my notes of the ASCB 2008 - San Francisco

A giant meeting, a lot of people, many many interesting things ...

Saturday, 12-13-2008

• [A. Weaver] ECM rigidity promotes invadopodia formation - breath cancer cells, using gelatin density to generate different rigidities
• [P. Keely] Tumor Associated Collagen Signatures - using multiphoton imaging the interface between cell-matrix interface; TACS3 predicts overall patients survival; cells invade out along radially aligned collagen fibers; an explant system, where collagen aligns between the explant and promotes invasion; MCF10A cells, low density - form cysts, high density - very invasive; Colla +/- (a collagenase resistant mutant) cross with MMTV-PyVT, more collagen, more progression, more invasive; FAK null, down regulates genes associated with metastasis
• [H. Kim] 3D migration modes: contact guidance - Quasi-1D, matrix guidance - Traditional 3D; use collagen-GAG scaffold to control the scaffold pore size; increased pore size, less migration, lower speed; junction micro-architecture enhances contract-guided migration; in collagen (2-4 mg/ml), EGF on serum starved U87MG cells enhance 3D motility directional persistence, Rac1 switches between persistent and speed; collagen density affects steric-hindered cell migration; treatment with GM6001, an MMP inhibitor, shows that directional persistence correlates with MMP, not cell speed; EGF in 3D stimulates both cell speed and directional persistence (persistence is highly collagen density dependent); some of the cell density effect on migration might be due to the happiness of the cells in different density
• [J. Brugge] anchorage independence of tumor cells, using soft agar assay; in early tumorigenesis, excess proliferation disposes cells from normal niches; MCF10A cells, mimic three stages of tumorigenesis - all need apoptosis, and there is impaired metabolism in addition to apoptosis; ATP reduction associated with autophagy ?? - suspension cells maintained high ATP through Akt/PI3K pathway; glucose uptake drops after 24-hour in suspension - rescued by overexpressing ErbB2; introducing pyruvate could rescue ATP decrease in suspension, non-metaboliable 2-DG suppressed ATP production; glucose is mainly for two pathways - pentose phosphates pathway to generate anti-oxidants, glycolysis for energy; anti-oxidant treatment leads to enhanced ATP levels in suspension - no change in glucose transport; an alternative energy pathway via fatty acid oxidation is blocked in suspension - due to elevated ROS from the pentose phosphatase pathway; rescue suspension cells by either ErbB2 overexpression - rescuing glycolysis, or anti-oxidant - by ROS; put anti-oxidant to MCF10A cells increases luminal filling - still having apoptotic clearing, which is also true in soft agar colony formation assay; survival of hyperproliferation tumor cells: 1. anti-apoptotic activity by oncogenes, 2. metabolic impairment, either by oncogene rescuing the glucose transport or by anti-oxidant rescuing ATP generation by other oxidation pathways - a way to survive outside the niche or under nutrient shortage; SOD2 differentially expressed in high grade human breast tumors; a paradox about anti-oxidants: 1. protect DNA damage, 2. in abnormal tissue, under metabolic challenge, anti-oxidant promotes tumorigenesis; human tumor cells are NOT overexpressing ECM, while mouse tumor cells are - consider the differences between human and mouse cancer models; ErbB2 stabilizes EGF and EGFR in suspension
• [K. Rejniak] IBcell modeling; using MCF10A to feed the model for acini development; BioSig / LBNL; the importance of cell division; lumen re-population
• [A. Ewald] 2.5 nM FGF for ex vivo branching; polarized tissue with un-polarized cells; permissive ECM for the invasion
• [M. Peifer] self-assembly of tissue and organism; tissues are organized by adhesion junctions; without adhesion, no morphogenesis; cytoskeleton during apical constriction; fly forms of mesoderm as the neural tube formation in mammal; Nectin/Echinoid+Afadin/Canoe as important as E-Cadherin; fly embryos complete lacking Canoe - cell adhesion is normally established, during gastrulation things went wrong - mesoderm invagination disrupted - they had the twist master mesoderm fate; Caneo rest at constriction - actin/myosin contrct uncoupled to the adhesion; Canoe colocalized with E-Cadherin at spotty adhesion junctions, especially enriched at tri-cellular junctions - the localization is not dependent on beta-Catenin; Canoe can bind to actin directly via the C terminus - Cyto. D treatment abolished the localization; Rab1 mutant phenocopied the Canoe null suggesting Rab1 is essential for the Canoe recruitment

Sunday, 12-14-2008

• [U. Mueller, 2] inner ear, hair cells, actin bundles linked by tip-linked filaments; Myo1C to reset the ground state after ion channel open; ENU mouse reverse genetic approach to screen hearing impairment and deafness - found Cadherins; CDH23, labels hair cells, not on the tip, only on the side; PCDH15 only labels the tip; using immunogold labeling found that PCDH15 and CDH23 linked together; based on His-Gold particle trick found that dimmers are in parallel form; found the interaction protein of CDH23 - Harmonin, which interacts with F-actin - without F-actin binding, loss tip localization and cause deafness; evolution view: tip-linked complex, actin based for fast response; while in worm, using microtubule
• [L.B. Vosshall, 3] reversed topology of insect transmembrane chemosensory receptor - peptide antibody and EM; knockdown Or83b causes problems in bulk trafficking to the tip of dendrites; ...
• [C. Montell, 4] fly genetic screen to find genes for visual transduction; PLC, Myosin II, etc; neural degenerative disease, TRPML1 - possible NMJ defeats, autophagy degradation pathway decrease (breakdown step failed in mutant, the important role is turning off mitochondria); not enough breakdown of mitochondria due to high pH; trpm1 mutant has decreased clearance of apoptotic cells - clearing requires trpm1
• [J.T. Lis, 6] Drosophila heat shock gene as the model; in living salivary gland, 2-photon imaging; translate of HSF protein upon heat shock; PolII-GFP also responses to heat shock, FRAP PolII 2 min recover - very close to the time of PolII stays on hsf gene; use RFP and activatable GFP to check local vs. long distance recruitment - early heat shock is different from late heat shock; confirm by FRAP; nucleosome spinning - lose nucleosome is independent of transcription; physical border for nucleosome lose
• [S. Gasser, 7] Epigenetics - memory; differentiation as a restriction of potential; 3D-EM of heterochromatin; active genes are mobile and relocate for maximal expression - use Lac and Gal-EGFP to image; FISH with probes for active and inactive genes; Whole mount FISH to distinguish random localizes vs. peripheral localized - activation causes shift; baf1-GFP-LacI/myo-3::RFP, inactive at the peripheral and H3K staining on them (heterochromatin) - since in muscle cells, where myo-3 expresses, they found the GFP signal, the conclusion is that the promoter is sufficient! ... in developing gut, pha4 promotes arrays de-condense upon induction; are peripheral localized genes active? using stress induced genes to check - heat-shock::GFP live the de-condense process after heat shock; FISH confirm - nucleosome position driving by transcription factors and nuclear structures; differentiation - genes move upon differentiation, which correlates with expression; peripheral localized gene can be active; nuclear reorganization during differentiation - heterochromatin ties to the peripheral
• [T. Misteli, 8] spacial organization in genome; non-random gene position - may be clustered based on function, may dissociate based on activation; LacO/LacR-ECFP(I-SceI)TetO/TetR-EYFP, positions are stable, Ku80 protein mediates stability, translocation only occurs when breaks; immobility is a protective mechanism - factors for immobility are tumor suppressors; amplification after DNA damage to spread DNA repair machine; no damage - still has DNA damage responsible pathway, why? chromatin structure, epigenetic changes; non-random organization for genome stability
• [B31, S. Kunii, 89] Chicken skin collagen, type I; 1% Pepsin (Asp. protease) to generate atelocollagen, most are beta and gamma forms; 1% Actinidain (Cys. protease) to generate AP-collagen; 1 mg/ml gelling on glass
• [B102, C.M. Waterman, 160] iPALM (interferometric PALM), PA-FP probes for focal adhesions; U2OS cells; focal adhesions have different levels; molecular clutch model
• [B125, R. Misaki, 182] spinning disk, Zeiss; 60x; manually fixation on slides
• [B197, T. Nishioka, 253] biosensors for lipids, FRET based, less than 10% signal, very high background; MDCK cells random migration; PI(4,5)P2 - PH of PLCgamma; DAG - C1 of PKCbeta11; PI(4)P - PH of FAPP1; PI(3,4,5)P3 - PH of GRP/Akt; PI(3,4)P2 - PH of TAPP
• [B204, H. Haga, 260] MDCK collective migration in 3D, 1.2 mg/ml collagen
• [B272, S. Sivaramakrishnan, 328] use MyoVI coated nano-sphere on detergent extracted keratocytes
• [B294, M. Shina, 350] Crn7 in Dicty, Triton-insoluble, sensitive to LatB/CytoA treatment; Crn7 phagocytosis of yeast/E.coli - no overexpression phenotype; Crn7 mutant inhibits phagocytosis uptake (knockdown - higher uptake); short Coronin mutant in Dicty has delayed devlopment and thinner stream, combined with Crn7 - double knockout resuces! Crn7 mutant has thicker stream; all the data support that in Dicty long Coronin functions upstream of short Coronin
• [B454, G. Mirriott, 505] rsCherryRev (Biophys.J. 95:2989-2997) - Monomeric Reversibly Switchable Red Fluorescent Protein; OLID - optical lock-in detection
• [B594, M. LaBarge, 632] mammary progenitor differentiation: microenvironment - array found Jagged1 and P-Cadherin; micropattern - luminal epithelia needs cell-cell contact/E-Cadherin
• [B609, A. Vasilyev, 647] collective movement of cells in fish towards proximal direction; CD41-EGFP cells
• [T. Pucadyil, 22] Membrane fission by Dynamin; in vitro liposome assays; glycerol induced tubulation - glycerol + GTP + Dynamin causes liposome fission; or, tubes break into small vesicles
• [P. Bashkirov, 23] neuron synapses; elastic deformation of the bilayer; the tilting of the lipid; nanotube of Dynamin - altering lipid concentration has different bending; Dynamin squeezes nanotubes, not immediately after GTP addition - conductance waves; leak free fission; hemi-fission reaction; fission needs to come over the hydration barrier
• [S. Ferguson, 24] Clathrin mediated endocytosis; knockout mice: Dynamin 2 - first week developmental problem and die; Dynamin 3 - born and die; Dynamin 1 - survives; knockout both Dynamin 1 and 2 - Clathrin pits accumulate, abundant tubules (involving bar domain proteins); add LatB to show that Arp2/3 not on pits, Endophilin pits gone, new tubules formed after wash-out
• [J. Stow, 25] TNF traffic to recycle endosome; OBCOL; endosome proteins are segregated in different domains; cytokines and cargos are segregated into sub-domains of recycling endosomes; Calcium mediated membrane fusion in vitro; V-cells and T-cells - cell fusion model, add proteins to media to study the interactions; CPX-1 mutant; super-clamp complex
• [J.K. Jaiswal, 27] Kiss and Run fusion; use TIRF to detect cargo fully release vs. partial release (comparing peak intensity, intergrade intensity, fluorescent area); partial release supports Kiss and Run; Dynamin for partial release - use small molecular inhibitor Dynasore; with CytoD, much more full release - no actin distribution change during release; no Clathrin, full release only

Monday, 12-15-2008

• [P. Newmark, 755] Planarian regeneration; Neoblasts; Schmidtea mediterranea; bacterially expressed shRNA for RNAi - in artificial food; Planarian intestine regeneration - epithelia (phagocytes, mintian glands cells); no circulation system; gut - niche for stem cells (evidence from BrdU experiments); no proliferation of intestine; neoblasts dynamics - migrate into new intestinal cells; morphallaxis - remodeling of pre-existing tissues in absence of new tissue growth; free iron beads - magnetized column to purify Planarian intestinal cells
• [D. Stainier, 756] regeneration during endodermal organ formation in Zebrafish; live imaging pancreas gut, gut-GFP fish line; promethus mutant appears to lack liver - encode Wnt2bb; Alk8 mediated Bmp signaling - heat shock blocking function; stem cell differentiation; nitroreductase system - not effective in liver; using MO fading trick to test the Wnt/Bmp/Fgf signaling; liver regeneration requires Wnt2bb, not Bmp or Fgf
• [B. Hogan, 757] progenitor cells in lung maintenance and repair - endoderm organ; Alveoli; cell types in lung - clara secretory cells, ciliated cells, neuroendocrine cells, type II cells, type I cells, basal cells; cell turnover is very slow in adult lung, but very rapid either during postnatal or after injury; repaired by stem cells or differentiated from progenitors (such as hepatocytes, beta cells of islets); linage tracing using Cre-Lox, Rosa26R-lacZ, Rosa26R-YFP; tamoxifen pulse; in bronchioles, labeled cells are ciliated not alveolar cells; in trachea is different, replaced by unlabeled cells; low dose of TmX to decrease the labeling efficiency; basal cells (Keratin 14+ 15+) behavior as "stem cells", stay with xxxx; trachea repair quickly after SO2, K5-GFP specifically labels trachea; bioengineered trachea
• [L27/L90] RhoA and RhoC activation observed by FRET based biosensors, from Condeelis and Hahn labs
• [K. Magudia, B386, 1177] Caco-2 cells, NDR1 depletion decreases proliferation; NDR1 depletion decreases cell migration and cell shape (using MDA-MB-231 and 16HBE cells)
• [S. Yamashiro, B303, 1095] UNC-94/tmd-1 mutant, severe wall muscle disorganization; cooperative not antagonistic with Cofilin/AIP and Profilin; promote the assembly of sarcomeric thin filaments
• [S. Balasubramanian, B256, 1048] FRAP beta-actin-GFP in adult feline cardiomyocytes
• [C. Yang, B180, 972] I-bar induced filopodia needs actin, no clear bundle; actin may be external, not reaching the tip or absent in the filopodia
• [H. Kim, B219, 1011] persistent random walk model ; 3D collagen, different density - EGF enhances migration via: low density - speed, high density - persistence
• [T. Svitkina, B333, 1152] low 75 um, high 100 um; reformation/restoration
• [M. Welch, B336, 1128] R. parkeri to S2 cells, and examine tail length and motility speed
• [J. Condeelis, 759] study metastasis at single cell and single molecular levels; multiphoton microscopy - infrared light penetrate tissue deep; MMTV-PyMT x MMTV-iCre / CAG-CAC-ECFP x c-fms-GFP; volume red and track - Coral-Dendra (photo-conversion, permanent conversion); peri-vascular macrophage required for intravasation - EGF required; in vivo invasion model in rat, mouse and human using matrigel/EGF filled needle to examine the invasion signatures; Cofilin pathway in metastasis; Mena - anticapping - promote cell motility in vivo; TMEM, a clinical evaluation value, using anti-Mena against metastatic cells and anti-CD31 against macrophages; study cells in vivo and do not do motility in culture
• [A. Huttenlocher, 760] Leukocyte trafficking; inflammasome - pro-IL-1beta to IL-1beta; Cryopyrin - Pyrin - WASP; Leukocyte migration and inflammation; reverse chemotaxis, to/out-of-back-to blood migration, during resolution of chronic inflammatory diseases; chronic disease model at 2.5 dpf, mimicking human "psoriasis" HAI-1; cross-talk between inflammation and EMT; what regulates reverse migration - PI3K pathway, persistant PIP3 in the leading edge imaged by PH-Akt; during gradient sensing, activating PI3K - sensing does not require PI3K; amplification of the signal; PI3K is recruited to wounds by attraction - for bidirectional migration/reverse migration; in fish, random vs. chemotaxic cells migration
• [J. Massague, 761] metastasis mechanism; initiation, progression, violence genes; sites: bone marrow sinusoid vs. lung capillary; courses: breast cancer - years to decades vs. lung adenocarcinoma - weeks to months; hypothesis: different organs select for distinct species of metastasis; ANGPTL4, priming for capillary distribution; TGFbeta signature: primary breast cancer to lung metastasis; BrMS17 signature for brain metastasis - mediator of blood-brain barrier breaking, such as Sialy Transferase - a brain not breast metastasis gene
• [I. Ayala, B647, 1428] Fgd1 in invadopodia, actin Cortactin Dynamin; WT - up ECM degradation, DN - down ECM degradation
• [C.P. Xavier, B316, 1108] Coro1C, kidney isoform about 200 kD, skeletal muscle about 67 kD; components of podosomes - macrophages with F-actin marker; knockdown 1C in U373, A172 - no invadopodia; low malignancy related cellular function
• [C. Higashida, B324, 1116] Swinholide A - analogous to LatB; overexpression mDia1 resistances to 100 nM LatB; mDia1FH2/AIP1 at base of lamellipodia
• [G.A. Quinones, B225, 1017] border cell migration; dmim mutant (I-bar) - delayed migration, less endocytosis and membrane dynamics; Cortact rescues dmim
• [R. Vale, B289, 1081] Spatin severs microtubules, Hereditary Spastic Paraplegia human patients with mutations in acidic ATPase domain
• [S. Koike, B20, 823] Enpp2^-/- mouse, decreased Cofilin phosphorylation - impaired lysosome biogenesis; rat serum from Charls River; in Tfn uptake experiments, yolk sac was not removed; Masayuki Masu
• [M. Anitei, B145, 946] AP-1/Clathrin trafficking with Arp2/3-NWASP machine
• [A. Adachi, B168, 961] screen for kinase regulated trafficking by InCell analyzer 100 with autofocus; p230 - green, C1-M6PR - red, transport between TGN and endosome
• [I. Konig, B183, 975] actin in lamellipodia trap proteins, by FRAP analysis
• [J. Zheng, B201, 993] rods, overexpressing Marchalin in CHO cells; binds MT and actin
• [Y. Matsushita-lshiodori, B290, 1082] SPAS-1 severs MT
• [C. Skau, B306, 1098] fimbrin dissociates Tropomyosin, both anti- and parallel forms; formin elongates twice fast
• [S.A. Koestler, B338, 1130] based on fluorescence before and after extraction, get the F/G-actin ratio is 3.1 in vivo; use FRAP to get the F-actin concentration, assuming bleached area only has fluorescence on the F-actin tips; phalloidin induces branching - no actin branch in vivo
• [A.S. Howell, B582, 1366] actin mediated symmetry breaking not guarantee xxxx in budding yeast; Bem1p-EGFP with SNARE
• [L. Cramer, 762] Actomyosin II organization in cell body is non-sarcomeric; filopodia seeds actin bundles; myosin II binds filopodia destined to bundles
• [R.T. Boettcher, 763] Profilin 1 is required for abscission - mouse model, full knockout died at 2-4 cell stage; Col2pfn1 mice developed dwarfism - caused by defects in chondrocyte rotation and proliferation; Profilin-deficient cells assemble contractile rings - normal, reduced tensile forces, impaired spreading and stress fiber formation; Profilin required for mDia1 function
• [D. Mullins, 764] JMY - p53 cofactor; binds to p300 acetyltransferase; JMY in nuclear, mammalian only, three WH2 domains, a MBL sequence between the second and the third WH2; C-terminus induces cellular actin polymerization; by itself, nucleates actin - only need the three WH2 domains; WCA activates Arp2/3 not actin
• [V.O. Paavilainen, 765] ADF-H/G-actin; Twf-C domain is very similar to ADF/Cofilin domain - structurally and biochemically; structure of Twf-C/G-actin complex; phosphorylation breaks 1 of 3 binding interfaces; fitting to get a better Twf-C coated actin filament
• [M. Welch, 766] WHAMM; 40C VSVg-GFP shift to 33C, GFP moves to Golgi; Rab1 + WHAMM has much more tubes; membrane and MT binding is important for the ER to Golgi transport
• [A. Bershadsky, 767] Dia1 to E-Cadherin junctions; Dia1 for Golgi disperson - Dynactin complex (Arp1 filament); mDia1 interacts with Arp1 filaments then initiates actin filaments elongation

Tuesday, 12-16-2008

• [R. Foisner, 1501] Nuclear Lamin for stem cell differentiation; LAP2alpha in nucleoplasm with A-type Lamin; Null LAP2alpha lacks Lamin A/C in nucleoplasma, can be rescued by WT full length but not the fragment missing C terminus; LAMIN - LAP complex; LAP2alpha binds to retinoblastoma protein (pRb); LAP2alpha and Lamin A bind to E2F-dependent genes; lack of LAP2alpha: lose contact inhibition, impair E2F-pRb pathway - regulate cell cycle arrest and hyperplasia in paw epidermis, delay in keratinocyte differentiation - hyper-proliferation with delayed differentiation; LAP2alpha is important for mesenchymal stem cells
• [T. delange, 1502] Telomere protection - endprotectin; telomeric DNA, a 3' overhang and a looped structure; Shelterin: 6 proteins, a telomere specific protein complex, function - regulate telomerase, repression of DNA damage response; telomeres with TRF2, active ATM pathway; ATM/ATR kinases activation requires telomeres; deletion of mouse POT1, actives ATR pathway - TRF2 and POT1 act independently to repress ATM/ATR; TRF2 deletion causes telomere function; telomeres block inappropriate NHEJ at chromosome sites - unexplained dependence of NHEJ on ATM; dammaged telomere promotes mobility - by live imaging; LatA treatment shows - not actin dependent, it depends on MT
• [M. Oser, B281, 1819] 1 min after EGF treatment - Cortactin Tyr phosphorylation and barbed ends peak; Cortactin required for N-WASP localization; Arp2/3, N-WASP binding not the Tyr site important for invalopodia formation; MMP is un-coupled
• [S.A. Ribeiro, B560, 2095] iXMcro, live and fixed screen (Woods Hole MBL course)
• [C. Choi, B289, 1827] AIP C terminus rescues polarity (by NHE1 staining) and chemotactic defects; full length AIP1 rescues as well; AIP-C binds to Cofilin, AIP-N binds to F-actin
• [Y. Bae, B286, 1824] siRNA Profilin-1, slower stable kymograph in MDA-MB-231 cells; siPfn, enhanced leading edge VASP/Ena staining; siPfn + mito-FP4, worst in motility and protrusion; it is PI3K dependent - by LY294002 drug
• [T. Yanagida, 1506] Single-molecular on Myosin V (GFP fused) - invention TIRF, FIONA + Q-dot to get nm/ms resolution, Cy3-ATP to check ATP hydrolysis; optical trap to manipulate the force; TIR dark field microscopy; Brownian motion - small energy, stochastic and ambiguous; noise plays positive role during cell signalling - spontaneous fluctuation of IP3K/PTEN; brain fluctuation - hidden figure perception driven by fluctuation; enzyme reaction - perceptual reaction
• [M. Plodinec, 1504] MT during congression and segregation; mechanism of spindle assembly - search/catch, chromatin-mediated MT nucleation; Kinesin-14, regulates spindle MT organization; kinetochores lack tension in cells and having motility defects - lacking K-fiber and HSET (Kinesin-14); Kiber does not require for congression but increases efficiency; CENP-E is needed, mediates congression of mono-oriented chromosome; ...
• [C. Walczak, 1505] Mechanobiology; bioscope AFM into phase contract and fluorescent; imaging and indentation test of AFM; Rat2 transfected for AFM - topograph; Rat2 sm9 fibroblasts - Gly245Asp mutation of beta-actin, generates large tumors, morphology is similar to normal Rat2 cells; on glass, sm9 has elongated stress fibers; Rat2, 3D spheroids; tumor is softer; Rat2 with desmin-GFP; SW13/+-vim cells; human breast cancer tissue is softer than normal; intermediate filaments for cell's mechanical behaviour - sensor for mechanics
• [M.C. Jonikas, B31, 1579] reporter based on GFP/RFP ratio
• [C.M. Ghajar, B60, 1607] fibrinogen gel, geling for 30 min, 2.5 mg/ml, with EGM-2
• [M. Pope, B70, 1617] segregation by Image Processing Tools - Matlab; H2B for nuclear
• [T. Onodera, B69, 1616] Salivary gland morphogenesis; Cleftin, micro-dissection then T7-SAGE, enhances scattering/migration, enhances branching, decreases E-Cadherin; siRNA on the organ culture - lung and salivary, kidney tried not huge on normal scope
• [J. Nelson, B102, 1649] PDMS, ECM micro-patterning - MDCK cells
• [M. Katoh, B173, 1712] mouse model tests their FRET result; CFP-Epac2-YFP; 0.3-1.0 range
• [J. Zhang, B181, 1720] PH of PLC-delta, PIP2-binding
• [A. Masedunskas, B191, 1730] Rat sectioned salivary glands for trafficing study, 2-photon imaging; dye injection
• [A. Kubo, B214, 1752] gene search - sentan; tip of cilia; overexpression stimulates actin filopodia but not stress fibers; in vitro cillogenesis in cultured mouse tracheal epithelial cells; curvature dependent
• [P. Rompolas, B235, 1773] LC1, IFT88 - planarin cilia; RNAi, reduced gliding
• [C. Waterman, B263, 1801] Myosin II, endothelial cells (3D collagen gel); soft/hard substrate
• [K. Yamada, B272, 1810] 1D topography mimics 3D fibrillar migration; 2D transition by increasing the width of the line of the 1D lane
• [K.I. Hulkower, B278, 1816] Oris^TM cell invasion assay, HT-1080, HT-1080DM
• [T. Chew, B280, 1818] 3-day endothelial in collagen:matrigel - artificial blood vesicles system; MLCK biosensor 2D 27% FRET efficiency; 3D ratio method has been published - scanning fast, 3D reconstruct then ratio CFP/YFP; actin stress shortening in velocity
• [L67] Redox-sensing GFP (c-roGFP1) in water stressed plant
• Crumbs complex: Crumbs, Stardust, Dlin-7, DPATJ; in fly eye photoreceptors; only PDZ of Crumbs in pupae to localize it, in adult more factors are required; important for conversion extension, conserved function between fly and mammal
• [J. Ziel, 1520] Netrin, ligand for cell invasion - a guidance factor; uterine-vulva connection; genetic control of AC invasion; the invasion machinery is polarized; UNC-6 for polarized actin regulation for invasion
• [T. Nystul, 1521] Healthy epithelial stem cells and niche; follicle stem cells are progenitors of follicle epithelial; signals for early follicle cell differentiation - Notch; screen for "hyper-replacement" mutants - dCRELD1; cross-migration for stem cell replacement
• [P.C. Rida, 1522] TBC1d19, mammal inner ear; PCP mutants, cilia mutants; Vangl2, a core compnent of mouse PCP; Y2H with the E17 cDNA library, TBC1d19, verify interaction by CO-IP - required for fish gastrulation, MO experiments phenocopy Vangl2, required for efficient dorsal convergence, reduced evacuation zone, PCP defects in the inner ear; localized to middle body during division, to gamma-Tubulin at centrosome
• [L.E. Dow, 1523] Scribble/Dlg/Lgl and cancer - down regulate or mis-targeted; rescue Ras loss, induce architecture changes, suppress Raf signaling; Ras suppression bypass screen Ras^V12+hScrb transformation assay; the bypass screen: mix, hairpin, pick the transformation - 20000 shRNA screen, 3cm² soft agar, about 3000 cells per dish, hand pick and sequencing - deep sequencing is faster (one target is LGN); scribble regulation of Ras transformation; Scribble conditional knockout mouse - early stage of prostate cancer
• [I. Macara, 1524] Par-3 in mammary gland morphogenesis; important for early embryo development; mammary gland transplant model, single cell, shRNA by lentivirus; Par-3 shRNA MOI=5 at least, last for two months - disrupts ducal morphogenesis, disrupts epithelial layers; model: without Par-3 - unable to differentiate

Wednesday, 12-17-2008

• [G. Storz, 2246] Toxic single transmembrane domain proteins; 28aa peptide encoded by AzuR
• [E. Heard, 2247] RNA acts on X inactivation; Mary Lyon 1961 through coat color of mice found the X inactivation; cascade events; X-inactive-specific-transcripts, 2006, Xist RNA compartment is depleted of PolII and TFs - what repeats there? what is in there; SINE-, LINE, the LINE hypothesis ... deep sequencing
• [G. Hannon, 2248] transposon control is critical - distinguish transposons from normal transcripts; fly, hyper-dysgenic - piRNA pathway, ping-pong mechanism for transposon silencing; what is maternal factors suppress dysgenesis - small RNA deposits, or, maternal inherited small RNA activates ping-pong in daughter cells; epigenetic inheritance by piRNA group
• [K. Hahn, B219, 2510] GDI-binding to Cdc42 sensor: mCer-mVen, FRET; MeroCBD binding sensor (Nalbant, 2004)
• [B. Grin, B208, 2499] vimentin, IF; Ser38, PKA site, phosphorylation after serum stimulation; mimic peptide causes disassembly to vim - induces Lp; DN vim no Lp
• [A. Hall, B563, 2847] Caco-2 model, CTX for 12-hour to stimulate lumen extension; identify GEF/GAPs by siRNA (SMART pool, 82 GEF, 66 GAP) - through Cdc42 regulates 3D epithelial morphorgenesis; fix and stain approach; GEF: Tiam2; GAP: ARHGAP17, TCGAP, ARHGAP9; KD efficiency proved by GFP fusion proteins
• [J.S. Biteen, B468, 2756] photo-switchable EYFP (Dickson, Nature 1997 388:355)
• [E. Derivery, B353, 2644] WASH complex has CapZ, controls endosome through Dynamin; IF of endosomal markers; he is interested in Coronin study
• [J. Kimble, 2250] Basic of stem cells; asymmetric cell division; C.elegans germline stem cells; niche and mitotic region - distal tip cells; Notch is required for germline self-renew; extrinsic signal - Notch, intrinsic for self-renewal - FBF, intrinsic for differentiation - GLD; FBF, PUF RNA binding, for a broad range stem cells not only in fly; GLD, poly A polymerase; RNA regulation of stem cells is ancient and important; PUF targets RNA and recruits deacylation complex; ERK/MAPK is a conserved target of PUF repression; uncommitted state - self-renew, transition from one state to the other, differentiation state
• [A. Kriegstein, 2251] epithelial organization of adult neural stem cells; SVZ astrocyte - amplifying precursor - OB interneurons; cilia on the ventricular surface; pinwheel architecture of the ventricle; hot spot of B1 apical surface; EGFP+B1 basal processes; OB has 6 types of inter-neuron for xxxx; NSC are multipotent in adult brain; different NSC to differentiate ventricular neurons, to OB, at different parts of the brain
• [H. Lin, 2252] Argonaute/Piwi; binds small RNAs, RNaseH-like; mili(-/-) failed to undergo self-renewing division; Piwi-associated piRNA in the fly genome; piRNA, about 60000; TAS-piRNA, has an epigenetic activation role in TAS; Piwi-HP1a interaction: HP1a is a central player in epigenetic regulation, binding interface recognized by NMR studies, interaction is required for epigenetic silencing; H3K9 methylation requires Piwi; HP1a binding to chromatin is Piwi-dependent; Piwi localizes xxxx on piRNA
• [L. Solnica-Krezel, 2265] conversion extension in fish; knypek and trilobite mutants encode components of non-canonical Wnt/PCP pathway; mid-gastrulation stage, cell polarity via PCP; Vangl2 in migration; MTOC during drosal migration - not polarized, bias towards later when moving dorsally; factors polarized in PCP, not during gastrulation - not sure aPKC or Par3/6; not perfect coordination between MTOC and direction of migraion
• [A. Martin, 2266] apical constriction of actin-myosin network; published in Science - ratchet model; myosin fibers are connected to adhesions
• [T. Schilling, 2267] cell migration and adhesion in fish; mesoderm/endoderm cells migrate and separate - beta1 Integrin is important; organ duplication in endoderm defect mutants; mutant: endoderm runs to A too quickly, detached; hypothesis: FN may present Cxcl2 (a chemokine ligand) to endoderm, RGD peptide phenocopied the Cxcl2 mutant, rescue by Ingegrin beta1 RNA while MO Cxcl2; chemokine-deficient cells lose adhesions to FN (dissociated fish cells to FN coated surface); Cxcl2 - Cxcr4
• [S. Saburi, 2268] planar cell polarity - chick, vertebrate inner cell hair, fly wing, fly eye, etc; Fat, DS - core PCP - tissue specific effectors; many Cadherin repeats; Fat4-/- mice died birth with curve tail; loss Fat4 failed PCP; Fat4-/- kidneys are cystic at birth - cysts and dilation of the tubules, because of polarized division is disrupted (spindle orientation is less orientated); Fischer et al 2006; Fat1-/-, no PCP defects
• [S.L. Gupton, 2269] neurite initiation and neuron development in culture; Tetanus toxin, an inhibitor of VAMP2 - regulator for exocytosis, blocks neurite extension only on poly-D-lysine not on Laminin; VAMP7, Tetanus toxin insensitive, DN does block the Laminin rescue; VAMP2 on poly-D-lysine, vesicles to projections, not Laminin; VAMP7 vesicles not to projections; pH sensitive GFP (pHluorin) - reveals exocytic events, VAMP2 exocytosis occurs more on PDL than Laminin, VAMP7 exocytosis more without Ena/VASP/Mena; alpha3beta1 and alpha7beta1 via antibody blocking - other DN and inhibitors; DN Arp2/3 blocks the Laminin dependent rescue
• [D. Yelon, 2270] cardiac morphogenesis; fish chamber curvatures emerge from a linear tube; cells change size and shape during chamber emergence; xxxx, contractility is independently required for cell morphogenesis, non-contractile cell is abnormal in WT enviroment (via transplantation experiments)

updated 2009-1-5: finally, all in!