Blog Search

Vincent Racaniello

Vincent Racaniello

Vincent Racaniello is a virologist at Columbia University and science communicator. He is using Zika Diaries to communicate the personal and behind the scenes experiences of his laboratory as it moves from working on poliovirus (for 35 years) to Zika virus.

Tuesday, 25 April 2017 02:21

TWiV 438 Letters

Sarah writes:

Hello TWiVsters,

Long time listener first time emailer…

In response to Bob’s letter on TWiV 437, about recent episodes being “boring” – I have to agree with the hosts, there is nothing boring about the in depth discussions of plaque assays! Anyone who has attempted a plaque assay has a story to share...

Tuesday, 25 April 2017 02:21

Drs. TWiV go to Washington - TWiV 438

On the eve of the March for Science, the TWiV team gathers at ASM Headquarters in Washington, DC with guests Stefano Bertuzzi and Susan Sharp to talk about the state of science communication.

Thursday, 20 April 2017 19:42

Microbiology is where it’s at - TWiM 150

In recognition of National Medical Laboratory Professionals Week, Robin Patel speaks with the TWiM team about directing a clinical bacteriology laboratory, and how an observation made by a laboratory technologist lead to the finding that Ureaplasma species can cause a system metabolic disturbance, hyperammonemia.

Monday, 17 April 2017 08:50

TWiV 437 Letters

Paul writes:

Some very sad news to pass along.  It’s a bit difficult to write about at the moment.

http://www.cbc.ca/news/canada/montreal/mark-wainberg-montreal-aids-research-dies-2017-1.4067843

Bob writes:

TWiV 436: Virology above Cayuga’s waters was NICE!

Last few TWiVs I have found boring, but #436 was very wide-ranging with interesting guests, and I liked it a lot.

As Vincent said towards the end, “Well I could go on forever, I love talking about viruses…”

Yup! Some of us out here in TWiVland agree!

Bob

Adam writes:

Dear TWiVsters,

Weather in Peoria Illinois is sunny and 5C with a high of about 25 today, a welcome respite from two weeks of raining.

A minor bit of bug pedantry – in TWiV 434 and several previous podcasts Vincent has hinted at his hope of doing a “bug podcast”.  While the popular perception of “bug” includes all insects and perhaps other creepy crawlies, the order hemiptera within the class insecta are technically the only true bugs.  The order includes aphids, cicadas, shield bugs, and various agricultural pests.  This of course leads us to a thrilling linguistic question:  how did the term bug become a stand-in for all insects?  Personally I find both diptera and hymenoptera to be a bigger nuisance, yet no one ever calls an aphid a fly or a wasp.  Many people know the story about Grace Hopper and “bug” entering computer lingo, but how did it become the norm in the first place?

At least Vincent didn’t pull a Will Shortz.  Once on the NPR Sunday Puzzle he referred to spiders as insects.  When asked to correct himself the next week, he replied “Oh my bad, I should have said spiders are bugs”.

And finally, an awful virology pun:

Question:  What is both a type of nuclear weapon and an exclamation from Beatrice Hahn* when she locates a potential viral sample from chimps?

Answer:  “ICBM”

Thanks,

Adam

*Substitute another field biologist if the joke is too obscure, but she is the only one that comes to mind when I picture falling feces.  

Nathan writes:

Dear Esteemed TWIV hosts,

Thank you for a great podcast!  Keep up the great work.  

Attached is an interesting paper about viruses several hundred feet under the ocean floor.  It would be great to have a discussion on a future episode.

It’s 47oF and sunny in Chapel Hill.

Joshua writes:

Hello, my name is Joshua, I’m 23 years old and I really want to be a microbiologist, but I don’t think I’d be able to handle the actual work at a job because I have a learning disability. I have borderline impaired working memory capacity; this basically means I can’t hold much information at all in my head and working with a set of information is very difficult and slow for me. I would appreciate if you would read this email and tell me if someone with my disability would be able to perform the day to day tasks of a Microbiologist, also please tell me what kinds of cognitive tasks a microbiologist does day to day. I would also appreciate other contacts/professors/scientists that I can talk to about this.

One example of how my impaired working memory capacity affects me is my ability to make decisions, I’m slow to consider all the options and each of their consequences. Another, is that, in school, I couldn’t takes notes because I can’t both listen to a stream of information while focusing on what to write or I’ll lose my place and forget or just completely miss what was said. If someone tells me a list of things I won’t be able to think of the whole list at once, I’ll need to write it down and then wait until I remember all the parts to complete writing the list. When my working memory is full I get completely stuck, new or related ideas have no room to fit into my memory so things stop occurring to me, I sometimes can’t recall my memories if they’re complex like a story or contain a lot of parts and I can’t think well and need some time to clear my head.

How well do you think a person like me could perform at being a microbiologist? Do you think I would be able to advance in this career? Who else can I talk to about what cognitive tasks a microbiologist does day to day? I would appreciate any info, contacts and, advice and thank you very much for reading my letter.

-Joshua

P.S. If you want a really good idea of how my learning disability works you can try a dual N-back test that requires you to remember two streams of information and if they repeat you press a key to mark it. An average person should be able to get a consistent 100% on “2-back” once they learn the rules. I can not perform this test at 2-back. I get 20%, I get 30%, I get zeros; I’m basically Guessing.

Kim writes:

Hello there TWIV team,

As many other graduate (and international) students, I see myself on a teaching assistant position this semester. I teach the “Phage Hunters Lab” at Washington State University (part of the SEA-PHAGES program) and I gotta say it’s a pretty sweet gig. Undergraduate students brave the inclement tundra we live in (I may be imagining it but Pullman’s had quite the rough winter) and collect soil samples to try isolate bacteriophages from the environment. If successful, we get to characterize these phages (TEM, endonuclease restriction analysis, sequencing) and even get to name them before uploading them to PhageDB. The idea behind it all is to keep students engaged and provide them with authentic, hands-on experience on the scientific method. Now, I’m not the brightest apple in the orchard (see what I did there? Apple State, anyone?) but even I have to admit that we all (specially the “phage parents” which are the labmates that isolate phage) get teary eyes and swell with pride whenever we see plaques…what a great time to be alive!

I listened to “TWiV 428: Lyse globally, protect locally” and will share it with my students so they can get inspired and start working on their Lab report. Most of them are hung up on the idea of using phages to control antibiotic-resistant bacteria. This paper is a good way to show them that not everything is roses in the phage dimension.

Sorry for the long email and please keep fighting the good fight. Best,

Kim Lam Chiok

Graduate Student

Department of Veterinary Microbiology & Pathology

College of Veterinary Medicine

Washington State University

Pullman WA

P.S. Here’s a link for the SEA-PHAGES program: https://www.hhmi.org/developing-scientists/science-education-alliance

YY writes:

Hello TWiV,

I have just started learning about viruses as a graduate student and I have a question about dsRNA viruses that maybe TWiV may be able to answer — do dsRNA viruses always have linear genome? Are there any viruses that contains circular dsRNA genome, or closed dsRNA genome? (Such as a continuous strand of RNA is folded to dsRNA by base-pairing, hence creating 2 (or more) stems.)

It seems that dsRNA are quite different than other viruses, which is quite fascinating to me. Although it seems that there are way less research or literature discuss dsRNA viruses.

Thank you. Looking forward to your response.

Best regards,

YY

Ricardo writes:

Hello Twiv friends. Just sending a confort message. I hope I’m not the 27th (I’m listening one week later 430), but if I am, it will be an honor to have a book from your shelf.

My best regards

Ricardo Magalhães

Judy writes:

Dear TWIV Team,

This is my first time writing in but I am a big fan of the podcast. I am graduate student in Terry Dermody’s lab, recently moved to the University of Pittsburgh and settling in. This past week as I was catching up in the episodes during my plaque assays (see attached), I listened to TWIV episode 428. It was almost serendipitous because as I was infecting  my assay you mentioned that you couldn’t imagine how someone could do a plaque assay and listen to Twiv at the same time. Then during the discussion of “Regional astrocyte IFN signaling restricts pathogenesis during neurotropic viral infection” Vincent jokingly mentioned “and a summary for all those doing plaque assays.” I laughed out loud and thought what a great addition to the episode- a summary of an in depth paper and talking points in case you missed anything. Finally, Kathy’s timing was perfect because just as I was overlaying she said “we know you are finishing up your plaque assays.” So thanks for keeping me company in the lonely hood during my 200 plate assays. Vincent- I hope you would be proud.

Thanks all!

Judy

Jarrett writes:

Hello all,

Just writing (again) to put myself in the running for a copy of Emerging Infections. Spring is certainly under way here in Austin, as the Redbud trees are in bloom. We have three varieties of this lovey tree in Texas; the Eastern, Texas and Mexican Redbud trees are all native to the area. Current temperature is a balmy 71 F. Looks like we’re in for a sweltering summer.

Thanks!

-Jarrett H.

Austin, TX

Megan writes:

Dear TwiV cohort,

I hope I am number 27 for the Emerging Infections book contest! I have been listening to TwiV since 2009, and have been hooked ever since.

I want to thank the TwiV team for providing knowledge in the wonderful world of viruses, and keeping my sanity in check. I am a recovering academic who is looking for a new career in virology or bioinformatics research in the industry or a non-profit organization. In times like these I am particular grateful to have TwiV as an old friend, where I can learn about the latest virology research from you all with humor and wit.

Besides all the TwiX podcasts, I also regularly listen to the wonderful Public Health United, 99% Invisible, RadioLab, the Sporkful (which occasionally features Fred Alt’s son Kenji), and the Hilarious World of Depression.  

The weather in Pittsburgh, PA is a rainy and unseasonably warm day at 15°C (59°F). Thank you for all your great work, and keeping TwiVing!

Best Regards, Megan.

David writes:

Dear Vincent,

I hope I have become the 27th listener to write in to win the emerging infections book.  Or if not, that I surpassed the limit so that some other person is lucky enough to get the book contest.

I think that most of the members in your audience have some scientific inclination – and that probably means they are all making estimated guesses how long they have to wait to win.

Thanks for the countless hours of viral fun!

Kind regards,

David

Matthew writes:

Dear Vincent and the TWiV-viridae

Hopefully by now you have already received the 27th email but if not this will you bring you one email closer! I am an undergraduate student from Northern Ireland studying Biochemistry at Queen’s University Belfast and I’m currently on my placement year working in industry. I listen to TWiV each day during my lunch break in order to keep my brain active and learn new things as in work I have done the same tasks day in day out for 9 months so TWiV is the only opportunity I have to quench my thirst for knowledge. Although I haven’t been a listener for too long (I think the first episode I listened to was 418) my first encounter with Vincent’s work goes back further than this! In the second year of my degree I was given the choice to pick a module, either Virology or Genetic Systems. I decided to pick Virology as I had come across Vincent’s lectures on Coursera and although I did not do the course at that time I downloaded all the videos so that I could use them when I started the module. Queen’s had some really good virology lecturers, particularly Dr Ultan Power who made sure to emphasise the importance of having an understanding of virology rather than just being able to recall processes and facts. In his first lecture he showed a graph of marks obtained vs pupil attendance and when it became clear that a lot of people failed the module every year I did notice a drop in class numbers as people frantically switched to Genetic Systems! I think at the end of one of another lecturers notes a TWiV episode was mentioned as extra reading and I admit I never did check it out at the time but at least I am here now! However I would have to say it was Vincent’s Coursera lectures and YouTube videos which made me really interested in Virology as a subject, I ended up revising for the exam pretty much only using Vincent’s videos (luckily using information not found in the his lecture material was encouraged by Dr Power) and I could not have got 70% in that module without them. Listening to TWiV has further peaked my interest and when I start back to university in September I am hoping to see if I could do something virology related for my Honours project but even if I am not able to I believe one of the modules I will have to do is virology related so at least I have that to look forward to.

And last but not least it is a normal March day here in Northern Ireland with I think the temperature being around 7’C, not too cold but not warm either! Keep up the good work with the podcast and thank you all for being so informative, entertaining and dedicated to the field of virology.

Kind Regards

Kevin writes:

Dear TWiVumvirate,

Here’s a listener pick. I think it’s lovely, and I suspect that all you TWIV hosts will agree.

https://www.bbg.org/collections/cherries

Best,

Kevin

Monday, 17 April 2017 08:38

Kathy's new spindle virus - TWiV 437

TWiV reveals new giant viruses that argue against a fourth domain of life, and discovery of viruses in the oceanic basement.

Monday, 17 April 2017 08:33

TWiP 131 Letters

Case guesses

Hannah writes:

Dear TWiP doctors,

Time to embarrass myself with another case guess! Apologies in advance for the long email.

If it really is an arthropod as you implied (and not e.g. a small mammal or snake), I see three possibilities here: 1. a non-venomous arthropod bite that got infected, 2. a venomous arthropod bite/sting, or 3. a venomous arthropod bite/sting that got infected. In the first case, it could be just about anything, although biting flies seem unlikely given the circumstances of the bite. Getting bitten while putting on pyjamas suggests that the arthropod was hiding inside, and that it was defending itself when crushed against skin. A lot of bugs (Hemiptera) have both the mouthparts and temperament to defend themselves in this manner, as do beetles and many many more.

Since I doubt you’d give us a case where the answer is “one of the several million arthropod species that could break your skin when squashed, letting unknown bacteria into the wound”, let’s move on to the a venomous arthropods. One of the many stinging bees, wasps and ants could conceivably cause these symptoms, at least in conjunction with a bacterial infection. Bees and wasps generally don’t hide in pyjamas, however, and while ants might crawl through clothing on their way somewhere else, it still seems unlikely, especially since there was only one bite/sting.

Centipedes are a real possibility. I don’t know what species are found in her region, but their venom can cause intense pain and swelling, and they could conceivably hide in clothing. I don’t think their venom is likely to cause the other symptoms, so this would once again point to some infection.

This brings us to the arachnids, specifically spiders and scorpions. A minority of species have medically important venom that can, all by itself, cause some or all of the symptoms experienced by the patient. If it’s a scorpion, I can’t speculate further – I know next to nothing about that group, though aside from the pain, the description of symptoms in Parasitic Diseases doesn’t seem to match.

Given that the patient is in Peru, the spider genus Phoneutria immediately comes to mind – Brazilian wandering spiders. Despite the common name, some species are also found in Peru. They are known to hide in clothes, but to the best of my knowledge, they are tropical forest spiders, so I wouldn’t expect to find them in the highlands. Much more likely are the genera Latrodectus (widows) and Loxosceles (recluses). Both widows and recluses are shy, non-aggressive spiders that may occasionally find themselves caught up in clothing. Latrodectus are more commonly encountered in their webs, however, and their bites are not necrotic. Any necrosis seen would be from an infection.

Loxosceles, on the other hand, do not weave webs, love to hide in clothing, and their bites are famous for being necrotic. While bites are typically painless, and necrosis usually takes longer than 2 days to develop, it seems like the most likely culprit. Many Loxosceles species can be found in Peru, but L. laeta is the most well-known, and bites from this species can cause both skin lesions and systemic reactions, including renal failure.

Before I sign out, I just want to share this excellent STAT article on delusional parasitosis (also known as Ekbom syndrome): https://www.statnews.com/2017/03/22/insect-delusional-parasitosis-entomology/ I’d be very surprised if you didn’t have a few listeners who suffer from this awful condition, and it may benefit them to know that they’re not alone and can get help.

Thank you so much for everything you do!

Cheers,

Hannah

P.S. Dr. Griffin: I’m the one who brought up some of the issues in the arthropods section via your website’s contact form a while back. I apologise if I came across as overly critical or rude – I really do think you guys are doing amazing work, and I’m thrilled that you got some entomologists on board to make this textbook even better!

Carol writes:

She was bitten by a wandering spider, or “banana” spider.

Carol

Wink writes:

Dear TWIP Team,

The case of an apparent bite and multi-organ system failure sounds like a dangerous arthropod to me. My guess this week is spider bite. I found the following excerpted information in Wikipedia: “Loxosceles laeta, commonly known as the Chilean Recluse Spider, is generally considered to be one of the most toxic species. It has a very wide range [including Peru] … and has been documented at elevations.”

Wink Weinberg (Atlanta)

John writes:

Hi TWiPerati,

My initial guess in the case of the Peruvian woman with the inguinal insect bite was that she had disturbed a recluse spider (either Loxoceles laeta  and  L. intermedia). That spider lives in South America; bites when disturbed in clothes; can cause lesions and necrosis.

If that is the case, direct treatment options for the woman are limited. Symptoms can be treated to give the body a chance to recover itself.

On the other hand, the family home should be nuked from orbit, it’s the only way to be sure.

https://m.youtube.com/watch?v=aCbfMkh940Q

However, I am not confident in the diagnosis. The timeframe is extremely short from bite to serious consequences.

The preview of the paper “A Mnemonic Device to Avoid False Diagnoses of Brown Recluse Spider Bites” (http://jamanetwork.com/journals/jamadermatology/article-abstract/2603498) indicates that ulcers would not be expected for a week. Unfortunately, it’s not open access and all I could read was the preview.

I look forward to the answer in the next episode,

Thanks and regards,

John in Limerick, Ireland.

(where it’s 11°C, cloudy with sunny spells)

Nita writes:

Greetings,

Hello, TWIP team. I have recently tuned into the podcast and find it really fascinating! I am a soon graduating medical student going into neurology, but I really like parasites and had been trying to find a good resource to learn about them! This is my first guess submission, so please be kind! I am going to Tokyo soon for my vacation, and I am excited to visit the Meguro parasitological museum! Hope I’m the lucky 14th emailer!

For our 24yo female Peruvian patient, my first instinct of a rapidly progressive necrotizing with black central dot is the brown recluse spider, but maybe that’s my affinity to spiders. After doing a little digging, I did find that the Chilean recluse spider is quite venomous in Peru, and recluse spider bites can cause breakdown of muscles that result in rhabdomyolysis and acute renal failure. However, looks like it doesn’t cause increased WBC count necessarily. Womp womp to this guess from a arachnid fan.

After some digging, such a rapid exacerbation of clinical course as well as the red lesion with a black enter sounds a burrowing sand flea tunga penetrans. The female has a black dot at the read end, and that’s what marks the change. However, I’m not sure of the time course.

Those are my two silly, sexy answers! Doing this in a rush so I didn’t get to think it through. Just jotted down the two “zebras” that popped into my brain.

John writes:

TWIPsters,

Greetings from Omaha, the city that hosted the very vibrant meeting of the American Society of Parasitologists (ASP) in 2015.

Check out these exciting and fun playing cards ASP made for our conference goodie bags:

http://www.anorak.co.uk/wp-content/uploads/2015/06/playing-cards-parasites-1.jpg

My students used them recently to help prepare for the Parasitology Lab practical. It doesn’t get any more vibrant than that!

I haven’t attended an ASTMH meeting, but ASP includes parasites of veterinary importance and others without medical importance such as gregarines and horsehair worms. ASP also addresses the evolutionary ecology of parasites, which may interest the environmental science major from Colby-Sawyer College. Many attendees enjoy the relatively small size of the meeting, which facilitates collegiality and is undergraduate-friendly. Also, no one tries to sell you anything.

My guess this week for the case study is the brown recluse spider, Loxoceles sp.

Although not a parasite, I look forward to incorporating this case study into my Zoology class.

I concluded my Parasitology Lab with the infamous #109 Case Study. I didn’t tell them about the “twist” in the case and they went nuts when they heard the big reveal. Encouragingly, two students guessed the correct parasite (but not host).

Peace

Suellen writes:

This one really has me stumped — which I guess isn’t saying much, considering that I’ve not gotten a diagnosis right yet.

This time, I tried to take more time and jump to fewer diagnostic conclusions, but I can’t find a parasitic disease that would manifest so quickly after a bite from a critter in one’s pajamas. My initial guess was cutaneous leishmaniasis, but that takes weeks or months to develop, and the lesions are not just where one is bitten, they are all over the body — but especially on the face and other exposed areas.

Next, I decided to rule out certain vectors. For example, a mosquito is unlikely to get into someone’s pajamas, and even if it did the person is not likely to be able to catch and bottle the mozzie a day later. Fleas fall into the same category, so I am ruling out mozzie-borne illnesses such as malaria and dengue, as well as anything that fleas might carry.

Sand flies? I don’t know much about them, so it’s hard for me to say whether one is likely to end up in pajama bottoms, or to be able to be captured easily, but the diseases that sand flies and other flies carry just don’t come on that quickly after a bite.

Tick-borne parasites? Again, everything I researched would take a week or more to become symptomatic. Same with bacterial diseases, they just don’t show up that quickly. And I ruled out Chagas disease because it also takes a while to show symptoms, and also because I don’t think a reduvid bug is likely to show up in someone’s pants leg. (Also, she has no fever.)

So I came to this: Either (1) the bite did not cause the illness, i.e., the patient was getting sick and just happened to get bitten or stung right before she began to feel really bad, or (2) this is a case of myiasis, where she’s actually got a fly larva of some type living in her skin, and that is what is making her sick.

Now, what I’ve read about myiasis seems to indicate that this is more of a tropical or sub-tropical problem, and our Peruvian patient lives in the arid mountainous region of the country, but I suppose it’s still possible. It also appears that usually you get more than one bite, but maybe our patient reacted quickly enough to avoid being bitten multiple times? And, of course, the scalp and neck are the regions where people most often get bitten . . . so, again, this diagnosis is looking a bit thin. A bite that occurs when you are putting on your pants seems much more like a defensive move on the part of the critter than a “oh, look, I think I’ll lay my eggs here while i’m being suffocated in this pants leg” kind of thing. But if I move along this line of reasoning, I need a critter. The only one I could find that seemed to fit the bill was Dermatobia hominis, the human botfly, which is endemic to the highlands of Central and South America. The problem is that the literature seems to be devoid of any symptoms other than the ones related to the skin — itching, etc. No mention of vomiting or other signs of illness. And I don’t see a botfly seeking out a pants leg when a scalp would be much more handy.

So I am left with the possibility that the bite and the illness are not related, but are simply coincidental, or that this is not a parasitic disease after all, but either poison from the bite of a spider or scorpion, or is just something Dr. Griffin thought up to make us all go crazy rooting around in Google. LOL — nah, he wouldn’t do that to us, would he? But I’m afraid that after all my research I really don’t have a diagnosis, but now that I’ve written all this I’m going to send it anyway, so you will know that I tried my best.

Thanks for keeping me guessing!

Carl writes:

Dear TWIPniks,

I was listening to TWIP 130, and as soon as I heard that the center of the unfortunate woman’s lesion had turned black, I hollered “Brown Recluse!”  Fortunately I was by myself and so did not frighten anyone.  Upon later consultation of Parasitic Diseases Sixth Edition, I discovered that I was wrong, as one would expect of an amateur diagnosis.  But I was close– right genus, wrong species.  This is a case of loxoscelism, caused by the bite of a spider in the genus loxosceles.  Given that the case is in Peru, and the severity of the systemic symptoms, the species is most likely loxosceles laeta.   

It’s sunny and a record-setting 87 Fahrenheit here in Lexington Massachusetts. 
–CarlF

email

Anthony writes:

Tracking zoonotic pathogens using blood-sucking flies as ‘flying syringes’

https://elifesciences.org/content/6/e22069

Dave writes:

Dear host. I had a very unusual parasitic experience while shearing sheep in the Kamloops area of BC. I’m used to seeing sheep keds but on this occasion I was shearing ewes and beside her udder was a fully engorged tick (not sure what type). I noticed is as I went through it with the shears. Now generally it takes a lot to creep me but this was at the far edge of weird sh#tometer. Out of the cut in half tick came a pile of baby ticks. These were the size of pinheads but fully formed and crawling. Now I hadn’t been doing drugs or drinking or suffering from any other hallucinations that would explain this so even though I have read and heard that ticks don’t give birth to live young what is the other explanation for this.

Thanks for this in advance and sorry that it isn’t human related but most of my parasitic experiences are of the ovine kind

Dave the shearer in sunny southern AB

ps yes Dickson the fishing is great. about 2 hours west of us is the Elk river famous for float fishing

Andrea writes:

Hi Twipitos!

You have probably already seen this one:

http://www.popsci.com/rat-lungworm-hawaii-prevention

Oh boy! Now paradise is off-limits!

It’s 59°F in Seattle with rain of course!

Love the podcast. Please keep it going even though I may never send in a guess. I do enjoy listening to the cases. Even those that creep me out! I now look at all mangos with suspicion.

Monday, 17 April 2017 08:11

Entomophagy - TWiP 131

Jonathan from the podcast Arthro-Pod joins TWiP to solve the case of the Peruvian Woman With Inguinal Insect Bite, and discuss warm autoimmune hemolytic anemic that develops after babesiosis.

At Cornell University in Ithaca, New York, Vincent speaks with Susan, Colin, and Gary about the work of their laboratories on parvoviruses, influenza viruses, and coronaviruses that infect dogs, cats, horses and other mammals.

Thursday, 06 April 2017 15:11

You’re going to learn R - TWiM 149

TWiM speaks with Pat Schloss about assigning sequence data to operational taxonomic units, and his experience with mSphere Direct, a new way of submitting papers for publication.

Monday, 03 April 2017 10:04

TWiV 435 Letters

Sam writes:

Hi TWIV Team,

I just listened to TWIV 433 and while I was very interested to learn about anti-viral mechanisms in my favorite nematode worm, I have to make a few points. C. elegans is a species of self-fertilizing hermaphrodites with a very low incidence of males. While there are some male-female Caenorhabditis species (such as C. afra), this is not the case with C. elegans. N2 is standard wild-type strain of C. elegans first isolated by Sydney Brenner. Nematode growth medium (NGM) is essentially a non-selective solid bacterial medium which is generally seeded with the E. coli strain OP50, which the worms eat. The worms cannot eat the NGM itself and once the bacterial lawn is eaten, will starve (they will adopt the dauer stage and can survive without food in this way for many months).

I’m a big fan of show. Keep up the excellent work.

Sam in Toronto, Ontario.

Steve writes:

Hi Vincent et al,

Interesting programme this week.

I love all the carefully thought up entomological and morphologically descriptive words–they are so much better than the alphabet soup being used to describe biochemical entities!–: good descriptive names for the various parts and life stages enable different species to be compared, so that you can see how evolution acts on each segment of, say ‘the fundamental segmented worm’, to gradually develop ‎the increasing complexity of all the vast variety of arthropods. A good name for each structural component of the basic ‘bug construction kit’ makes it possible to describe very complex features with great accuracy, on a ‘bug blueprint’, so that readers know exactly where to look to see what you want to draw attention to.

I’m not an entomologist, and I’ve not read the paper, but, when I hear you wondering if ‘secondary sexual features’ is a mistake‎, I can imagine, that, if you are dealing with something that affects the development of an insect into functional or sterile males and females, you might want to distinguish between the functional females, and the phenotypical females that cannot reproduce (as in the case of honey bees, for example). Your authors probably mean to make sure that they can determine the effective sex ratio, separately from the outward sex ratio suggested by the visible phenotype, following each phase of the experimentation. That would be my guess if it isn’t a mistranslation.

If you want to see some more brilliant words, you might like to check out the Wiki on screwworm‎ flies, which you could then cover in TWiP, as the outbreak in Florida has just been brought under control by successive release of sterile males–which works in this species because the females only have one breeding cycle. I’m sure that Dickson would relish describing the gory details of the infestation by the live-flesh-eating ‘primary screwworm’, as compared with the dead-flesh specialising ‘secondary’ screwworm–which is also useful in estimating time of death in found corpses, and even cause of death, where poisons are found in the insects’ guts.

http://wwww.promedmail.org/post/4923534

https://en.m.wikipedia.org/wiki/Cochliomyia

_______

Knowing Kathy’s love of Lego, and, now hearing that she says she has never seen ‘Alien’, you might like to get her interested in the idea, by showing her this famous scene from the movie:

https://m.youtube.com/watch?v=ZRfNqvJ264I

And here compared, blow by blow, with the original:

https://m.youtube.com/watch?v=DU-5XEdPgYU

Love that they even included the cat. 

All the best,

Steve

Luton

Bedfordshire

England

Where Spring is sprung, the clocks have just gone forward, and wild plum blossom is ablaze in my overgrown garden. 

Jimholy (Jim-Hoe-Lee) writes:

Dear Vincent et. al

        I thoroughly enjoyed your discussion on parasitoids, everyone was friendly and made the discussion fun. At the time of this writing it is a dreary 40֯ F, there is still snow everywhere. I’d like a chance to win that book. You guys are the first science podcast I have ever listened to, as a millennial I normally consume my science via YouTube videos (most notably scishow). I am a senior Molecular Biology major at Skidmore College taking Dr. Hilleren’s Virology, RNA and Biology of Cancer classes, so there is a fair amount overlap between the classes.

In China, they have already begun genetically engineering 3n human embryos to cure lung defects. https://link.springer.com/article/10.1007%2Fs13238-015-0153-5. What are your thoughts on genetically the engineering the viruses to skew the sex ratio in the other direction as a way form of improving pest control? There is a C2c2 CRISPR derived system that can edit targeted mRNAs.  http://science.sciencemag.org/content/early/2016/06/01/science.aaf5573

Sincerely,

Jimholy (Jim-Hoe-Lee)

P.S In traditional Chinese symbolism the Yin-yang each swatch contains the seed of its opposite, I thought it was a clever play on symbolism where you would have the seed of male skewing viruses inside of the females (not sure how intended that was). In standard Mandarin Pronunciation Song is pronounced (Soong), and zhe (zh-ugh) (like you’re soft grunting), he (h-ugh). I really appreciate that you guys trying to get the pronunciations correctly.

Eric Delwart writes:

Dear Vincent and Twivome

This study shows how human genomic data can be repurposed or mined to analyze a part of the human virome. To put the scale of the analysis in context: The 1 petabyte amount of data used here is the equivalent of 100 thousand runs of the smaller MiSeq Illumina machine typically used for viral genomes. The amount of data restricted the analysis to finding viruses using nucleotide sequence similarity only, rather than the computationally much more demanding translated protein similarity searches needed to detect divergent (ie “new”) viruses. The focus was on a small fraction of that starting data (~0.000005) that matched viral sequences.

As most of the people sampled were likely healthy, the viruses detected, with a few exceptions, are typical commensal blood borne viruses. The focus on blood cells left out the large majority of human viruses that are usually restricted to respiratory, skin, or enteric tissues.  Because of the way human genomes are sequenced the viruses detected were largely limited to those that are associated with blood cells and have double stranded DNA genomes or at least form a dsDNA during their replication cycle. The dominance of the Herpesviridae reflects the focus on cellular DNA rather than plasma where these viruses are more rarely detected.  Anellovirus were also commonly detected despite their single stranded circular DNA genome likely because they were caught in the act of replicating as rolling circle dsDNA intermediates. As expected the very common blood borne RNA pegiviruses (in Flaviviridae family) were not detected.

As you often state in TWIV finding viral genomes does not prove that the virus is infectious. Sequences from viruses known to replicate in bacteria, algae, amoeba, or fungi were also detected likely reflecting DNA contamination in the many reagents used to generate human genome libraries. Human tropism for these viruses has not been shown. Papillomaviruses and polyomaviruses sequences where also detected despite their known tropism being restricted to epithelial cells. Their detection in blood may reflect either other sites of replication or sample contamination with skin cells during phlebotomy.  

So despite the bias of the starting material (blood cells), focus on dsDNA, and lower sensitivity relative to targeted PCR studies, the study shows that analysis of raw human genomic data can reproduce the known epidemiology for some viruses like the higher prevalence of HTLV proviruses in people of African ancestry. If similarly analyzed the growing amount raw human genomic data will allow large scale epidemiology for blood cell associated dsDNA viruses. Data from the major human populations located in either their ancestral or new homes may facilitate studies of the relative roles on these infections of human genetics versus geography and lifestyle. By combining the human genomic and viral information the identification of human genome polymorphisms associated with particular infections or high viral loads will also become possible.  

Lots of these analysis will depend on available computing power. Maybe Facebook, Google or Amazon will have some to spare?

Andrea writes:

Suggestion, perhaps you could pick a random email out of the emails that you receive in a specific amount of time, say two weeks for example, this way people that listen to the podcast early and send in an email have the same chances as those that listen later.

I am assuming, of course, that you want to get the contest over as early as possible so that you can continue to clean out your office of all the extra books.

Seattle

Ken writes:

Vincent & Crew-

When I heard you were giving away books, I assumed they’d be gone long before I could type your address on my email. If you have not yet, please consider this submission.

I have been listening for a little over a year, since my friend Lauriel introduced me while we were talking about her research on AAV. She met you in Portland, and I remember hearing about your trip on TWIV.

I was also pleased to hear you read her email detailing the capsid proteins, on which her thesis was written.

I am a software engineer, and my knowledge of viruses is very limited, but I am a huge fan of science, and learn as much as I can find the time for. That is why I love listening to TWIV. I have to pause often and look up terms and papers– it keeps me on my toes. Keep up the good work!

P.S. It is cloudy, windy, and about 10°C here in Portland today, with a lot of rain in the forecast.

Ken

Alexandra writes:

The emerging infections book is still up for grabs! I just got into the wonderful world of viruses three months ago & you have definitely infected me with great fascination.

Alexandra Ortiz Rosa, M.Sc.

Virology Laboratory Research Assistant

Department of Microbiology & Medical Zoology

University of Puerto Rico – Medical Sciences Campus

Donna writes:

Dear TWiV crew

I heard on TWIV 428 that you had not yet received email #27 for the Emerging Infections book – would  be great to add this to my collection. Even if I’m not the winner, I want to thank you for the TWiV podcasts

I’ve been listening since the Joan Steitz interview. My graduate work was in virology (VSV inhibition of splicing in Jack Keene’s lab in the 1980s). I meandered into other topics for postdoc and beyond.  I am a lecturer at RPI (non-tenure track: 10+ years) where I teach a variety of  molecular biology-related courses. I was excited when Virology was added to my teaching duties in 2015; this led me to your podcast via ViralZone.

I especially enjoyed your discussion of VSV UV inactivation as that was a technique I used extensively in my graduate work.

Thanks so much for your podcasts

donna

Donna E. Crone, PhD

Lecturer

Rensselaer Polytechnic Institute

Dept of Biological Sciences

Neil writes:

“Sparrow Urgent Care Physician Dr. Song Yu says although it feels similar to the flu, it’s actually a virus.”

Some other good quotes from this MD in the article:  http://wlns.com/2017/02/19/viral-infection-going-around-mid-michigan-how-you-can-protect-yourself/

Maybe Kathy can try to do some in-state education…

Wow.

PS to add to the other podcasts list: Freakonomics. Especially my listener pick, 3 episodes called “Bad Medicine”…  

http://freakonomics.com/podcast/bad-medicine-part-1-story-98-6/

http://freakonomics.com/podcast/bad-medicine-part-2-drug-trials-and-tribulations/

http://freakonomics.com/podcast/bad-medicine-part-3-death-diagnosis/

———————————————————–

Neil Parkin, Ph.D.

Data First Consulting, Inc

Belmont, CA

Sidd writes:

Hi TWIV team!

It’s 6C in Saint Louis, and I’d love to get a copy of the Emerging Infectious Diseases book!

I’m a PhD candidate at WashU studying RNA phages and viral dark matter. I’ve been listening to your podcast for about 8 years now (primarily TWIV and TWIM) and I think it’s great!

Thanks!

Sidd

Page 1 of 114

TPL_asm2013_ADDITIONAL_INFORMATION

TPL_asm2013_SEARCH

73545:vincentracaniello