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TWiM 133 Letters

Arthur writes:

Hello TWIMers!

I'm a graduate student working in mycoplasmology and I  must say I've been overjoyed to hear the past few episodes mention our tiny friends!

Elio's mention of their unique mechanism of moving ("Gliding Motility") made me think of a recent paper from the group in Japan under Dr. Miyata - you may find the paper quite interesting (attached)! They've done a lot of work on mycoplasma motility, and local US researchers such as Dr. Mitch Balish at Miami University also have made great advances in this field.

In discussion of the Mip/Mib system, one thing that has caused some head scratching in our lab has been why the microbe cleaves the Fab portion rather than the Fc? The human species (M. genitalium and M. pneumoniae) don't have the serine protease (at least based on homology searches) and bind to IgG nonspecifically - it makes you wonder why the microbe has conserved that binding protein? Quite a neat area that needs more work!

Thanks for such an interesting podcast and keeping me preoccupied during my hours in the mouse facility!

Warmest Regards,

Arthur

https://www.ncbi.nlm.nih.gov/pubmed/27073090

Frank writes:

Dear Drs. of TWIM,

Two observations on pili conduction.

TWIM #51 featured Hazel Barton discussing her discoveries of microbial excavation of caves.  Barton’s comments on the role of Geobacter electron transport in speleogenesis would be very interesting.

Secondly bio-batteries would seem to be far ahead of their time.  These energy sources that are so valuable to low C/V biological systems are likely not going to be useful in our crude, relatively high C/V electronics.  I have to imagine that our current electronic technology will eventually discover and utilize biomolecular processes to accomplish computing and communication.  At that time, bio-batteries will come into critical use and we can start to approximate the complexity and elegance of multicellular organisms.

August Gloom pervades the northern California coast where the temperature is Ugh point 7 (15.5C) and the humidity is only a optical tease of much needed falling water.
Thanks for all the education.  Your importance can’t be overestimated!

Best Regards,

Frank
Aptos, CA

 

TWiM 132 Letters

William writes:

Hi TWiMers;

It is a nice late July evening here in Berkeley - 60F/15.5C - no fog, but we have had a bit less than usual summer fog this year.

Ran across this article which is fascinating  because it falls into the category of "what you thought was obvious, in fact is not."

"Lichen: Apparently Happy Couple Really A Threesome"
.......
"Lichens come in two basic flavors. One forms a thin, film-like layer on rocks and trees. The other kind is composed of "macrolichens" that grow big leafy, branching or vine-like structures. It's the latter that seem to harbor the yeast.
The discovery started when Toby Spribille, a postdoctoral fellow in McCutcheon's lab, was studying two lichen species collected from the mountains around the Missoula, Montana campus - Bryoria fremontii and B. tortuosa. The two species are distinguished by the presence of vulpinic acid in B. tortuosa, which also gives it a yellow colour. However, genetic tests showed that the known fungus and alga in both lichen species were identical.
But Spribille and McCutcheon found the genetic signature of a third species - a basidiomycete yeast, present in both of the lichen species but more abundant in the yellow version. They and their colleagues went on to test 56 different lichens from around the world, and found each had its own distinct variety of basidiomycete yeast."
See "Lichen: Apparently Happy Couple Really A Threesome"http://www.science20.com/news_articles/lichen_apparently_happy_couple_really_a_threesome-177105
Bill (William) Johnston
Berkeley, CA

Anthony writes:

https://www.theguardian.com/science/blog/2016/jul/27/lets-celebrate-150-years-of-beatrix-potter-author-scientist-and-fungus-lover

:...
Until quite recently, Potter’s accomplishments and her experiments in natural science went unrecognised. Upon her death in 1943, Potter left hundreds of her mycological drawings and paintings to the Armitt Museum and Library in Ambleside, where she and her husband had been active members. Today, they are valued not only for their beauty and precision, but also for the assistance they provide modern mycologists in identifying a variety of fungi.
In 1997, the Linnean Society issued a posthumous apology to Potter, noting the sexism displayed in the handling of her research and its policy toward the contributions of women.

Christoph writes:

Dear TWiM overlords (in a gender neutral way)!

Michael had a very interesting interpretation of what coccolithophores were, when commenting on Kyle's letter in TWiM 131!

He correctly identified two out of the three Greek/Latin words in there, but that steered him in a in funny direction, as he thought they were rock eating cocci and not Haptophyte algae.

Let's see what I can remember from learning two dead languages in "Gymnasium" (German grammar school):

Cocco-litho-phore consits of "cocco-" from Greek kokkos = berry (score Michael) , "-litho-" from Greek lithos = rock (score Michael) and "-phore" from Latin ferre = to bear / to carry (this one Michael got confused with trophos = feed)

So Michael turned the "Cocci-Rock-Bearers" into "Cocci-Rock-Eaters". Close, but no cigar!

Indeed the, the "Cocci-Rock-Bearers" got their name from carrying tiny scales of calcium-carbonate, the coccoliths (I presume this was close enough to be called "rock" since their fossilised remains makes those impressive cliffs of Dover in the UK). Their ability to turn carbon dioxide into calcium carbonate combined with their high abundance in temperate oceans makes them highly important to the global carbon cycle, but unfortunately also highly susceptible to ocean acidification. One of their prettiest members Emiliania huxleyi has even been featured on TWiM before (TWIM 34 https://en.wikipedia.org/wiki/Emiliania_huxleyi).

Hope I didn't screw this up too badly and embarrass my former Latin/Greek teachers...

Keep up the great work, the TWiX empire is awesome!

Maybe you could feature more free living eukaryotic microbes (and their viruses)?! It seems like they get lost somewhere in the gap between TWiM and TWiP, but their rare appearance is always a delightful listen (like TWiM 94)!

Chris

PS: The weather in Vancouver BC is currently 21˚C, 73% humidity, 0% chance of precipitation and apparently pretty windy with 29km/h (although a quick look out the window can't confirm this..)

 

TWiM 129 Letters

Steven writes:

Dear Vincent et al,

Firstly, congratulations for keeping up such a wide range of thought provoking podcasts, and maintaining such a tremendous output. I find they all leave me with more questions than answers, which is, I think, a sign of good science.

On the latest TWiM, I listened with fascination to Elio's round up of species able to manage without mitochondria (I wonder: will Wolbachia ever be reduced to the status of organelle?), but then I found myself feeling decidedly uneasy as I listened to the review of the paper on using a phage lysate as a novel antibiotic against bacteria.

Our 'traditional' approach to antibiotics (and, indeed, anti-cancer drugs, and pesticides), through simply prospecting for active chemicals in the environment‎, and then using them in a haphazard way--both through the profit motive, and misuse--has, in every case, led to the development of resistance and the danger of a return of morbidity to pathogens long thought 'tamed'.

Isn't it time we learnt our lesson?   This new attack on the natural resource offered by phage, clearly shows that we have not. By all means, search for an active phage, but, for all our sakes: don't go spiking its guns!

I found myself with a sense of deja vu as I recall my concerns when B.t. products began to be used as pesticides, even though the live bacteria had long been used as a proper biological control--no patent fortunes to be made in that, of course.   

Using the natural process, bacteria multiply in the target species and destroy it from within: using bacterial products as sprays that don't multiply, the pest may or may not absorb a lethal dose, and resistance is much more likely to develop (Applying it via the GM route, pests are still able to sample a leaf, and reject it and go somewhere else: not so if they had swallowed whole bacteria.).‎

No doubt, resistance develops more slowly in insects than with the case of antibiotics and bacteria, but I think that the end result is inevitable: a useful living biocontrol has been rendered ineffective, due to our obsession with finding the active ingredients of everything and using them 'pure'.  (The same thinking was applied to the food industry when 'nutrition' kicked off in the 19C and gave us white bread and sugar, from which we still have not recovered.)

Whilst prospecting for antibiotics has been recently given a second chance through the new methods of cultivating bacteria‎ 'in the wild', it seems clear that there is every intention of going on with 'business as usual', mass producing every new find, and then cashing in until resistance develops.

Meanwhile, other countries have, apparently, been using the much more logical approach, of letting whole phage target, and destroy, pathogenic bacteria, all along.   Why are the 'Westernised' countries not pursuing what would seem to be a much more likely way to  combat bacterial drug resistance than carrying on the way we have been?  [Presumably the drug cos don't see fortunes in that approach.]

The rather lame 'excuse' seems to be that us fussy 'Westernised' people would not accept 'live' viruses inside us, whereas we don't mind poisonous chemical drugs. I think that the willingness with which we shovel 'probiotic' yogurts, and even consider stool transplants, demonstrates that it would not be so difficult to market phage as the next big natural medicine--And in this case, it really would be medicine!

Undoubtedly, phage therapies will have their own intrinsic problems to overcome--getting around our immune defenses for one--, but the fact of their quite long history of use shows that ways have been found.   So: What right do we, who have squandered all our 'magic bullets', have to start stripping down the medicinal phages used by other nations, to their basic components, in order to extract and squander the magic from them too?  

What we witness in the phage lysate paper discussed on TWiM, is the start of an assault on the essential medicinal resources of other nations, that could saddle them with pathogenic bacteria made immune to their natural phages, and, leave them and ourselves powerless to fight disease.   And, in a worst case scenario, we might even upset the entire balance between phage and bacteria that has kept the latter under control for billions of years.

I am, of course, only a lay observer of all this, but it rather strikes me, that playing loose and free with the essential tools and weapons with which phages prevent our world from simply piling up with bacteria, when we know that our own methods always result in resistance‎, is a much more dodgy thing to contemplate, than all those 'gain of function' experiments we argue about.   These, indeed, could be called 'loss of function' experiments, because, used the way we know they will be used, they, indirectly, could result in the reduction in effectiveness of some of the most vital housekeeping components of our ecosphere.

I hope I'm wrong, but I think history is on my side.

Sincerely,

Steve
Bedfordshire
England.

Ben writes:

Dear Twimers,

I recently discovered your excellent podcast and have been going back through your archives discovering many gems. My favorites so far include the discussion about the Bobtail Squid with Margaret McFall Ngai in TWiM #10, the discussions of Ehux in TWiMs #34 and #37 and the discussion of Centenulid Flatworms in TWiM #21.

I'm an artist and have no scientific training so I listen without expecting to understand everything, but when things get a little too technical I'm always sure that you all will bring the discussion back around to a point that I can readily understand. This is something I really appreciate so thank you for your effects to clearly communicate the intricacies of the fascinating and exciting world of microbial science.

I recently came across this paper that I thought might be of interest

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144270

This is an example of a substance that is generating what seems to be a beneficial alteration of the gut microbiota. I found it particularly interesting that the species involved is Akkermansia muciniphila-one that regulates mucus in the gastrointestinal tract. Given that the mucosal lining of the intestine is an important area for communication between host and microbe I wondered whether the ecology of the intestinal mucosa might be in interesting subject for a future TWiM.

Kind Regards

Ben

Sydney, Australia

Anthony writes:

Experimental evidence of a symbiosis between red-cockaded woodpeckers and fungi

http://rspb.royalsocietypublishing.org/content/283/1827/20160106

 

TWiM 128 Letters

John writes:

Dear TWIM Team,

First of all, thanks for the supremely informative and entertaining podcast. As a biologist who stumbled into my passion for microbiology almost by accident (as a student, I began my research as a herpetologist and was converted while working with the cutaneous microbial assemblages of woodland salamanders), your podcast serves as a primer for many topics that would otherwise require hours of comparatively boring research.

One trend that I hear often repeated is that every microbiology student can't hope to be a PI in an academic lab, which is very true. I currently work in the R&D department of a small biocatalyst company, and wonder if more attention shouldn't be paid to careers for microbiologists in the private sector. While R&D doesn't afford one the same sort of research freedom that academia can boast (I have had to leave numerous interesting but commercially irrelevant questions relegated to the margins of my notebook), it does give you the opportunity to research a variety of interesting aspects of applied microbiology.

There are a few research conferences coming up this year, namely the Society for Industrial Microbiology and Biotechnology (SIMB) annual meeting (http://www.simbhq.org/) and their more specific Recent Advances in Microbial Control (RAMC) symposium (http://simbhq.org/ramc/). Perhaps the list of topics might provide the basis for a TWIM exploring some of the applications of microbiology in agronomy, animal husbandry, bioremediation, wastewater treatment, and other areas. Academic and clinical microbiology seem to get all the attention, and perhaps deservedly so, but there are other options out there for a microbiologist open to branching out.

Thanks again for the fantastic podcast, keep up the great work.

Best Regards,

John

Ross writes:

Hey TWiMers. I very much enjoyed your discussion of the content of pro-biotics a couple weeks ago. It was interesting to me as previous research I have seen indicated many of those probiotics had little effect on the microbiome, or even had very few live bacteria reaching the gut. Certainly the consensus seems to be they are not very helpful as a health product. But the fact many of those products contain what they claim for the most part was enlightening. This latest research out of Copenhagen may be of interest to you, it seems to further cement the idea that these products are essentially worthless as health supplements. I wonder how this compares to the TWiMers assessment of the current literature? https://www.theguardian.com/science/2016/may/10/probiotic-goods-a-waste-of-money-for-healthy-adults-research-suggests
 
P.S I applied to be a communication ambassador this year for the Australian Society of Microbiology and am very excited to have been successful. I would love TWiM listeners to follow me @rossbalch and the society @aussocmic and keep up with my adventures in my PhD in respiratory virology as well as sharing and talking about the latest in microbial science throughout the year.
 
Regards, Ross Balch
BAppSc(MedSc), BAppSc(Microbiol), BBiomedSc(Hons)
 
School of Biomedical Sciences
Queensland Institute of Technology
Centre for Children’s Health Research (CCHR)
Institute of Health and Biomedical Innovation (IHBI)

Hunter writes:

Greetings!
 
I came across this article today and had to share it. I wasn't sure which show to send it to, as the microbe described is related to Giardia and Trichomonas, but I figured TWiM was still more appropriate than TWiP.
 
Surprise! This eukaryote completely lacks mitochondria:
http://phys.org/news/2016-05-eukaryote-lacks-mitochondria.html
 
The article mentions that they're using sulfur with a system acquired from bacteria to replace the mitochondria, and that the researches want to try to find when the mitochondria were lost. However, I didn't see anything mentioning evidence that mitochondria were ever there.
 
Is there some evidence that the microbes used to have mitochondria but lost them, or is it just assumed that they must have had them at some point and lost them?

It seems to me that it would be possible that some microbes could have evolved similar traits to other eukaryotes without having taken up mitochondria.
 
I also was thinking about the possibility that two organisms could evolve to have similar looking genomes completely independently of each other simply because similar pressures in different places could cause similar genetic patterns to emerge. The result being two organisms with one or more major differences that appear far more closely related than they really are.
 
With ongoing increases in information that we can gather about organisms, it seems like our current system for categorizing life is becoming less and less able to accurately represent the way different organisms are connected. When I was in school (not too long ago) we were taught to remember the hierarchy of life using: Kings Play Cards On Fat Green Stools, but this system only goes down to the species level, which seems to leave out at least one level of categorization out.
 
If the finding that this eukaryote doesn't have mitochondria, which seems like a pretty major difference to others, I would expect to see a new tier added between the currently existing top level eukaryote category and all the current sub-categories that splits the mitochondria and non-mitochondria having eukaryotes, with the currently existing eukaryotes mainly existing under the new mitochondria having category.
 
With current technology, it seems like it would be more efficient to focus on cataloging organisms and their traits and thinking of them as a relational database where you look for things based on one or more traits with less focus on trying to specifically build a family tree like hierarchy that can be more difficult to adjust to fit new information. For example, with a trait based model, a new finding like this would simply become a new attribute on any appropriate organisms. This, in turn, would cause said organisms to be listed if you were querying all organisms that were both eukaryotic AND lacking in mitochondria without needing to change the categories, or make changes to any other organisms.
 
With that kind of data, it seems like constructing a hierarchy could be done programmatically, at regular intervals (annually, for example) and with all the needed changes to make sure all life on the tree is at an appropriate level (and that there are enough levels).
 
Anyway, I don't know if most of this sounds like the rambling of someone that clearly doesn't have a background in biology, but I figured I'd share some of the thoughts I had after reading the article.
 
Hope all is well back East. It's currently 24C and partly cloudy here in Irvine, CA with a 51% chance of rain that I'm sure we won't see.
 
PS: For the hardcore condition fans:
It feels like 24
Wind is out of the SW at 14km/h
Visibility is 16.1km (not counting the fact that between walls and other buildings I probably can't see more than 100 meters.
 
____________________
Hunter Curren
QA Analyst 3 : Hearthstone
Blizzard Entertainment

William writes:

An interesting anomaly that you might be interested in discussing:  A eukaryote without a mitochondrial organelle
A. Karnkowska, et al. A eukaryote without a mitochondrial organelle. Current Biology. Vol. 26, May 23, 2016. doi: 10.1016/j.cub.2016.03.053.

 

TWiM 127 Letters

Stefan writes:

Just discovered this nice episode.
Well made and nicely discussed comment on our pack-hunting paper; quick reply to the question what would happen if you add one single amoebae: it would multiply and a clonal pack would do the same thing as observed (they were actually grown from clonal cultures).
But let's say if only one amoeba was existing before trapping the nematode- no idea if that would be able to kill it alone - would be a nice side study!
very interesting hypotheses you came up with, we should study some of it
Keep on with this great work!
Stefan

Anthony writes:

Branchial nitrogen cycle symbionts can remove ammonia in fish gills

Just looking at the abstract, I wonder if the relationship really is commensal.  Without the bacteria in the gills, won't the ammonia still be carried away from the fish?
# # #
Branchial nitrogen cycle symbionts can remove ammonia in fish gills
http://onlinelibrary.wiley.com/doi/10.1111/1758-2229.12407/full

Abstract
Knowledge of the mechanisms by which fish excrete their metabolic nitrogenous waste and insights into nitrogen cycling in aquaculture systems is of utmost importance to improve the sustainable commercial production of fish. In fish, most nitrogenous waste is excreted via the gills as ammonia, a potentially toxic nitrogenous compound. In this study; activity assays, physiological experiments, molecular analysis and microscopy were used to show that the gills of fish harbor a unique combination of hitherto overlooked nitrogen-cycle microorganisms that can theoretically detoxify excreted ammonia by converting it into inert dinitrogen gas. By doing so, these microorganisms may benefit from the ammonia supply by the host and prevent the build-up of this compound to toxic concentrations. This novel relationship between vertebrates and microorganisms may shed new light on nitrogen handling by ammonotelic fish species. This article is protected by copyright. All rights reserved.

And

Copper pajamas?

http://www.mrsaidblog.com/2016/03/04/copper-pajamas-an-18-year-old-school-girl-beats-scientists-to-a-mrsa-remedy/

"...
So by the time Gemma was in the hospital fighting for her life, Amber was ready. She brought in copper pajamas, bedding, socks, and a hospital gown for Gemma. (Since copper is a metal the fabrics were a blend of 60% copper, 20% cotton, and 20% bamboo.) Gemma was skeptical at first but within a couple days she felt much better and noticed the open wound was decreasing in size. “It was incredible,” said Gemma, “the nurses took swabs from my stomach daily and they always came back infected with MRSA, but a few days after wearing the copper-infused clothing, they came back negative. You wouldn’t think something so simple could make such a huge difference but I could feel the difference in my skin almost overnight. Instead of feeling lethargic I felt brighter, more alert and healthier. More importantly, I was healing. It was a miracle.”

Clinical trial mentioned in response…
http://www.sciencedirect.com/science/article/pii/S1201971214000599


Suzanne writes:

You're right, I do hear women saying "guys" plural to others in a group of women. But I still argue that if I said "That guy over there." you'd be more likely to expect to turn and see a man than a woman. So it isn't really neutral.

I vote for the spread of y'all!

PS. I catch myself at it, too. I will also try to be more vigilant!

Pat Schloss writes:

Hey gals,

Although I’ll never be accused of being part of the language police, I was taken aback by Vincent and Michael’s reaction to Michele’s comment on TWiM #125 regarding the use of “guys” when referring to people that are involved in computer programming. As you may know, it is thought that there are many small biases throughout the career development of female scientists that discourage them from pursuing specific disciplines - particularly computer science. So it would be worth reconsidering the collective nouns we use to refer to people within science.

To bring some data to the conversation, here’s a large, but admittedly non-scientific survey of 2300 individuals (http://jvns.ca/blog/2013/12/27/guys-guys-guys/).  The survey showed that men are more likely to think that “guys” is gender neutral when referring to people within a computer science context. Regardless, I think we owe it to our female colleagues and trainees to use the terms that are the most inclusive.

As someone that runs a lab with a heavy bioinformatics focus, it is very important to me to maintain a strong balance between men and women knowing that this is difficult given the poor representation of women in computer science. Both programmers that have worked for me have, in fact, been women. To call them “guys” would be obviously wrong. All kidding aside, I would be unlikely to call them “gals” as well. Instead, I have been working cut “guys” out of my language and go back to my Missouri roots by instead saying “y’all”. If nothing else, every time I force myself to use this odd slang, I remind myself to check my unconscious biases and to be better.

Happy Sciencing!
Pat Schloss

 

TWiM 126 Letters

 

Anthony writes:
An Abandoned Sailor’s Infirmary in NYC Where Cholera Bacteria Was Discovered
http://untappedcities.com/2016/03/10/an-abandoned-sailors-infirmary-in-nyc-where-cholera-bacteria-was-discovered/

Neva writes:

Hello clever TWIM ers,
A rather urgent detective story that TWIM might be interested in talking about. People in the area must be very spooked.
Neva in Buda
Deadly disease outbreak in Wisconsin baffles public health officials
A common and usually harmless microbe is causing a mysterious cluster of deadly bloodstream infections in Wisconsin.
http://www.statnews.com/2016/03/14/disease-outbreak-wisconsin/

Dennis writes:

Hi Docs, this cnn article gives some info on a continuing Elizabethkibgiam outbreak.
Rarely seen blood infection outbreak continues; source remains mystery
CNN
The rarely seen blood infection Elizabethkingia has been found in a Michigan resident. It has sickened dozens in Wisconsin since November. Read the full story


Best,

Dennis

vr: see http://www.promedmail.org/post/4158063

Elizabeth King (used to be Flavobacterium)

Suzanne writes:

Guys isn't gender neutral it's gender absorptive. It's used the same way it became standard over the last few hundred years to use he as a general third person singular pronoun (before that they was acceptable). Just because some women are OK with it doesn't mean the rest of us can't be annoyed by it. If your students will call a specific, individual woman a guy then I guess I'm wrong and it's honestly becoming gender neutral. But I never hear anyone doing that.

 

TWiM 125 Letters

Inspired by William:

Dear TWiMers;
Greetings from Berkeley where miracle March (water-wise) was perhaps half a miracle, but that is definitely better than none. At least we will not run out of water this summer.

I found this quasi-synthetic biology result to be very interesting on several levels.

First, it does not surprise me that Craig Venter was the one to do it. Thirty years ago I ran the computing group that supported the DOE Human Genome center at LBNL when it was run by Charles Cantor.  The focus was on sequencing long fragments which was hard but the reassembly was relatively easy.

Venter went off on his own and said that shotgun (as I recall the term) sequencing was the way to go: make lots of short fragments that can be sequenced quickly and then use statistical methods to reassemble computationally. He, of course, was right.

Second, I found it fascinating that "... after 20 years of concerted effort, his group has built - essentially from scratch - the minimal life form.
And in the process demonstrated that we have a very incomplete view of how life works at the most basic level.
However, now that they know the 30% unknowns, they can systematically tackle those genes one at a time to figure out their essential role." (The Atlantic article.)

Even when they infer that function of some of these from looking at similar genes in other organisms where their function is know, they still end up with 17% that are essential to this minimal life form that they have no idea what they do. No idea ... surprising.

Thirdly, "In a parallel experiment that didn't wind up in JCVI-syn3.0 , the scientists reorganized about an eighth of the genome to put genes with similar functions next to each other. Venter called this process "defragging the genome," as one would do with a computer's hard drive. In this parallel experiment, the defragging of that section of the genome didn't seem to harm the organism."

I would have thought that gene placement on the genome would be the result of some important optimization evolution, but that is apparently not the case. (THe San Diego Union article - see the nice diagram of this.) THough this may be the key:" "Despite extensive reorganization, the resulting cell grew about as fast as syn1.0, as judged by colony size," the study said. "Thus, the details of genetic organization impinge upon survival in hypercompetitive natural environments, but the finer details are apparently not critical for life." (San Diego Union) So the organization may only be non-critical in a very benign environment.

Fourthly, I like this:  'This philosophy of learning basic biology by building stuff is the best bit of the syn3.0 story, says Drew Endy from Stanford University. “Too often in biology we end up with only data, a computer model, or a just-so story. When you actually try to build something you can’t hide from your ignorance. It either works or it doesn’t.” (The Atlantic article.)

Anyway, it would be interesting to hear you take on this.

The ARS Technica article (http://arstechnica.com/science/2016/03/minimalist-genome-only-473-genes-synthesized-and-used-to-boot-up-a-cell/) gives some of the experimental technique and a pointer to the scientific paper ( Science, 2015. DOI: 10.1126/science.aad6253 )

The best of the popular articles is this San Diego Union Trib. article. (Unsurprisingly - given all of this sort of activity in the San Diego / La Jolla area -  they have a lot of good molecular biology articles.)

J. Craig Venter Institute unveils bacterium with smallest functional genome
http://www.sandiegouniontribune.com/news/2016/mar/24/minimal-genome-bacteria-venter/

Jenna writes:

Everyone at TWiM,

I wanted to thank you again for the interest you and your colleagues have taken in our Cell Host & Microbe paper "Fungal Mimicry of a Mammalian Aminopeptidase Disables Innate Immunity and Promotes Pathogenicity," which was expertly reviewed in your most recent podcast.  It was wonderful to hear someone as enthused with our findings as we were.  However, I just wanted to clarify a minor point.  While it is accurate that Alana completed most of the neutrophil work for this paper, for the past two years now my own research has primarily focused on further teasing apart how B. dermatitidis modulates neutrophil function by acting on other cytokines and chemokines using both neutrophil-like cell lines and peripheral primary neutrophils.  Again, I very much enjoyed the podcast and appreciate the interest in our work.

Best,
Jenna Lorenzini

Ph.D. Graduate Student, Klein Lab
University of Wisconsin-Madison

Kevin writes:

Dear TWiM Team,

In episode 124 (Fungal Parasites) a listener asked if quorum sensing was involved in development of abx resistance.

Dr. Melanie Blokesch studies how quorum signals induce competence in V. cholerae.  This phenomenon particularly happens in aquatic environments when V. cholerae forms biofilms on chitinous surfaces.  These aquatic biofilms can incorporate multiple V. cholerae strains, and the subsequent DNA transfer between strains could promote the spread of abx-resistance genes. However, I was unable to identify a paper that was specifically tracking the movement of Abx resistance genes between species.

Really enjoying the podcast, looking forward to the next one.

-Kevin

Anthony writes:

http://www.cdc.gov/tb/worldtbday/

Each year, we recognize World TB Day on March 24. This annual event commemorates the date in 1882 when Dr. Robert Koch announced his discovery of Mycobacterium tuberculosis, the bacillus that causes tuberculosis (TB).

Too many people in our country and around the world still suffer from TB. Anyone can get TB, and our current efforts to find and treat latent TB infection and TB disease are not sufficient. Misdiagnosis of TB still exists and health care professionals often do not "think TB."

The theme of World TB Day 2016 is “Unite to End TB” CDC and its domestic and international partners, including the National TB Controllers Association, Stop TB USA, and the global Stop TB Partnership are working together to eliminate this deadly disease. But we need your help.

# # #

In some areas of Jersey City, every day is Tuberculosis Day.

FWIW

Anthony

Also from Anthony:

http://www.elinthomas.com/

Above is the Link to the artist's Site for the Petri dish art.

Thank you.

And

Kim D'Alessandro writes about TWiM

 

TWiM 124 Letters

Anthony writes:

This image was posted on Facebook by Kim Dallesandro, the wife of the Warhol star Joe Dallesandro.  I don't know where it's originally from.

http://tinyurl.com/z8bbfnn

Larissa writes:
Hi Drs. Racaniello et. al,
I have a specific case study of Yersinia pseudotuberculosis which I think may be of interest to you or listeners:
I recently acquired a toddler. At the time the toddler arrived to my house, she was 18 months old, eating only formula from a bottle, was not toilet trained, and did not have a habit of putting things into her mouth. Her previous living conditions are unknown, but it is safe to say they were generally unclean. Her primary caregiver was a vegetarian and an IV drug user.
The toddler had frank diarrhea 6+ times a day upon arrival. Also upon arrival she was switched from formula to "real food" and water. I took her to multiple doctors regarding the diarrhea who across the board suggested that she had a gluten intolerance or a lactose intolerance.
As an owner of multiple dogs who drink out of woodland puddles, I know infected poop when I see it.
After a string of doctors and taking a watch/wait approach, I finally walked into an ER and demanded that a doctor test her for parasites (after lying to the doctor that I had, in fact, removed her from gluten for a period of 4 weeks), and low and behold - the toddler had Yersinia pseudotuberculosis, was treated by antibiotics for about 3 weeks, and is now ~6 months out and 100% symptom free.
A happy ending to a sad story.
Best regards,
Lara

Heather writes:
Dear TWiM,
I want to apologize for not writing much lately due to excessive "grad studenting" (yes, this is now a verb). However, I would like to request that you please discuss the hyperthermophile microbes of Peru's Boiling River. I assume you have seen it all over the news last week. I listened to the audiobook and was very impressed. I am anticipating another potential Taq polymerase, or something even more mind-blowing, to come out of this and would love to hear what the learned TWiM hosts have to say about it and the interesting (and potentially academically risky) stance of Andres Ruzo. Back to excessive "grad studenting" now.
Regards,
Heather

Wink writes:
Michael,
I think ticks are such good transmitters because they stay on you, feeding, for hours to days.
Wink Weinberg

Supti writes:
hello i am Gargee from India and i am a regular listener of your podcasts. I have a question, can development of antibiotic resistance be related to quorum sensing? Have any studies been made on this topic?
thank you


Anthony writes:
Washington Post - Plague alive and well in Madagascar
http://tinyurl.com/hhoszfm

"...
Plague victims’ corpses are to be buried immediately to prevent the spread of the disease. This means that they may be interred near a city hospital, instead of in the family crypt. But families will go so far as to stealthily unearth their loved ones to bring them back to their own villages for burial. Plus, there is a chance that families may anticipate not being able to bury their family members properly and decide to not bring their relatives to the hospital at all, said Ken Gage, chief of Flea-Borne Diseases Activity at the CDC. Among officials’ tactics is burying the corpses with concrete tombs to try to discourage the unearthings, Werner said.

Madagascar has seen lower numbers of deaths from the plague in the past two years, but an alarmingly higher rate of contracting the pneumonic form of the disease — the kind that is airborne and can kill you in 24 hours.

Mike writes:
Hello professors TWiM,

Thanks for the great podcast. I have often wondered why we so frequently prescribe single antibiotics to patients. At this point we know that bacteria are rapidly evolving resistance. It strikes me that this is exactly the same problem as we have with HIV infections, with the primary difference being a question of the speed of evolution. Human immunodeficiency virus evolves very fast, to the point that resistance evolves within just a few years (or less) in a single host. With bacteria, the exact same process is happening, but bacteria are much larger and slower evolving, so the process takes decades and many hosts. However, the solution is still basically the same: if it takes a decade plus a few million infected hosts to evolve resistance to a single drug, surely it would take centuries to evolve resistance to a combination therapy?

So then the question is: why does this never happen? I recognise that the resistance issue is not only an issue of medical prescriptions, the massive use of single-drug antibiotics in stock animals is probably an even bigger concern, but still: doesn't it seem that using a triple therapy of antibiotics would be more effective for the patient, as well as being better at preserving our antibiotic supply?

I recognize the immediate response would be: we don't give more drugs than we have to. My answer to that is easy: we have to, we are running out of antibiotics. The next obvious response is that antibiotics have side effects and that this means you should minimise their use. Is that the main reason that we don't do this? Is there a reason we can't give a single pill with multiple antibiotics in it and just give anti-nausea and anti-diarrhea medicines to the patient to take as needed? The side effects of a single antibiotic are primarily due to the death of so many bacteria in the gut, would adding two more antibiotics to the mix actually make those symptoms that much worse? I have no idea, but I would really like to know.

Thanks so much again for your fantastic podcast.

All the best,

Mike

 

TWiM 122 Letters

Hunter writes:

Greetings TWiM crew!
 
I recently learned of a new game (currently getting ready for Alpha and crowd funding) where players will edit microbes at the genetic level and pit them against microbes created by other players. The game is called CURE, and can be found here: http://curethegame.com/
 
It claims to be accurate based on current scientific knowledge, and to have been reviewed by teachers and scientists.
 
Being a gamer and super interested in Microbiology, this was right up my ally and I figured I probably wasn't the only TWiX fan who would be interested in this.
 
____________________
Hunter
QA Analyst 3 : Hearthstone
Blizzard Entertainment

Anthony writes:

Tardigrade creed art
https://cottonbureau.com/products/live-tiny-tardigrade


Dennis writes:

Hi Docs, regarding TWIM #120 and tubeworm metamorphosis stimulated by a bacterium, what a fascinating observation. Dr. Lynn Margulis and Dorian Sagan in their book, “Acquiring Genomes”, have a chapter titled Seaworthy Alliances in which Dr. Donald I. Williamson’s work is quoted in which he claimed that invertebrates owed their transformations from larval forms to radically different looking adult forms to “acquired genomes”. He did experiments to cross Invertebrate sea urchin fathers (Echinua escalentus) with Chordate mother sea squirts (Ascidia mentula). “Not only did the fertilized eggs survive this bizarre coupling but they developed fully paternal larvae, the immature forms called plutei.” … “Some of these weird hybrid forms survived up to 90 days from hatching.” There’s much more detail and he begged for some independent group to try the same experiments but I’ve never heard more of this kind of work. Margulis’s entire book was dealing with the question of how some animals develop with wildly different phases, for example from embryo to larva to pupa to adult. I wonder if the observation of the bacterium stimulating a tubeworm transformation will also stimulate more work in either expanding on or correcting the theory of acquired genomes in higher forms of animals. Have you any thoughts on the theory of acquired genomes? We know that many life forms acquire viral DNA (and bacterial DNA?). How about higher forms of acquired DNA? Thanks,
Dennis

 

Listen to TWiM

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TWiM 119 Letters

Jeanne writes:

Dear TWiM,
 
With regard to the question about culturing gut microbes from Drosophila:
 
I was lucky enough to take a sabbatical in the lab of Dr. Angela Douglas (http://angeladouglaslab.com/) in the Fall of 2012, where I worked on the gut microbiota of Drosophila.  Her lab found that the diversity of gut microbes in lab-reared  Drosophila is quite low, comprising just 5-6 taxa, almost entirely Lactobacillus and Acetobacter (Wong ACN, Ng P and Douglas AE, 2011. Low diversity bacterial community in the gut of the fruitfly Drosophila melanogaster. Environmental Microbiology 13: 1889-1900. Pubmed link).  These are easily culturable, although they grow better in low-oxygen environments.  Cultivation techniques for these bacteria can be found here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3911109/.
 
Hope that helps!
Jeannie
 
**********************************************************************************************
Dr. Jeanne Kagle
Professor of Biology
169 Grant Science Center
Mansfield University
Mansfield, PA 16933

Steve writes:

Hi Microbophiles,

Happy New Year (And Happy Birthday to Vincent).

I have to say it was good to hear a TWiM (118) where I understood every word! :)   Having bee‎n a mushroom collector in my time, it was like revising the morphology section--right down to the sterigmata!

I had often wondered how the spores managed to 'stop' and fall down‎ between the gills, but perhaps the air viscosity is sufficient as Elio says. A further point to note may be that the mushroom cap is elevated on the stipe so as to get the spores above the lamina airflow that hugs the ground, close to, and into the turbulent air that carries them aloft.  [You might also observe that the gills are always gravitationally aligned, even if the stipe is bent: the spores have to be able to fall down unimpeded.]

Where it comes to the assertion of the importance of fungal spores to cloud formation, I have to refer you back to your programme on EHux, and other phytoplankton, where we were told that the production of dimethylsulphide as a result of breakdown of sulphur-containing metabolites, was the key to controlling the World's weather, as the DMS leads to the formation of sulphate aerosols that act as nucleation foci for water droplets, much as the fungal spores are mooted to do in today's podcast.

Without reading into this before writing whilst it's still fresh in my mind, I would suspect that, as they are derived from molecular processes, the aerosol particles may be smaller than even the fungal spores, and give more nucleation foci  ‎per m3 than obtained from even the large number of spores mentioned.   

So, on the whole, I think I am more inclined to stick with the phytoplankton than the mushrooms in importance as rainmakers, though I think that almost any dust particle, including spores, will act as a nucleus too...

...Or do the sulphate aerosols need particles to condense on just as the water vapour does?  :/

Many thanks for all your great podcasts, and I look forward to many more in the New Year, especially as I have now caught up with the story so far on TWiV, TWiM, and TWiP.

All the best,

Steve
Luton
Bedfordshire
England

Steve writes:

Hi Vincent,
           TWIM is one of my top 3 podcasts-an excellent way to relax-thanks for a great job. I enjoyed Bullers drop, fungal spore ejection and discussions of potential life on MARS but what about some discussion of life in Earths subsurface, where most microbes on/in Earth live, at depths down to several kilometers and at very low metabolic rates! They play a major role in geochemical cycles and natural resource formation. The paper below is an old one from Casey Hubert at UoC and talks of bacterial spore transport and so on. I think survival and transport of micro-organisms within and between planets would make an interesting episode for readers. Discussion in more detail of microbial survival on interplanetary transport and landing via meteorites would also be interesting, which you touched on in the spore/MARS episode.

Thanks and best wishes. cheers steve

Hubert, Casey, Alexander Loy, Maren Nickel, Carol Arnosti, Christian Baranyi, Volker Brüchert, Timothy Ferdelman et al. "A constant flux of diverse thermophilic bacteria into the cold Arctic seabed." Science 325, no. 5947 (2009): 1541-1544.

Peter writes:

Dear TWiM team.
I saw this advert for a two year postdoctoral position for a microbiologist at the UK Centre for Astrobiology, University of Edinburgh and thought it may be of interest to  other listeners.
I do  not have any connection with the University of Edinburgh other than having taken their Coursera astrobiology course.


Here is the description:


A two-year STFC-funded PDRA position is available at the UK Centre for Astrobiology, University of Edinburgh to investigate the behaviour of microorganisms in space, using the International Space Station. Your work will involve understanding the effects of extreme space conditions, including microgravity, on microbial communities and use these data to advance our understanding of how we can look for biosignatures of life elsewhere and develop new methods to look for those signatures. You will work to help develop new experiments using orbital and space facilities. You will lead both laboratory based and theoretical research to apply this research to STFC science. You should also have an interest in technology transfer. Working at the interface between biology and planetary sciences (astrobiology), at Edinburgh, your responsibilities will include advancing work on space experiments and the use of space facilities to carry out research. You should have a PhD in biological sciences.

You will be a member of the UK Centre for Astrobiology. You will play a wider role in developing astrobiology. This includes working on our ‘Astrobiology in the Classroom’ initiative which, through the Astrobiology Summer Academy, involves developing lesson plans with primary and secondary school teachers to use astrobiology as a vehicle to advance science education in the UK. We seek a self-motivated scientist who will play an active role in creating links with space agencies and other astrobiologists. You will also be responsible for supervision, training and oversight of other staff.

The start date is 1 April 2016. This is a fixed term 2-year position.


You can apply here: http://www.ed.ac.uk/human-resources/jobs
The job vacancy is 035130

Geoffrey writes:

Doctors:

     First of all, thank you for reading and commenting on my talmudic question about unleavened bread. I hope that it got some of your listeners thinking.

     Second, I had a few thoughts that I thought might or might not help amplify your discussions in this episode.

1) Thanks for the article of amoebic pack hunting. I think that I’ve heard of similar tactics with other microbes. Dr. Racaniello kept referring to nematodes in a negative sense. One nematode function that he particularly picked on was “parasitism”. I’d like to point out that nematodes are as diverse a group as they are because they occupy nearly every ecological niche available somewhere in the world. While many of them are quite nasty, nearly all are valuable contributors to the environment. Because of the differences in scale, we tend to think of plant-eating nematodes as infestations while we tend to think of plant-eating ungulates as cattle. Also, think about the difference (or lack of differences) inherent in nematodes that graze on bacteria and nematodes that graze on algae. Thinking on their level is probably one of the most fascinating things about this group.

2) One of the reasons that I have a small interest in nematodes is exactly their occupation of so many ecological niches. Dr. DesPommier (if he hasn’t already heard of this) may be interested to know that Dr. Sharanbir S. Grewel (formerly of the Ohio State University) has been working on a method to measure soil health by microscopic assays of nematodes in a soil sample. Unlike many systems that have used nematodes to generate soil health indices, Dr. Grewel’s methodology relies only on identifying the categories of mouth types in the sample’s nematodes. Since these mouth parts are fairly characteristic for the nematodes’ soil services, they are much quicker and easier to identify that species. The numbers and ratios of the service (mouth) types can give a fairly good idea of how “alive” and diverse the soil is. Unfortunately, Dr. Grewel left OSU before I could work with him to develop a gardener’s guide to using this technique and I have not seen that he has published the basics of it yet.

3) Thanks for the article on fungal spore dispersion biophysics as well. I have to say that I disagree with their assessment of evolutionary advantage. I think that:

A) being a point of droplet nucleation would help ensure that the spores could be carried in the clouds further than naked spore because naked spore would be subject to more chaotic and, therefore, shorter overall paths. Genetic dispersion can be an advantage.

B) In the open atmosphere, spores are vulnerable to UV exposure. It seems to me that thicker aqueous coatings would reduce UV exposure and, again, portage inside a cloud would provide some further protection.

C) Being a rain droplet nucleation site would also help ensure that a spore lands with an initial bolus of water to help initiate sporulation. This would take advantage of a short-term survival strategy that requires only an initial exposure to water. It might be that non-ballistosporic spores take advantage of longer-term survival strategy of initiating sporulation only after water has been available long enough to make a water steady state more likely.

4) I suspect that there is a lot that we can learn about hydrophobic / hydrophilic metamaterial surface design from studying these spores.

5) Much of water droplet formation seems to be based on nucleation site chemistry. That might be the mannitol. That might be part of the surface structure of the spore itself. It might be a combination. I saw little reference to this chemistry in the paper. If they aren’t already in talks with someone, then I would suggest that the authors need to collaborate with a meteorological chemist to look at the surface chemistry of the aquated and non-aquated spores more closely. If this hasn’t already been studied in some detail, then the estimates of atmospheric spore concentrations suggest that it should be. The fact that spore surface chemistry changes may be a point overlooked in previous nucleation site studies.

6) In addition to studying spore effects on droplet nucleation in a cloud chamber (I believe that that’s what the warehouse-sized buildings are called, not the atomic tracing chambers), I would suggest that a potentially less expensive test would be a correlational study between the atmosphere and cloud concentrations of the two types of spores versus rain formation based on mannitol biotracer monitoring might be possible.

7) To chime in on Chris’ martian pathogen question, I would say that it might be possible even if there wasn’t a microbial exchange between Earth and Mars. As long as the martian life-form requires carbon, oxygen, nitrogen, and water, I could envision a decomposer-type organism which doesn’t so much hijack the host body but chemically decomposes it and scavenges the chemically-shattered remnants. It could be something along the lines of acid-based hydrolysis which would have the added advantage of liberating needed minerals in the martian soil. The bigger question would be if any extremophilic microbial survivors on Mars could survive the (relative) superabundance of water in Earth organisms. Such extremophilic organisms might also grow so slowly as to be swamped out by the abundance of life in most Earth organisms. On the other hand, if a dead body were left on Mars and mostly dried out, then those organisms would be all over the body like bone worms on a whale carcass in the deep blue terrestrial sea.


Thanks for another stimulating episode!


Anthony writes:

What Happens to Your Microbiome If You Own a Dog
http://www.ubiomeblog.com/what-happens-to-your-microbiome-if-you-own-a-dog/

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