Author Archives: Ramy

Edwards lab 2010 all-day meeting

We are now celebrating the first anniversary of Edwards labsite as we are sitting in the SDSU Coastal Waters Laboratory to plan for the coming year, and the coming summer in particular.

All lab members will now present short summaries of their work in the past few months then their plans/objectives for the following months.

New lab members will also join the labsite very soon… Stay tuned

PhiGenometrics1

Phage Genometrics. I’m only 23 years late!

“Eureka! If I just ran these analyses 23 years earlier!”

This is what I was telling myself few minutes after I was so excited at looking at the nice graphs I generated by analyzing the GC% statistics of about 600 phage genomes (graphs below).

As any good scientist (although they would tell you otherwise), I did the analysis before digging the literature deeply. I just got this urge to perform all kind of calculations on the phage codons and compare them to the phage overall GC%. Of course I know well that the third nucleotide in a codon is under much less pressure than other nucleotides, and thus varies depending on which genome it is located in (depending on many factors including the translational machinery of the host). However, I didn’t know whether anybody bothered to look at the difference between codon GC statistics and genome GC statistics, or the slopes of codon GC% versus genome GC%.

Whether the data below are new or not (they are new of course, since they are done on new sequences, but old since the conclusion was reached in 1987–before some of our lab members were born–, or maybe earlier), the figures look really cool! Another neat study from 1997 is here.

PhiGenometrics1

Fig. 1: GC% statistics for individual protein-coding genes (all phage proteins in PhAnToMe)

PhiGenometrics2

Fig. 2: GC% statistics for individual phages (all phages in PhAnToMe)

PhiGenometrics3

Fig. 3: nucleotide GC% (first and second derivatives) vs genome GC% statistics for individual phages (all phages in PhAnToMe)

The PhAnToMe Blog is out

Well, phantome.org is hosted locally, as you know. However, for several reasons–including that WordPress is a more developed blogging tool that Joomla! blogs, and that maintaining and securing a blog is a nightmare–I started a PhAnToMe blog (to the world).

Why a PhAnToMe blog? We already have a set up PhAnToMe insider blog, but this one is a closed blog that is only accessible by the PhAnToMers and is mainly a developer’s blog. The PhAnToMe blog, on the other hand, is addressed to the entire world to publicize the PhAnToMe project and post specific stories about interesting phages, interesting subsystems, interesting modules, and interesting problems.

Check it soon; test it; visit it; and comment on its posts.

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Phages without borders (1)

Phages are everywhere. We know this very well. But where is everywhere? Can we locate particular phages in certain ecosystems? Is there a pattern there?

This new PhAnToMe Labs tool may help us answer this question, or at least get the right questions:

1) Are cyanophages enriched in certain marine metagenomes?

2) Are enteric bacteriophages enriched in mammalian fecal samples?

3) Can we locate a certain phage entirely in one metagenome (remember the classical riddle: can one locate the same virus twice somewhere?)

 


 

Here are some examples:

Continue reading

Joomla tips (1)

I don’t know what Joomla!® stands for; but the word “Joomla جملة” in Arabic means “sentence or clause”! It also means “lump or wholesale,” in another context. Regardless of its etymology, Joomla! is the content management system (CMS) used for this labsite (at least until now) and for the PhAnToMe website as well.

Needless to say, we (hmm.. at least I and someone else) are learning Joomla! by the golden method: trial and error. Being a good CMS, Joomla! is modular and felxible, with almost no usable defaults. And, while the Joomla! features always seem obvious and straightforward once we discover them, I thought to write some of them down because I WILL forget them when I need them again.

  1. Admin is no longer a top-rank position. You need to be a Super Admin to do things from the back-end. You can’t change the configuration unless you’re a Super Admin. For example, to make the links look pretty (i.e., http://phantome.org/index.php/phantomers instead of http://www.phantome.org/index.php?option=com_content&view=article&id=7:who-are-we&catid=8:current&Itemid=14).
  2. Golden rule: Almost everything in Joomla needs to be set as a ‘Section’ (sometimes a Category is crucial too) and then as a ‘menu item’ to be visible even if it’s ‘published.’ Many features won’t appear until a Module is activated for them. For example, you may have a very well set–and published–Main Menu, but it won’t actually appear on the site until you activate the Main Menu module, and tell it where to put the menu (and this is largely dependent on your template–some templates will not show your menu if you choose to put it at the ‘top’).
  3. There is a Web Links option in the Components menu of the administrator page. No need to re-invent the wheel. When you get this one activated, you can create a menu item that belongs to ‘Web Link Category List Layout,’ and this one will show the web links.

To be continued

And now.. Cell phone microscopy!!

I thought this article may be of particular interest to the lab.

Here is the abstract:

Light microscopy provides a simple, cost-effective, and vital method for the diagnosis and screening of hematologic and infectious diseases. In many regions of the world, however, the required equipment is either unavailable or insufficiently portable, and operators may not possess adequate training to make full use of the images obtained. Counterintuitively, these same regions are often well served by mobile phone networks, suggesting the possibility of leveraging portable, camera-enabled mobile phones for diagnostic imaging and telemedicine. Toward this end we have built a mobile phone-mounted light microscope and demonstrated its potential for clinical use by imaging P. falciparum-infected and sickle red blood cells in brightfield and M. tuberculosis-infected sputum samples in fluorescence with LED excitation. In all cases resolution exceeded that necessary to detect blood cell and microorganism morphology, and with the tuberculosis samples we took further advantage of the digitized images to demonstrate automated bacillus counting via image analysis software. We expect such a telemedicine system for global healthcare via mobile phone – offering inexpensive brightfield and fluorescence microscopy integrated with automated image analysis – to provide an important tool for disease diagnosis and screening, particularly in the developing world and rural areas where laboratory facilities are scarce but mobile phone infrastructure is extensive.

And now.. Cell phone microscopy!!

I thought this article may be of particular interest to the lab.

Here is the abstract:

Light microscopy provides a simple, cost-effective, and vital method for the diagnosis and screening of hematologic and infectious diseases. In many regions of the world, however, the required equipment is either unavailable or insufficiently portable, and operators may not possess adequate training to make full use of the images obtained. Counterintuitively, these same regions are often well served by mobile phone networks, suggesting the possibility of leveraging portable, camera-enabled mobile phones for diagnostic imaging and telemedicine. Toward this end we have built a mobile phone-mounted light microscope and demonstrated its potential for clinical use by imaging P. falciparum-infected and sickle red blood cells in brightfield and M. tuberculosis-infected sputum samples in fluorescence with LED excitation. In all cases resolution exceeded that necessary to detect blood cell and microorganism morphology, and with the tuberculosis samples we took further advantage of the digitized images to demonstrate automated bacillus counting via image analysis software. We expect such a telemedicine system for global healthcare via mobile phone – offering inexpensive brightfield and fluorescence microscopy integrated with automated image analysis – to provide an important tool for disease diagnosis and screening, particularly in the developing world and rural areas where laboratory facilities are scarce but mobile phone infrastructure is extensive.