RT @MolSystBiol: Sunney Xie's lab: RNA dynamics at sub‐minute time resolution in E coli http://t.co/WU9QICMc53 http://t.co/biTpXO9A0a
2:35pm January 14th 2015 via Hootsuite
To everyone tweeting and listening in from #PAGXXIII - many thanks for the conversations and interest! Until next year #PAGXXIV
12:30pm January 14th 2015 via Hootsuite
CW:Was able to pull out milk proteins. Natural state in mammals is lactose intolerance. Can track back to Bronze Age using MS #PAGXXIII
12:22pm January 14th 2015 via Hootsuite
CW:Was able to determine dietary gDNA sequence - 'the German diet has changed little in 900y' (!) 4 livestock spp. #PAGXXIII
12:21pm January 14th 2015 via Hootsuite
CW: Looking at periodontal disease - fig from 2014 Nature Genet http://t.co/nJMhE2lFyo #PAGXXIII
12:19pm January 14th 2015 via Hootsuite
Someday, I want to slide down into an Austrian salt mine. #PAGXXIII #bucketlist
12:14pm January 14th 2015 via Hootsuite
CW:Onto calculus: <1ng DNA/mg sample. A recent OA paleomicrobiology review: http://t.co/gWeKqceywM Dentine yield much lower #PAGXXIII
12:13pm January 14th 2015 via Hootsuite
CW: Austrian salt mine, Iran mummified; 70-80% ancient microbiome seq. 'Looks close to modern' Prominent: bifidobact. in Austria #PAGXXIII
12:07pm January 14th 2015 via Hootsuite
CW:Hinds Cave USA - very early site, very little preserved. One context: salt mines (Iron Age Celtic and Iran) #PAGXXIII
12:06pm January 14th 2015 via Hootsuite
CW: Tyrolean iceman - much rural human; dry cave - also. But vast majority of samples: just composts in-place, then preserved #PAGXXIII
12:05pm January 14th 2015 via Hootsuite
CW: Fig of coprolites - grass, sticks (!) 2012 PLOS One http://t.co/Q0PIFLhRbA Comparing across many samples & modern sources #PAGXXIII
12:04pm January 14th 2015 via Hootsuite
CW: Calculus though: fig from 2014 Nature Gen paper http://t.co/WmjjTst7HS #PAGXXIII
12:02pm January 14th 2015 via Hootsuite
CW: Ancient DNA - bone and teeth. Mummies are rare, often no organs; Some do preserve: feces in dry or cold (coprolites) #PAGXXIII
12:01pm January 14th 2015 via Hootsuite
CW: Ref 2012 Science http://t.co/oF3w36gp9H on relationship to the immune system (i.e. Crohn's) #PAGXXIII
11:59am January 14th 2015 via Hootsuite
CW: Joey shown: needs microbiome to avoid toxic effects of leaves consumed. Chart of microbial diversity by diet, obesity #PAGXXIII
11:57am January 14th 2015 via Hootsuite
CW: We are a superorganism, or a holobiont (i.e. coral reef). Microbiome term coined by Lederberg in '01. http://t.co/4nTwjf8cex #PAGXXIII
11:55am January 14th 2015 via Hootsuite
CW:One bowel movement: 9% of cells lost (!); in mouth, about 100mg. Van Leeuwenhoek's page shown. 3.3M est bact genes #PAGXXIII
11:54am January 14th 2015 via Hootsuite
CW: Human est 10T cells + 100T bacterial cells. 100T is 300x the 300B stars in Milky Way. 1.5kg of bacteria/human. Abt 1 brain #PAGXXIII
11:52am January 14th 2015 via Hootsuite
CW:"We know almost nothing about the evolution of the microbiome." Shows DAPI-stained image of tooth surface. #PAGXXIII
11:50am January 14th 2015 via Hootsuite
Last plenary: Christina Warinner (Univ OK): "Reconstructing Our Ancient Microbial Self" #PAGXXIII
11:48am January 14th 2015 via Hootsuite
GO:A2:Still looking - but engineering in cereals helpful in finding out what ancillary signals needed #PAGXXIII
11:47am January 14th 2015 via Hootsuite
GO:Q:How does a legume tell which signal is given? A:Same common signalling, nodule forms one vs another. TF not found yet #PAGXXIII
GO:Q:Has the reverse been tried in rice w/ CCaMK? A:Yes - but legume-spec xcr factors still needed. #PAGXXIII
11:44am January 14th 2015 via Hootsuite
GO:Marchantia - liverwort, is being looked at as another model, haploid, many attractive features #PAGXXIII
11:42am January 14th 2015 via Hootsuite
GO:We need this kind of throughput - as plants are so much more complex than bacteria used in synthetic biology. Biggest challenge #PAGXXIII
11:41am January 14th 2015 via Hootsuite
GO:Found barley most efficient transformation; 100's of constructs this year. Not a rapid cycle. Synth bio: 80k-100K #PAGXXIII
11:40am January 14th 2015 via Hootsuite
GO:Design, build, test, repeat: an engineering cycle. Uses GoldenGate cloning 2014 PLOS ref http://t.co/jSFfbSPUrU #PAGXXIII
11:39am January 14th 2015 via Hootsuite
GO:Looking at complementation of ccamk w/ constitutive promoters; finding which work best for which gene in legumes #PAGXXIII
11:37am January 14th 2015 via Hootsuite
GO: Engineering the NOD factor kinases upstream; downstream. 'Shown as straightforward' #PAGXXIII 2012 fig http://t.co/OzpU41nYJG
11:36am January 14th 2015 via Hootsuite
GO: Complex figure of activation shown: CCaMk+Cyclops+TF+RNAPol activates ERN1, NIN for nodulation. #PAGXXIII
11:33am January 14th 2015 via Hootsuite
GO:Downstream: have two gain-of-fn mutations (CCaMK and Cyclops) for nodulation formation. Complex map of symbiosis signalling #PAGXXIII
11:31am January 14th 2015 via Hootsuite
GO: Shows calcium spiking in rice from diff oligosaccharides. Legumes vs non-legumes: lyto-keto-oligosaccharide specificity #PAGXXIII
11:30am January 14th 2015 via Hootsuite
RT @YiliangDing: @giles oldroyd is giving a marvelous keynote talk at #PAGXXIII ----fix nitrogen in cereals!!! http://t.co/fEH4ipQoWE
11:27am January 14th 2015 via Hootsuite
GO:Simpler engineering problem: no need for calcium signalling. Cereals have it - just activate w/ Myc factor & downstream signals #PAGX
GO:Fungus at the root & can't get in. Legumes don't fn diff, just added on NOD function and later nodulation. Core conserved #PAGXXIII
11:26am January 14th 2015 via Hootsuite
GO:This myc signalling pathway at the base. Fig from 2002 TIPS ref http://t.co/MSvYTlGkvB Wheat have this pathway, unactivated #PAGXXIII
11:23am January 14th 2015 via Hootsuite
GO:Phylo tree of plant kingdom: nodulation 60MYA, but mycorrhizal about 450MYA, the earliest land plants. Thus myc everywhere #PAGXXIII
11:22am January 14th 2015 via Hootsuite
GO:Called symbiosis signalling pathway: both myc factor strigolactone (from microrrhyzo fungi) and NOD factors. #PAGXXIII
11:20am January 14th 2015 via Hootsuite
GO: 2006 Nature ref http://t.co/a0AFkeAuj8 engineered gain-of-function in CCaMK pathway, entire NOD pathway to coord. dev #PAGXXIII
11:19am January 14th 2015 via Hootsuite
GO:Ca2+ oscillations in root-hair shown - when NOD factor present. Transmitting NOD factor presence into nucleus #PAGXXIII
11:17am January 14th 2015 via Hootsuite
GO:Wt vs nsp2 mutant - can't make nodules. Assembled signal transduction pathway, for the NOD factor production. Movie root hair #PAGXXIII
GO:They are at step 1: rhizobial recognition into cereals. Steps 2-4 require more knowledge in legumes. Used forward genetics #PAGXXIII
11:16am January 14th 2015 via Hootsuite
GO:'The biggest challenge: engineering bacterial infection.' But there are simpler ways in other legumes. Env.: restrict O2 #PAGXXIII
11:15am January 14th 2015 via Hootsuite
GO:Lots of complex development, engineer in pieces. Steps: rhizobial recognition; nodule formation; bacterial inf.; environment #PAGXXIII
11:14am January 14th 2015 via Hootsuite
GO:NOD factors - showed structure from S. meliloti. Known for 25y, showed developmental process in root hair. Infection thread #PAGXXIII
11:12am January 14th 2015 via Hootsuite
GO:Legumes have to find the N2-fixing bacteria; flavenoids released from plant, NOD factors released from bacteria, nodules form #PAGXXIII
11:11am January 14th 2015 via Hootsuite
GO:Thus for small-holder famers: if 3-5kg goes to 25-50kg their yield will double or triple. Could also reduce fertilizer use #PAGXXIII
11:10am January 14th 2015 via Hootsuite
GO:Much simpler than pea: less efficient but still useful. Graph of kg ha^-1: ave 134kg max yield. Small-holders: only 3-5kg #PAGXXIII
11:09am January 14th 2015 via Hootsuite
GO:Legumes the prototype: self-fertilizing crops. A false assumption: need for nodule on a cereal root. Pea nodule the pinnacle #PAGXXIII
11:07am January 14th 2015 via Hootsuite
GO:Greatest potential is sub-Saharan Africa,. @gatesfoundation supported: Engineering the nitrogen symbiosis for Africa #PAGXXIII
11:06am January 14th 2015 via Hootsuite
