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.

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.

Examples:

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.

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.

Tags: annotation, Bibliotheca Alexandrina, biochemistry, BioVision Alexandria 2010, COMBREX, database, DNA sequencing, domains of unknown function, drawbacks, DUFs, E. coli, Helicobacter pylori, human genome project, New England Biolabs, Nobel laureates, open reading frames, ORFs, Richard Roberts, sequence similarity, synthetic life

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:

• Publishers: Peter Binfield, Managing Editor, PLoS One
• Libraries: Marcus Banks, Manager of Education and Research Services, UCSF
• End Users: Ansuman Chattopadhyay, PhD, Bioinformatics, University of Pittsburgh
• Tools: Ramy Arnaout, MD PhD, Chairman and CEO, Pubget

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, Del.icio.us, 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

Tags: Ansuman Chattopadhyay, CiteULike, DeepDyve, Delicious, double-matrix technology, eTBLAST, Google-like, GoPubMed, GoToWebinar, JANE, librarian, Marcus Banks, Mendeley, Novoseek, Peter Binfield, PLoS ONE, Pubget, Ramy Arnaout, RefShare, Ryan Jones, scientific articles, sharing tools, text-similarity, trackback, UCSF, University of Pittsburgh, webinar, Zotero

What is bioinformatics?

It can simply be defined as a link between biology and computer science, in which the biological data is processed and computed through software, to yield an output, that is later interpreted in different ways.

Biological data indicates the nucleic acid or protein sequences, their simple or complicated forms, whereas the software is the computer program, specially designed for processing these data in a certain way, done using a certain algorithm (it is a recipe to solve a program problem). The data output is usually numerical or visual (often graphical), but mostly it needs to be well understood. The last one is the key point in the bioinformatics.

What is the need of bioinformatics?

In the research field, we need to be led to certain road, to choose one way or another, or to try many options until we define our research plan. Bioinformatics simply brings the solutions into your hands by a few mouse clicks.

One simple example to make it all clear is the PCR (Polymerase Chain Reaction). We always need to design a primer to trigger our reaction. If we did this through the ordinary ways, we would have to practically try out so many primers and this would surely take a tremendous amount of time. Now, what if you are computer- and internet-literate? You can simply use software to get many primer options for the DNA piece under investigation; doesn’t this save time, efforts and money?

Can bioinformatics be useful in different ways, other than the PCR example?

Some people may think that using bioinformatics is limited to some fields of biological research, and some others might think it is only a matter of prediction, which always needs to be evaluated for its accuracy, specificity and efficiency. But indeed, bioinformatics can be used in the analysis of nucleic acids and proteins.

Analysis?!! That is a vague word, how can you analyze a protein using bioinformatics?

Now you’ll see what bioinformatics can do for protein analysis:

1. Retrieving protein sequences from different databases, either specialized or general databases and it is not an easy job if you would think so.
2. Computing a protein or amino acid sequence to obtain:

• So much of the physicochemical properties of you sequence like the molecular weight, and isoelectric point…etc
• Hydrophilicity / hydrophobicity ratio

Both of the above can provide us with the probabilities of one protein acting as a receptor on the cell surface or it might be antigenic or even secreted outside the cell.

3. On the prediction aspect, we can predict:

• Some sequences of certain importance, e.g. the prediction of signal peptides that can lead us to know the secretory proteins of one organism
• 2ry structure of your protein
• 3ry structure of your protein

The last two points are applications of what is called structural bioinformatics, through which computer is capable of predicting the 2ry and 3ry (3-D) configuration of your protein, using special programs with advanced algorithms and artificial intelligence. Amazingly, this may be useful in understanding the receptor-substrate interactions.

4. Comparing sequences to obtain the best alignment (it means compare 2 or more sequences to find their relation to each other, i.e. finding similarities and differences), it will help in:

• Classifying your protein and relate it to its protein family
• Making your evolutional expectations about your protein to define whether it descends from another protein or not. This is called phylogenetic analysis, at which the proteins under investigation are studied to know which protein is considered a mother to the others, which are the daughter, the grand daughter, and so on
• Detection of the common domains, this will help us understanding the functions of unknown protein when it is compared to sequences of other proteins of known functions

Then, what will we gain if we compute DNA? Or you can say, what can bioinformatics do for DNA research?

On the same level as with protein, though different applications, we can use it in:

• Retrieving DNA sequences from different databases
• Computing a sequence to obtain information about its properties (like proteins) e.g. GC% which could be used with other properties to identify a gene
• Assembling sequence fragments (usually DNA is sequenced in the form of fragments which are needed to be assembled in the best way, bioinfo. does this in a faster and more accurate way rather than the ordinary assembly)
• Designing a PCR primer
• Prediction of DNA and RNA secondary structures (e.g. prediction the stems and loops of the t-RNA)
• Performing alignments between 2 or more sequences that can lead to many applications (as those mentioned above in protein alignments)
• Finding of repeats, restriction sites, Single Nucleotide Polymorphism (SNPs), and/or open reading frames, all of which have so huge applications in the medical and paramedical fields and typically in the research activities.

Tags: algorithms, alignment, analysis, artificial intelligence, Bioinformatics, biology, computer science, DNA, PCR, phylogenetic, phylogenetic analysis, protein, RNA, sequence, signal peptide, single nucleotide polymorphism, SNPs

From a humble point of view, as I was attending a bioinformatics and genomics workshop held in FOPCU, the lecturer was pointing to us, that up until now, no one has managed to come up with a method capable of converting a full-functioning protein back into the original nucleotide sequence on its corresponding gene. At that instance, the following thought occurred to me, as to why this would ever be needed?

For starters, we already have the protein in hand, its 3D structure is, for many, completely figured out and some even their orientation in space, their actions and functions. Then, as far as I understand, being the mould from which a protein is later assembled is the only function a gene, or one which is expressed anyways, has. Knowing that for instance, in gastrin hormone, the 4^th amino acid is leucine, would it matter whether it was translated from the codon CUA and not UUG?

Now three thoughts impose themselves. I could only imagine that the presence of SNPs (which is basically a nucleotide that varies among individuals and thought to influence certain traits) within the nucleotide sequence of the gene is the reason behind the researchers’ attention. However, this ultimately means, that if a method were to exist, it would have to produce a different nucleotide sequence for proteins coming from different people. Simple logic.

Another probable explanation, that could come to mind, would be the existence of a difference in the structure of the leucine amino acid, held on tRNA molecules with varying anticodons, where each would have some “characteristic” features that distinguish it from the other tRNA. If that were the case, then it probably has managed to fly below the radar for quite some time, as no matter which reference I turn to, it is taken for granted that these amino acids are carbon copies. So being non-identical in any way, would cause the resulting protein to function in a slightly different manner, which could explain the diversity of their actions in varying individuals. Who knows?

Last, but not least, is the possibility of gaining fast insight into the genome of a previously undiscovered species of living organism, where one can quickly figure out all the expressed genes through this simple task of “reverse translation”. However sequences of the unexpressed genes would still have to adopt the old-fashioned way. No choice there!

Just wondering what the future has in store.

Tags: Bioinformatics, fopcu, gene sequence, genome, genomics, nucleotide, protein, research, reverse translation, sequence, translation, workshop

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.

GOOD LUCK

* 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.

Tags: alignment, Bioinformatics, Cn3D, COG, crystal structure, functional site, homolog, motif, PDBSum, Pfam, phylogenetic analysis, PIRSF, PROSITE, protein family, PSI-BLAST, related structures, SCOP, superfamily, uncharacterized protein, UniProtKB, VAST

Hello, hello. You’re now tuned to your favorite blog: micro-writers.egybio.net. Tonight we have this very special guest, live, online. After two months of waiting, we finally got this exclusive interview with the emerged Streptococcus pyogenes strain, the most dangerous ever, M1T1. We have it here, with us, in the studio.

- Hello, M1T1. Welcome in our studio.
- Hey there.

- We knew from our resources, which are totally classified, that you got yourself in trouble recently.
- (Interrupting), I did NOT get myself in trouble. EID set me up.

- M1T1, Would you please calm down & tell us a little more about yourself?
- Well, I belong to Group A streptococci (GAS) aka Streptococcus pyogenes. M1T1 is my serotype; I’m just a clonal strain. As you know, S. pyogenes colonize human skin & throat causing either non-invasive (sore throat, tonsillitis & impetigo) or invasive (necrotizing fasciitis NF, scarlet fever & streptococcal toxic-shock syndrome STSS) infections. Actually, NF gave me my nick: Flesh-eating bacteria.

- So, you cause all people NF & STSS?
- No, kid. It depends on their genetic susceptibility, what you call “Host–pathogen interactions”. I was isolated from patients with invasive as well as non-invasive infections during 1992–2002. This is NOT entirely my fault; humans can make me extra virulent by selecting the most virulent members.

- Back to your history, when have you exactly been isolated?
- M1 & her sisters were the worst nightmare in US & UK in the 19^th century as they caused the famous pandemic of scarlet fever. “Nevertheless”, early 1980s was the golden age of my strain as well as my very close sisters M3T3 & M18. We caused STSS & NF in different parts of the world. Great times, great times!

- Only for you, I suppose! So, what made you hypervirulent? What caused you this “epidemiologic shift”?
- Two reasons Dr Ramy K. Aziz identified that improved my fitness to humans: the new genes I got from phages & “host-imposed pressure”. Both resulted in the selection & survival of me M1T1 the hypervirulent strain. Dr Aziz’s work at Dr Kotb’s lab resulted in identification of a group of genes I got from phages that changed my entire life.

- Interesting! Tell us more about that. How did phages “change your life”?
- Dr Aziz proved that I differ from my ancestral M1 when he found that I have 2 extra prophages (lysogenized phages didn’t get the chance to lyse me, so they became integrated in my genome):
1. SPhinX which carries a gene encodes the potent superantigen SpeA or pyrogenic exotoxin A (scarlet fever toxin).
2. PhiRamid which carries another gene encodes the most potent streptococcal nuclease ever, Sda1.
3. He also found that phages conversion from the lytic state to the lysogenic state resulted in exchange of toxins between our different strains (aka Horizontal Gene Transfer). Phages are very good genetic material transporters, what makes “strains belonging to the same serotype may have different virulence components carried by the same or highly similar phages & those belonging to different serotypes may have identical phage-encoded toxins.” What a quote from Rise and Persistence of Global M1T1 Clone of Streptococcus pyogenes.

- Well, It was not that interesting. So, what? What’s the significance? How that made you hypervirulent?
- You can’t get it? You’re not that smart, are you? Tell me, what made M1 hypervirulent causing scarlet fever in the 1920s and me hypervirulent causing STSS in the 1980s with a 50-years decline period?

- Superantigen?
- Exactly. You do have your moments! Superantigen encoding-gene was present in us and absent in strains isolated in the period between them. The interesting part, for me of course, that humans after 50 years of absence of hypervirulent strains had absolutely no superantigen-neutralizing antibodies. That was the real invasive party. Superantigen causes high inflammatory response because of its non-specific binding to immune system components (antibodies & complements) causing an extremely high inflammatory response. In fact, SuperAg inflammatory response is “host-controlled”.

- So, what about Sda1?
- Streptodornase (streptococcal extracellular nuclease) helps me to degrade neutrophils that entrap me in the neutrophil extracellular traps (NETs). So, I can invade humans freely & efficiently and be able to live in their neutrophils. Dr Aziz proved in his paper “Post-proteomic identification of a novel phage-encoded streptodornase, Sda1, in invasive M1T1 Streptococcus pyogenes” that it’s all about C-terminus in my Sda1; the frame-shift mutation increased my virulence while deletion decreased it.

- Now we know about your SuperAg & nuclease (DNase), what’s the “host-imposed pressure”?
- I have my own SpeB (Protease), I use it to degrade my other proteins (virulence factors), which provides me with a good camouflage & gives me access to blood. When the host immune system recognizes me, it traps me in NETs. At this time, I secret Sda1 to degrade neutrophils. Actually, SpeB protects you, humans, from my Sda1& my other toxins. When SpeB was compared in patients with severe & non-severe strep infections, it was found that SpeB wasn’t expressed in case of severe infection. Expression of SpeB may be host-controlled, as host selects the mutants with a mutation in covS, a part of my regulatory system which regulates my gene expression including SpeB gene.

- Finally, M1T1. How do you see your future?
- More new phage-encoded genes, more selection of the hypervirulent strains by the host & more regulation of expression of my virulence factors. Pretty good future! I also count on humans to not develop immunity against me like what happened in 1980, when I got new virulence factors or allelic variations in my old ones.

Thank you, M1T1. Pleasure talking to you…….M1T1? M1T1, where are you? Why do I feel this strange pain in my throat?

Image credits:
Streptococcus pyogenes: http://adoptamicrobe.blogspot.com/

Tags: covS, epidemiologic shift, flesh-eating bacteria, global M1T1 clone, group A streptococci (GAS), horizontal gene transfer, host-imposed pressure, host–pathogen interactions, impetigo, M1T1, Malak Kotb, necrotizing fasciitis, neutrophil extracellular traps (NETs), phage-encoded toxins, pyrogenic exotoxin A, Ramy K. Aziz, S. pyogenes, scarlet fever, sore throat, streptococcal nuclease Sda1, streptodornase, STSS, superantigen SpeA, tonsillitis

“It’s an honor to announce that we’ve successfully discovered, cloned & characterized the densonucleosis virus (DNV) Antigen, which will be able to infect Anopheles gambiae. That will hinder its ability to transmit Malaria parasite, Plasmodium or, at least, reduce its lifespan. I’ve to tell you this: This will be the latest in Malaria control.” Well.. those are my words but, of course, it is not my discovery. It’s the team of researchers from Johns Hopkins who discovered it. To realize how big it’s; we first need to know the previous approaches & trials in Malaria control.

To think, just think, about control/ prevention of any of those vector-borne parasites; automatically researchers think about these:
1- Prevent infection – disease – transmission.
2- By looking at: the parasite’s life cycle – the mosquito – the human immune system.
3- So, it’ll look like that: get humans vaccinated – develop genetically modified mosquitoes incapable of transmitting the parasite or simply “I was so naive to think that it’s simple” kill them with insecticides (anti-vector measures) – target the parasite at any stage of its life cycle.

For decades, DDT (dichloro-diphenyl-trichloroethane) & Chloroquine were successfully used in eradication of Anopheles & Plasmodium respectively, “I do like this word, makes me sound like a pro”. Chloroquine was used in treatment as well as prevention, till the emergence of chloroquine-resistant Plasmodium parasites and DDT-resistant Anopheles mosquitoes. Yes, they overcame the humans’ arsenal. So, preventing spread of resistant parasites is the #1 priority.

We can’t talk about all control strategies today, so we’ll talk about anti-vector measures. What do they use in control programs as anti-vector measures?
1- Insecticide-treated bednets (ITNs) & long-lasting ITNs (LLINs) it helped kids to survive. The only allowed insecticides to be used in ITNs are pyrethroid insecticides, so when the pyrethroid resistance emerged, as usual, it was really bad.
2- Indoor residual spraying (IRS) using DDT
One word about the mechanism of action of DDT & pyrethroids, both target voltage-gated Na-channels. So, when a set of mutations change the protein structure; Congratulations! It’s resistance to both DDT & pyrethroids.
3- New approach: Molecular talk; Know more about “blood meal” host selection. Yes, Anopheles smells the host, so researchers want to identify that pathway.
4- Another new approach: They are investigating genes which encode proteins that may interrupt the development of the parasite in the Anopheles.

The latest as an anti-vector measure is using Paratransgenesis or “the genetic manipulation of insect symbiotic (mutualistic, commensal or parasitic) microorganisms”, I can’t get the term or the definition. I’ll say it like that: “Any other m.o. has a relationship with the vector”. The steps are:
1- Know the Ag (Pick the gift)
2- Get the gene(s) engineered to be successfully expressed (Wrap the gift)
3- Delivery to Anopheles (Deliver the gift)
So the gift will be the non-enveloped ssDNA virus called (DNV). Its genome is very small, when they say for a viral genome that it’s small, so it has to be small (4–6 kb). The entire genome can be placed in a plasmid.

Back to the story of the discovery, they were doing a totally unrelated experiment when they found that strange band/ zone. They isolated it from the gel, cloned, sequenced, ran through BLAST which showed that it looks like DNV of Aedes aegypti (AeDNV) but not the man himself. They did multiple tests to identify the Ag, e.g. Immunofluorescence assay. There was a trial to infect Anopheles gambiae with DNV of Aedes aegypti which wasn’t successful in infecting adults from Anopheles gambiae. But the novel “AgDNV is highly infectious to An. gambiae larvae, disseminates to adult tissues, and is passed on to subsequent generations.”

Tags: AeDNV, AgDNV, anopheles gambiae, anti-vector measures, DDT, IRS, ITNs, malaria, paratransgenesis, plasmodium

                                                                          (image source) 

Aetiology and epidemiology

Meninigococcal meninigits and septicemia are devastating diseases caused by Neissieria meningitidis. Although infants and young children are the most susceptible to the disease, adults are also affected but with less incidence. N.meningitidis is a gram negative capsulated bacterium that has been classified into five serogroups (A, B, C, Y, W135)  based on their polysaccharide capsule.

The challenge

Over forty years, developing a vaccine against this dangerous bacterium proceeded with little success. In 1960, the purified polysaccharide antigens were used to develop a vaccine against four groups (A, C, Y, W135) . Unfortunately, this vaccine was highly effective in adults but didn’t give protection to young infants and children who represent the age group most susceptible to the disease. Another challenge is that this vaccine didn’t show success against serogroup B (known as:MenB).

More attempts to overcome the new challenge

Using capsular polysaccharide antigen, as a vaccine against MenB, wasn’t a very good idea. This is due to the fact that MenB capsular polysaccharide is highly similar (nearly identical) to N-acetyl neuraminic acid which is widely distributed in human tissue and that means it is a self antigen. The new vaccine was poorly immunogenic (and thus provide poor protection) and also it might elicit auto-antibodies.

As scientists never give up, they switched into the new trend in vaccinology: Reverse vaccinology. Due to the formerly mentioned, N.meningitidis was expected to be a very promising candidate for reverse vaccinology.

RV provides help

Using in silico technique (computational biology), the genome sequence was fed into a computer, 570 proteins of the bacterium surface were predicted. Going for more refinement, only 350 of these proteins were successfully expressed in E.coli and and used to immunise mice. The sera assays allowed the identification of certain proteins that elicit bactericidal antibodies and surprisingly, were conservative among different strains and this meets the criteria for a good vaccine.

Going forward

As research is proceeding to deprive our pathogen from enjoying its life inside our bodies, this work suggested further research of other pathogens such as: Streptococcus pneumoniae, Chlamydia pneumoniae, Bascillus anthracis, T.B and group B Streptococcus. 

Reference:

A universal vaccine against serogroup B meningococcus.

Tags: meningitis, reverse vaccinology, vaccinology

For many decades, conventional vaccinology has faced many obstacles. One major problem is that among several antigens of the microbe, you have to identify the most immunogenic (and thus protective) antigens (such as virulent factors, toxins, surface-associated proteins, etc.) suitable for vaccine development. This process is very fastidious and costs a lot as it relies mainly on traditional biochemical and microbiological methods. As a summary, it is carried out as following:

• Firstly, you have to cultivate the microbe and harvest proteins.
• Then you have to identify the antigens one by one.
• After that you can pass to vaccine development stage.

Introducing genomics has greatly contributed to providing a new impulse to vaccinology field. The major role it plays is in the antigen discovery stage. As the genome sequence of many microbes has been identified, the integration between the sequence, proteomics and microarray has introduced what is called “reverse vaccinology” . Reverse vaccinology (RV) means to identify and characterise the antigen using bioinformatics. In RV, you start from the genome and not from the pathogen itself i.e.  you start from the opposite direction, that’s why it is called “reverse”.

RV will provide solutions to some problems that usually come up during vaccine development as:

• It will provide fast access to almost all antigens including:less common antigens and antigens not expressed in vitro.
• It represents a new approach for non culturable microorganisms.

On the other hand, the major disadvantage of RV is that it cannot be applied to non-proteinaceous antigens such as lipopolysaccharides and glycolipids.

Tags: GBS, genomics, reverse vaccinology, vaccinology

Two years ago, the project of sequencing the Neanderthal genome started. They (Max Planck Institute & 454 Life sequencing) promised to end by this year. Well, they kept their promise. Frankly, some mitochondrial DNA sequences (mtDNA) have been published but contamination was the major defect in those published sequences. They collected more than 60 bone specimens from museums (We’re talking about 38,000-year-old bone); they repeated the sequencing for 35 times in the same clean room of extraction to avoid contamination with human DNA.

From the total 13 protein-encoding genes of the sequenced mtDNA, they identified only one with amino acids difference than the human sapien version. It is cytochrome c oxidase subunit 2 (COX2 – part of the respiratory chain), but even this difference has no significant effect on the functional domain of COX2. They hope to answer this questions in a few months: Why Neanderthals died out & human didn’t?!

We already know that Neanderthals & humans share 99.5% of the sequence, but answering questions about having a common ancestor & extinction through absorption (bred with humans) needs lots & lots of researches, collecting & sequencing samples at different time intervals to come with hypotheses. The mtDNA is not enough as Trinkaus (an expert on Neanderthal biology and human evolution) said: “The genome sequence data may tell us something about the selection of a couple of proteins, but it tells us nothing about language or social behavior.”

Image credits:
Reconstruction of a Neanderthal child from Gibraltar: http://en.wikipedia.org/
First complete Neanderthal genome sequenced: http://www.nature.com/

Tags: 454 pyrosequencing, genomics, human genome, human genome project, max planck institute, mtDNA, neanderthal