10 April 2006

Still digging out . . .

Controllable Snail-Paced Light in Biological Bacteriorhodopsin Thin Film Physical Review Letters 2005, 95:253601 KEYWORDS: physics, optics, ultraslow light, cute science, photonic, optical switch, halobacteria, refractive index VOCAB: group velocity, optical density NOTES: -"electromagnetically induced transparency" -"The induced dipole moment interferes with the dipole driven directly by the probe field, leading to a redution in the absorption of the probe with an extremely narrow frequency interval (~1/tao). This indicates that the refractive index increases rapidly over the same spectral region . . . " -quantum yield of 65% -". . . we are able to control teh group velocity from the order of 10^-4 m/s to normal light speed." -what polymer is the matrix? -does this only work for 568 nm light? Decatenation checkpoint deficiency in stem and progenitor cells Cancer Cell 2005, 8:479 KEYWORDS: biology, checkpoint, wound-healing, stem cell, cancer VOCAB: decatenation (disentanglement by topoisomerase II of chromosomes during cell division), aneuploidy, aneuploid, pseudomitosis ("spindle formation and kinetochore poleward movement in the presence of entangled chromosomes, which results in aberrant chromosome segregation") NOTES: -"checkpoint efficiency increased when embryonic cells were induced to differentiate . . " -->are stem cells part of the cancer problem? -->the "SIGNIFICANCE" box in this journal is a fine, fine touch. -"chromosome gain and loss have been observed during the ex vivo culture of human and mouse ES cells and could be a consequence of the inefficient decatenation checkpoint." DRUGS: retinoic acid, colchicine, KRF-193 (Topoisomerase II inhibitor) Sipa1 is a candidate for underlying the metastasis efficienty modifier locus Mtes1 Nature Genetics 2005, 37:1055 KEYWORDS: metastasis, bioinformatics, confluence, adherence VOCAB: transgene, locus, orthologous, multiple cross mapping, MCM, variable tandem repeat, VTR, minisatellite, PDS domain ("frequently implicated in protein-protein interactions"), nephrogenic, missense, bromodomain NOTES: -"The control Mut1 cell line produces many rounded cells when grown to confluence compared with the flat sheet observed in the shRNA knock-down cell line" --> normal (less prone to metastasis) cells die when grown to confluence in vitro -rounded cells at confluence "suggestive of strong cellular adherence"

Photonics, Wow!

Design, fabrication, and optical characterization of quantum cascade lasers at terahertz frequency using photonic crystal reflectors Optics Express 31 October 2005 13(22):8960 KEYWORDS: physics, photonic, photonic crystal, terahertz, THz VOCAB: lensed mirrors, stop-band NOTES: -applications for THz: imaging, chemical sensing, astronomy -photonic crystals at "stop-band" energies = reflectors -"single plasmon waveguide (sic) are easily fabricated and enable high power structures with little out-of-plane losses -lases at 77 K PROTOCOLS: -5 nm Ti/50 nm Au --> surface plasmon -alloy at 400 deg C for 1 minute: 10 nm Ni/20 nm Ge/50 nm Au/20 nm Ni/200 nm Au

Notes on style.

I plan to render titles as given. Keywords and other notable text will follow British spelling conventions (typos aside). Links will lead to Google search results (safesearch off, on principle) except where I thought it worth pointing somewhere specific. Please note in comments if any links are dead--maybe the equilibrium state will be all links leading simply to Google search results.

Two old biology papers

The effect of surgical wounding on tumour development Eur. J. Surg. Oncol. 1999 25:231-243 KEYWORDS: biology, wound-healing, extra-cellular matrix, ECM, hypoxia, hypoxic VOCAB: cytokine, autochthonous (originating where it is found), stroma (connective tissue existing for support alone), mitogen (a chemical that triggers mitosis, i.e. cell division) NOTES: -growth factors: EGF (epidermal growth factor), TGF-a (transforming growth factor), TGF-b, bFGF (basic FGF), IGF I (insulin-like growth factor), IGF II, PDGF (platelet-derived growth factor) -wounding stimulates some cell lines (How? Via what factors?) -wound healing stages: inflammatory, proliferative, repair & remodeling -“wound macrophages phagocytose wound debris” and trigger the next stage (proliferation) -“fibroblasts produce many of the extracellular matrix (ECM) components that result in scar tissue formation” -p53 is a tumor-suppressor -fibrinogen (via transglutamation) --> cross-linked fibrin -kDa = 1.1(residue count)/10 -bFGF (basic FGF) is highly angiogenic -this article considers treats as hypoxic concentrations below 50 ppm oxygen (presumably in medium) -ECM components: fibronectin, laminin, collagen, vitronectin, fibrinogen, thromospondin

Oxygen Tension Regulates the Expression of Angiogenesis Factor by Macrophages Science 23 Sept 1983 KEYWORDS: biology, wound-healing, angiogenesis, hypoxia VOCAB: debridement, Permanox culture dishes, lactalbumin hydrolysate, mitogen, mitogenic NOTES: -“sealed culture chambers”? -oxygen concentration in atmosphere reported -cultured cells at 20%, 10%, 5%, 2%, 0% oxygen in air --> corresponds to what in media? are some of these points saturated/otherwise indistinguishable? -“near-anoxia” = “sealed” chamber is not so sealed?

09 April 2006

Walk the Planck length

No doubt we're jumping the gun here, but this link leads to some science books I'd like to read one of these days.