Author Archive

This post on Microbe World entitled: “Software for Programming Microbes” did attract my attention, and I followed its source in the MIT Technology Review: An amazing article presenting a fascinating newly emerging technology of programming bacteria to do whatever we want them to do, produce drugs more efficiently, clean up oil spills, anything… useful! But the methodology was quite beyond my imagination.

I was extremely lucky to be able to interview Dr. Christopher Voigt, Associate Professor at the University of California, San Francisco, who is the project leader. Dr. Voigt has published over 34 articles indexed in Pubmed and you can find more about his projects on his lab website.

Now I will leave you with the interview! I thank Radwa for reviewing it.

Dr. Christopher Voigt

Dr. Christopher Voigt

1. May you please simplify the term “genetic circuit” to the micro-readers? What drove you to use software to genetically modify bacteria?
A genetic circuit functions like an electronic circuit, but uses biochemical interactions to do the computation. I am a computer programmer at heart and find living cells to be the ultimate challenge.
2. We used to hear a lot about the use of genetically modified bacteria in cleaning up toxicants or oil spills, producing drugs and biofuel. How is “programming bacteria” different from the “regular” definition of genetic engineering, which might be based on inserting a gene, a regulatory gene, or an operon that encodes for a certain needed functionality?
Genetic programming controls the timing and conditions under which those processes occur.  It doesn’t refer to the pathways by which molecules are made or degraded.
3. In MIT Technology Review, you mentioned that like for a computer, programming bacteria is about writing a program to be encoded on a piece of DNA to implement a function. How can bacterial cells understand the code? How can the software make them sense the outer media?
The DNA contains codes for when molecules like proteins and mRNA should start and stop being produced and under what conditions. A protein can change its state when it senses a condition and bind to DNA to cause genes to be turned on or off.  This acts like a sensor.
4. Honestly, I can’t imagine writing a piece of code to link bacterium to one another, because node->pRight!=NULL ? I just can’t imagine it. Is there any risk of overloading natural functions by accident?
5. How can programing bacteria make use of quorum sensing?
Quorum signaling enables cells to be programmed to communicate with each other.
6. How can drug discovery and production benefit from programmable bacteria in the near future?
It makes it easier to access and control those pathways.
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Recently, I have been working on an essay for my last year in college.  I titled it: “Parkinsonism: Disease and Treatment”, scary enough? NO!!??  I turned it in, anyway. In it, I identified the neurodegenerative disease that targets the basal ganglia and deprives it of the inhibitory neurotransmitter (NT), dopamine. No dopamine means no balance between the excitatory action of the NT, Acetylcholine, and the inhibitory action of dopamine, leading to the well-known clinical picture of parkinsonism that Jankovic (2007) gave the acronym TRAP: Tremor at rest, Rigidity, Akinesia/bradykinesia and Postural instability.

Parkinsonism can be classified into:

  1. Primary/idiopathic “of unknown cause” which is mostly due to degeneration of dopaminergic neurons (a.k.a Parkinson’s disease)
  2. Secondary to viral infection as encephalitis & meningitis; drug-induced, e.g., antipsychotics; or due to brain damage caused by trauma, anesthetics,  or toxins as MPTP (a contaminant of street-drugs).
Arvid Carlsson

Arvid Carlsson

You may know that the Nobel Prize associated with Parkinson’s disease didn’t go to Dr. James Parkinson who described it in an essay he wrote back in 1817 calling it “The Shaking Palsy”.  It went jointly to Arvid Carlsson, Paul Greengard, and Eric R. Kandel in 2000 (To find out more about the story, here’s the Nobel lecture by Dr. Carlsson). Carlsson and colleagues discovered dopamine as a potential NT in 1957. After that, in 1960, Hornykiewicz and his postdoctoral fellow, then, Ehringer observed the decrease of dopamine levels in Parkinson’s disease patients, and levodopa successful trials started after that, in 1961.

J. Robin Warren

J. Robin Warren

What does Dr. Warren, the scientist whose discoveries led to a paradigm shift in physiology, who said out loud that peptic ulcer is an infectious disease caused by Helicobacter pylori, the gut bacteria? What does he have to do with parkinsonism? Note that: J. Robin Warren and Barry J. Marshall also won Nobel prize in medicine for 2005 for their discovery.

Helicobacter-induced parkinsonism!!

What I am trying to say here—and didn’t say in my essay—is that there is a hypothesis, Helicobacter-hypothesis, that strongly provides another cause of idiopathic parkinsonism, which will not be idiopathic any more, and this cause is H. pylori (Altschuler, 1996). Or to be more accurate, I will say parkinsonism associated with H. pylori. Dobbs and colleagues have carried out well-controlled studies and observed a significant conversion in patients with Parkinson’s disease from malignant into benign parkinsonism after successful eradication of their H. pylori, even with no levodopa administration. The rationale behind this theory is that: H. pylori induces an autoimmune reaction against mitochondria, then a systemic inflammatory response with the whole gang of inflammatory mediators and antibodies reaching and crossing the deficient areas or areas with increased permeability of the blood-brain barrier, causing parkinsonism. And the blood profile can prove the Helicobacter-hypothesis.

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I had the chance to attend the international conference BioVision Alexandria 2010 held at the Bibliotheca Alexandrina Conference Center in Alexandria, Egypt, from 12-15 April 2010. I really want to share with you the >50 talks that I attended, given by Nobel laureates and other remarkable scientists specialized in health-related topics.

Dr. Richard J. Roberts

I will start with this talk by Dr. Richard Roberts, who received the Nobel Prize in Physiology or Medicine in 1993 for the discovery of split genes and mRNA splicing in 1977. He is now joint Research Director at New England Biolabs. Dr. Roberts entitled his talk: “Collaborating to bridge the gap between computation and experimentation”. I will try to sum it up for you.

I. Let’s start with stating this fact that Genomics is rapidly taking over the field of biology, at the research level at least.


  1. Sequencing of the human genome or “The Human Genome Project” provides the basis of the emerging field “personalized medicine”.
  2. Plant genomics are unbelievably important for food and –maybe- for energy production purposes, unicellular plants mostly.
  3. Ocean organisms are very interesting, as they produce potential new antibiotics and many other useful substances.
  4. Bacteria and archaea are making up to 50% of the living biomass.

Bacteria are everywhere, they live in the oceans, the soil -plants require them for nitrogen fixation- animals and us; our gut, skin, nose and mouth. Most of these bacteria we know absolutely nothing about because we can’t grow them on cultures.

But this is about to change now thanks to DNA sequencing.

II. So, the core of today’s science is DNA sequencing… but unfortunately, DNA sequencing has its drawbacks.

1) DNA sequencing is getting faster and cheaper in a rate that is exceeding our ability to understand the function or the biochemical pathways of every single gene sequenced. Or, if we’re really lucky, we can make a guess –based on sequence similarity– that this gene, for example, encodes for a “hydrolase”, but just a hydrolase with no clue about the exact biochemical pathways it’s involved in or its substrate.

Dr. Roberts gave this interesting simile that getting more and more DNA sequences of bacteria is like getting a car with a list of all its parts with no idea about how they fit together or how they work. Biology is about understanding how life works. If we’re talking about synthesizing life today, we have to understand how life works first. He dreams that before he dies, he can understand how a very simple bacterium actually works, what is the chemistry that is going on there?

So, the first problem is in the very rapid growth in DNA sequencing without a similar growth in annotation/renaming/finding the function. Here’s a quite older graph showing the growth of sequence databases and annotations from 1982 till 2006, close to the one Dr. Roberts presented, from 1995 till 2009. If you can get to a newer one, please do not hesitate to comment on the post and add its link.

The growth of sequence databases and annotations (1082-2006) - Argonne National Laboratory

2) The computer is not enough! Do the biochemistry in the lab! In spite of the large amount of money spent on sequencing different organisms; we still are not making any progress in understanding them. This might be that when we get the DNA sequence, translate it into its corresponding amino acid sequence, our best shot then is to compare it to the existing protein sequences in the databases to know how it looks like what and thus predict its function. If two protein sequences look the same, there’s a chance, not a guarantee, that they have the same function, because if there’s a one amino acid difference, they may have different substrates and thus different functions. How to tell? The computer is not enough! Do the biochemistry in the lab! This will lead us to the third problem.

3) All substrates are not available to all labs all the time. So, one lab can’t determine the function of all genes on earth. He gave this example: if you want to assay a specific disaccharide hydrolase; to determine its substrate, you need to have disaccharide combinations of all possible sugars and test it on them.

4) Lack of good funding for biochemistry. Funding agencies think that biochem- is an “old-fashioned” field! They are funding the more appealing genome-wide studies, which is very superficial.

III. Dr. Roberts’ suggestions for a solution: “COMBREX”
Identifying Protein Function—A Call for Community Action.

Dr. Roberts and colleagues have got an NIH fund in October 2009 to establish COMBREX (maybe: COMputational Biology Reading EXperiments). The work flow will be very much like this:

Step1: Establishment of a database. From 1200 complete bacterial and archaeal genome sequences, computational biologists groups generate protein families/domains of unknown function (DUFs), predict the function based on sequence similarity and establish a database.

Step2: Coordination of the efforts between biochemistry labs, experimentalists/biochemists (young grads, even technicians) offer a proposal to test those predictions, gain an exclusive access to those genes of interest for 6 months + a small grant (5,000-10,000 USD) to carry out single gene studies. If we know one protein’s function, we know the function of the whole protein family.

Step3: Making of a Wikipedia-type page for suggestions and predictions.

Step4: Establishment of a journal to publish the findings.

IV. What genes should we focus on/start with?

Dr. Roberts suggested this list, which is ordered in a descending order:

1) Genes abundant in many many different organisms; in humans, animals, bacteria… etc. Those are likely to have conserved important functions.

2) E. coli, the most widely used and so-called “the best studied” organism, we can make a full characterization of it.

3) Helicobacter pylori, to understand the biochemistry of such an important pathogen that we know nothing about.

4) Identify cloned, translated and frozen open reading frames (ORFs) products.

V. Who can help?

Dr. Roberts said almost everybody, computational biologists to predict, biochemists to test, geneticists, as personnel university students -even high school students it can help them to get a genuine science project-, retired professors to supervise and maybe get back to the lab, and funding agencies.

You can watch this talk and most of the conference’s talks via the Bibliotheca Alexandrina webcast.

Dr. Roberts' talk at BioVision Alexandria 2010

Richard Roberts with BioVision Alexandria 2010 attendees

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I had the chance to attend this interesting webinar hosted by Pubget, a new search engine for life-science PDFs. The webinar was held on Friday, December 11, 2009 (you can catch the recording here). There were 160 attendees and the GoToWebinar tool enabled live interaction with the speakers.

The webinar meant to have speakers who are experts in their areas and to cover different segments dealing with searching, analyzing, and reusing scientific articles. The webinar was moderated by Ryan Jones, President of Pubget, and the speakers represented:

Peter Binfield talked about his experience with PLoS One as a journal established in the digital era, and all of its content is digital. He was much concerned with how to monitor the “reuse” of an article and the tools incorporated in PLoS to achieve that. PLoS uses multi-dimensional, article-level metrics rather than a monolithic system like impact factor. PLoS metrics system enables every one to know the exact usage of an article, downloads and views. PLoS also enables commenting, rating, discussing, selecting a part/line and writing a note about it, sharing/bookmarking, and showing trackbacks to blogs and citations.

Marcus Banks said that the digital “libraries” are still in need of a librarian to analyze, organize and link publications. He also talked about the need of a tool that enables researchers to highlight only the parts of a publication that they need, instead of consuming time reading through the whole publication. He talked about sharing tools like: Zotero, Mendeley,, RefShare, CiteULike, and Pubget.

Representing the end-users was Ansuman Chattopadhyay on the stand. His presentation was entitled: “Beyond PubMed: Next generation literature searching”. With PubMed, it’s difficult to narrow down your search and reduce the number of the results/hits, but this could be achieved by the newer Google-like tools such as:

  • GoPubMed, which gives the users suggestions as they are typing
  • Novoseek, which categorizes search results into: diseases, pharmacological substances, genes/proteins, procedures, organisms, etc.

and text-similarity tools like:

  • eTBLAST, a web server to identify expert reviewers, appropriate journals and similar publications (the paper)
  • JANE, Journal/Author Name Estimator
  • DeepDyve

One point I didn’t get is the need of a “daily journal of negative results”.

Ramy Arnaout presented Pubget as a search tool that is:

  • like an on-the-web Acrobat Reader (the search results are the PDFs of the papers)
  • able to deliver science at speed
  • legal and free, as researchers use their institution’s license to get to all publications including the non-open-access ones
  • user-friendly, as a user chooses from a list of publications a paper that opens in the same window

The concerns that all four speakers expressed at the end of the webinar were mostly:

  • How to achieve the balance between delivering science and preserving copyrights, a problem that is being partly solved by Open-Access journals.
  • How to tell the end-user what is related to his/her field.
  • Although everything is “online”, the challenge is how to get to it and use it.
  • How to interact with the end-users and make them discover the tools/features of search engines, this can be solved by workshops and tutorials.

I do thank Pubget for giving me the chance to attend this very informative webinar by making it  freely available.

Edited on Dec 22, 2009 09:31 p.m. CLT

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Is it a luxury to “think like a microbe” and to publish blogs such as “Adopt a Microbe and books like “The Other End of the Microscope: the Bacteria Tell Their Own Story (find it on Google Books)? Is it just about understanding or “getting to know” bacteria, or is it a necessity to be “microbe-oriented” for better understanding of pathogenesis and for developing the appropriate eradication and prevention strategies (I can’t think of better examples other than Reverse Vaccinology and H. pylori)?

When I first read this commentary “The Case for Biocentric Microbiology”* by Dr. Ramy Aziz, published by the journal “Gut Pathogens, I was shocked! The article was presenting a very different perspective, at least different from what I always dreamed of as a pharmacy student, to kill the bad bugs by designing an effective, highly selective chemotherapeutic! Plus it was my first time to read an opinion article, and I used to take the microbiology courses for granted; “this is a bad microorganism, causing this bad infectious disease with serious manifestations including these, diagnosed by the following and the antibiotic of choice is this.” And then Dr. Aziz came with this article with the cool, simple and exciting writing style that keeps one alerted the entire article, gathering all those thoughts and examples of our human-centered/self-centered view of microbiology.

Four parts I enjoyed the most in the commentary:

  • The tabular form of “differences between the anthropocentric and biocentric views of microbes.”
  • The final balancing paragraph –the conclusion.
  • The “competing interests” part, which is funny.
  • The questions part, which is an excellent idea to open up discussions, especially for those who are not-natural-born brain stormers like me!

Even though microbiology is a new science, it suffers from anthropocentric view that Galileo suffered from; starting with the field’s name itself, “microbiology” -liked what Dr. Elio Schaechter mentioned: “Small,” says who? Not the microbes… till the funding agencies that give priority to studying bad microbes (i.e., pathogens), and good microbes (i.e., fuel-producing and yogurt-making bacteria) nothing else!

Bacteria conversation -

Bacteria convention -

We, in our human-centered view; automatically classify any newly-discovered bacterium to fall into one of three categories: the good, the bad and the ugly… no, not that one! They are: the useful guys, the harmful guys and the just-existing guys. Now, let’s take a look at the biocentric view of microbes: Humans and microbes share many ecosystems. To microbes, humans are just an ecosystem that is a “relatively safe” habitat with a source of nutrition.

As victims, we think about pathogenesis/infection as it’s shedding from the immune system, invasion and toxin production; but microbe-oriented microbiologists/bacteria whisperers know that, to bacteria, pathogenesis is  just defense, seeking nutrition, and excretion of metabolic byproducts. Being pathogenic or opportunistic is not their reason of existence, it’s just a form of adaptation to survive in this hostile environment (aka the human body).

You do not believe me!? OK, bacteria lived –happily- thousands of millennia before mammals and humans, so their reason of existence can’t be to harm humans, like what Dr. Aziz is mentioning: “Who attacks whom”, are the bacteria the “one” that start the fight, or is it the human immune system that starts the war against them?  A very interesting example to understand adaptation is Legionella pathogenesis, and how they adapted to human macrophages because they used to survive in amebas, which are similar to our macrophages.

Back to the basic question, is it a luxury or a necessity?

Studying “all” bacteria from their perspective will help us in understanding pathogenesis and subsequently developing strategies to combat infectious diseases (immunization and design highly selective chemotherapeutics), will give us a better idea of the tree of life and the metabolic map, and studying environmental microbiology will allow us to meet new “useful” microbes like what happened with the PCR Taq-polymerase, we knew how to make use of this bacterial polymerase that can work at those very high temperatures required for the PCR steps.

Here are two interviews about the commentary covering two segments of readers, the first one is with Dr. Betsey Dyer, Professor of Biology at Wheaton College, and the second one is made with Radwa Raed, a micro-writer and a final-year FOPCU student:

1- What is your opinion about (the commentary)? To what extent do you find it compatible with your bacteriocentric view of bacteriology? How strong are the arguments?

Dr. Betsey D. Dyer, Professor of Biology at Wheaton College.

“I thoroughly enjoyed Ramy Karam Aziz’s article “The Case for Biocentric Microbiology.” I think he is absolutely right that some old fashion thinking about the divisions of microbiology and anthropocentrism in general have hindered a more complete understanding of the microbial world. I also think Dr Aziz is quite bold and daring. I’m not sure I could have gotten such forceful statements accepted for publication! Good for “Gut Pathogens” to print it! I hope Dr Aziz gets lots of readers and citations.”

2- How did (the commentary) change your point of view? Are you with or against the biocentric view for microbiology? Do you think about it as a view against, or at least far from, your beliefs as a pharmacy student dreaming of fighting diseases? What are your opinions regarding studying environmental microbiology in pharmacy school?

Radwa Raed, Pharmacy student, Faculty of Pharmacy, Cairo University – Egypt.

“From my humble point of view, I would have to agree (with the biocentric view of microbiology). It goes without saying that studying more about certain bacteria “the ones some would consider to be of the least priority” will definitely expand our knowledge about the overall, and in many cases analogous or even similar, methods of survival, adaptation to existing conditions, etc.., which all pretty much ultimately serve medical microbiology. Plus, leaving a whole chunk, simply unexplored, can only raise several “what if” questions; one of which, that comes to mind, is what if the simplicity and less dramatic forms of life could help researchers better grasp the machinery behind these fascinating little creatures 🙂

As for studying environmental microbiology in pharmacy schools, I would have to oppose the idea, because the field of pharmaceutical science is taught so the future students can come to understand, and hopefully later suggest, treatment methods against pathogenic microorganisms, prophylaxis, and so studying the harmless ones would not point in this direction. It can only lead them to drift away from the pharmaceutical science branch of study into a more microbiology-oriented career.”

You can read the paper, share your comments and debate the arguments here, and you can also vote for it on BioWizard.


*Full Citation:

Aziz, R. (2009). The case for biocentric microbiology Gut Pathogens, 1 (1) DOI: 10.1186/1757-4749-1-16

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Dr. Betsey Dexter Dyer is a professor of Biology at Wheaton College, Massachusetts, USA. She received her Ph.D. Betsey Dexter Dyerfrom Boston University. Among her research interests are symbiosis, evolution of cells, field microbiology and genomics. She is also part of the Genomics Research Group, a student project that she launched in collaboration with Mark LeBlanc, professor of Computer Science. Dr. Dyer has written several books, including

The Modern Scholar: Unseen Diversity: The World of Bacteria (Audiobook), The Origin of Eukaryotic Cells (Benchmark Papers in Systematic and Evolutionary Biology, 9) (1986), Tracing the History of Eukaryotic Cells (1994 – with Robert A. Obar), Explore the World Using Protozoa (1997 – coauthor), A Field Guide to Bacteria (2003) and Perl for Exploring DNA (2007 – with Mark D. LeBlanc).

I recently read about her book “A Field Guide to Bacteria” and wanted to know more about her view on “Bacteriocentrism,” and how one becomes “bacteriocentric.” I was so lucky to be introduced to Dr. Dyer, who was kind enough to accept to be interviewed for Micro Writers, and immediately answered my questions about her book and her student project, Genomics Research Group, via email. So, here I am, sharing with you this very interesting interview.

1. Why did you decide to write the book “A Field Guide to Bacteria”? Field microbiology and symbiosis are among your research interests ; is this one of the reasons that made you dig deeper in bacterial populations and “think like a microbe”?

I first got the idea of a field guide when I was a graduate student and was very fortunate to be on a field microbiology expedition (in Baja California Mexico) with some world famous field microbiologists. I realized at once that a field guide should be written and one of them should write it and probably would! It did not occur to me that I would write it.   It took me years to get to the point of being secure enough with my career. First I had to get a PhD, then a job, and then tenure. I also got married and had two children. Finally, about 15 years after that original idea, I realized that I had been accumulating enough information that I should begin to write. And so I did. However, I am still a bit surprised that nobody else wrote it.
I am naturally drawn to tiny things. I got a microscope for a present when I was 11 years old and it transformed some of my views of biology. I found that I loved the microscopic world. But I also like miniatures in general such as tiny furniture and dishes and things in dolls houses. I have in my library at home, some shelves devoted to a doll house and two miniature rooms.

2. What is meant by “becoming bacteriocentric”? And how does this lead to better understanding of the biology of bacteria?

We humans are mostly visual and auditory, the primary senses by which we perceive and analyze the world. It is probably impossible for us to be otherwise. Furthermore, we are gigantic and multicellular and terrestrial in marked contrast to the vast majority of organsims on Earth. Nonetheless, I think it is an excellent exercise for any biologist at least to try bacteriocentricity. The bacterial or microbial world is primarily olfactory and tactile. They are single celled (intimate with their environments), tiny and aquatic. I cannot avoid being anthropocentric but I can at least be more aware of the limitations of my size, habitat, and senses. My goal is to have as much humility as I can manage when I observe the world of microbes.

3. “Many groups of bacteria can be easily identified in the field (or in the refrigerator) without a microscope” and “Bacteria can be seen and smelled”, as a pharmacy student, I want ask how could that be achieved?

Well, do you have the book yet?  There are many examples but the basis of all of them is that bacteria, when they are in an appropriate environment, are likely to do quite well: reproducing abundantly, taking in and transforming molecules, sending out wastes. In many cases (surprisingly many) the abundance is on a level perceptible by humans. The field marks just need to be revealed and interpreted. Otherwise, they may be easily overlooked or misunderstood. My first experience with this as a graduate student was being shown the distinctive pigmentations and odors of bacteria in sulfur cycles in Baja California.

4. You have a project with Dr. Mark LeBlanc, professor of Computer Science, called “Wheaton College Genomics Group.” Why did you do such a project for undergraduate students? How did it raise their potential?

One day about ten years ago, Mark asked me if I had any large datasets that his computer science students might analyze in their course on algorithms. It happens that I teach genetics and am fascinated with genomes. At that time, genome sequences were becoming more available at NCBI. I had not realized that it would be so easy to collaborate with a computer scientist. I had lots of questions about genomes and we just started right in with devising some answers. Right now, we are interested in characterizing horizontal transfer events of distantly related bacteria and archaea.  There are hundreds of complete microbial genomes at NCBI and most have not been completely analyzed. Therefore, there is plenty for us and our students to do.
We ended up writing a book on the topic because we wee in need of a text that could be used both by biologists and computer scientists.

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Yediot Ahronot (Literally: Latest News)

Cure for radiation sickness found?

Published: 07.17.09

A team of scientists has succeeded in developing an anti-radiation. “The process that led up to the medical innovation dates back to 2003, when Professor Gudkov –the head of the team- came up with the idea of using protein produced in bacteria found in the intestine to protect cells from radiation.Mice received that purified protein survived the amount of radiation that killed the control group.

What kind of news is that?! Do that legendary bacteria and that miraculous protein actually have names?! If so, why don’t newspapers include it? Should bloggers do everything?!

Professor Andrei Gudkov – Chief Scientific Officer at Cleveland BioLabs, is interested in protecting cells against apoptosis induced by cancer therapy as well as radiotherapy. He worked on p53 –the famous tumor suppressor- and found that p53 has a role in inducing apoptosis. The research group suggested that p53 inhibitors can protect normal cells against chemo- and radiotherapy, and it’s been found that it sensitizes tumor cells to the therapy (PMID: 15865929). They also showed that PFTmu (pifithrin-mu), a small isolated inhibitor of p53, protected primary mouse thymocytes from p53-induced apoptosis caused by radiation (PMID: 18403709).

The breakthrough discovery mentioned above has been published in Science – 11 April 2008. It is about the injection of “flagellin” purified from Salmonella enterica serovar Dublin into mice and monkeys. It causes suppression of apoptosis by binding to Toll-like receptor 5 (TLR5) and activation of the nuclear factor–kappaB (NF-kappaB) pathway, the same mechanism used by tumor cells to inhibit the function of the p53 pathway (PMID: 18403709). To reduce its immunogenecity and toxicity, they engineered a polypeptide derived from flagellin with the “important” domains only, N and C termini separated by a linker. The engineered protein (named: CBLB502) was found to provide radioprotection in rhesus monkeys and mice against lethal doses of gamma-radiation and accompanied hematopoietic system and gastrointestinal tract acute radiation syndrome, with no alteration of the efficacy of the radiotherapy.

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When you hear/ read the term “Phage Therapy“, you’ll be automatically directed to the concept of using bacteriophages, the virus-like particles that infect bacteria, to kill/ lyse the resistant bacterial strains, instead of the “useless” antibiotics that allowed bacteria to fool them & develop resistance against them. The initial target of phage therapy was to kill the bacteria using phages; because they act like any other virus; get in, multiply and lyse the cell. But, by this way, bacteria develop resistance against phages more rapidly. So, they may become useless by time. In this paper from PNAS: “Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy,” two bioengineers, Timothy K. Lua and James J. Collins, from Boston University successfully engineered the Enterobacteria filamentous phage M13 to weaken bacteria not to kill it. Sounds strange, right? By engineering M13, they gave us a variety of options:

1st, we may make M13 overexpress a bacterial protein named lexA3 which inhibits the ability of the bacteria to repair their damaged DNA by the action of Ofloxacin –as pharmacophils, who had 2 consecutive chemotherapeutics courses, we may recall that quinolones’ MOA is generation of ROS. So, the repressor suppresses the bacterial SOS mechanism. Very promising results were observed; the adjuvant therapy increased the survival rate of mice infected with resistant E. coli. It was also observed that the adjuvant therapy reduced the rate of developing mutations/ resistance within the E. coli population.

Schematic of combination therapy with engineered phage and antibiotics

2nd, bacteriophage can be responsible for expression of certain proteins that can attack gene networks in bacteria which are not target for existing antibiotic classes. I will mention just one example here, expression of CsrA which is a “global regulator of glycogen synthesis and catabolism, gluconeogenesis, and glycolysis, and it also represses biofilm formation,” biofilms is thought to be related to antibiotic-resistance and OmpF porin which is used by quinolones to enter the bacterial cell, it may enhance its entrance.

Engineered phage producing both CsrA and OmpF simultaneously (csrA-ompF) enhances antibiotic penetration via OmpF and represses biofilm formation and antibiotic tolerance via CsrA to produce an improved dual-targeting adjuvant for ofloxacin

Now, thanks to the engineered phages, we can use the old beloved antibiotic classes to treat bacterial infection using the engineered phages as an adjuvent therapy to potentiate the cidal action of the antibiotic on the former-resistant strains. A precaution was made to ensure that no lysogeny would take place in the human cells is that the phages were engineered to be “nonreplicative”. But we still have two problems regarding Phage Therapy in general: identifying the strain responsible for the infection & making sure that the human immune system won’t elicit an immune response against phages, they’re “foreigners” after all!

Image credits:

1- “Schematic of combination therapy with engineered phage and antibiotics. Bactericidal antibiotics induce DNA damage via hydroxyl radicals, leading to induction of the SOS response. SOS induction results in DNA repair and can lead to survival. Engineered phage carrying the lexA3 gene (lexA3) under the control of the synthetic promoter PLtetO and an RBS acts as an antibiotic adjuvant by suppressing the SOS response and increasing cell death”:

2- “CsrA suppresses the biofilm state in which bacterial cells tend to be more resistant to antibiotics. OmpF is a porin used by quinolones to enter bacterial cells. Engineered phage producing both CsrA and OmpF simultaneously (csrA-ompF) enhances antibiotic penetration via OmpF and represses biofilm formation and antibiotic tolerance via CsrA to produce an improved dual-targeting adjuvant for ofloxacin”:

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Microbiology, Immunology & Biochemistry Dept.*

Faculty of Pharmacy

Cairo University

Bioinformatics Practical Exam – Winter 2010**
Time allowed: Lab computers will automatically hibernate after 2 hours.***

Target: Assigning the function of the uncharacterized protein O67940_ AQUAE from Aquifex aeolicus ****

A suggested procedure:
1- Get the amino acid sequence of the protein from UniProtKB
— Run it through BLAST to find homologs (related sequences). Do not forget to choose Blastp & PSI-BLAST
— Check the assigned hits (known function & solved crystal structure) which have highest possible similarity (highest score/ highest % id) to your query.
2- Check obtained BLAST alignment of those proteins against your query.
3- Check if the protein belongs to any protein family using PIRSF & COGs
— Check if the protein shares any conserved domain with assigned function using Pfam.
— Using PROSITE the functional site database, check if the protein shares any sequence motifs with other proteins
4- Check if the protein belongs to a superfamily using SCOP database, which provides structural and evolutionary relationships between proteins.
5- As you don’t have the crystal structure of your Aquae protein & you have the structure of the closest assigned protein, use VAST to search & align protein related structures to yours.
6-  Extract homologs.
7- Multiple alignment (structure-guided alignment) using Cn3D
—  Neighbor-joining (NJ) phylogenetic analysis using CDTree
8- Use PDBSum to obtain an overview of the protein–ligand interactions available for your query.
9- Alignment of homologous sequences to identify conserved functional residues.
10- Evidence-based assignment of biological function of query O67940_Aquefix.


* What have I got to lose?!
** I have faith.
*** I can provide that; I know a guy who knows a guy!
**** Frankly, I wanted to pick a different protein, but I hesitated.

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Watson - Crick DNA modelOn February 28, 1953, James Watson and Francis Crick announced to their friends that they have discovered the chemical structure of the DNA. After publishing their paper in Nature on April 2, the official announcement took place on April 25.

That is what I have read in Al-Ahram newspaper today. What a discovery! Imagine if they had not done it, we would have had no clue about genes & protein synthesis, no recombinant DNA tech- & no sequencing. We would have had no molecular biology departments in universities! Abby from NCIS & Greg from CSI would have had no job!

So, what was the real story? To what extent are the “rumors” saying that Rosalind Franklin is the real discoverer of the DNA double helix right? Is she really the “Dark Lady of DNA”?Rosalind Franklin

I hope we can get the story through your comments after we read this:

1- Crick papers from the National Library of Medicine.

2- Watson’s interview with a group of top North Carolina high school students in 2003.

3- BBC celebrating the 50th anniversary of DNA structure discovery in 2003. (really interesting)

4- Rosalind Franklin: Dark Lady of DNA by NPR (National Public Radio)

Image credits:
Watson – Crick DNA model:
Rosalind Franklin:

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