TWiV 214
Rich writes:
Rich writes:
Dear TWiX gang,
Rich stumbled and fell again in TWiV 213 over polydnavirus nomenclature. You would think that after all these years he’d get it straight. Bracoviruses and Ichnoviruses refer to two different lineages of polydnaviruses. They both package multiple circular dsDNAs and have similar life cycles, however they inhabit different families of wasp, they have different capsids and modes of egress, and they package and deliver different host genes. These facts suggest independent evolution. Nudivirus refers to a modern dsDNA containing insect virus that is most like the virus that probably integrated into the wasp genomes long ago to provide the capsid and transcription genes that contribute to polydnavirus replication.
Get it right next time.
Love the show.
Rich
Richard Condit
Trudy writes:
Hi TWiVers,
I’m writing this email in response to Rich’s comment about Nudiviruses in episode 213. In my prep notes for this episode (since I was a guest on this particular episode 179), I made the following summary to help me understand the relationship between Bracoviruses and Nudiviruses:
“The hypothesis is that the viral origin of these Bracoviruses goes back to Nudiviruses, which are large dsDNA viruses that are closely related to the Baculoviridae and which often establish persistent infections in arthropods. In this paper, they did a deep sequencing analysis of both viral and wasp genes during replication of Bracoviruses, to address the question of whether other nudivirus-like genes exist or whether the genes identified to date are present in all Bracovirus-carrying wasps.”
I hope this helps!
And I really didn’t mean to insinuate that Alan is SHORT. He just SOUNDS really tall.
Happy New Year!!
Trudy
Winkler writes:
Dear TWIV panelists,
I never miss an entire podcast — THANKS!
Please allow me to expand on Alan’s point that the human genome is now being examined to predict idiosyncratic drug reactions, as it is to understand viral susceptibility and virulence.
I played a small part in the very first use of pharmacogenomics in clinical medicine. This was a multicenter, multinational effort spearheaded by GSK, the company that previously started modern antiviral therapy (acyclovir) and antiretroviral therapy (AZT). We found that subjects who have the B*5701 HLA marker might experience a fatal allergic reaction when exposed to the antiretroviral drug abacavir. HLA B*5701 negative individuals are not at risk for this side effect. Now, all patients get this blood test before abacavir is prescribed.
Thanks again for keeping me so informed about the rapid evolution of virology.
Winkler, MD
Robin writes:
Educated by TWIV
As mentioned by Dr. Firestein, teaching is lighting fires rather than filling buckets.
Well, a small fire was lit in this retired Emergency Physician:
Thanks to TWIV I looked up Wikipedia and discovered that placental mammals appeared before the extinction of the dinosaurs, 75 million years ago according to paleontology, and up to 100 million years ago according to molecular phylogenetics.
Appreciate TWIV for all it does.
Howard writes:
Hi Vincent,
During your recent conversation with Stuart Firestein, he mentioned the first President of Israel Chaim Weizmann had been trained as a chemist but had not worked as one. Although better remembered now as one of the early proponents of the 20th century Zionist movement to create a home land for the Jewish People, it was his brilliance as a scientist that prepared the way for his passion to become a reality.
Weizmann was a pioneer of using large scale fermentation to create industrial chemicals. He developed the ABE process using Clostridium acetobutylicum to produce acetone, butanol, and ethanol (3:6:1 ratio) from anaerobic fermentation of starch. Weizmann’s adopted nation of the United Kingdom had a munitions problem during WW1 because the main supplier of acetone used to make the explosive cordite had been Germany. Several British breweries were commandered to use Weizmann’s ABE process which enabled the UK to continue munitions manufacture. The acknowledgement of this and a couple of additional chemistry based achievments led to the next steps. Weizmann had known former UK Prime Minister Balfour for quite a while and is believed to have been crucial in developing the Balfour Declaration of 1917 promising creation of a homeland for Zionists in Palestine. The Weizmann-Prince Faisel agreement in post war negotiations was also helpful when Faisel became the First King of the newly created country of Iraq. The rest of the story is too well known to go into but although he was honored as Israel’s first President for his political efforts, these were made possible because of his scientific contributions. There is a current ironic twist to the story. Although it’s been said that God gave Israel everything but oil, modern versions of Weizmann’s ABE process may make enormous petroleum reserves less valuable. The primary product of the process is butanol which can be used as a direct replacement for gasoline as a transportation fuel and unlike ethanol, has equivalent power density and can be shipped by pipeline. The process can be carbon neutral but production still needs to be made more efficient which several university and commercial labs are doing.
This may be an example for Dr. Firestein’s hope for more basic science since when Beijerinck first isolated this anaerobic bacterium he was just describing the range of environmental microorganisms that were not involved in disease processes and was probably amazed at it’s eventual use.
Another topic: I am looking forward to being in the audience at the ASM General Meeting in Denver this year for recording of a new episode of your wonderful series.
Best regards,
Howard
Jennie writes:
Dear TWiVome,
I was very interested in your thoughtful discussion of Chadwick’s letter in Episode 213 and the challenges of balancing a science career with raising a family. As a person raised by two scientists, I thought you might be interested in what it is like from this side of the bench.
My father was a doctoral student in biology when I was born, and my brother was born during Dad’s first year as a postdoc. My mother went back to school for her doctorate in molecular biology when my brother and I were in elementary school, and I was in high school when she received her degree.
My parents both worked full time while I was growing up, but they were always home for dinner. We had family time in the evenings and on weekends, and I know my parents frequently brought work home to do after they put us to bed. I am embarrassed to say I once selfishly accused my mother of not being a “normal” mom like the stay-at-home moms of my friends, but I now appreciate that she was an incredible role model for me. It cannot have been easy to be a female doctoral student with kids during the 1970s and 80s, especially in a field like molecular biology. But my mother’s perseverence and success taught me that I could pursue my own challenging career and succeed.
What is it like to be the child of scientists? In a word: COOL. My parents’ labs were home to us. I loved going to work with my dad on the weekends. He would set us up at a bench with a roll of brown paper and some crayons and let us go to town while he and his students worked around us. His students became part of our family, and we loved the cookouts and lab parties and journal club/pizza nights at our house. My natural curiosity was constantly encouraged and reinforced by everyone in my parents’ science circles. And when it was time for science experiments for school, I had access to the kind of equipment that made it possible for me to find the LD50 for bleach in a minnow tank (and an unlucky grad student even helped clean up the mess). No one in my school could match that.
Dinner table conversation at our house was (and still is) about endangered species, electron microscopy, climate change, gels, grant proposals, Cold Spring Harbor, manuscript submissions and the agonies of academic life. Sometimes it was hard, especially when my Dad was away in the field. But I treasure the memories (and excellent stories) of being a scientist’s kid. Most kids didn’t have salamanders in their fridge, or a crocodile head in the freezer. Most kids didn’t earn money by writing out reprint cards (for Dad’s sophisticated index card filing system), 5 cents a card. Most kids couldn’t spell schistosomiasis, let alone know what it was.
Finding success while raising a family is a challenge for many professionals, including scientists. There were definitely occasions when the lab came first, and that was hard for me to understand at the time. But my parents shared their science-lives with my brother and me in ways that shaped who we are and how we think. I consider this to be a tremendous gift.
My only regret is that I never asked my Mom to show me how to do a plaque assay before she left the lab for freelance science writing. After listening to 213 TWiVs, I realize that that would have been COOL.
Cheers,
Jennie
Carolyn writes:
I just wanted to thank you both for featuring our placenta work on TWiV. I awoke to an inbox full of emails from folks who had listened to the most recent podcast (as I intend to do today). I assume you have heard this many times, but I just wanted to reiterate what a really fantastic influence TWiV has had on our graduate students (microbiology and molecular virology (MVM)) here at Pitt. By listening to TWiV, our students have been introduced to new areas of microbiology and science that they otherwise would not have been. Because of TWiV, you are directly influencing an entirely new generation of scientists, which is really quite powerful.
Thank you again,
Carolyn
Carolyn Coyne, PhD
Assistant Professor
Department of Microbiology and Molecular Genetics
University of Pittsburgh
Kelly writes:
Ni Hao TWIV Crew,
I graduated two years ago from a BS/MS program, and now work as a technician in a HIV/AIDS research lab in China, where the weather is a breezy -10˚C, and, sunny somewhere above the pollution cloud.
I wanted to contribute to the discussion on the grad student struggling at the bench, because her story was nearly my own. In high school, I was diagnosed – along with a brother and three cousins – with ADHD, after years of lost iphones, countless missing mittens, and the near-theft of my boyfriend’s car when I left the keys in the door overnight. Psychiatric care and current Rx never effectively addressed these issues (buying cheaper accessories did). Furthermore, ADHD has often been associated with creativity, and indeed, I found the medication negatively affected my artistic side – writing and drawing. I decided to go off the treatment.
Diagnoses aside, the characteristics described in her letter – good at analytical abilities, solid experiment design, synthesizing and writing papers – are aspects of how she thinks. Changing her neurology would also affect these aspects. Of course, associated attention-related errors are detrimental and even dangerous in a lab setting. As a student, I was given similar advice – that I was good at writing papers, but possibly not cut out for lab work.
Then I moved to China. There is no correlate of “ADHD” here. When I described my disability to my co-workers, they laughed. At first, I found this frustrating and considered it backward. But then, instead of discouraging me, they showed me tricks and practice to prevent attention-related errors. The saying goes measure twice, cut once. For me, it was measure five times, then double check again. Progress seemed painfully slow and meticulous, and I was assigned to monotonous, low-resource, low-risk technical work. At times, it took a weekly dose of TWIV to remind me what the heck I was doing this for. But their faith in me was encouraging. As I gained experience, I found I built up experiment habits that made execution almost mechanical. It reminded me of my years as a soccer player, where through repeated practice the body develops muscle memory. The effort and extra prep work was not fun by any standard, but I was encouraged by my PI, who saw that I was working hard and was highly motivated to pursue a career in a bio lab.
His attitude was due, in part, to the Chinese approach towards learning that, unlike the US, puts less focus on whether students are innately ‘talented’ or ‘good at certain things’ Instead, intelligence is believed to be products of how much individual effort you put into your education.
(Excellent NPR episode in this: http://www.npr.org/blogs/health/2012/11/12/164793058/struggle-for-smarts-how-eastern-and-western-cultures-tackle-learning)
I do not suggest that anyone struggling is not trying hard enough. But attitudes on whether we are ‘made’ for science direct our belief in ourselves, and our future careers. I think telling students they have a disorder, or are not ‘cut out’ for science, would be a great loss to benchwork. New ways of thinking inject new insights and new connections that might otherwise never be found.
My first year was a struggle, but the efforts have paid off. Although I still often leave my keys in the door, I do extremely well in lab, and do it quickly with few errors. I don’t think I could have reached this point enrolled in PHD program, trying to work out how to address these problems while balancing coursework and other pressures. Much of this was due to my decision to take a few years off, and having found such a supportive environment. I am applying to programs in the coming fall, and I no longer worry that my alternative thinking style, (some in the US call a ‘chemical imbalance,’) will not hinder my progress.
Anyway, thanks so much for the show, and the perspective and personal motivation it provides. I wanted to add this advice to others hoping to peruse (pursue?) careers in science – if you want something bad enough, and are willing to work long and hard enough, anything is possible.
Happy Holidays from around the globe!
新年快乐
KC
Russell writes:
TWIV
This is a follow-up to the letter from Fernando in TWIV 111 about the hantavirus outbreak in Yosemite. This is a link to a nice article in Outside describing the outbreak.
As Fernando noted in his letter, the signature tent cabins had double walls – apparently two pieces of plywood. The deer mice were happily living in the space between the walls. Also, in contrast to the canvas tents, they allowed food to be stored in these hard-walled tents. (This is in response to the bear problem.) After they figured out what was going on, they closed the double-walled tents and tried to close all of the gaps that allowed the mice to get in – a quarter inch was all that was necessary for them to get in. They reopened the tents but the mice soon returned and were happily living between the walls again. So they are tearing down the double-walled tents and replacing them with canvas tents. The critters win again.
Merry Christmas to all of you. I’m visiting my daughter in Washington State and we may have a white one. The temperature here is 6 C/43F … and rain of course.
Russ
___________________________________________
Russell Van Dyke M.D.
Section of Infectious Diseases
Department of Pediatrics
Tulane University Health Sciences Center
Jim writes:
Hi all,
Have noticed that a few of my favorite podcasts are requesting donations this time of year. You guys put on my favorites of all. Do you fund them with donations?
Jim writes:
This Quora item about academic research has a link to this 20-page PDF about applying to Ph.D. programs in computer science that may be of interest to students who are considering pursuing any Ph.D.
Regards,
Jim
Smithfield, VA
Geoffrey writes:
Dr. Et Al and Able-Minded Assistants:
Two quick notes
1) Episode 210 – As I understand it, silk worm cocoon threads are long but do not extend the entire cocoon. Chinese silk worms have a much longer thread (presumably bred for that). Indian silk worms have much shorter threads. That is why indian silk is considered slightly inferior to chinese silk.
2) Episode 212 – Haven’t heard this yet but saw Glofish mentioned on the webpage. Have you started to expand your podcast empire to include TWICG (This Week In Children’s Games)? Glofish is the famous children’s card game, right?
Thanks for the great show,
Geoffrey
Charles writes:
I was wondering if you could comment on this story and the future if using the HIV virus to deliver viral payloads.
http://www.youtube.com/watch?v=M61x6g_H7qQ
Robin writes:
Here is what some physicists think about the future of technology:
http://physics.ucsd.edu/do-the-math/2012/10/futuristic-physicists/#more-1275
Ricardo writes:
Hello Vincent and the rest of the TWIV gang. I hope for the Very best to all of You and TWIVPM.
One more nail on correlation danger.
Ricardo Magalhães
Correlation between autism diagnosis and organic food sales
http://boingboing.net/2013/01/01/correlation-between-autism-dia.html
