All posts; Tags Include "Synthetic Biology"
- October 5, 2016
- 09:06 AM
- 211 views
Of microbes and men: Evolving as one and terraforming earth
by gdw in FictionalFieldwork
Me and my microbes In the past decade or so, the microbiota, the community of microbes that makes its home in the guts of humans and other animals, has become quite a popular research topic. Quite rightly so, since our little guests seem to affect aspects of our lives that we wouldn’t necessarily consider to […]... Read more »
Faria VG, Martins NE, Magalhães S, Paulo TF, Nolte V, Schlötterer C, Sucena É, & Teixeira L. (2016) Drosophila Adaptation to Viral Infection through Defensive Symbiont Evolution. PLoS genetics, 12(9). PMID: 27684942
Solé RV, Montañez R, & Duran-Nebreda S. (2015) Synthetic circuit designs for earth terraformation. Biology direct, 37. PMID: 26187273
- September 22, 2016
- 09:27 AM
- 248 views
Will tardigrades get humanity into space?
by gdw in FictionalFieldwork
The mighty water bear Tardigrades, aka water bears, are tiny animals that can be found just about everywhere on earth, with a slight preference for the moisture in moss. They happily amble along on their four pairs of legs and slurp up plant cells, algae, and even smaller invertebrates that can’t get away fast enough […]... Read more »
Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Nishimura EO, Tintori SC, Li Q, Jones CD, Yandell M.... (2015) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proceedings of the National Academy of Sciences of the United States of America, 112(52), 15976-81. PMID: 26598659
Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, & Blaxter M. (2016) No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. Proceedings of the National Academy of Sciences of the United States of America, 113(18), 5053-8. PMID: 27035985
Hashimoto T, Horikawa DD, Saito Y, Kuwahara H, Kozuka-Hata H, Shin-I T, Minakuchi Y, Ohishi K, Motoyama A, Aizu T.... (2016) Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein. Nature communications, 12808. PMID: 27649274
- September 8, 2016
- 09:16 AM
- 278 views
CRISPR on my plate, and some GMO’s on the side
by gdw in FictionalFieldwork
A CRISPR recipe Less than a month ago, the world’s first official CRISPR/Cas9 meal was served. CRISPR/Cas9 is a fairly new technology to edit genomes, and cut and paste genes at will. Well, it’s not exactly that new. It’s actually been around for a long time. CRISPR, or *humhum* Clustered regularly interspaced short palindromic repeats […]... Read more »
Snell C, Bernheim A, Bergé JB, Kuntz M, Pascal G, Paris A, & Ricroch AE. (2012) Assessment of the health impact of GM plant diets in long-term and multigenerational animal feeding trials: a literature review. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 50(3-4), 1134-48. PMID: 22155268
Panchin AY, & Tuzhikov AI. (2016) Published GMO studies find no evidence of harm when corrected for multiple comparisons. Critical reviews in biotechnology, 1-5. PMID: 26767435
- September 1, 2016
- 10:19 AM
- 296 views
Responsible resurrection: The ecology of de-extinction
by gdw in FictionalFieldwork
March of the mammoths Improvements in our genetic tinkering capabilities have led several people to suggest potential uses for our newfound powers. Although we ought to add some nuance and note that those powers are still in development. In any case, one of those powers is quite impressive. De-extinction, or the process of bringing back […]... Read more »
Seddon PJ, Griffiths CJ, Soorae PS, & Armstrong DP. (2014) Reversing defaunation: restoring species in a changing world. Science, 345(6195), 406-12. PMID: 25061203
McCauley, D., Hardesty-Moore, M., Halpern, B., & Young, H. (2016) A mammoth undertaking: harnessing insight from functional ecology to shape de-extinction priority setting. Functional Ecology. DOI: 10.1111/1365-2435.12728
- May 25, 2016
- 09:00 AM
- 601 views
Are our gut bacteria the key to immortality?
by gdw in FictionalFieldwork
The fight against aging Ever since the ancient Sumerians, men has sought eternal life. We still do. Anti-aging science has become quite an industry. As we dive deeper and deeper into our biological foundations, we’re learning more and more about how and why we age. A lot of mysteries remain, but there’s still talk about […]... Read more »
De Winter, G. (2014) Aging as Disease. Medicine, Health Care and Philosophy, 18(2), 237-243. DOI: 10.1007/s11019-014-9600-y
Biagi E, Franceschi C, Rampelli S, Severgnini M, Ostan R, Turroni S, Consolandi C, Quercia S, Scurti M, Monti D.... (2016) Gut Microbiota and Extreme Longevity. Current biology : CB. PMID: 27185560
- May 10, 2016
- 07:40 AM
- 441 views
Do dragons dream of tasty crickets?
by gdw in FictionalFieldwork
(Also appeared on United Academics) Sleep cycles When we leave the day behind us and nestle ourselves in our cosy beds, we sleep. Sleep, however, comes in stages that repeat themselves. It’s a five-stage cycle that last about 90 minutes in humans. Four stages of non-REM sleep are followed by a period of REM (Rapid […]... Read more »
Ólafsdóttir HF, Barry C, Saleem AB, Hassabis D, & Spiers HJ. (2015) Hippocampal place cells construct reward related sequences through unexplored space. eLife. PMID: 26112828
Shein-Idelson M, Ondracek JM, Liaw HP, Reiter S, & Laurent G. (2016) Slow waves, sharp waves, ripples, and REM in sleeping dragons. Science (New York, N.Y.), 352(6285), 590-5. PMID: 27126045
- April 15, 2016
- 09:12 AM
- 553 views
Rewriting life: Adding letters to the ABC of DNA
by gdw in FictionalFieldwork
(Also appeared on United Academics.) The alphabet of life The grand tale of life is long and complicated. Storylines intertwine and many subplots twist and turn unexpectedly. Amazingly, this billion-year-spanning story is written in an alphabet that contains only four letters, the alphabet of DNA. A for adenine, C for cytosine, G for guanine, and […]... Read more »
Malyshev DA, Dhami K, Lavergne T, Chen T, Dai N, Foster JM, Corrêa IR Jr, & Romesberg FE. (2014) A semi-synthetic organism with an expanded genetic alphabet. Nature, 509(7500), 385-8. PMID: 24805238
- March 28, 2016
- 11:00 PM
- 435 views
Minimum Viable Cell
by Paco Jariego in Mind the Post
Craig Venter is on a quest to find the Minimal bacterial genome. It seems the task is 70% complete now. We still don’t understand 30% of the minimum viable organism that we are able to build today, which means that, although we cannot understand what we cannot build, we need not necessarily understand what we can build.... Read more »
Hutchison, C., Chuang, R., Noskov, V., Assad-Garcia, N., Deerinck, T., Ellisman, M., Gill, J., Kannan, K., Karas, B., Ma, L.... (2016) Design and synthesis of a minimal bacterial genome. Science, 351(6280). DOI: 10.1126/science.aad6253
- February 29, 2016
- 07:30 AM
- 582 views
I love thial-S-oxides so much I cry
by Shane Caldwell in Helical Translations
What exactly is behind the tear-inducing chemical in onions?... Read more »
Eady CC, Kamoi T, Kato M, Porter NG, Davis S, Shaw M, Kamoi A, & Imai S. (2008) Silencing onion lachrymatory factor synthase causes a significant change in the sulfur secondary metabolite profile. Plant physiology, 147(4), 2096-106. PMID: 18583530
- February 9, 2016
- 12:00 PM
- 545 views
WATCH: Cockroach-Inspired Robots Could Save You
by Jenny Ludmer in Rooster's Report
The fear of cockroaches is so common there’s a name for it, katsaridaphobia. And yet, there are apparently scientists out there with nerves of steal. By working with these creepy critters, they’ve actually created a roach-inspired robot. Just like the real thing, it can slither through tiny cracks, and if it doesn’t scare the dickens out of you, it might just save your life one day.... Read more »
Kaushik Jayarama, & Robert J. Fulla. (2016) Cockroaches traverse crevices, crawl rapidly in confined spaces, and inspire a soft, legged robot. PNAS. info:/10.1073/pnas.1514591113
- December 2, 2015
- 09:45 AM
- 519 views
Video Tip of the Week: KBase, DOE’s Systems Biology Knowledgebase
I’ve been following the development of KBase for a long time. A couple of times I started draft blog posts to highlight them. But it always seemed like they were just about ready to launch some new features-so I figured I’d wait-or they had a beta interface in testing and about to change a lot […]... Read more »
Benedict, M., Mundy, M., Henry, C., Chia, N., & Price, N. (2014) Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models. PLoS Computational Biology, 10(10). DOI: 10.1371/journal.pcbi.1003882
Wilke, A., Bischof, J., Harrison, T., Brettin, T., D'Souza, M., Gerlach, W., Matthews, H., Paczian, T., Wilkening, J., Glass, E.... (2015) A RESTful API for Accessing Microbial Community Data for MG-RAST. PLoS Computational Biology, 11(1). DOI: 10.1371/journal.pcbi.1004008
- November 11, 2015
- 08:40 AM
- 759 views
Where Do All Those Leaves Come From?!
by Mark Lasbury in The 'Scope
As you grab your rake or leaf-blower this fall, you might wonder how it is possible for trees to make so many leaves. Learn where they all came from.... Read more »
Pijpers, J., Winkler, M., Surendranath, Y., Buonassisi, T., & Nocera, D. (2011) Light-induced water oxidation at silicon electrodes functionalized with a cobalt oxygen-evolving catalyst. Proceedings of the National Academy of Sciences, 108(25), 10056-10061. DOI: 10.1073/pnas.1106545108
- August 7, 2015
- 07:38 AM
- 913 views
Seeing With Bionic Eyes!
by Viputheshwar Sitaraman in Draw Science
Pulse trains to percepts: the challenge of creating a perceptually intelligible world with sight recovery technologies.... Read more »
Fine I, & Boynton GM. (2015) Pulse trains to percepts: the challenge of creating a perceptually intelligible world with sight recovery technologies. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 370(1677). PMID: 26240423
- December 7, 2014
- 11:23 AM
- 940 views
Synthetic gene circuits with a memory!
Imagine having a USB port in the body that we could use to insert a "flash drive" and transfer genetic data, therapies, or monitoring devices. The flash drive would have to be some kind of removable biological entity that has no problem getting in and out of the body. If you think about it, bacteria are the perfect candidates to be such devices. So, what if bacteria could be used as storage for genetic memory? This is not so far-fetched if you think that recent studies have shown for example tha........ Read more »
Ausländer D, Ausländer S, Charpin-El Hamri G, Sedlmayer F, Müller M, Frey O, Hierlemann A, Stelling J, & Fussenegger M. (2014) A synthetic multifunctional mammalian pH sensor and CO2 transgene-control device. Molecular cell, 55(3), 397-408. PMID: 25018017
Farzadfard, F., & Lu, T. (2014) Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science, 346(6211), 1256272-1256272. DOI: 10.1126/science.1256272
- November 4, 2014
- 08:00 AM
- 1,255 views
Where Do All Those Leaves Come From?!
by Mark E. Lasbury in The 'Scope
You rake leaves and lug them to the curb, or you push them into your neighbor’s yard with your blower. Either way, do you know where the matter/mass in all those leaves comes from? You won’t believe the answer. But the leaf may be passé. New research is showing how artificial leaves can produce oxygen for space travel and hydrogen for fuel cells.... Read more »
Pijpers, J., Winkler, M., Surendranath, Y., Buonassisi, T., & Nocera, D. (2011) Light-induced water oxidation at silicon electrodes functionalized with a cobalt oxygen-evolving catalyst. Proceedings of the National Academy of Sciences, 108(25), 10056-10061. DOI: 10.1073/pnas.1106545108
- October 15, 2014
- 08:00 AM
- 1,172 views
Frankenstein Meets Genetic Modification
by Mark Lasbury in As Many Exceptions As Rules
Halloween conjures up monsters, like Mary Shelly’s Frankenstein. Her story is just as applicable for us today – the story of science being responsible for what it creates. The so-called Frankenfoods are called dangerous – but why? Studies that label them dangerous have been retracted or are merely correlative. New studies have shown that genetically modified crops are safe for livestock and humans. However, there are valid concerns, so every GMO must be tested rigorously.... Read more »
Goldstein, D. (2014) Tempest in a Tea Pot: How did the Public Conversation on Genetically Modified Crops Drift so far from the Facts?. Journal of Medical Toxicology, 10(2), 194-201. DOI: 10.1007/s13181-014-0402-7
Tufarelli V, & Laudadio V. (2013) Genetically Modified Feeds in Poultry Diet: Safety, Performance and Product Quality. Critical reviews in food science and nutrition. PMID: 24915369
Van Eenennaam AL, & Young AE. (2014) Prevalence and impacts of genetically engineered feedstuffs on livestock populations. Journal of animal science, 92(10), 4255-78. PMID: 25184846
Snell C, Bernheim A, Bergé JB, Kuntz M, Pascal G, Paris A, & Ricroch AE. (2012) Assessment of the health impact of GM plant diets in long-term and multigenerational animal feeding trials: a literature review. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 50(3-4), 1134-48. PMID: 22155268
McCall WV, Andrade C, & Sienaert P. (2014) Searching for the mechanism(s) of ECT's therapeutic effect. The journal of ECT, 30(2), 87-9. PMID: 24755719
- October 9, 2014
- 12:35 PM
- 773 views
Keep Calm and Evolve On
by Lauren Richardson in PLOS Biologue
Lauren Richardson, Associate Editor for PLOS Biology, discusses a new paper published in the journal. We generally think of evolution as a beneficial process, letting organisms adapt and excel in new and different environments. But as we all know, not … Continue reading »The post Keep Calm and Evolve On appeared first on PLOS Biologue.... Read more »
Szamecz, B., Boross, G., Kalapis, D., Kovács, K., Fekete, G., Farkas, Z., Lázár, V., Hrtyan, M., Kemmeren, P., Groot Koerkamp, M.... (2014) The Genomic Landscape of Compensatory Evolution. PLoS Biology, 12(8). DOI: 10.1371/journal.pbio.1001935
- July 30, 2014
- 08:10 AM
- 1,000 views
Does Life Come In XXXS?
by Mark Lasbury in As Many Exceptions As Rules
Is there a minimum size for life? How would you measure it, cell volume or genome size? People do both. The current minimum example of life is Mycoplasma genitalium, at just 200 nm by 600 nm in well-fed cultures. M. genitalium also has the smallest known genome for a free-living organism (520 genes, we have about 27,000). Some organisms have fewer genes (137 or so) but are endosymbionts, so they can get away with trashing some of their DNA. New research shows that M. genitalium is a pathogenic o........ Read more »
Manhart LE. (2013) Mycoplasma genitalium: An emergent sexually transmitted disease?. Infectious disease clinics of North America, 27(4), 779-92. PMID: 24275270
Wu CY, Young L, Young D, Martel J, & Young JD. (2013) Bions: a family of biomimetic mineralo-organic complexes derived from biological fluids. PloS one, 8(9). PMID: 24086546
Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM.... (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science (New York, N.Y.), 329(5987), 52-6. PMID: 20488990
- June 3, 2014
- 02:00 PM
- 1,039 views
Will genetically engineer bacteria for Biofuel
by Dr. Jekyll in Lunatic Laboratories
Utter the word biofuel in the wrong circles and someone is likely to be stabbed. Let’s just say that the topic can be polarizing, but for good reason. Biofuel offers […]... Read more »
Daehwan Chung, Minseok Cha, Adam M. Guss,Janet Westpheling. (2014) Direct conversion of plant biomass to ethanol by engineered Caldicellulosiruptor bescii. Proceedings of the National Academy of Sciences. info:/10.1073/pnas.1402210111
- June 3, 2014
- 09:56 AM
- 800 views
Gene Scissors
by Viputheshwar Sitaraman in Draw Science
Gene scissors allow scientists to cut out any gene: a dream for gene therapy! [Infographic]... Read more »
Gaj, T., Gersbach, C., & Barbas, C. (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in Biotechnology, 31(7), 397-405. DOI: 10.1016/j.tibtech.2013.04.004
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