Biology is a science of three dimensions. The first is the study of each species across all levels of biological organization, molecule to cell to organism to population to ecosystem. The second dimension is the diversity of all species in the biosphere. The third dimension is the history of each species in turn, comprising both its genetic evolution and the environmental change that drove the evolution. Biology, by growing in all three dimensions, is progressing toward unification and will continue to do so.
ALPHA-HEMOLYSIN from STAPHYLOCOCCUS AUREUS Protein Data Bank code 7AHL
From the side
From the top of the structure, showing its wonderful symmetry.
Space-filling model from the top, revealing the symmetry of seven sub-units that unite to form the complete structure.
Space filling model from below, showing how the sub-units create the barrel-like structure seen in the first image.
Hemolysin’s name provides a vital clue to its function. Staphylococcus aureus inserts hemolysin into the membranes of red blood cells, resulting in their rupture, leading to potentially fatal episodes of meningitis, pneumonia, and toxic shock.
Scientists used X-rays at the Advanced Photon Source at Argonne National Laboratory to characterize the first enzyme in the pathway that bacteria use to convert methane to methanol. This important breakthrough is helping researchers improve the synthesis of methanol—a process that would make natural gas a viable energy alternative to petroleum.
Credit: A.C. Rosenzweig and R.L. Lieberman (Northwestern University) using Argonne National Lab’s Advanced Photon Source
We only need to look at our own bodies to discover mysterious monsters and amazing creatures—if one can agree that such things sometimes come in very small packages. In case you didn’t know, you are a minority in your own skin. You are a walking ecosystem of immense complexity and diversity. So much so, that the space occupied by your body is less “you” and more “other creatures.” By this I mean that some ten trillion cells are “yours” in the sense that they contain your DNA, but there are more than one hundred trillion parasites, predators, freeloaders, and helpful cohabitants that…
”The ribosome is, in fact, a nano-scale computer and is very much analogous to the ‘CPU’ of the cell,” he said.
A supercomputer simulation of the ribosome dating back to 2005. It simulates 2.64 million atoms in motion. The in motion is key as the molecular machinery of a ribosome can only be comprehended when its relation to the motion of the cellular environment and how it utilises motion in manufacturing peptides can be considered.
Kevin Sanbonmatsu of Los Alamos National Laboratory ran the simulation on 768 of the “Q” machine’s 8,192 available processors. The entire project took 6 months of work: the end animation equates to 20 nanoseconds of simulated ribosome machinations
Molecular model of a bacterial ribosome showing the RNA and protein components in the form of ribbon models. In the large (50S) subunit the 23S RNA is shown in cyan, the 5S RNA in green and the associated proteins in purple. In the small (30S) subunit the 16S RNA is shown in yellow and the proteins in orange. The three solid elements in the centre of the ribosome, coloured green, red and reddish brown are the transfer RNAs (tRNAs) in the A, P and E sites respectively. The anticodon loops of the tRNAs are buried in a cleft in the small subunit where they interact with mRNA. The other ends of the tRNA, which carry the peptide and amino acid, are buried in the peptidyl transferase centre of the large subunit, where peptide bond formation occurs.
Zhou, Y., Larson, J. D., Bottoms, C. A., Arturo, E. C., Henzl, M. T., Jenkins, J. L., … & Tanner, J. J. (2008). Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA. Journal of molecular biology, 381(1), 174-188.
Peng, L., Oganesyan, V., Damschroder, M. M., Wu, H., & Dall’Acqua, W. F. (2011). Structural and functional characterization of an agonistic anti-human EphA2 monoclonal antibody. Journal of Molecular Biology, 413(2), 390-405
The CGSociety had a contest that challenged digital artists to illustrate how the Human Immunodeficiency Virus (HIV) attacks critical immune system defense cells in human blood, causing the disease AIDS. Alexey Kashpersky (mrRIDDICK) from Poltava, Ukraine won first prize for his image (top). The other images show details of his work in progress.
Kashpersky on his work:
As for the artwork, in fact, I was pretty worried about its position among the works of other participants. Before I get started, I’ve learned a lot of materials, reviewed hundreds of photos, and studied the AutoPACK 3D model. How and what is there. And over some time realized that I had somehow change the initial “correct” form of HIV, in the direction of artistic exaggeration, since I did not want just to render a model, but to express in the form and shape the depth of the problem, and I decided to stop on this. Consciously decided to make an artistic exaggeration, but knowing that my work can cause a controversial reaction from respected judges. Because they DO know how real HIV looks like!
I am very grateful to them for the fact that my thoughts and what I wanted to express in the form, in some way violating the “truth”, understood and appreciated. This means I did it! I have express in this work the pain, suffering and fear of unknown, which in inconceivable tandem go hand in hand with physical beauty, light feelings of love and passion.
Your mind is a universe inside a universe. The cells of your body resonate with the energy of your environment, and cells of your brain resonate with those of your body. Consciousness is a fractal of the Universe simulating itself.