Ramu Punna (Cornell Univ) "Identifying Genetic Load By Whole Genome and Transcriptome Sequencing of Cassava Breeding" #PAGXXIII
7:43pm January 13th 2015 via Hootsuite
EM:Q:What 5 mutagens? A:EMS, MMS, but spectrum may not be wide enough. Thus the need for add'l ones #PAGXXIII
7:42pm January 13th 2015 via Hootsuite
EM: Transgenics only generated for proof-of-concept. Will do large-scale on model variety 60444. Credited @gatesfoundation #PAGXXIII
7:41pm January 13th 2015 via Hootsuite
EM: Have generated ALS kill curves. Chlorsulfuron most effective; flumetsulam and imazapyr about same. Roots most sens. #PAGXXIII
7:39pm January 13th 2015 via Hootsuite
EM:They are optimizing mutagenesis; 5 mutagens tested, 5K plantlets, 2K sent for sequencing. Showed mutant phenotypes #PAGXXIII
7:37pm January 13th 2015 via Hootsuite
EM: KeyGene lots of experience w/seed-based crops. Easy to get seed; cassava is vegetatively propagated. http://t.co/xGylGVfRIT #PAGXXIII
7:35pm January 13th 2015 via Hootsuite
EM:17 unique Nigerian farmer-preferred varieties. 3.5k SNPs via KeyGene GBS. Presented complex ALS gene family #PAGXXIII
7:32pm January 13th 2015 via Hootsuite
EM: Pilot phase, SNP genotype, char ALS gene families for mutation, develop tissue culture protocols, larger scale mut/selection #PAGXXIII
7:30pm January 13th 2015 via Hootsuite
EM:Three other efforts, supported by @gatesfoundation - ALS + glyphosate via CIBUS, also Danforth #PAGXXIII
7:29pm January 13th 2015 via Hootsuite
EM: Aim for ALS-tolerant cassava via random mut, collab between ETH and KeyGene (Netherlands) #PAGXXIII
7:28pm January 13th 2015 via Hootsuite
EM:A social problem as well - women & children perform >90% of hand-weeding. Financial return with herbicide treament >80% #PAGXXI
7:27pm January 13th 2015 via Hootsuite
EM: Weeds are a real problem - photo of a cassava farm in Nigeria. Also Cambodia. Small holders: hand-labor (200-500hr/ha) #PAGXXIII
7:26pm January 13th 2015 via Hootsuite
Emily McCallum (ETH Zürich) Development of Herbicide-Tolerant Cassava Using Random Mutagenesis #PAGXXIII
7:24pm January 13th 2015 via Hootsuite
JB:Q:Evidence of introgression into LatAm? A:Yes, going back to structure data #PAGXXIII
7:22pm January 13th 2015 via Hootsuite
JB: GBS of 288 African cassavas 'reveals cryptic identity, relatedness'. v5.1 genome at http://t.co/BpZ1PGLrgB #PAGXXIII
7:20pm January 13th 2015 via Hootsuite
JB: Tree cassava genomes best explained as M. esculenta w/ varying amts of M. glaziovii introgression #PAGXXIII
7:15pm January 13th 2015 via Hootsuite
JB: Only two cassava chloroplast haplotypes found globally (!) Wang 2014 Nature Comm ref http://t.co/oTMqcq16Ig #PAGXXIII
7:14pm January 13th 2015 via Hootsuite
JB: Cassava genetic diversity: PCA analysis from WGS clusters into 3; background G3 2014 http://t.co/NN1uz5760Z #PAGXXIII
7:12pm January 13th 2015 via Hootsuite
Jesson Bredeson (UC Berkeley CA) Genome Sequence and Genetic Diversity of Cassava and Its Wild Relatives #PAGXXIII
7:10pm January 13th 2015 via Hootsuite
DM:They hope to double insert sizes within the next few months #PAGXXIII
5:48pm January 13th 2015 via Hootsuite
DM:Looked for a single gene, found 117/960. Combined short-read with long mate-pair libraries. #PAGXXIII
5:47pm January 13th 2015 via Hootsuite
DM:'BAC Sudoku Sequencing': a row, column, pool strategy. 10 plates, 12 columns, 8 rows (total 40) #PAGXXIII
5:46pm January 13th 2015 via Hootsuite
DM: Used Blue Pippin from @sagebio and collected longer and longer inserts for human. Was able to get fragments past 100kb #PAGXXIII
5:43pm January 13th 2015 via Hootsuite
David Mead (Lucigen, WI) "100 Kb Long Span Reads and Beyond" #PAGXXIII
5:41pm January 13th 2015 via Hootsuite
MV: Laboratory website: http://t.co/FnNU62dvE0 #PAGXXIII
5:38pm January 13th 2015 via Hootsuite
MV:Reports Lucigen mate-pair efficiency of >90%, chimera codes help reduce chimeras - have non-pairing codes #PAGXXIII
5:35pm January 13th 2015 via Hootsuite
MV: Wheat has 124k protein coding genes, alohexaploid. Using PacBio, sequenced 672 BACs, enhanced w/ long mate-pairs #PAGXXIII
5:33pm January 13th 2015 via Hootsuite
Miroslav Valarik (Inst of Exp Botany, Olomouc, Czech Republic) Mate Pair Libraries for Enhancing Wheat BAC Assemblies #PAGXXIII
5:29pm January 13th 2015 via Hootsuite
KS:Q:Relevance of miscanthus to bioenergy? A:Most benefit is to sugarcane. Miscanthus also has potential but a way to go #PAGXXIII
5:28pm January 13th 2015 via Hootsuite
KS: Est grass duplication ~70Mya. Shows data that Miscanthus genome better reference for sugarcane than Sorghum #PAGXXIII
5:19pm January 13th 2015 via Hootsuite
KS: 300 scaffolds pieced together. Resulted in 87% of scaffolds >50kb. Now 'the fun stuff' - diff in genes & their expression #PAGXXI
5:16pm January 13th 2015 via Hootsuite
KS: Some evidence of clonal redundancy, filter out wrong orientation reads, >40kb; keep all <40kb. 4-cutters worked best #PAGXXIII
5:14pm January 13th 2015 via Hootsuite
KS: Sent tissue to Lucigen, 960K fosmid clones (15x) using 5 different RE's to effectively sample fosmid ends #PAGXXIII
5:10pm January 13th 2015 via Hootsuite
KS: (NB - Lucigen's Mate Pair technology highlighted here http://t.co/MVWvS2WiOe for @iontorrent ) #PAGXXIII
5:08pm January 13th 2015 via Hootsuite
KS: With help from @Hudsonalpha have 8kb jumping libraries. Now Lucigen's 40kb NGS mate-pair fosmids: restricted size #PAGXXIII
KS: A doubled haploid Miscanthus sinensis line developed - no allelic var. Many repeats, dupl's: Need larger PE insert sizes #PAGXXIII
5:06pm January 13th 2015 via Hootsuite
Kankshita Swaminathan (Energy Biosciences Institute, IL) Construction and analysis of a Miscanthus sinensis gene space assembly #PAGXXIII
5:02pm January 13th 2015 via Hootsuite
KT: Platform has scheduler to optimize node usage; data compression uses gzip w/FPGA board; 2.5Gb/s; working on CRAM #PAGXXIII
4:53pm January 13th 2015 via Hootsuite
KT: I/O intensive processes: +processing power doesn't help. Extreme example of Casava 1730min vs 107min by caching library #PAGXXIII
4:47pm January 13th 2015 via Hootsuite
KT: GATK optimized on their Power8 system; HaplotypeCaller optimization laid out here http://t.co/przVRB5ywC #PAGXXIII
4:45pm January 13th 2015 via Hootsuite
KT: Tape drives to save energy (and highly reliable), also data compression appliance http://t.co/zek1v0CGlq w/open source apps #PAGXXIII
4:42pm January 13th 2015 via Hootsuite
Kathy Tzeng (IBM NY) "Accelerating Genomics Research Using an Integrated High Performance Computing Solution" #PAGXXIII
4:41pm January 13th 2015 via Hootsuite
RT @davidfuzzylime: Awesome correction in today's @guardian, to be filed under "why hyphens are important" http://t.co/BMHgyht6ak
3:30pm January 13th 2015 via Hootsuite
MW:Showed histogram of ID'd GNPS dataset - most in 1-5% range. But ID's are increasing over time. Now at 187 datasets #PAGXXIII
3:15pm January 13th 2015 via Hootsuite
MW: MassIVE is their MS repository. A 'continuous identification' - automatically searching db's for ID #PAGXXIII
3:09pm January 13th 2015 via Hootsuite
MW: Their solution GNPS. Note: Behind the Bench blog post from ASM http://t.co/OEI4pBkoXz #PAGXXIII
3:08pm January 13th 2015 via Hootsuite
MW:Many rediscover what has already been done. Already: NIST, MassBank, ReSpect, Metlin - but incomplete and grow slowly #PAGXXIII
3:05pm January 13th 2015 via Hootsuite
MW:Leveraging social networking for mass-spec: one problem they work on is compound ID. Normally NMR, manual interpretation #PAGXXIII
3:04pm January 13th 2015 via Hootsuite
Mingxun Wang (UC San Diego) "GNPS - The Future of Community Wide Collaboration and the Power of Social Networking in Mass Spec" #PAGXXIII
3:01pm January 13th 2015 via Hootsuite
AB:Proteomic analysis problem - 2D gels may have multiple forms (i.e. glutamine de-amidation); 40 spots for 5 isoforms #PAGXXIII
2:56pm January 13th 2015 via Hootsuite
