William writes:
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.)
- 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
Anthony writes:
Above is the Link to the artist’s Site for the Petri dish art.
Thank you.
And
Kim D’Alessandro writes about TWiM
One comment on “TWiM 125 letters”