”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.
Glial cells send ‘care packages’ including protective proteins and genetic information to nerve cells
Researchers at Johannes Gutenberg University Mainz (JGU) have discovered a new form of communication between different cell types in the brain. Nerve cells interact with neighboring glial cells, which results in a transfer of protein and genetic information. Nerve cells are thus protected against stressful growth conditions. The study undertaken by the Mainz-based cell biologists shows how reciprocal communication between the different cell types contributes to neuronal integrity. Their results have been recently published in the journal PLOS Biology.
Brain function is determined by the communication between electrically excitable neurons and the surrounding glial cells, which perform many tasks in the brain. Oligodendrocytes are a type of glial cell and these form an insulating myelin sheath around the axons of neurons. In addition to providing this protective insulation, oligodendrocytes also help sustain neurons in other ways that are not yet fully understood. If this support becomes unavailable, axons can die off. This is what happens in many forms of myelin disorders, such as multiple sclerosis, and it results in a permanent loss of neuron impulse transmission.
Like other types of cell, oligodendrocytes also secrete small vesicles. In addition to lipids and proteins, these membrane-enclosed transport packages also contain ribonucleic acids, in other words, genetic information. In their study, Carsten Frühbeis, Dominik Fröhlich, and Wen Ping Kuo of the Institute of Molecular Cell Biology at Johannes Gutenberg University Mainz found that oligodendrocytes release nano-vesicles known as ‘exosomes’ in response to neuronal signals. These exosomes are taken up by the neurons and their cargo can then be used for neuronal metabolism. “This works on a kind of ‘delivery on call’ principle,” explained Dr. Eva-Maria Krämer-Albers, who is leading the current study. “We believe that what are being delivered are ‘care packages’ that are sent by the oligodendrocytes to neurons.”
While studying cell cultures, the research group discovered that the release of exosomes is triggered by the neurotransmitter glutamate. By means of labeling them with reporter enzymes, the researchers were able to elegantly demonstrate that the small vesicles are absorbed into the interior of the neurons. “The entire package of substances, including the genetic information, is apparently utilized by the neurons,” said Krämer-Albers. If neurons are subjected to stress, cells that have been aided with ‘care packages’ subsequently recover. “This maintenance contributes to the protection of the neurons and probably also leads to de novo synthesis of proteins,” stated Carsten Frühbeis and Dominik Fröhlich. Among the substances that are present in the exosomes and are channeled to the neurons are, for instance, protective proteins such as heat shock proteins, glycolytic enzymes, and enzymes which counter oxidative stress.
The study has demonstrated that exosomes from oligodendrocytes participate in a previously unknown form of bidirectional cell communication that could play a significant role in the long-term preservation of nerve fibers. “An interaction like this, in which an entire package of substances including genetic information is exchanged between cells of the nervous system, has not previously been observed”, stated Krämer-Albers, summarizing the results. “Exosomes are thus similar to viruses in certain respects, with the major difference that they do not inflict damage on the target cells but are instead beneficial.” In the future, the researchers hope to develop exosomes as possible ‘cure’ packages that could be used in the treatment of nerve disorders.
Image A: Exosomes (red arrow) are small vesicles that contain proteins and nucleic acids. They are commonly present in close proximity to nerve cell axons where they are ideally positioned to supply protective substances.
B: The JGU researchers were able to show that exosomes are absorbed by the nerve cells and thus help protect these against stress.
When Greg Dunn finished his Ph.D. in neuroscience at Penn in 2011, he bought himself a sensory deprivation tank as a graduation present. The gift marked a major life transition, from the world of science to a life of meditation and art.
Now a full-time artist living in Philadelphia, Dunn says he was inspired in his grad-student days by the spare beauty of neurons treated with certain stains. The Golgi stain, for example, will turn one or two neurons black against a golden background. ”It has this Zen quality to it that really appealed to me,” Dunn said.
Scientists have come up with a way to make whole brains transparent, so they can be labelled with molecular markers and imaged using a light microscope. The technique, called CLARITY, enabled its creators to produce the detailed 3D visualisations you see in this video.