What A Chromosome Really Looks Like.
A chromosome is essentially a hybrid structure that contains our genetic information. It is predominantly visualized as X-shaped, but in reality chromosomes only exist like that when they are about to divide. Recent research by scientists at the BBSRC-funded Babraham Institute have created a new technique to generate models of how chromosomes really exist.
The new technique combines molecular measurements of chromosomes and uses the latest DNA sequencing technology. From which they have created a 3D model of how the DNA folds within a chromosome.
These findings reveal the structure of chromosomes which are directly linked to when and how much genes are expressed. This field of study into how the structure contributes to genome control is known as Epigenetics. Additionally 3D models of chromosomes will allow for mapping of specific genes and other important genomic features onto the structures giving further insight into how chromosome structure affects genomes.
The first gif zooms into a cell showing how chromosomes are normally visualized. The second gif shows four typical cell nuclei in which only one of the chromosomes has been dyed in green and all other DNA with a blue dye, note how different chromosomes actually appear. The final gif shows the created 3D chromosome structure.
I could never get tired of all the ways scientists model molecular structures, and with such accuracy. Especially chromosomes, so much complexity. So glad to see modelling really get the acclaim it deserves for being so critical in various fields like epigenetics. Even the Chemistry Nobel this year went to computer modelling (multi-scale models).
Political and academic ramifications de damned.
That study on the new Dmanisi skull (skull 5) by Lordkipanidze et al. is the biggest load of rubbish and spurious science I have read in a long time. I don’t know how they even got it published, let alone how they can stand behind it as scientists.Edit: It’s also deplorable behaviour that the same lot routinely prevent all but a select group of academics study the Dmanisi material. Dishonest science is that absolute worst.
Many of you may not know about this, and I know this blog is cell biology-centric, but it’s incredibly important. I have been disgusted for days with the awful articles coming out about skull 5.
Kyle Marian was kind enough to supplement the (incredibly disappointing) Science article from the “hoarders” of the fossils, if you will. You can access the article on her blog here.
Early Interactive Molecular Graphics
wetwareontologies introduces us to an early 3D visualization system displaying molecular structure wireframe models:
Eric Francouer helped rescue this crucial archive of early uses of interactive computer graphics in understanding the molecular realm of intracellular biology. These movies document the very early days of interactive computer graphics and their maiden scientific use (in practical science at least) in working out macromolecular structures.
The first system for the interactive display of molecular structures was devised at MIT in the mid-1960s.
Cyrus Levinthal and his colleagues designed a “model-building” program to work with protein structures (Levinthal 1966). This program allowed the study of short-range interaction between atoms and the “online manipulation” of molecular structures. The display terminal (nicknamed Kluge) was a monochrome oscilloscope, showing the structures in wireframe fashion.
Three-dimensional effect was achieved by having the structure rotate constantly on the screen. To compensate for any ambiguity as to the actual sense of the rotation, the rate of rotation could be controlled by globe-shaped device on which the user rested his/her hand (an ancestor of today’s trackball) (NOTE - this is a fantastic historical parallel to the use of the Leap Motion to control data from the Protein Data bank [link])
Speaking of his invention Levinthal said:
"It is too early to evaluate the usefulness of the man-computer combination in solving real problems of molecular biology. It does seems likely, however, that only with this combination can the investigator use his "chemical insight" in an effective way. We already know that we can use the computer to build and display models of large molecules and that this procedure can be very useful in helping us to understand how such molecules function. But it may still be a few years before we have learned just how useful it is for the investigator to be able to interact with the computer while the molecular model is being constructed."
Uh-mazing. To think, computers still can’t completely predict how a protein will fold into its complex three-dimensional structure (although we’ve gotten much closer)