A model organism – the virtual bacteria.

stanfordmycoplasmagenitaliumI was reading an article in Scientific American today that got me thinking about the complexities of biology – the article described the production of a virtual bacteria using computing to model all of the known functions of a simple single cell.  The article was a very compelling read and presented a rational argument of how this could be achieved, based on modelling of a single bacterium that would eventually divide.  The benefits of a successful approach to achieving this situation are immense for both healthcare and drug development, but the difficulties are equally immense.

In order to simplify the problem the organism chosen to be modelled is a bacterium with the smallest genome size – Mycoplasma genitalium a bacteria that has only 500+ genes all of which have been sequenced.  This bacterium is also medically important, which adds weight to the usefulness of a virtual organism.  The problem of programming the computer was divided into modules, each of which will describe a key process of the cell all of which could feedback in a way that described actual binding coefficients for protein-protein and protein-DNA interactions.

As I read the article, I began to realise that there were some simple problems associated with the description of how the computer would “manage” the cell and when the author described doubling protein concentrations prior to cell division I knew there were problems with their model – this simplistic approach is not what happens in the cell – cellular control is an important aspect of this modelling and must be correct if the cell is to be realistic.  I can illustrate what I mean with one example – plasmid replication.  A plasmid in an autonomous circle of DNA, often found in bacteria, that are easy to understand and ubiquitous in nature.

Replication of plasmid DNA:

ReplicationThe number of copies of a plasmid are tightly controlled in a bacterial cell and this control is usually governed by an upper limit to an encoded RNA or protein, when the concentration of this product drops, such as AFTER division of the cell, replication will occur and the number of plasmids will increase until the correct plasmid number is attained (indicated by the concentration of the controlling gene product).

This is a classic example of cellular control and is a lot different to a model based on doubling protein concentration in anticipation of cellular division.

Mycoplasma genetics and the complexity of biology:

This whole problem also got me thinking about my own subject area and my brief excursion into the study of restriction enzymes from Mycoplasma. Restriction systems are a means for bacteria to protect themselves from viral invasion and, despite the small size of the genomes of Mycoplasma bacterial strains, they encode such systems.  There is clear evidence that such systems are “selfish” and may be they are fundamental to the long term survival of bacteria, so I think they need to be dealt with in the model organism.  However, things begin to get complicated when you look at the well described system from Mycoplasma pulmonis (a slightly more complex version of the organism used for the model).  Instead of a single set of genes for a restriction system, as usually found in other organism, the restriction genes of Mycoplasma pulmonis  are capable of switching in a way that can generate four different proteins from a single gene.  This is where the complexity of modelling an organism occurs and while the organism used may have a simple genome, it is important to know of how even simple organisms can increase their genetic complexity without increasing their DNA content.


I think the work at Stanford is both interesting and important and I think they have achieved a very important step along the road to modelling a living cell, but I also think they may need more information and have more complex modules available to them as they try to be more accurate with even these simple organisms.  It will be a long road before we have a model of a human cell, but what an incredible thought that would be!


Future wish list – technology frontiers

I remember from reading computer magazines that a popular article was always based around what the future holds and what we would really like to see developed.  So, I thought I might have a go at this myself and create a list of ideas or developments in technology that I would really like to see (comments are welcome and I will add ideas I agree with).  I am not as up to date with technology as some think I am, so my list may be out of date!   The  order is not necessarily linked to how important I think the technology might be:

  1. fibre-opticFibre-optic broadband – this is not new technology, but I think the roll out of this capability has been too slow and too random.  The available speeds for internet access, for many people (including myself) are poor (8 Mb) and very variable.  The internet will never be fully useful until download speeds improve.
  2. 3G and mobile networks – also not new technology, and soon we will have 4G, but what I would like to see is a seamless switch between data handling and telephone/text capability.  There is nothing worse than having a Wi-Fi signal but no network connection, so a phone call is impossible!  It must be possible to use both communication systems to handle any type of data, after all we can have internet telephone calls.
  3. displayDisplay screen on laptops and tablets– everyone knows where the use of laptops and tablets falls down, it is in direct sunlight, but we all have seen The Kindle displays with the paper white screen that is easy to read in daylight.  So, why can’t we have a combination of these technologies, backlit LCD and reflective white screen, so that a tablet/laptop can be read anywhere at anytime.
  4. Universal-Charger-300x217Power supplies and batteries – this is a slight re-hash of a previous blog and reflects my continued annoyance at having to carry chargers, batteries and cable connectors.  Why can we not have a universal charger for all electronic equipment and a simple mechanism to charge batteries that does not require us to switch off to swap a run-down battery (hot-swap technology).  A charger should have a universal connector for direct charging batteries, which should all have the same connector layout, and a single connector for all equipment – how difficult is that?
  5. Wireless sound systems – another technology that is already available, but my desire is a simpler system (for example Bluetooth is often hard to get to work and unreliable in some situations) and one that can easily be understood before purchase such that you buy the right thing!  It is sometime impossible to find a device that does what you want it to do, which should be stream high quality music from any source to an amplifier and speakers, and then knowing it will receive signals from all sources becomes a jumble of abbreviations and acronyms!

Okay, that is a start I will come back to this article I am sure

High-level equipment and its impact on science

A recent article (Hamrang, et al. Trends in Biotechnology, 2013) made me think about the impact modern technology is having on how scientific research is developing and, in particular, my own experience of applying some of this technology.  I thought it might be interesting to detail some of this technology and how it has influenced my own research and how it might both develop to provide new approaches for the advancement of science and how this will change requirements in teaching.

AFM1A good place to start is SINGLE MOLECULE ANALYSIS a concept I had never thought of in my early research career, but it became a possibility during the 1990s.  The first time I  heard of single molecule analysis was something called a Scanning Tunnelling Microscope, but I could not see uses for this device outside of chemistry as the objects to be visualised were in a vacuum.  However, this device quickly developed into the Atomic Force Microscope (AFM) and the study of biological molecules was soon underway.  This device measures surface topology and can visualise large proteins as single molecules – my first involvement was to visualise DNA molecules translocationthat were being manipulated by a molecular motor.  The resolution was astounding, but more importantly we were able to use this technology to study intermediates that had been biochemically “frozen” in position and resolve features we never expected to see.  Further studies allowed us to also study protein-protein interactions and super-molecular assembly of the motor.  The wonderful thing about this technology is that interpretation of the data has quickly moved from the negativeness of “artefacts” and a lack of faith that images showed what was thought to be there, to a situation where major advancements are possible through direct topology studies.  Developments of this technology are likely to include automatic cell identification, in vivo measurements using fine capillary needles and measurements of ligand-surface target interactions on cells – this could influence drug development and biomedical measurements.  Another developing technology related to AFM is the multiple tip biosensor that can sense minute amounts of material in a variety of situations (a “molecular sniffer” – one use I heard of directly from the developer was for wine tasting/testing!
Magnetic TweezerMy second single molecule analysis involved a Magnetic Tweezer setup which is able to visualise movement of a magnetic bead attached to a single molecule (in our case DNA), which allowed us to determine how a molecular motor moves DNA through the bound complex, but, perhaps more importantly, this led us to develop a biosensor based around this technology that could be used to determine drug-target interactions at the single molecule level and perhaps allow single molecule sensing in anti-cancer drug discovery.  This technology is also closely related to optical tweezer systems that have been used in similar studies and the future is certain to make such technology cheaper and easier to use and their application in biomedical research.  The key to this development will be the increased sensitivity of single molecule studies and how this will enable more detailed understanding of intermediate steps in molecular motion induced by biomolecules. I imagine as newer versions of these devices become more automated, then they will be used as biosensors to study more complex systems that involve molecular motion.  In the short term, it seems to me that there is scope for the application of these devices in understanding protein amyloid formation and stability with a view to determining mechanisms for destabilising such structures.

SPRThe best known system in this category of analytical devices is Biacore’s Surface Plasmon Resonance (SPR), which uses a mass detection mechanism based on changes to the Plasmon effect produced by electrons in a thin layer of gold. We have used this to study protein-DNA interactions and subunit assembly and the technique provides a useful confirmation of older techniques such as electrophoresis. I have been involved in discussions about the application of this technology in the field, but reliability and setup problems remain a problem. In comparison, the Farfield dual beam interferometer can use homemade chips that simplify setup and seems more reliable for similar measurements. Where I see a potential for these devices is in the study of protein aggregation, which has tremendous potential in the study of amyloid-based diseases. This idea sprang from discussions with Farfield about using their interferometer to detect crystallization and would be an interesting project. However, if these devices are to have a major impact in biomedical sciences, they need to be easier to setup, more reliable and smaller.  recent advances are leading SPR toward single molecule sensing (Punj, D., et al., Nat Nano, 2013). I believe the real key to implementing this technology as a biosensor is to incorporate two technologies in the same device. We proposed to have a dynamic system, on an interferometer chip, whose activity would switch off the interferometre when active. This could be used in drug discovery, targeting the drug at two systems simultaneously. If massively parallel systems can be developed, possibly based around laminar-flow, I can see a use in molecular detection of hazardous molecules using either antibodies, or aptamers.

cyroEMI have not directly used this technology, but I have seen the results applied to the molecular motor that I have worked with. The value of the system is that cyroEM allows the gathering of many images of a large protein complex, which allows structural studies of systems that cannot be crystallized or visualized using NMR. My feeling is that as computing power increases this technique combined with molecular modelling in silico, will provide structural information for many complex biological systems. The impact of this knowledge will greatly influence the design of drugs and will aid the biochemical analysis of complex systems. My feeling is that further development of this technology will revolve around combining it with other techniques for visualising biomolecules, one I have mentioned before is Raman Spectroscopy, which could allow studies of these complexes in situ another could be single molecule fluorescence (Grohmann, et al. Current Opinion in Chemical Biology). I can easily imagine collaborative research projects that will bring a variety of such techniques to the production of the 3D image of real biological systems isolated from cells. Such research would have to follow existing models of bidding to use such equipment in centres of excellence. Such centres would bring together visualization techniques with single molecule analysis and data from genomics and proteomics. The research lab of the future will depend on much more international collaboration than we have seen up to now!

The current technology in this area divides into two types of nanopores, physical holes in a surface and reconstituted biological pores. I have used a physical nanopore to investigate the separation of proteins from DNA using electrophoresis across the nanopore, the beauty of this system is that it also quantifies the number of molecules crossing the pore. I imagine that such devices will develop using surface attached biomolecules around the pore, which will introduce specificity into the device, but what I would have liked to develop is a dynamic device for ordered assembly of molecules (an artificial ribosome) where the nanopore allow separation of the assembly line and the drive components – such are the dreams of a retired scientist!
nanopore_x616[1]Biological nanopores are the main focus for single molecule sequencing of DNA and the future must be portable, personal sequencing devices (DNA sequencing information must reside with the source of the DNA and for humans this will eventually lead to personal devices. However, the level of available data will be enormous and the growth of the “omics” research will require new ways to store, organise and access this information. A new method for studying biological systems is already underway in which analysis of data allows a better understanding of complex systems. This will eventually become a part of biomedicine and will be supported by personalised medicine.

I was once asked by a student what future Biology holds, and I now know it will be an area of significant growth for many years to come, but this requires the right focus for investment and a new direction for undergraduates in their studies – good luck to those I have taught, who now have to lead these developments.

Windows Live Messenger has gone!

windows messengerThis week my copy of Messenger stopped working, well, strictly speaking it started insisting I upgrade to Skype, so I uninstalled it.  This  is not because I don’t want to use Skype, but because I already have Skype and don’t want to merge the two accounts.  I am not even sure there is a simple way to merge the two accounts, or import required contacts from Messenger into Skype – I have done this manually, but that does mean I have to ask my contacts to accept me, which means they also have to use Skype. I think Microsoft have made a complete mess of this change for Windows live and that there should have been a better way to integrate Messenger into Skype.  I am also unsure what happens with my Android app that contacts Messenger contacts, are they now permanently offline – we need more information!

Broadband speeds – slow progress?

Internet speeds can be quickly determined at this site, the results for my line are:

Line speed

Having just moved house (May 2012) I find i have gone from a Virginmedia connection (formerly NTL fibre optics) to a BT landline (through Sky) and what a difference I notice in download and especially upload speeds!  This subject seems to have disappeared out of the news, but there is still a major issue to be addressed by the government, if they are to make good use of modern internet capabilities within the economy.

The reason for this blog is that I am disappointed with the speed I get from out BT landline, but also because I think this is a typical example of a missed opportunity – a new housing estate with poor internet speeds.  I cannot understand why there is no fibre optic capability on this new estate, nor any sign that there may ever be such a fast connection.  It seems to me this is one place the government could provide regulation (just as they have regulated the energy use of new buildings) by insisting that a new housing estate should be provided with fibre optics and a choice of supplier who can use this facility!

speed4As you can see from the data at the top of this blog, I am only getting 5Mb/s download speed (against a maximum offered speed of 8 Mb/s; although the advertisements suggest upto 14 Mb/s) and an upload speed of only 0.68 Mb/s!  This illustrates the other area that needs government regulation – advertised speeds are theoretical maximums, not actual situations.  This is very misleading and should not be allowed – it is the use of the phrase “upto” with the offered speeds that is particularly misleading.  Although, I could choose another supplier (other than Sky) this is unlikely to help me as they all have to use the BT landline.  I have asked Virginmedia if they plan to lay fibre optics in the area, but they may not be able to gain access to do so!  BT would make no comment about upgrading our area to fibre optics.

So, I imagine that nothing will change in this area, the government simply make noises when they have to, but implement no policy changes.  The suppliers are only competing on price (except for Virginmedia) and there is no coherent policy to introduce fibre optics in areas that could be upgraded without too much disruption – very disappointing!

Skydrive replaces Live Mesh? Maybe not – updated!

I have updated this blog after a week or two of trying to understand the problems of using Skydrive – the comments that are most recent are marked ADDENDUM:

I have used Windows Live Mesh to synchronise my laptops and PC for a few years now, and I have even used Mesh to distribute science notes in our lab environment.  However, recently Microsoft announced the removal of Mesh from Windows Live utilities.  Their suggestion is to replace Mesh by Skydrive and a recent update to the Skydrive application for PCs allowed selection of files to synchronise, but will it accomplish the same tasks as Mesh, will it work?

I hope this blog might answer those questions and provide an insight into the problems that occur.  First, let me explain what I want to do and how well that worked with Mesh.  I have two laptops (mine and my wife’s) and a PC that we both use.  What I want is to ensure that specific folders are the same on all three computers and to back these up to an external source (I used Carbonite until the change to Skydrive was announced).  Mesh was installed on all three computers and you could choose specific folders that would be synchronised between computers (there was also a small space on the Mesh servers to store some files).  You could also share these folders with another person, who had to sign into Mesh, and they would be shared and synchronised when they were signed in.  But, there were two major problems:

  1. Outlook – the data file for the email program Outlook could not be synchronised by Mesh and so emails were only accessible on one computer, which was our individual laptops.
  2. Special folders – Pictures, Videos, Downloads and My Documents are special folders in Windows and synchronizing these on one shared PC was a major problem.
    What happened when trying to synchronise these folders and sharing them, was a new folder was created with the first letter missing – “My Documents” became “y Documents”!

Although this was messy I was able to synchronise files and have all the computers identical.  I was even able to synchronise some files that were not simple documents files such as Favourites and Office Templates.

The Skydrive application, installed on a PC is meant to replace Mesh.  You can upload all of your files to the Skydrive server (purchasing extra space as required) and then link to them by means of the Skydrive application, selecting which folders to synchronise.  However, all the folders must be within a specially created “Skydrive” folder, but you can at least determine the initial location of that folder.  Sadly, that means folders such as Favourites are not synchronised, so already a major difference from Mesh.

So, how did this work for me?  Well, first of all it took a long time to have all my files upload to the Skydrive server (about two weeks for 80 Gb), I also uploaded some folders that would not be synchronised, just to store them.  Then I had to create a Skydrive folder on each PC, but deselect all folders at first.  Then I moved all files/folders into the Skydrive folder on each PC (this was to be quicker than waiting for downloads.  On the PC I also allowed sharing of all of these folders with my wife’s account on that computer.  I then had to ensure all Libraries pointed to the new location (e.g. Pictures, Videos etc) and that links to these files worked.  Then I enabled synchronisation of specific folders via the Skydrive application.
Copying the files to the Skydrive folder was meant to save a lot of download time, but, unlike Mesh, the policy for avoiding overwriting is not clear for Skydrive and what I quickly discovered was that the files already on the laptop (the computer is called Portege) were renamed with “-Portege” appended to the filename.  This meant my hard drive quickly filled up with duplicates and some files (such as outlook.pst needed to be renamed to avoid being out of date!  This is not a great feature of Skydrive and Microsoft need to think about their synchronisation/duplication policy.

CaptureAll seemed well until I started to use the PC, my first problem arose when I tried to open Outlook – I pointed the program at the new location for my PST files, which opened fine and seemed well, but after signing my wife on to do the same, a problem arose on my desktop, I was unable to open Outlook as I was not allowed access to my PST file!  I checked the sharing setting and that indicated I was the owner and it was shared with my wife!  A mystery that was solved when I used the properties tab of the file to enable Home Users full access.  But, why am I not able to open a file I am owner of?
This problem of Administration of a shared computer has turned out to be more than just a bug bear, but in fact, a major issue!  I am not sure I really understand the real nature of the problem, but I will summarise what I think is happening.
It seems to me that when you first set up a shared computer the first owner, who automatically is classed as an Administrator, has a different set of ownership rights over files.  So when I set up my account on my wife’s PC and created a Skydrive account, I ran into issues of file ownership that I was not expecting.  In fact, I quickly discovered that Skydrive was not synching on my desktop and that I could not open my online account.  However, when I created the Skydrive account (using my login details) within my wife’s account not only could I access my online files, but the Skydrive folders were now synching.  As a consequence I have closed the Skydrive application within my account on this shared PC!  Not a very satisfactory solution to be honest, which also relates to the fact that Mesh allowed sharing of files that could also be downloaded automatically, but Skydrive shares the files online only – they cannot be synched unless you have the Skydrive account working!
A few weeks later, now, I have all the files synchronised, but I cannot open the online Skydrive from my account on this shared computer, only when logged on as my wife can I access the online files – something of a nuisance!  I also found that Media Player would not load the music files in the shared Library until I enabled as an administrator and asked it to restore the library – it seems okay now.  Finally, I find that many programs, that need access to the shared folders (e.g. Internet Explorer for picture saving) need to be run as an administrator, even though I have administrator rights for my account – this issue is much more complex than it seems!  Recently, I have found a better solution to this problem and that is to go to the root folder of each synchronised folder, open properties and then Security and then use the edit button to add the other user’s name to the list of names allowed full rights.  This seems to solve the sharing problems.

The problem of not being able to open the online Skydrive account is interesting and I tried to find out more about it recently.  What happens is that instead of opening the list of folders when you sign into your Skydrive account, the IE page cycles or repeats trying to load.  I discovered a forum description of this that said you should check the privacy setting for Internet Explorer to make sure live.com is not one of the trusted sites.  I checked this and I had indeed added live.com to the trusted site list and when I removed it the online folders opened as expected!

This ownership problem was repeated for a number of files I needed to access – one was an MNY file I use with MSMoney to keep my accounts – one common denominator seems to be the files autosave.

So, I am now waiting to see what problems we run into and to see if I can understand the nature of these problem.  What is my conclusion?

  1. Skydrive ONLY allows synchronisation of folders within the created Skydrive-folder, which means any system files cannot be synchronised; whereas, Mesh allowed favorites and Office Templates to be synchronised, but this is not now possible.
  2. Skydrive duplicates existing files to avoid overwriting, so care must be taken about loading files into the Skydrive folder, this is best done from the online source either manually or automatically using synchronisation, rather than copying them across folders on the computer.
  3. Sharing files that are to be synchronised presents some issues, especially with key folders such as the default Pictures, Videos and My Documents folders that have to be moved to the Skydrive folder.  However, this was also a problem with Mesh.
  4. Administrator rights influence how Skydrive works on a shared computer and this situation is complex – the best solution is that the computer owner (first user) should install Skydrive and synchronise files that are the shared to other user, but there may still be problems.
  5. Uploading is fairly slow and the system does not synchronise as fast as Mesh.

Therefore, my overall feeling is that this system is neither as good nor as versatile as Mesh and Microsoft will have to rethink how this works for it to solve the problem of synchronizing computers, especially computers with shared accounts.

A SMART TV–The Toshiba 40 inch 40RL953B

I recently bought a new TV for the lounge of the new house, we have a large gap on the TV cabinet and a 40” set fills this perfectly!20121003_092

When choosing the TV I decided I would explore these SMART TVs, which connect to the internet and a local network.  The TV also has a sound outlet, through a headphones socket, which allows the volume to be set for a output via my HiFi amplifier (which you can see just below the TV on the left) and the TV speakers to be switched off via the setup controls.

The TV was bought via Amazon and was less that £400, which is quite reasonable I thought.  Delivery was very prompt and setup was easy – the TV has Freeview available, but we connect through a Sky Anytime+ HD box (visible on the right under the TV).  As I mentioned above I connected the headphone output to the auxiliary input of my amplifier, set the volume level with the TV speakers set to a minimum and then muted the TV speakers through the TV setup.  This means the volume level is fixed, adjustable only through the amplifier volume control, but the TV mute button doesn’t work Sad smile .  The sound output from the TV, through the amplifier, is excellent, but the TV speakers are poor because they are so thin (I guess).  The picture in HD is very clear and refreshes very fast, so is good for sport.  Various screen modes are available, but I tend not to use them.  I connected the TV to my home network using a cable connection to a Powerline network adapter and the TV found the local network quickly and without problem (WiFi connection needs a USB adapter).

m1-T2ubJdnPTuC3TXY8I2tgThe TV has BBC iPlayer, which is handy for catch up TV as Sky have not implemented this yet!  This loads quite fast, but the sound level, through my system is very high and this can be a shock if I forget to turn down the amplifier sound – I cannot find a way to offset the level for iPlayer!

It also has Youtube, but I have not used that much yet, so I will have to come back to this part and update it.  Finally, there is Toshiba Places, which provides music, radio, movies (pay as you go) and social networking connections.  Again, I have not made much use of this facility yet, so I will have to come back and update the blog.

The network connection allows media streaming and I have managed to get the TV to talk to the main computer (required setting the streaming setting in Windows Media Player) and it loads and plays music (again the level is higher than I would prefer, as with iPlayer), but switching between albums is a little slow.  This slowness probably reflects the number of albums/folders that it has to display, but can take as long as a few minutes for a large music collection.  The display of the music/albums is neat and it picks up playlists, genres, artists, albums etc., as displayed in media Player.  I like this network media player and use it a lot.  I understand it should be possible to play from the computer, to the TV, but I have yet to accomplish this yet!  Music and movies can also be played through the USB port, from a FAT formatted memory stick or external hard drive and this works really well for movies.  The music folder displays the folders, so you should see the artists names if you store music like I do, but it is not a well designed player and is a little clunky in places.  Recording to the USB memory stick / hard disk is also possible, but I am unlikely to make too much use of this as I record to the Sky box – we will see if it is useful.

Overall, after a week of using this TV I am very happy with it and think it is both good value and very versatile.  I would recommend it to others, but I will update more about the features as time passes.