In 1953, Cambridge researchers Watson and Crick published a paper describing the interweaving ‘double helix’ DNA structure – the chemical code for all life.

Now, in the year of that scientific landmark’s 60th Anniversary, Cambridge researchers have published a paper proving that four-stranded ‘quadruple helix’ DNA structures — known as G-quadruplexes — also exist within the human genome. They form in regions of DNA that are rich in the building block guanine, usually abbreviated to ‘G’.

The findings mark the culmination of over 10 years investigation by scientists to show these complex structures in vivo — in living human cells — working from the hypothetical, through computational modelling to synthetic lab experiments and finally the identification in human cancer cells using fluorescent biomarkers.

The research, published January 20 in Nature Chemistry and funded by Cancer Research UK, goes on to show clear links between concentrations of four-stranded quadruplexes and the process of DNA replication, which is pivotal to cell division and production.

By targeting quadruplexes with synthetic molecules that trap and contain these DNA structures — preventing cells from replicating their DNA and consequently blocking cell division — scientists believe it may be possible to halt the runaway cell proliferation at the root of cancer.

“We are seeing links between trapping the quadruplexes with molecules and the ability to stop cells dividing, which is hugely exciting,” said Professor Shankar Balasubramanian from the University of Cambridge’s Department of Chemistry and Cambridge Research Institute, whose group produced the research.

“The research indicates that quadruplexes are more likely to occur in genes of cells that are rapidly dividing, such as cancer cells. For us, it strongly supports a new paradigm to be investigated — using these four-stranded structures as targets for personalised treatments in the future.”

Physical studies over the last couple of decades had shown that quadruplex DNA can form in vitro — in the ‘test tube’, but the structure was considered to be a curiosity rather than a feature found in nature. The researchers now know for the first time that they actually form in the DNA of human cells.

“This research further highlights the potential for exploiting these unusual DNA structures to beat cancer — the next part of this pipeline is to figure out how to target them in tumour cells,” said Dr Julie Sharp, senior science information manager at Cancer Research UK.

“It’s been sixty years since its structure was solved but work like this shows us that the story of DNA continues to twist and turn.”

The study published January 20 was led by Giulia Biffi, a researcher in Balasubramaninan’s lab at the Cambridge Research Institute.

By building on previous research, Biffi was able to generate antibody proteins that detect and bind to areas in a human genome rich in quadruplex-structured DNA, proving their existence in living human cells.

Using fluorescence to mark the antibodies, the researchers could then identify ‘hot spots’ for the occurrence of four-stranded DNA — both where in the genome and, critically, at what stage of cell division.

While quadruplex DNA is found fairly consistently throughout the genome of human cells and their division cycles, a marked increase was shown when the fluorescent staining grew more intense during the ‘s-phase’ — the point in a cell cycle where DNA replicates before the cell divides.

Cancers are usually driven by genes called oncogenes that have mutated to increase DNA replication — causing cell proliferation to spiral out of control, and leading to tumour growth.

The increased DNA replication rate in oncogenes leads to an intensity in the quadruplex structures. This means that potentially damaging cellular activity can be targeted with synthetic molecules or other forms of treatments.

“We have found that by trapping the quadruplex DNA with synthetic molecules we can sequester and stabilise them, providing important insights into how we might grind cell division to a halt,” said Balasubramanian.

“There is a lot we don’t know yet. One thought is that these quadruplex structures might be a bit of a nuisance during DNA replication — like knots or tangles that form.

“Did they evolve for a function? It’s a philosophical question as to whether they are there by design or not — but they exist and nature has to deal with them. Maybe by targeting them we are contributing to the disruption they cause.”

The study showed that if an inhibitor is used to block DNA replication, quadruplex levels go down — proving the idea that DNA is dynamic, with structures constantly being formed and unformed.

The researchers also previously found that an overactive gene with higher levels of Quadruplex DNA is more vulnerable to external interference.

Authors: Andrzej Polanski · Marek Kimmel

ISBN 978-3-540-24166-9 Springer Berlin Heidelberg New York

Download link: Bioinformatics.pdf

PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. These Web pages, by Joe Felsenstein of the Department of Genome Sciences and the Department of Biology at the University of Washington, contain information on PHYLIP and ways to transfer the executables, source code and documentation to your computer.

Let's assume that you have fetched the appropriate executables archives (if any) for your machine, together with the Documentation and Sources archive.

These archives are not simply a single executable for general use. Instead they are a (large) number of files, squished together into one file, and thus called an "archive". You have to go through a step which involves getting all the files out of the archive and into a folder on your machine.

We will give these instructions for four different kinds of systems, Windows, Mac OS X, Linux or Unix systems, and Mac OS 8 or 9. Then we will describe how to access the documentation after installing the package.

Windows
Our main method of distributing PHYLIP for Windows systems is in a self-extracting archive. A self-extracting archive has a small self-extraction program on its front, and when you run them as programs they extract themselves and write many files into your folder.

On the Windows system you will have a self-extracting archive called phylip-3.69.exe. Place it in a folder where you will want PHYLIP to reside. After it self-extracts, it will make a folder called phylip-3.69 there, in the folder where you place the self-extracting archive. So if you place the archive on the Desktop, it will make that folder there.

To self-extract the archive simply double-click on it. If your Windows system does not allow the archive to self-extract, you may have to right-click on the archive and select "Run as administrator". Accept the default settings, making sure that it will extract into the folder that you want it in, and when a dialog box comes up, click on Unzip. When the extraction is complete, select Close. You will find the folder phylip-3.69 in the same place as the archive.

After the self-extraction is done, you will find the phylip-3.69 folder which has three folders within it, called doc, exe, and src. There is also a web page phylip.html. You should read this in your browser. It contains links to the main documentation web page main.html and to the other documentation pages and programs.

Note: There has been a report that on Windows Vista (specifically the report was for Service Pack 2 on Home Edition) that if you extract the files into a folder that is somewhere under Program Files, they may not work properly. You can avoid this problem if you extract them into a folder which is somewhere in your own folders.

Macintosh Mac OS X

The archives for Intel iMac and PowerMac Mac OS X are in the Apple .dmg disk image format. There is one .dmg disk image distributed. It is 6.8 Megabytes in size, and is compressed; when uncompressed it is several times larger. (Note that Mac OS X version 10.0 did not support compressed disk image files, so the .dmg file we distribute will not work on it).

It contains what looks like a normal folder called phylip-3.69, but you should not use the programs while they are in that folder. It is important that you use a copy of the contents of the disk image elsewhere on your system. Decide where the folder phylip-3.69 is going to reside, and copy that folder to that new location. Within it is all the source code, documentation, and executables.

The executables are 32-bit "universal binaries" that will run on either the newer iMacs (which has Intel processors) or the older G3's, G4's or G5's that have PowerMac processors. (Basically they are each simply a pair of executables set up so that the processor chooses the right one and runs it).

There is also a set of links in the exe folder to enable you to run the programs by simply typing their name. If these are absent, which they should not be, there is one additional set of steps you need to do:
Open a Terminal window (which you will find in the Utilities folder of the Applications folder).
At the prompt, change to the folder where the PHYLIP executables are kept. For example, if you have folder phylip-3.69 on your desktop, type in the command
cd Desktop/phylip-3.69/exe
Change the permissions of the script linkmac which you will find there to allow it to execute:
chmod +x linkmac
Then execute the script by typing: ./linkmac

The result will be that the executables folder will now have a set of links, one for each program, that allow the programs to be executed simply by typing their names. Thus the programs in that folder can then be executed either by clicking on their icon, or by typing their name (in lower case) preceded by ./ to indicate the current folder, such as ./dnaml

This setting up of these links needs to done only once, and they will be available thereafter.

Linux and Unix

You can easily install PHYLIP and compile it yourself on a Linux or Unix system, provided that you have a C compiler on your system. (On some Linux systems and in some recent versions of Mac OS X the C compiler is not installed by default, and you may have to make sure that it is installed).

The archive for Linux or Unix systems is just the Documentation and Sources archive. You can extract the files from the archive by putting it into a folder by itself, getting into that folder, and giving the command

gunzip phylip-3.69.tar.gz

This uncompresses the archive so that it will now be bigger and be called phylip-3.69.tar. Now it is a "tar archive".

Now just issue the command

tar xvf phylip-3.69.tar

The archive will be extracted and a phylip3.69 folder created that contains within it three folders, doc, exe, and src, as well as a web page phylip.html. You should start by reading that web page. It contains links to the documentation web pages, including the main documentation web page main.html.

To make executables, use your C compiler. It is probably as simple as going into the src directory and typing the command

make install

which will cause the programs to be compiled and the executables and font files installed in the exe directory. If there are problems with the compilation, read the relevant sections of main.html and also the beginning of the Makefile.

Compiling on Ubuntu (or other Debian-family) Linux

I have found that to compile PHYLIP 3.69 on an Ubuntu system, and presumably on other Debian-family Linux releases, you need to load some X11 libraries before compiling. Try the following:
Make sure you have enough administrative privileges for the following (or go get the help of those that do).
Load the X11, Xt and Xaw libraries by doing these commands:

3. sudo apt-get install libX11-dev

4. sudo apt-get install libxt-dev

5. sudo apt-get install libxaw7-dev
If all those installations work, you can then get into the src folder, and as indicated above, just execute the command

7. make install

With luck this will work. After the compilation the executables and their font files will be in folder exe.

Macintosh Mac OS 8 or Mac OS 9

We don't think there are many Mac OS 8 or Mac OS 9 machines around any more -- Apple has abandoned that operating system, and it is probably not wise to use it on the Internet as it has not been upgraded to cope with recent security threats. We no longer distribute Mac OS 8 or 9 executables for our most recent versions of PHYLIP. Nevertheless, we do make available a Stuffit (.sit) archive of executables for PHYLIP 3.65, just in case anyone needs it.

Downloading the single Stuffit archive

The archives for Mac OS 8, Mac OS 9 Macintoshes are self-extracting archives. If you are fetching the files using a Web browser directly from your Mac, it will probably automatically invoke Stuffit Expander to unpack the archives into self-extracting archives. Self-extracting archives are archives with a small self-extraction program on their front, so that when they are run as programs they write a great many files into a folder.

Our default distribution is of a single large (4.9 Megabyte) Stuffit archive called phylip3.65.sit. This should automatically be unstuffed as it is downloaded. It contains the source code, documentation, and Mac OS executables.

However, at the moment we have reports of trouble running the unstuffed archives. Recent versions of Mac OS 9, and also the Classic environment under Mac OS X, seem to regard the executables files as text files, and they try to open them under SimpleText, which of course does not work.

Downloading multiple smaller Stuffit archives

Some people may wish instead to download these as a series of four archives. This might be necessary, for example, if you wanted to transfer them to a machine that was not connected to the Internet, and needed them each to be small enough to write onto a floppy disk.

If you choose to download these instead of the single Stuffit archive, and our system does automatically invoke Stuffit Expander, four self extracting archives will be created on your desktop, and their file names will end in .sit. If you have Stuffit Expander, you can use it to expand them.

Once the archives are downloaded and extracted, they will put folders on the desktop. One is called phylip and contains folders doc and src as well as a web page phylip.html. There are 307 files in all, as these include the documentation files, source code files, and compilation support files. You may have to be patient while the archive is being extracted.

The three archives of Macintosh Mac OS 8 and Mac OS 9 executables will create folders exe, exe.1, exe.2 and exe.3 on the desktop when they are extracted. For some reason we could not create these inside the phylip folder, but that is where these files need to be put. Do the following:

1. Move the exe folder inside the phylip folder.
2. Open the exe.1 folder, and mark all of its files (you can do this using the Select All menu option in the system Edit menu).
3. Drag this group of marked files into the exe folder which is now inside the phylip folder.
4. Now do the same for exe.2 (mark the files and drag them into exe).
5. And do the same for exe.3 (mark the files and drag them into exe).
6. You can now discard the folders exe.1, exe.2 and exe.3 (if any). If you have four folders named phylip3.65.0.sit, exe.1.sit, exe.2.sit, and exe.3.sit on your desktop, these can be discarded too.
7. The phylip3.65 folder can now be moved to wherever you want it to be.

Source: http://evolution.gs.washington.edu/phylip

Nanotechnology is science and engineering at the scale of atoms and molecules. It is the manipulation and use of materials and devices so tiny that nothing can be built any smaller.

How small is small?

Nanomaterials are typically between 0.1 and 100 nanometres (nm) in size - with 1 nm being equivalent to one billionth of a metre (10^-9 m).

This is the scale at which the basic functions of the biological world operate - and materials of this size display unusual physical and chemical properties. These profoundly different properties are due to an increase in surface area compared to volume as particles get smaller - and also the grip of weird quantum effects at the atomic scale.

If 1 nanometre was roughly the width of a pinhead, then 1 metre on this scale would stretch the entire distance from Washington, DC to Atlanta - around 1000 kilometres. But a pinhead is actually one million nanometres wide. Most atoms are 0.1 to 0.2 nm wide, strands of DNA around 2 nm wide, red blood cells are around 7000 nm in diameter, while human hairs are typically 80,000 nm across.

Unwittingly, people have made use of some unusual properties of materials at the nanoscale for centuries. Tiny particles of gold for example, can appear red or green - a property that has been used to colour stained glass windows for over 1000 years.

Nanotechnology is found elsewhere today in products ranging from nanometre-thick films on "self-cleaning" windows to pigments in sunscreens and lipsticks.

Nano is born

The idea of nanotechnology was born in 1959 when physicist Richard Feynman gave a lecture exploring the idea of building things at the atomic and molecular scale. He imagined the entire Encyclopaedia Britannica written on the head of a pin.

However, experimental nanotechnology did not come into its own until 1981, when IBM scientists in Zurich, Switzerland, built the first scanning tunnelling microscope (STM). This allows us to see single atoms by scanning a tiny probe over the surface of a silicon crystal. In 1990, IBM scientists discovered how to use an STM to move single xenon atoms around on a nickel surface - in an iconic experiment, with an inspired eye for marketing, they moved 35 atoms to spell out "IBM".

Further techniques have since been developed to capture images at the atomic scale, these include the atomic force microscope (AFM), magnetic resonance imaging (MRI) and the even a kind of modified light microscope.

Other significant advances were made in 1985, when chemists discovered how to create a soccer-ball-shaped molecule of 60 carbon atoms, which they called buckminsterfullerene (also known as C₆₀ or buckyballs). And in 1991, tiny, super-strong rolls of carbon atoms known as carbon nanotubes were created. These are six times lighter, yet 100 times stronger than steel.

Both materials have important applications as nanoscale building blocks. Nanotubes have been made into fibres, long threads and fabrics, and used to create tough plastics, computer chips, toxic gas detectors, and numerous other novel materials. The far future might even see the unique properties of nanotubes harnessed to build a space elevator.

More recently, scientists working on the nanoscale have created a multitude of other nanoscale components and devices, including:

Tiny transistors, superconducting quantum dots, nanodiodes, nanosensors, molecular pistons, supercapacitors, "biomolecular" motors, chemical motors, a nano train set, nanoscale elevators, a DNA nanowalking robot, nanothermometers, nano containers, the beginnings of a miniature chemistry set, nano-Velcro, nanotweezers, nano weighing scales, a nano abacus, a nano guitar, a nanoscale fountain pen, and even a nanosized soldering iron.

Engineering wonder

Engineering at the nanoscale is no simple feat, and scientists are having to come up with completely different solutions to build from the "bottom-up" rather than using traditional "top-down" manufacturing techniques.

Some nanomaterials, such as nanowires and other simple devices have been shown to assemble themselves given the right conditions, and other experiments at larger scales are striving to demonstrate the principles of self-assembly. Microelectronic devices might be persuaded to grow from the ground-up, rather like trees.

Researchers are also finding ways to put proteins, DNA, viruses and bacteria and other micro-organisms to work in building nanomaterials, and also taking other inspiration from the natural world.

Some problems have arisen due to a lack of consistency in measuring distances at the nanoscale, but an atomic lattice nanoruler could improve accuracy.

Great potential

In the short term, the greatest advances through nanotechnology will come in the form of novel medical devices and processes, new catalysts for industry and smaller components for computers.

Source:  http://www.newscientist.com

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Artificial Intelligence and Molecular Biology - Lawrence Hunter