Goethe's Faust

German poet, novelist, playwright, courtier, and natural philosopher, one of the greatest figures in Western literature. In literature Goethe gained early fame with The Sorrows of Young Werther (1774), but his most famous work is the poetic drama in two parts, FAUST. Like the famous character of this poem, Goethe was interested in alchemy. He also made important discoveries in connection with plant and animal life, and evolved a non-Newtonian and unorthodox theory of the character of light and color, which has influenced such abstract painters as Kandinsky and Mondrian.

Noble be man,
Helpful and good!
For that alone
Sets him apart
From every other creature
On earth.
(from The Divine, 1783)

... heard Goethe from Siga's site http://www.trappedinspace.com/numerology

Stuff Stuff

Stuff

- hiked the Chief http://www.stawamuschiefpark.ca/
- X-Men Origins: Wolverine http://www.youtube.com/watch?v=k6cRSvyC3Ws
- Swine Flu outbreak in Mexico http://health.asiaone.com/Health/News/Story/A1Story20090427-137660.html
- A rescuer's / scientist dream ... http://www.news1130.com/more.jsp?content=20090424_103647_5396
- Canucks defeats St. Louis Columbus BlueJackets http://www.vancouversun.com/health/Gallery+Canucks+Blue+Jackets/1342909/story.html

Can't and Can Quotes

You can't decide the length of life, but you can control how you want to live it.
You can't control the weather, but you can control your mood.
You can't change your look, but you can smile.
You can't control others, but you can control yourself.
You can't foresee tomorrow, but you can utilize today wisely.
You can't win everything, but you can try your very best to achieve that.

Hannes ...

http://www.cbc.ca/canada/british-columbia/story/2009/04/24/bc-north-shore-rescue-glacier-death.html?ref=rss

http://communities.canada.com/theprovince/blogs/newsroom/archive/2009/04/24/north-shore-search-and-rescue-member-dies-in-fall.aspx

http://www.chem.ubc.ca/personnel/faculty/withers/group/group/muelleger/muellegger_main.htm

http://zymeworks.com/about/management/

Improvisation

http://en.wikipedia.org/wiki/Improvisation

Improvisation is the practice of acting, singing, talking and reacting, of making and creating, in the moment and in response to the stimulus of one's immediate environment and inner feelings. This can result in the invention of new thought patterns, new practices, new structures or symbols, and/or new ways to act. This invention cycle occurs most effectively when the practitioner has a thorough intuitive and technical understanding of the necessary skills and concerns within the improvised domain. Improvisation can be thought of as an "on the spot" or "off the cuff" spontaneous activity.

Life's not written with a pencil

Life's not written with a pencil

Nice quote from the movie, 'Call for Love'

http://en.wikipedia.org/wiki/Call_for_Love

katakana

http://thejapanesepage.com/node/gif/katakana.gif

http://thejapanesepage.com/beginners/katakana/page01

~ tara （～たら）expresses condition.

Ken kara dattara inaitte itte.
ケンからだったらいないって言って。

I'm not here if it's from Ken.

少し (すこし) sukoshi ... a bit

かれは少しおそいですね。[kare ha sukoshi osoi desu ne.] [ex #869]
He's a bit late isn't he?

Korean Movie - Romantic Island

This was a pretty good movie with a happy ending ;p

http://www.hancinema.net/korean_movie_Romantic_Island.php

http://www.mysoju.com/romantic-island/

There's actually 3 couples but they only show the two youngest ones -o-

Methanogens -- oxygen producing bacteria

http://en.wikipedia.org/wiki/Methanogen

Methanogens are archaea that produce methane as a metabolic byproduct in anoxic conditions. They are common in wetlands, where they are responsible for marsh gas, and in the guts of animals such as ruminants and humans, where they are responsible for the methane content of flatulence.[1] In marine sediments biomethanation is generally confined to where sulfates are depleted, below the top layers.[2] Others are extremophiles, found in environments such as hot springs and submarine hydrothermal vents as well as in the "solid" rock of the Earth's crust, kilometers below the surface.

Methanogens play the vital ecological role in anaerobic environments of removing excess hydrogen and fermentation products that have been produced by other forms of anaerobic respiration. Methanogens typically thrive in environments in which all other electron acceptors (such as oxygen, nitrate, sulfate, and trivalent iron) have been depleted. In the deep rock they obtain their hydrogen from the thermal and radioactive breakdown of water.

Closely related to the methanogens are the anaerobic methane oxidizers, which utilize methane as a substrate in conjunction with the reduction of sulfate and nitrate.[10] Most methanogens are autotrophic producers, but those which oxidize CH3COO- are classed as chemoheterotrophs instead.


http://www.canada.com/Technology/Thank+oxygen+producing+bacteria+your+existence/1478323/story.html

oxygen-producing microbes, which transformed the oceans and the atmosphere and fuelled evolution of creatures that eventually crawled out of the sea, a Canadian-led team reports Thursday in the journal Nature.

"If the oxygen-producing bacteria had never taken over, we wouldn't be here right now," says lead author Kurt Konhauser, a geomicrobiologist at the University of Alberta.

The nickel-poor waters would, however, have been very hospitable to oxygen-producing microbes. And they soon took over as the dominant microbes, pumping oxygen into the oceans and air.

Marine scientist Mak Saito, of the Woods Hole Oceanographic Institution, describes the findings as both "exciting" and "sobering." It suggests "a single geological change can starve a major oceanic microbial community and thereby change the trajectory of life on Earth," Saito notes in a Nature commentary.

As the methanogen microbes died off, there would have been a big drop in atmospheric levels of methane gas, a potent greenhouse gas. This could have cooled the atmosphere, triggering the glaciation.

http://www.space.com/searchforlife/mars_conditions_020819.html
Kral led the experiment and presented it to colleagues during a bioastronomy conference in Australia last month.

"Our goal is first to get the organisms to grow well, then systematically experiment with conditions found on Mars," Kral said last week.

Mars' atmosphere contains large amounts of carbon dioxide with almost no oxygen. Assuming that hydrogen and some water are present under the surface, the basic requirements for methanogen growth are met on Mars. And even if hydrogen is not present, carbon monoxide is, and some methanogens can use this instead of hydrogen.

Since methane is a "greenhouse gas" that traps heat near a planets surface, methanogens could theoretically be used to raise Mars surface temperature, eventually "terraforming" the planet so that it could support life and provide a potential refuge for humanity.

http://zipcodezoo.com/Key/Archaea/Archaea_Kingdom.asp
Achaea kingdom, consists of crenarchaeota, nanoarchaeota, euryarchaeota
- single-celled microorganisms
- prokaryotes - have no cell nucleus or any other organelles within their cells
- Classifying the Archaea is still difficult, since the vast majority of these organisms have never been studied in the laboratory and have only been detected by analysis of their nucleic acids in samples from the environment.
- Despite this visual similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes: notably the enzymes involved in transcription and translation. Other aspects of archaean biochemistry are unique, such as their reliance on ether lipids in their cell membranes. The archaea exploit a much greater variety of sources of energy than eukaryotes: ranging from familiar organic compounds such as sugars, to using ammonia, metal ions or even hydrogen gas as nutrients. Salt-tolerant archaea (the Halobacteria) use sunlight as a source of energy, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no species of archaea is known to do both. Archaea reproduce asexually and divide by binary fission, fragmentation, or budding; in contrast to bacteria and eukaryotes, no species of archaea are known that form spores.
- archaea in plankton may be one of the most abundant groups of organisms on the planet
- One example are the methanogenic archaea that inhabit the gut of humans and ruminants, where they are present in vast numbers and aid in the digestion of food. Archaea have some importance in technology, with methanogens used to produce biogas and as part of sewage treatment, and enzymes from extremophile archaea that can resist high temperatures and organic solvents are exploited in biotechnology.

Metagenomics

dels.nas.edu/dels/rpt_briefs/metagenomics_final.pdf
dels.nas.edu/metagenomics/

"Metagenomics provides a new lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual microbial species. This new approach will bring to light the many abilities of the microbial communities that drive Earth’s energy and nutrient cycles and support the health of its inhabitants. Metagenomics will vastly enhance our knowl-edge of microbial communities and can lead to major advancements in many areas, includ-ing human health, agriculture, energy production, and environmental remediation."

unculturable - nothing grows on the plate, why? one reason could be that it lacks nutrients, what better way to find this? observe the organism in its natural environment -- see 1911 paper of Twort and G. Ingram [Proc. Roy. Soc.LXXXIV, pp. 517-542], Mycobacterium pseudotuberculosis which needed a form of Vit K obtained from dead cells of Mycobacterium phlei

lots of potential in this field, ranging from harvesting energy (Dr. Stephen Larter: Canada Research Chair in Petroleum Geology; microbes to convert athabasca oil sands back to good methane http://en.wikipedia.org/wiki/Athabasca_Oil_Sands), global climate change (eg oxygen minimal water zone, Dr. Steven Hallam UBC MBB), microbes in mouth and gut -> antibiotics Dr. Fergus Shanahan: Director, Alimentary Pharmabiotic Centre and the BioSciences Institute
--topics covered from Genomics Forum 2009
http://www.genomebc.ca/whatnew_press/upcoming_events/2009/genomics_forum_apr09.htm

Introduction to biology

http://themedicalbiochemistrypage.org/
http://research.cs.queensu.ca/~shatkay/490papers/HunterIntroMolecularBiology.pdf
http://www.ebi.ac.uk/microarray/biology_intro.html

Poster tips

http://www2.lut.fi/~jkamarai/misc/poster/latexhelp.html
http://www.swarthmore.edu/NatSci/cpurrin1//posteradvice.htm

I would say that in general, the posters that did the best were very clear and required little explanation. They had good leading headers above all figures, basically outlining in a few words what the figures showed. They had summaries or conclusions that were very clear, and it was clear from the verbal exchange what the presenter had contributed to the research and that the presenter was an expert in their field.

the Pimp My Poster group icon
Pimp My Poster
http://www.flickr.com/groups/688685@N24/

Dr. Miller and Dr. Borchers

My two judges at the poster competition

http://www.pac.dfo-mpo.gc.ca/sci/mgl/staff_profiles/miller_e.htm#Area
Dr. Kristi Miller (Saunders)
Primary work on Marine Ecological Genomics and Adaptation Group (MEGA)

http://www.genomebc.ca/research_tech/researcher_profiles/c_borchers.htm
Dr. Christoph Borchers
Genome BC Platform Leader

Too bad I didn't win, but it was a good experience!

Biomarkers

http://en.wikipedia.org/wiki/Biomarker

A biomarker is a substance used as an indicator of a biologic state. It is a characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention.

It can also be a substance whose detection indicates a particular disease state, for example, the presence of an antibody may indicate an infection (see biomarker (medicine)). More specifically, a biomarker indicates a change in expression or state of a protein that correlates with the risk or progression of a disease, or with the susceptibility of the disease to a given treatment. Once a proposed biomarker has been validated, it can be used to diagnose disease risk, presence of disease in an individual, or to tailor treatments for the disease in an individual (choices of drug treatment or administration regimes). In evaluating potential drug therapies, a biomarker may be used as a surrogate for a natural endpoint such as survival or irreversible morbidity. If a treatment alters the biomarker, which has a direct connection to improved health, the biomarker serves as a surrogate endpoint for evaluating clinical benefit.

An NIH study group committed to the following definition in 1998: "a characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention." [1]

In the past, biomarkers were primarily physiological indicators such as blood pressure or heart rate. More recently, biomarker is becoming a synonym for molecular biomarker, such as elevated prostate specific antigen as a molecular biomarker for prostate cancer, or using enzyme assays as liver function tests. Biomarkers also cover the use of molecular indicators of environmental exposure in epidemiologic studies such as human papilloma virus or certain markers of tobacco exposure such as 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK).

Immunology

- b-cells (bone marrow) has antibodies that bind antigens, then it makes clones of these b-cell types and the clones secrete antibodies into the blood stream, eg IgG, IgM (pentamer) (Y structure)
- t-cells 'killer' (thymus) has t-cell receptors which also has immnuglobulin (antibody) folds that recognizes antigens that are bound to mhc complex of infected cells (U structure only)

IgG (humoral, B-cell antibodies):
- immunoglobulin fold has 4 chains, 2 light and 2 heavy chains, 2 anti-parallel beta sheets packed against each other forming a barrel
- fc = crystalizable fragment, fab - antigen binding fragment
- fc and fab connected together by hinge region / flexible linker
- constant domain (ch1, cl) - 4+3 beta strand connected by short loops, linked by disulfide bonds, sheets are 90 degrees, hydrophobic interactions, 4 strands (longest sheet) in the middle, 3 strands in the outside
- variable domain (vh and vl) - 4+3+2 beta strand, long loops for antigen binding, cdr1-3 (complementarityy determining region) or hypervariable region on the same side, c' and c'' forms cdr2, cdr1 connects sheet 1 and 2 (crossover turn), cdr3 has the most variability, 5 strands in the middle (longest sheet) and 4 strands on the outside, c" not involved in packing (outside the barrel)
- epitope (Antigenic determinants) - part of antigen recognized by antibody (vs paratope - part of antibody recognize epitope)

T-Cell Receptors:

Protein crystallography

crystallography
- shine x-ray (1.5A = 1x10^-10 wavelength) on crystals (protein + h2o)
- treat reflections as summation waves (constructive interference = intensity)
- Bragg's Law: n(x-ray wavelength) = 2dsin(theta), d=lattice plane separation distance=resolution, theta is the incidence=reflection angle bouncing off the lattice plane, n=integral number of wavelengths in path length (extra distance travelled by beam on the 2nd lattice plane)
- structure factors (F) - wave equations that describe the reflections
- recombine structure factors to get an image of the molecular structure in the unit cell
- fourier transform - transforms reflections (diffraction patterns in reciprocal space) to electron density function in real space (and vice-versa)
- need to measure intensity and position (+ angle of reflection) of dots (miller indices hkl - name of reflections) in diffraction patterns, not errors (sigma)
- large unit crystals (proteins) produce reflections closer together (inverse relationship of theta and d in Bragg's Law)
- For a unit cell edge of 40 Å, and data collected to 2 Å resolution (d spacing)
40/2 = 20 planes = 20 spots along that direction
- For a unit cell edge of 80 Å, you now have 40 spots in the"same space"
so the reflections are twice as close together
- "as cell gets bigger, diffraction info is more + more compressed"
- phase problem - phase information is lost in the experiment, work arounds:
- MAD (multiple anomalous dispersion) - use SeMet, estimate Se atom phase from difference in Friedel mates, need to collect lots of data to find extent of error
- MIR (multiple isomorphous replacement) - soak crystals in heavy atoms (HA) while keeping the protein (P) isomorphic (same form), then we take the difference in structure factors, F(HA+P) - F(HA) = F(P), distance shown in Patterson map
- MR (molecular replacement) - homology, need at least 35% sequence identity, performs rotational and translational operations to match model with unknown
Methods for phase improvement:
- solvent flattening - ignore solvent envelope from e- density and mask it out
- histogram matching
- non-crystallographic symmetry (NCS) averaging