February 2015

RK:HMP - 4.5Tb of sequence data; saved as a graphical PCA plot; each cluster per body site (oral, skin etc.) #AGBT15

9:44am February 28th 2015 via Hootsuite

RK:Also impt for drug responses - acetominophen's effect on liver toxicity depending on microbes in the gut #AGBT15

9:41am February 28th 2015 via Hootsuite

RK: What do our microbes do? Perh why you get more mosquito bits NB: his TED talk Feb 14 online here: http://t.co/fpbLOQeTTR #AGBT15

9:39am February 28th 2015 via Hootsuite

Rob Knight, UnivColorado, Boulder: Dynamics of the Human Microbiome and its Evolving Genomes #AGBT15

9:38am February 28th 2015 via Hootsuite

MF:Q:What abt biofilms? A:Pseudomonas has efflux pumps, Fe-chelating molecules. Still many exported/imported molecules #AGBT15

9:37am February 28th 2015 via Hootsuite

MF:Q:Other bact resistant? A:G+ pathogens seem sensitive (vaginal); broader Q in soil, how do these grow? Perh not growing as fast #AGBT15

9:36am February 28th 2015 via Hootsuite

MF:Q:G+ organisms, potent but resistance? A:Most have mech of host-resistance; say a pump for efflux #AGBT15

9:35am February 28th 2015 via Hootsuite

RT @CIgenomics: MF: "What are the top ten molecules in your gut" no-one knows! And they probably differ in individuals; #AGBT15 http://t.…

9:34am February 28th 2015 via Twitter Web Client

With MF's opening talk, what a great and fun way to start the day! (From a standing start to 100mph.) #AGBT15

9:33am February 28th 2015 via Hootsuite

MF: They are present in high concentrations, change from indiv to indiv, and are present for years #AGBT15

9:32am February 28th 2015 via Hootsuite

MF: What are the top 10 spp. in your gut? But what about gut metabolites? Busy slide with dozens. There in high conc. #AGBT15

9:31am February 28th 2015 via Hootsuite

MF: What are the microbiota doing to each other; what are they doing to the host? Now metatranscriptomic reads (very few datasets) #AGBT15

9:30am February 28th 2015 via Hootsuite

MF: Thousands of potent drug-like molecules synthesized all around us (!) #AGBT15

9:30am February 28th 2015 via Hootsuite

MF: Microbiota 'do an end-run - they make these compounds and they are there' #AGBT15

9:29am February 28th 2015 via Hootsuite

MF: Lactocillin ID'd - a potent antibiotic against gram-neg. 'It overturns a paradigm - drug companies dev - FDA app - people' #AGBT15

9:29am February 28th 2015 via Hootsuite

MF: Thiopeptides from the human microbiota (again Donia et al ref), found mutant vs WT - spectra shows significant. 120L grown up #AGBT15

9:28am February 28th 2015 via Hootsuite

MF: A family of molecules, a 'little bit of biochemical modification by the bacteria' #AGBT15

9:28am February 28th 2015 via Hootsuite

MF: Found family of BGC's for thiopeptide antibiotics - 13 post-transl mods (!), incl. pyrimidine ring http://t.co/ZtWVyyx85b #AGBT15

9:27am February 28th 2015 via Hootsuite

MF: Three thiopeptide antibiotics, real drugs. Bind 50S subunit, potent against G+ bact. Harms 2008 paper http://t.co/ysV1en2JIB #AGBT15

9:25am February 28th 2015 via Hootsuite

MF: Complex chemically, and how much business it could mean (!!) #AGBT15

9:24am February 28th 2015 via Hootsuite

MF: Ave gut has 599 gene clusters; ave oral cavity, 1,061 gene clusters. Saccharides predominate; well-studied BGC 'are rare' #AGBT15

9:24am February 28th 2015 via Hootsuite

MF: 44K predicted biosynthetic gene clusters; 14K in known classes; 3.1K BCG's in HMP metagenomic data. #AGBT15

9:23am February 28th 2015 via Hootsuite

MF: Next - ID gene clusters in the microbiome. 3K biosynthetic gene clusters from the HMP (2.3K genomes) http://t.co/FoZnsoXUP4 #AGBT15

9:22am February 28th 2015 via Hootsuite

MF: Carotenoids from Gram-pos, APEs Gram-neg have >1000 clusters. "No one ever thought it was this wide" #AGBT15

9:21am February 28th 2015 via Hootsuite

MF:One of the most widely distributed biochemical synthetic pathways on the planet. Onto cartenoid pigments - 870 clusters #AGBT15

9:20am February 28th 2015 via Hootsuite

MF: APE ec/vf the largest family in the database; both discovered previously never connected. 'A chemical marker' for xanthomonadin #AGBT15

9:20am February 28th 2015 via Hootsuite

MF: What are the biosynth functions most unknown, not seen before for active biomolecules? Gram-neg 'large family of gene clusters' #AGBT15

9:18am February 28th 2015 via Hootsuite

MF: Oligosacch - hard to study, hard to char, but via MS/NMR the 'payoff is going to be huge'. Perh most impt molecules synthesized #AGBT15

9:18am February 28th 2015 via Hootsuite

MF: A broader view of the biosynthetic world - edge and node graph between genes, you can see largest network oligosaccharides #AGBT15

9:17am February 28th 2015 via Hootsuite

MF: 30K putative biosynt gene clusters (!!), via their bioinformatic method 2014 Cell paper http://t.co/uhDrwJurtL : #AGBT15

9:16am February 28th 2015 via Hootsuite

MF: 'Genomics reveals cryptic natural products' - sequence reveals what it is doing, rather than going to the corners of the earth #AGBT15

9:15am February 28th 2015 via Hootsuite

MF:Justification of forward genetics method - for erythromycin, 2007 Nature Biotech http://t.co/EfaSIntPDR #AGBT15

9:14am February 28th 2015 via Hootsuite

MF: From gene cluster to molecule - genes, domains mapped, make high res predictions, then pred structure 'all on the computer' #AGBT15

9:13am February 28th 2015 via Hootsuite

MF: Connecting molecules to genes - 750 known examples. Very slow, also we learn about known molecules, not unk ones #AGBT15

9:11am February 28th 2015 via Hootsuite

MF: Recently forward genetics. 150 examples where genes have been discovered '98 pub http://t.co/6ublnr04LK Chloroeremomycin #AGBT15

9:11am February 28th 2015 via Hootsuite

MF: The old paradigm - quite alive today, similar to when penicillin discovered; chemical purified from supernatants then screened #AGBT15

9:09am February 28th 2015 via Hootsuite

MF: Daptomycin synthetase - ~3000 kDa (!) 37 proteins, to make 1 small molecule. Why this kind of devotion! #AGBT15

9:08am February 28th 2015 via Hootsuite

MF: How to microbes interact w/each other, and w/human hosts? And - nature products- 2003 Newman review http://t.co/6pyXgGoe97 #AGBT15

9:08am February 28th 2015 via Hootsuite

Michael Fischback, UCSF: Insights From a Global View of Secondary Metabolism: Small Molecules From the Human Microbiota #AGBT15

9:06am February 28th 2015 via Hootsuite

RT @CLCbio: Aaand, the official Arcade Champ of #AGBT15 is... Miguel from Vanderbilt! By a large margin, even. Congratulations! http://t.co…

6:58am February 28th 2015 via Hootsuite

Part 3 - first goats, then sheep. RT @washingtonpost: Map: Llamas are literally everywhere http://t.co/i5iOd7C6R2 http://t.co/6GIFkgPWSW

6:20am February 28th 2015 via Hootsuite

fMRI in PNAS RT @wef: How the language you speak changes your brain http://t.co/fdFexk2BUy #neuroscience http://t.co/3emMVRvbdy

5:15am February 28th 2015 via Hootsuite

RT @vocativ: Here's NASA's First Global Map of Rainfall and Snowfall by @JoshKrisch http://t.co/WMdOPmmihx http://t.co/xfwOx7UUWX

4:10am February 28th 2015 via Hootsuite

RT @OmicsOmicsBlog: The ability of @DaleYuzuki to live tweet with URLs to key references never fails to impress me #agbt15

1:10am February 28th 2015 via Hootsuite

The 6 Issues That Will Guide the Future of Museums http://t.co/giXHjdVhFk

11:45pm February 27th 2015 via Hootsuite

VM:Q:Ever notice chimeric Pacbio reads? A:No, but something to look at #AGBT15

9:22pm February 27th 2015 via Hootsuite