the reported quantities of frozen methane hydrate clathrates on the ocean floor that would likely be fairly easy to extract. Some estimates are that there is more than 10 times the amount of energy stored there than in all the oil we have ever used. Obviously none of these fossil fuels address the CO2 generation concerns that many people have.

Wind, solar, hydro and even nuclear power all have their places and I hope their niches keep growing as the technology improves, but nothing comes close to competing with chemical energy as a cheap, portable, high density source of energy. One just needs to look at biology to see the truth of this; plants fix the suns energy into chemical forms that then cascade through the food chain ever evolving into more complex forms. How cool is that!

Thanks for helping me stretch my brain each week! Thus ends "This Week in Chemical Engineering"!

Warmest Regards,

Joe Griebstein
EH&S Manager, LSG

Robin writes:

How about phage fossils?

Now that we know that phages have an apparently symbiotic relationship with mammals, is it too farfetched to imagine that some phages were once incorporated into - and expressed - in metazoa?

One line of research might be a search for such fossil sequences in the genomic databases that already exist. Perhaps someone is already doing it?

The reference to salicylates in my last email was prompted by Dr. Schacter's comment that methyl salicylate reminded him of acetylsalicylic acid, and to show how the acetyl group was important in the clinical effects of the latter.

Thanks for such thought-provoking and paradigm-shifting discussions!

TWiM 6 Letters

Don writes:

I was intrigued by the comments on the antimicrobial effects of Cu, having used silver sutures in contaminated cases in the 60s. It struck me that an easy and cheap test would be to copper plate [which uses very little ] the door .faucet and toilet handles in an ICU  and see if the Hospital acquired infections changed. This is fairly low tech requiring a screwdriver, a auto battery and some CuSO4 [root killer.] or could be done by many firms who do it commercially. Thanks for the really good podcast

zowawih writes:

Hi, I am a big fan of your great education/entertaining programs. I would like to suggest Vincent to invite experts in antimicrobial resistant bacteria in his newly launched TWiM program. This problem is very serious and thus the WHO themed their day with the antibiotic resistance issue. Likewise the CDC chose a week on September last year to address the devastating health related issue. Inviting Experts and pioneers in this field will highlight and explain queries.

Chris writes:

I recall hearing about a bacterial contamination of cantaloupe years ago, which is when I started to wash them in soapy water before slicing.

Of course, I try to follow the rules. We actually cut meat products on the counter between the stove and sink, and the rest on the kitchen island to prevent cross contamination. Often I will prep for cooking by cutting the veggies on a dishwasher proof cutting board on the island, put them in bowls and set aside. Then move the cutting board to the counter, cut the meat and either put it in the bowl or the pan. Then put the cutting board in the dishwasher, set the knife to be hand washed next o the sink. Then cooking is quicker because I have everything ready, using a food safe mise a place.

The other day I was watching an old cooking show with Julia Child. I just about gagged when I saw the other chef she was working with put an herb stuffing between the breast and skin, and then reach over to pick up salt from a bowl with his fingers without washing his hands or using a spoon!

I have a TWiM idea from watching cooking shows, especially one that showed all of the varieties of salt: pink salt, which gets its color from an extremophile bacteria (a tidbit I want to share at the local upscale kitchen store when I get a chance!). Oh, cool, just checking the halophile wiki, I learned they are essential for some fermented foods like soy sauce, sauerkraut, anchovies, etc: http://en.wikipedia.org/wiki/Halophile

Frank writes:

First:  Thanks for making a career of TWI-Podcasts!  A great service and an entertaining and educational format.

In TWIM #1 you reviewed the antibacterial properties of copper and it’s potential for control of MRSA compared to other methods being pursued.  While the science of antibiotic mechanisms is fascinating, we may be blinded by the technology instead of understanding the logic of the problem.  The references below are a few of the many showing (not surprisingly) that the people who spend their days around hospitals are the reservoirs for MRSA.  Anywhere from 6% to 21% of healthcare workers (in this case anyone working in a hospital) have been shown to carry MRSA in their nares.  This is higher than the rate in incoming patients.  Remove the reservoirs and control is much easier!

While we are great at technical solutions, we are close to powerless at social, particularly politically social solutions.  It would seem that a major reduction could be achieved through regular testing of healthcare workers (<$10 & <24hrs) to identify carriers, their removal from patient care, treatment with mupirocin (I believe topically) and return to patient care.  Hospitals object to the cost of testing although as carriage rates decrease so would costs.  Unions object to the potential unpaid removal from work during treatment as well as the treatment cost.

Doctors generally refuse to be tested, even for hepatitis or HIV.   Despite the enormous monetary cost of MRSA to hospitals and to our overall healthcare system, plus the unnecessary deaths, our society insists that “magic bullet” pharmaceuticals and antibacterial hardware are the only way to solve this problem.  Pogo had it right about “the enemy”.

Thanks again for the education and entertainment.  Vincent and your TWIV, TWIP, TWIM teams are an exceptionally bright spot in scientific education!

Best regards,

Frank Shinneman,

NY, NY

 

Prevalence and Characteristics of Staphylococcus aureus Colonization among Healthcare Professionals in an Urban Teaching Hospital infection control and hospital epidemiology june 2010, vol. 31, no. 6

Prevalence of Staphylococcus aureus Nasal Colonization in Emergency Department Personnel Annals of Emergency Medicine, Volume 52, No. 5: November 2008, p.525 – 531

Incidence and Prevalence of Methicillin-Resistant Staphylococcus aureus Nasal Carriage Among Healthcare Workers in Geriatric Departments: Relevance to Preventive Measures INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY  Vol. 24 No. 6, p.456-458

How Often Do Asymptomatic Healthcare Workers Cause Methicillin-Resistant Staphylococcus aureus Outbreaks? A Systematic Evaluation infection control and hospital epidemiology october 2006, vol. 27, no. 10

Successful Control of Widespread Methicillin-Resistant Staphylococcus aureus Colonization and Infection in a Large Teaching Hospital in The Netherlands infection control and hospital epidemiology august 2007, vol. 28, no. 8

TWiM 59 Letters

Oscar writes:

This is the greatest TWiM ever. (#58)

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

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

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

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

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

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

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

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

Thanks for the great TWiM!

Oscar Prill
Technology Director
Lionsgate Academy


Mark writes:

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

But this is not the reason I am writing.

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

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

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

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

Keep up the good work!

Cheers

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

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

Robin writes:

TWiM #58: The brain microbiome

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

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

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

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

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

Eli writes:

Hi Vincent et al!

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

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

Quote from the episode:

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

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

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

Joe writes:

Hi guys

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

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

Cheers,

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

Dave writes:

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

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

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

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

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

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

dave

Tim writes:

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

- Tim

Bernadeta writes:

Dear TwiM podcasters,

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

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

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

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

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

Regards,
Bernadeta

Andy Camilli writes:

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

-Dr. Camilli

Charlotte writes:

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

Peter writes:

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

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

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

Jim writes:

Dr R:

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

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

Regards,

Jim
Smithfield, VA


Jim writes:

Hi Y'all,

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

Thanks.

Jim Vandiver
Smithfield, VA

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


Peter writes:

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

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

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

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

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

Regards


Jacob writes:

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


Jim writes:

Hi,

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

Jim
Smithfield, VA

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