This one is a transmitted light image through a pear tree leaf after it had changed to its autumn colouring. You can see the leaf veins as white networks among the pink cells. The cell vacuoles are filled with a water soluble pigment which produces the red colouring:

This is a photo of a coleus leaf showing the mix of green and pink cells which make up the beautiful colouring of these plants:

And, as promised for Blogtoberfest (check it out over at Big Cat's Emporium), your daily dose of buttons, with a red theme for Ruby Tuesday!

Some of my favourite Art Deco casein buttons, and a great Deco buckle.

Bakelite with celluloid inset, and the red and yellow is a bakelite 'cookie' button.

 Ruby Tuesday, brought to you Work of the Poet

  from Big Cat's Emporium!

The promise of solving atomic-resolution 3D structure of biological proteins with X-ray Free Electron Lasers has several obstacles. First one is to have fast enough x-ray pulse to image molecules before it starts to undergo "Coulomb explosion". But even that is not sufficient to produce atomic-scale structure due to low scattering cross-section of hard x-rays - so the experiment will need to be repeated many (thousands?) times to improve statistics. Luckily, protein molecules are identical, so the fundamental 3D structure of the sample could be considered the same - however, the orientation of protein molecule is going to be different each time.

There are two ways to solve the "random orientation" problem - one is to try to align the molecule, for example with a laser beam. However this has to be done with a very high precision and is difficult to achieve in practice. Another approach is to do experiment thousands of times with random orientations of molecules, catalogue all resulting projections, and then use mathematical algorithms to "fold" the projections into a unique 3D object that is consistent with all resulting projections.

Russel Fung et al. provide an algorithm that does just that - by simulating realistic conditions of 4th generation synchrotron source, X-ray Free Electron Laser, with collection of 100,000 photons, 72,000 repeated diffraction patterns from single shot experiments and scattering rates as low as 0.01 photons per pixel at large wavevectors corresponding to 1.8 Angstrom.

The result of folding using Generative Topographic Mapping for protein chignolin in random orientations is shown in figure above, for 3D movie of this reconstructed molecule see Abbas Ourmazd's webpage at UW Milwaukee.

"The crisis command centre in certain bacteria cells is a large molecule, dubbed a 'stressosome' by the scientists behind today's research. These cells have around 20 stressosomes floating around inside them, and although scientists knew they played an important role in the cell's response to stressful situations, the complexities of this process had not been fully understood until now" Science Daily

Does anyone still believe in adaptation through environment? It was taught when I was in school and promoted in such programs during the 70's. We know so much more now than back then.

For example, we know that there is no wire or connection linked with experience to the reproductive cells. So if someone is born pretty healthy and during his or her lifetime, they loose an arm in a car accident, nobody is going to be born without a arm as a result thereafter through the family linkage.

This discovery opens up various questions. Could this cell survived without it's complex crisis command center? Since there is no link to the reproductive cells, how could this cell through an unthinking process create such a complex mechanism that is able to ID particular threats to it's existence? Logic is a thinking process not a chaotic unthinking one.

Only a designer, namely God could create such abilities which help the creature to survive. It's fine tuned complexity is a special design for these one-cell animals. We know Darwinism didn't have this ability to know what we know now as he view one-cell animals as simple creatures, but his observations were wrong, and so are the Neo-Darwinists of our time.

Using cutting edge electron microscopy is true science and it's truly exciting to learn of what it can teach us about the microscopic world.  Something that is measurable and repeatable without the massive speculation (trying somehow to fit the data which is not agreeing with a particular dogmatic theory in evolution).

Clot forming in artery on Flickr - Photo Sharing!.

Both these images are of a dye called safranin. The liquid dye was evaporated, leaving these amazing crystal patterns. This one deposited crystals in a fractal formation.

I love this - it reminds me of a red night sky.

Here are some shots from my training session this morning at the Beckman Institute's Scanning Electron Microscope (SEM).  I haven't used SEM for years- wow!  Great fun.  Click on each image to enlarge.

For contrast, here's a photo of a wasp in the same genus taken with my standard Canon macro gear:

We'll be deciding over the coming months which type of images to use for our project.  As you can see, there are some advantages to the SEM: crisp, clean images that give much better detail about the the structure of the insect.  But there are drawbacks as well.  SEMs don't look very much like what people see under a regular microscope, they lack color, and they are expensive. Hmmm...

]]> http://nanotechnews.wordpress.com/?p=516 Fri, 19 Sep 2008 21:52:30 +0000 vascoteixeira http://nanotechnews.fr.wordpress.com/2008/09/19/3-post-doc-positions-in-nanotechnology-at-inl-international-iberian-nanotechnology-laboratory-braga-portugal/ Ref 2PD-OG-02 - Study of Nanoparticles clusters through ultrasensitive microscopy techniques

This position is offered in collaboration with Dr O. Gang, Center for Functional Nanomaterials-Brookhaven National Laboratory, New York, USA. Bimolecular linkers make it possible to create clusters of inorganic nanoparticles with well-controlled interparticle separation. This project will focus on the understanding of the dynamics of energy and electron transfer in model hybrid nanoscale clusters built from inorganic nanoparticles and bimolecular linkers. The dependence of the energy/electron transfer processes on interparticle distance and architecture design will be studied using a combination of ultrasensitive microscopies, e.g., single-molecule spectroscopy and scanning probe microscopy.

Postdoctoral position involves a time frame of 4 years and includes a 1-2 year research stage at the, Center for Functional Nanomaterials-Brookhaven National Laboratory, under the guidance of Dr Oleg Gang. After 4 years, researchers may have the opportunity of continuing their research career at INL.

The INL offers, according to the Postdoctoral experience, a highly competitive compensation plan similar to those offered by the Marie Curie Program and other high quality fellowships. The INL will also offer additional training in relevant areas of entrepreneurship and R&D management.

Ideal candidates Successful will hold a recent PhDs in Physics, Chemistry, Biology, Medicine, Engineering and other scientific fields, show a strong innovative mind-set, a goal orientated attitude and geographic flexibility. Preference will be given to candidates with relevant experience in the scientific fields involved.

Excellent communication skills are required; fluency in English is mandatory.

Application Deadline: November 2nd, 2008

Ref 2PD-NN-02 - Low-field and Solid State NMR applied to food quality control (Post-Doctoral, Portugal)
This position is offered in collaboration with Dr N.C Nielsen, iNano-University of Aarhus, Denmark. This project is concerned with the application of combined low-field and solid-state NMR and chemometrics (PCA/PLS) methods to on-line food quality control. The instruments to be used are based on low-cost 0.3 to 1.5T permanent magnets and homebuilt of controllers which together with sophisticated pulse and gradient methods have enabled construction of non-expensive “mass-production” equipment with sufficient spectral resolution to identify nanoscale biomarkers for high-throughput food control.
Postdoctoral position involves a time frame of 4 years and includes a 1-2 year research stage at the Interdisciplinary Nanoscience Center (iNano)-University of Aarhus under the guidance of Dr N.C:Nielsen. After 4 years, researchers may have the opportunity of continuing their research career at INL.

The INL offers, according to the Postdoctoral experience, a highly competitive compensation plan and health insurance package. The INL will also offer additional training in relevant areas of entrepreneurship and R&D management.

Ideal candidates will hold a recent PhDs in Physics, Chemistry, Biology, Medicine, Engineering and other scientific fields, show a strong innovative mind-set, a goal orientated attitude and geographic flexibility. Preference will be given to candidates with relevant experience in the scientific fields involved.

Excellent communication skills are required; fluency in English is mandatory

Ref 2PD-TJ-02 - Super-resolution microscopy based on QDs and other multi-parametric nanoparticle (Post-Doctoral, Portugal)

This Position is offered in collaboration with Dr T. Jovin, Max Planck Institute for biophysical Chemistry, Göttingen, Germany. Functionalized QDs and other nanoparticles [e.g. core-shell structures with magnetic properties (MNPs), noble metal 5-20 nm NPs, and small luminescent nanoclusters] will be incorporated into strategies based on multiparametric plasmon and scattering phenomena, and fluorescence (intensity, spectral distribution, lifetime, anisotropy, energy transfer). The aim is to exploit biochemical/photophysical regimes offering greatly improved spatial (< 50 nm) and temporal resolution in advanced microscopes such as the Programmable Array Microscope (PAM) under joint development by our laboratory and Cairn Research Ltd., and a new single-molecule module incorporating evanescent fields and a high-field magnetic trap. One will explore means for creating “fluorogenic” NPs, determining FRET by new more efficient means, and achieving spatial resolution using reagents combining NPs and organic dyes. Possible applications will include new ultrasensitive diagnostic procedures for infectious and degenerative diseases, gene transfer for cancer therapeutics, visualization of tumor boundaries during surgical excision, and hyperthermal therapy based on MNPs. Attention will be paid to correlative microscopies (AFM+EM+light microscopy) and innovative “Google Cell” approaches to data visualization and interpretation.

Postdoctoral position involves a time frame of 4 years and includes a 1-2 year research stage at the Max Planck Institute for biophysical Chemistry, under the guidance of Dr Thomas Jovin. After 4 years, researchers may have the opportunity of continuing their research career at INL.

The INL offers, according to the Postdoctoral experience, a highly competitive compensation plan similar to those offered by the Marie Curie Program and other high quality fellowships. The INL will also offer additional training in relevant areas of entrepreneurship and R&D management.

Ideal candidates Successful will hold a recent PhDs in Physics, Chemistry, Biology, Medicine, Engineering and other scientific fields, show a strong innovative mind-set, a goal orientated attitude and geographic flexibility. Preference will be given to candidates with relevant experience in the scientific fields involved .

Excellent communication skills are required; fluency in English is mandatory.

Application Deadline: November 2nd, 2008 (00:00 UTC +0)

Online applications at INL website.

eyeball 1 on Flickr - Photo Sharing!.

M. Bogan, W. Benner, S. Boutet et al., “Single Particle X-ray Diffractive Imaging,” Nano Letters 8, 310-316 (2008)

A study of SiN etched "logo" pattern x-ray induced destruction, similar to Chapman's Nature Physics 2006 work (Cowboys holding hands logo, doi:10.1038/nphys461):

A. Barty, S. Boutet, M. J. Bogan et al., “Ultrafast single-shot diffraction imaging of nanoscale dynamics,” Nat Photon 2, 415-419 (2008)

Lens-less imaging of Fresnel Zone Plate using ptychography - scanning coherent diffraction - improvement in resolution and illumination function from FZP reconstruction by Rodenburg et al. PRL 98, 034801 (2007):

P. Thibault, M. Dierolf, A. Menzel et al., “High-Resolution Scanning X-ray Diffraction Microscopy,” Science321, 379-382 (2008)

Tabletop coherent soft x-ray microscopy by UColorado group - an exciting alternative to large XFEL machines:

R. L. Sandberg, C. Song, P. W. Wachulak et al., “High numerical aperture tabletop soft x-ray diffraction microscopy with 70-nm resolution,” Proceedings of the National Academy of Sciences of the United States of America 105, 24-7 (2008)

X-ray holography with 5 reference beams is obviously better than holography with 3 or 1 reference beams. How about 1,000,000 reference beams? This is what can be accomplished with uniformly redundant arrays:

S. Marchesini, S. Boutet, A. E. Sakdinawat et al., “Massively parallel X-ray holography,” Nat Photon 2, 560-563 (2008)

Coherent imaging of 80-100nm particle (in SAXS mode, similar to work by Miao group) with 5nm resolution, but done at 15 keV. Coherent fraction of the beam drops off as lambda^2, and efficiency of area x-ray detectors is substantially reduced at higher energies too. But at higher energies one can capture more of the Q range for the same solid angle defined by scattering geometry. Still, 5 nm number is better resolution that I expected - this should imply there are at least 15-20 highly visible fringes in diffraction pattern, instead of 7 or so. Maybe it's log scale of intensity that hides extra fringes...

C. G. Schroer, P. Boye, J. M. Feldkamp et al., “Coherent X-Ray Diffraction Imaging with Nanofocused Illumination,” Physical Review Letters 101, 090801-4 (2008)

A review article on coherent x-ray diffractive imaging of small particles:

J. Miao, T. Ishikawa, Q. Shen and T. Earnest, “Extending X-ray crystallography to allow the imaging of noncrystalline materials, cells, and single protein complexes,” Annual Review of Physical Chemistry 59, 387-410 (2008)

This is a "monster" culture cell - a huge mutant with two nuclei and one centrosome. A normal cell can be seen at the lower right.

"monster" cell - triple labeled on Flickr - Photo Sharing!.

Morphology: Thrombocytopenia, 4+ schizocytes, 3+ spherocytes, 4+ polychromatophilic rbc.

Diagnosis: Disseminated carcinomatosis with DIC

DIC With Microangiopathic Hemolytic Anemia on Flickr - Photo Sharing!.

"The whole thing is truly compact--it could be put in a cell phone--and it can use just sunlight for illumination, which makes it very appealing for Third-World applications," says Changhuei Yang, assistant professor of electrical engineering and bioengineering at Caltech, who developed the device, dubbed an optofluidic microscope, along with his colleagues at Caltech.

The new instrument combines traditional computer-chip technology with microfluidics--the channeling of fluid flow at incredibly small scales. An entire optofluidic microscope chip is about the size of a quarter, although the part of the device that images objects is only the size of Washington's nose on that quarter.

"Our research is motivated by the fact that microscopes have been around since the 16th century, and yet their basic design has undergone very little change and has proven prohibitively expensive to miniaturize. Our new design operates on a different principle and allows us to do away with lenses and bulky optical elements," says Yang.

The fabrication of the microscopic chip is disarmingly simple. A layer of metal is coated onto a grid of charge-coupled device (CCD) sensor (the same sensors that are used in digital cameras). Then, a line of tiny holes, less than one-millionth of a meter in diameter, is punched into the metal, spaced five micrometers apart. Each hole corresponds to one pixel on the sensor array. A microfluidic channel, through which the liquid containing the sample to be analyzed will flow, is added on top of the metal and sensor array. The entire chip is illuminated from above; sunlight is sufficient.

When the sample is added, it flows--either by the simple force of gravity or drawn by an electric charge--horizontally across the line of holes in the metal. As cells or small organisms cross over the holes, one hole after another, the objects block the passage of light from above onto the sensor below. This produces a series of images, consisting of light and shadow, akin to the output of a pinhole camera.

Because the holes are slightly skewed, so that they create a diagonal line with respect to the direction of flow, the images overlap slightly. All of the images are then pieced together to create a surprisingly precise two-dimensional picture of the object.

Yang is now in discussion with biotech companies to mass-produce the chip. The platform into which the chip is integrated can vary depending upon the needs of the user. For example, health workers in rural areas could carry cheap, compact models to test individuals for malaria, and disposable versions could be carried into the battlefield. "We could build hundreds or thousands of optofluidic microscopes onto a single chip, which would allow many organisms to be imaged and analyzed at once," says Xiquan Cui, the lead graduate student on the project.

In the future, the microscope chips could be incorporated into devices that are implanted into the human body. "An implantable microscope analysis system can autonomously screen for and isolate rogue cancer cells in blood circulation, thus, providing important diagnostic information and helping arrest the spread of cancer," says Yang.

The paper, "Lensless high-resolution on-chip optofluidic microscopes for Caenorhabditis elegans and cell imaging," will be published July 28 in the early online edition of the Proceedings of the National Academy of Sciences.

Source: California Institute of Technology

Cardiomyocytes (red) and fibroblasts (green) isolated from chicken embryo heart.

Heart cells on Flickr - Photo Sharing!.

IEEE Spectrum: Face of Evil
This sinister-looking gingerbread man is actually a cross section of some melted metal interconnects as seen with a focused ion beam. The focused ion beam is an instrument similar to the scanning electron microscope, except that it uses gallium ions to image a sample instead of electrons.

Secret Worlds: The Universe Within is a slideshow created at Florida State University which moves through a series of images beginning 10 million light years from Earth and progressing to the microscopic and the subatomic universe, at intervals of the tenth power of magnitude. As you view this slideshow, you can control its speed. Once you arrive at the quark level you can reverse it and return to outer space.

There are other wonderful things to explore on this site, especially for artists who are interested in the amazing patterns of nature.

Aside from the incredibly inspiring visuals, this slideshow has an immediate meditative effect on me. It's nice to see that there's a screensaver available for download. I may decide to get it.

I hope you have great creative plans this week.

The system, with 1920 x 1080 resolution at 30 f/s, uses 3CCD prism block technology to deliver true color, bright contrast and extraordinary detail from the small camera head. A C-mount lens flange and RS232C serial interface and multiple outputs for HD-SDI (SMPTE 292M), analog RGB or Y/Pb/Pr are standard.

Accessories include a 4 - or 15-mm lens and camera cables in 3-, 6-, 10- or 30-m lengths.

The IK-HD1 has already been used for filming reality television shows including "American Gladiators" and "Cash Cab"

TOSHIBA IK-HD1 Accessories include:

• CABLES
  • EXC-HD03 ~ 3 Meter Cable
  • EXC-HD06 ~ 6 Meter Cable
  • EXC-HD10 ~ 10 Meter Cable
• POWER SUPPLY
  • AC-Y415A
• LENSES
  • TF15DA-8
  • TF4DA-8