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All the Patent Sequences are in Genbank, right? - No!

sqipdb — Mon, 01 Feb 2010 19:39:07 +0000

A very common misconception about sequences derived from Patents is that they are ALL available in the GenBank or EMBL sequence databases.

They are NOT – and limiting your searches to these datasets is a huge mistake.

The SQIP release of 12/31/2009 contained 49,684,446 unique nucleotide sequences and 3,287,071 unique protein sequences.

Compare that to GenBank’s gbpat division which contained 6,728,032 unique nucleotide sequences or to the EMBL equivalent with a subset of 6,700,532 unique nucleotide sequences. That represents only 13.5% of the SQIP dataset. (The EMBL and GenBank sets are typically in sync, or near to it).

EMBL’s patent division contains 1,786,723 unique protein sequences (GenBank has no protein division). That represents only 54% of the SQIP dataset.

The bottom line is that if you only search against the patent sequences in GenBank/EMBL you are missing out on a huge amount of data.

GenBank and EMBL are, rightly, viewed as the reference sources for publicly available sequence information. But it is clear that this is not the case for patent sequences. SQIP, and the other patent sequence databases, derive their data from a broad range of sources (including GenBank and EMBL) and so are able to offer a far more comprehensive set of data.

So why isn’t it all in GenBank/EMBL?

The main reason is that the various patent offices do not provide freely available and comprehensive feeds of their sequence data.

Some offices do not require that patent applications include machine readable versions of sequence listings, which adds greatly to the problem. Many of the listings submitted to WIPO, while they meet the requirements of the WIPO ST.25 standard, are only available as TIFF or PDF image files which require the use of optical character recognition software in order to extract sequence data.

Where do GenBank and EMBL get their data from?

It is unfortunate that neither organization is clear on the way they get data from patent offices. It would be extremely useful if either the databases or the patent offices would publish specific details on which sequences are transferred, the rationale behind that selection, and the schedule on which the transfers happen.

Both databases appear to only include granted patents, which is a huge limitation for anyone trying to assess the IP landscape around a sequence. Published applications, whether they are eventually granted or not, represent a major source of information for both patent professionals and research staff.

Furthermore neither GenBank nor EMBL represent RNA sequences as such. Instead they are converted to DNA. While this may make some sense in terms of sequence comparison, it represents a ‘loss of information’ in the dataset. Being unable to distinguish between DNA and RNA in sequence comparison results can be an issue in assessing IP, especially in the area of small RNA sequences.

The bottom line is that searching GenBank and EMBL patent sequence divisions, on their own, will not deliver the coverage of the patent literature that your work demands.

SQIP not only offers comprehensive datasets, but a superb user interface and project management system in which to perform your work.

Broad Consensus on Gene Synthesis Guidelines

BBVM — Thu, 21 Jan 2010 18:41:44 +0000

Participants at a January 11^th forum on Minimizing the Risks of Synthetic DNA, held at the American Association for the Advancement of Science, appeared to be in general agreement on the principles behind proposed US guidelines to safeguard the rapidly advancing technology of gene synthesis.

Synthetic biology, a new field made possible by developments in genome sequencing and genetic engineering, seeks to take an engineering-based approach to biological problems. The story of the malaria drug Artemisinin provides an example of the advances that this new approach can produce. The drug is currently made from a plant extract, and crop quantities are insufficient to meet global demand. Through synthetic biology, scientists have been able to engineer yeast capable of performing the multiple reactions necessary to create the drug’s precursor.

However, engineering life also presents the opportunity to create existing, augmented, and/or novel pathogens. Current restrictions on select agent pathogens, such as Smallpox, are based on the physical safeguarding of live bacterial and viral stocks to keep them from malicious users. With modern gene synthesis technology, a would-be attacker could potentially obtain a complete pathogen genome by ordering it from commercial DNA providers.

It is in this context that Monday’s forum brought together a wide variety of stakeholders, ranging from Federal regulators to major gene synthesis firms and research organizations. Though the specifics of guideline implementation were occasionally questioned, there was a surprising degree of consensus concerning future policies implemented by private industry.

Building Self-Policing Standards

The US Federal Government’s National Science Advisory Board for Biosecurity (NSABB) first weighed in on the gene synthesis issue in a December 2006 report, recommending in part that:

“…establishing uniform and standardized screening practices among providers of synthetic DNA would help safeguard against the intentional or unintentional circumvention of the [Select Agent Regulations].”

As the US government worked to clarify policies on this technology, synthetic DNA providers began similar efforts. The fruits of these separate efforts were finally revealed in November 2009.

On November 3rd, the International Association Synthetic Biology (IASB), a group that includes biotechnology and gene synthesis companies in the US, Germany, and China, announced that it had completed its year-long effort to draft a code of conduct covering “ethics, biosafety and biosecurity aspects of gene synthesis.” Shortly thereafter, on November 18^th, five major gene synthesis companies – Blue Heron, DNA 2.0, Genart, Genscript, and Integrated DNA Technologies – announced that they were forming the International Gene Synthesis Consortium (IGSC). This group, which claims to represent 80% of the world’s gene synthesis capacity, issued a similar screening pledge.

Finally, on November 27^th, the US Department of Health and Human Services (HHS) issued the draft guidelines titled “Screening Framework Guidance for Synthetic Double-Stranded DNA Providers”. The guidelines, which are open for public comment through January 26^th, were the subject of the AAAS forum.

The Proposed Standards

All three proposals are in broad agreement as to the basic procedures needed to prevent malicious double-stranded DNA orders. Potential customers would be screened to verify their identities as legitimate researchers, while the ordered sequences would be examined to assess their similarity to pathogen genes. In the event of red flags in either area, companies would further investigate orders to ensure that malicious individuals do not obtain potentially dangerous materials. Representatives from industry groups did not feel that these procedures would add substantial costs to order processing or delays in shipping the final product.

Technical details of the policy will require further evaluation. Researchers expressed concern that start-up companies without the support of an established research institution might have trouble demonstrating their legitimacy, which would now be required in order to request pathogen-related sequences. Some scientists and providers questioned the validity and arbitrariness of a proposed 200 base-pair threshold for screening scrutiny, which was intended to exclude smaller, single-stranded oligonucleotides from safety proposals aimed at synthesis of full-length genes.

The question of which method should be used to determine the sequence origin – either the so-called “best match” model, which utilizes databases such as GenBank, or other sequence matching algorithms – was also a hot topic of discussion. Indeed, some participants felt that this issue showcased an advantage of the voluntary nature of the proposed non-binding Federal guidelines. The intentionally flexible language would allow the policy specifics, such as the matching algorithm, to evolve in the face of technological advances that move far faster than either formal rule making or legislation.

This voluntary approach may also facilitate global cooperation within the rapidly expanding international gene synthesis industry. One DNA provider explained that their company would generally apply the most stringent standards mandated anywhere in the world they do business, rather than attempting to apply differing standards to individual orders depending on local regulations.

Ongoing Developments

The US guidelines for synthetic double-stranded DNA providers will be open for comment through January 26^th, and will be revised and reissued in final form later this year. The NSABB is also continuing to investigate the promises and perils of synthetic biology; the board approved a new draft report in December 2009 calling for increased oversight, education and outreach concerning the dual use potential of synthetic biology.

Even as the details continue to be discussed, it is encouraging to see nigh universal consensus on the measures to safeguard the public from harm, while preserving the potential for societal advances presented by this growing field.

New York Has a New Roach

frigginloon — Tue, 29 Dec 2009 01:22:15 +0000

OK, this isn't funny, help me up!

WTF, two teens have discovered a new species of roach living in New York City (or more specifically in a friggin supermarket). Sheez, it sure is a melting pot! The students Brenda Tan and Matt Cost were involved in a science project which required then to collect samples of stuff found on the streets of New York City which would be later tested using the Barcode of Life Database and GenBank. The cockroach sample came from a supermarket. What? Ewh! Anywho, after testing it was discovered the roach had been genetically modified (hope it wasn’t from eating those friggin GM strawberries the size of melons). Everybody panic! The duo also collected DNA from an ostrich, paddlefish, bison and even a giant flying squid. Hell, it’s a friggin jungle out there!

First Tamiflu Resistant Pandemic H1N1 Virus Isolated In Italy

flutrackers — Sun, 22 Nov 2009 21:30:10 +0000

Hattip Florida1, Ironorehopper, NS1

The H274Y mutation that confers resistance to Oseltamivir (Tamiflu) was found in a genetic sequence in Italy

The thirteenth TamiFlu Resistant specimen with a publicly available sequence, A/Pavia/21, was deposited Friday at GenBank with only Segment 6 (NA). The sample is contemporary and was taken 2009-11-16 on a nasal swab from a host with no gender or age identification in Pavia, a city of 71,000 in the Lombardy region of north central Italy. This Neuraminidase is remarkable due to the number and range of polymorphisms though the sequence is truncated 35 bases from the end.

http://www.flutrackers.com/forum/showthread.php?p=321644#post321644

The Largest Hockey Stick in the World. Sort of.

Michael Jung — Mon, 16 Nov 2009 09:52:35 +0000

GenBank Growth. The Biggest Hockey Stick.

The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced at National Center for Biotechnology Information (NCBI) as part of the International Nucleotide Sequence Database Collaboration, or INSDC. GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms. GenBank continues to grow at an exponential rate, doubling every 18 months. Release 155, produced in August 2006, contained over 65 billion nucleotide bases in more than 61 million sequences. GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers. (Wikipedia)

The Next ‘IT Industry’

When technology was given individuals, growth and innovation turned out to be exponential. Now we are reaching the stage where an individual can fabricate and re-design biological components and systems that do not already exist in the natural world at a fraction of the cost 20 years ago.

————————

Week11: Clearer point of view (29-09-09)

Kratip — Thu, 01 Oct 2009 02:08:11 +0000

This week, the discussion has made me clearer two important point of views as followings:

(i) How big do training set and test set have?

Due to sample sequences of my proposed work, it has been clearer that we can deal with sample sequences although the data set will be small number e.g. 50 classes. My supervisor suggested that we can determine one line of sequences (60 each) to be training set and the rest of sequences to be test set or vice versa. We can also split a training set to 10 each and the rest to a test set. This is clear about data sets problem although we will have sequence only 50 classes, we can generate lots of instances of training set and test set.

(ii) Setting a Java Machine Learning Library (Java-ML) in eclipse classpath.

My supervisor demonstrated how to set a classpath in eclipse and suggested me to try building a new java classifier from Java-ML library. We can start with choosing an easy classifier, copy, rebuild with my own, compile, and run in order to see how the new classifer working. This is clear about my coding program with Java and how to use eclipse generate Java programming.

Notes on Biological Databases (Part 1/2)

gurarslan — Fri, 18 Sep 2009 16:01:04 +0000

A Collection of Biological Databases

Here is a list of notable biological databases available on the Internet. I took notes about each of them, trying to see the distinctive feature of each one:

1) SWISS-PROT/TrEMBL

Succeeeded by UniProt
Father of Swis Prot format

2) GenBank

Convenient and quick Submission via Bankit
Entrez support
GenBank continues to grow at an exponential rate, doubling every 18 months

3) EMBL

SRS Search screen provides a navigation bar where various tools are listed that can be used to process fetched results
Integr8 has proteome analysis information on a large number of organisms.
Genome Reviews are a set of reannotated proteomes, based on manually curated data from UniProt.

4) RefSeq

Unlike GenBank, RefSeq provides only one example of each natural biological molecule for major organisms ranging from viruses to bacteria to eukaryotes.
non-redundancy
explicitly linked nucleotide and protein sequences
updates to reflect current knowledge of sequence data and biology
data validation and format consistency
distinct accession series (all accessions include an underscore ‘_’ character)
ongoing curation by NCBI staff and collaborators, with reviewed records indicated

5) UniProt

Possible to get help instantly
Advanced Web Design makes it easy to navigate
Allows downloading results
Allows boolean expression search

6) Kyoto Encyclopedia of Genes and Genomes (KEGG)

KEGG is a computer representation of the biological systems. For that, it uses KEGG Objects
Maintains five databases;

7)PDB – Protein Data Bank

3d Structure View
Educational resources
Flash animations
Molecule of the month

8)GOLD – Genomes OnLine Database

Poor Web Design
Global Project tracking system

9)UCSC Genome Browser

Extensive tranining material
Extensive tools

10)Ensembl

The Ensembl Genome Browser provides the best possible automatic annotation, graphical views and web-searchable datasets for a number of eukaryotic genomes including human, mouse, drosophila, anopheles, zebrafish with others to follow.
Perfect annotation
ability to automatically generate graphical views of the alignment of genes
Ensemble is easy to mine via BioMart

11)Entrez Gene

Cross Databse search made possible by Entrez
- Allows boolean expression search
- Indexing service makes searching even more comprehensive
- Putting search constraints made easier by Limits

12)Sanger Institute

Information about ongoing proejcts
Up to date site
Knockout mouse portal
Cancer genome project

13)J. Craig Venter Institute

Best source for sea organisms

14)FlyBase

Important tools like
Contributes to GO Project

15)Saccharomyces Genome Database (SGD)

Part of GO Project
Community Pages

16)MGI

Specilalized mouse database

17)InterPro

Stores signatures

–
Ömer Gürarslan – Fri, 18 Sep 2009 – 15:31:33

Peter Bogner's Excellent Skiing Techniques and Killer Flu Database

monotreme1000 — Thu, 17 Sep 2009 02:42:39 +0000

Want to know how to ski better?

Talk to Peter Bogner. He demonstrates how in this video: Skiing Techniques (1985)

Want someone to organise a Yacht race?

Talk to Peter Bogner. He organised the Speed world challenge sailing 2003.

From a prestigious skiing dynasty and no less passionate about sailing, Peter Bogner the Chief Executive of the Bogner Organization brings his media experience and his management skills to the speed challenge. He says his strategies for sailing and running a business intersect at the point of using speed and state-of-the-art technologies to reinforce leadership.

Want access to H5N1 sequences? To pandemic H1N1 sequences?

Talk to Peter Bogner.

Huh? WTF!!!

That was my first reaction when I realised that a ski instructor/yacht racing organiser/media impresario would have control over the most significant nucleotide sequences in the world.

How did this happen? No-one seems to know.

When it was first announced, it was spun as some sort of good thing. Sequence data that had been kept secret in WHO vaults would be made publicly accessible. (See A nonscientist pushes sharing bird-flu data for more).

The thing is, if people really want to make sequences public, there is a simple way to do this: deposit them in GenBank. In every field of biology, with the glaring exception of influenza science, sequences are uploaded to GenBank and then made freely available to anyone who wants them with no pre-conditions whatsoever. This database is paid for by the US taxpayer via funding from the National Institutes of Health, a division of the Department of Health and Human Services (DHHS).

Want all the new H1N1 sequences deposited in GenBank? Here they are:

GenBank sequences from pandemic (H1N1) 2009 viruses

So, since there is already a publicly funded, completely accessible database for nucleotide sequences, why do we need a privately funded one for flu sequences? Hint: Because the data are not freely available. Instead, there are a number of preconditions attached to access. The contract you must agree to is more complex than the one I signed to buy my house. Some highlights: First, you must register by providing your name, address and other personal information. If Peter, the Ski Instructor, thinks you are OK, you will use a password and username to access the database. Every access of data will be monitored by Peter, the Ski Instructor. If you attempt to disclose the information to anyone else without gaining the permission of the person who submitted the sequence data, you lose access to the data. If Peter, the Ski Instructor, decides to cut you off at any time, then, no sequences for you!

These conditions greatly limit the utility of the data. If you want to analyse a large dataset, you need to get permission from all the many contributors. If you want to publish an idea that contradicts the hypothesis of one of the contributors, they may make it difficult for you. If you want to discuss your ideas with a colleague down the hall, you can’t. If you want to discuss an important result at a meeting, you may not be able to if you cannot get permission from all the sequence contributors in time.

This may surprise you, but it turns out that being a ski instructor is not the best preparation for building a nucleotide sequence database. So Peter, the Ski Instructor, contracted out the actual sciency part of the project to the Swiss Institute of Bioinformatics (SIB). SIB and Peter the Ski Instructor recently had a dispute about ownership of the database. So, access to these critical sequences was interrupted….

IN THE MIDDLE OF A FRAKKING PANDEMIC!!!!!

Sorry, I get that way when buttheads endanger all of humanity due to extreme greed and stupidity.

To all the researchers who deposit your flu sequences in GISAID instead of GenBank, please, go buy a soul and have it inserted into your meat sack. Historians are going to record what you did. And if a lot of people die in this pandemic, a pretty good bet at this point, your wax image is going to be in the Bad Boys section of Madame Tussauds.

Recomendo o artigo extraído da Veja de 2006

delfinaguimaraes — Tue, 25 Aug 2009 15:56:35 +0000

Medicina Letal por natureza Pesquisadores americanos descobrem por que o vírus da gripe espanhola ma

Swine Flu Conspiracy Goes to Court

ahrcanum — Fri, 24 Jul 2009 15:46:41 +0000

Tipping the scales of justice.

Think about all the money being poured into swine flu by pharmaceutical companies with their vaccines and treatments, let alone the funding from politicians and governments.

Is it fear mongering, warnings or plain old profiteering from the A/H1N1 Swine Flu virus and its mutations?

Insane or billiant, Austrian journalist Jane Burgermeister- blog her at http://birdflu666/wordpress.com is sure that swine flu was created as a mean of mass population reduction and has filed a lawsuit against WHO, UN, FBI and a who’s who of government officials in an effort to substantiate her claim.

She asserts that there is a covert bioweapons program involving Baxter pharmaceuticals and that these bird and avian flu viruses have been lab engineered so that a mass vaccination program would be implemented around the world. She also claims that the vaccines are worse than the disease it is designed to eradicate believing that the vaccines will contain toxic biological agents that will be weaponized to cause death and injury to perhaps millions.

She resides in Vienna where the case was filed, but we could all be dead by the time this case got to trial as slow and backlogged as the court systems are.

Baxter applied for a patent on H1N1 some two years prior to the pandemic. If you don’t own it and you didn’t make it, why bother to patent it? Who owns the common cold bug?

Tons of Influenza genome sequences are available on line at GenBank alsong with other influenza resources free for terrorists and scientists alike. http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html How many of these have a patent?

More flu related posts on the tab above labeled A/H1N1 Flu Report or

Open wide, say ahhh and check out these posts on the A/H1N1 Swine Flu from Ahrcanum, where the conspiracy spreads as fast as the virus itself . Our disclaimer-Swine Flu Conspiracy theory can sometimes be triggered by real world events. http://ahrcanum.wordpress.com/swine-flu-report/

Week1: Start doing Ph.D. project (14-07-09)

Kratip — Tue, 14 Jul 2009 11:00:36 +0000

I have met supervisor since February 2009. Today (14 July 2009) this is an official meeting as a full-time Ph.D. candidate. Again, we have discussed an overview project, scope, and methodology as followings:

Database  –> Problem 1  –> Problem 2    –> Problem 3      –> Tool
GenBank &      Feature         Classification      Presentation
EMBL               Extraction                                Visualization
How big?
Is it problem?

To Do Lists:
1. Count % of A’s, % of C’s, % of G’s, and % of T’s gene samples
2. Classify the class of lemon grass (yes/no) by using WEKA and choose suitable algorithms including an interpretive visualization

Tarmboll

grodd — Mon, 01 Jun 2009 16:15:31 +0000

Jag skulle lätt kunna inbilla mig att kulan på magen är en liten gravidmage.
Men efter mitt samtal med barnmorskan då jag bokade vårt första besök upplyste hon mig om att det förmodligen är en tarmboll. Tarmarna och livmodern möblerar om och det kräver tydligen lite space.

Problemet är att det syns när jag har mina tighta jobbskjortor på. Och mina chefer kommer inte tänka tarmboll… De kommer tänka bäbis.

I lördags på bröllopet fakeade jag fylla på ett föredömligt sätt. Jag ägde dansgolvet. Bytte diskret champagneglas med N. Smuttade på alkoholen och svalde luft. Gick runt med min vattenfyllda ciderflaska. Sluddrade, vinglade och sa lite fjantiga saker. Alla mina sjukligt observanta tjejkompisar gick på det.

N blev orolig för maten dock. Han såg att gravida H inte åt sin lax. Så idag har jag läst på om kostråden. Jag är skeptisk till alla överdrivna råd och kommer inte nojja i onödan. Så jag kollade vad som gäller hos livsmedelsverket och laddade ner denna trevliga guiden med kostråd för gravida. Ingen större fara med maten alltså. Och ingen panik över laxen.

I morse vaknade jag 04.00 och insåg vad som håller på att hända. Det börjar smälta in nu.
En kompis till mig bloggade nyligen om hur stort allt känns i nuet, men om man ser tillbaka på sitt liv så är det samma sak nästan hela tiden. Jag hoppas att grodden inte kommer innebära ett helt nytt liv. Jag är mycket nöjd med mitt och vill inte att det ska ändras. Till exempel vill jag gärna kunna dra iväg och bada med N spontant som vi gjorde igår.

N är ett praktexemplar. Vem skulle inte vilja avla med N?
Vilken genbank!
*nöjd*

GIGO y la importancia de los biocuradores en las bases de datos

Rubén — Thu, 14 May 2009 12:34:47 +0000

Durante estos últimos años la biologia ha generado volumenes inmensos de información, tanto genética

Bioinformatics of Swine Flu

aurametrix — Tue, 28 Apr 2009 23:07:42 +0000

By Aurametrix

The swine influenza A (H1N1) virus is is an RNA virus coding for 8 genes. The sequences of these genes from strains isolated in Texas, California, New York and Kansas can be downloaded from GenBank:

Another collections of sequences with bioinformatics tools can be found at http://www.flugenome.org, but this resource is not updated with the current data and can’t be used for genotyping of the latest sequences.

HA encodes hemagglutinin (about 500 molecules of hemagglutinin are needed to make one virion). This protein determines the extent of infection into host organism, bronchial epithelial cells, lungs and other organs.
NA encodes neuraminidase (about 100 molecules of neuraminidase are needed to make one virus particle).
NP encodes nucleoprotein.
M encodes two matrix proteins (the M1 and the M2, which is an ion channel) by using different reading frames from the same RNA segment (about 3000 matrix protein molecules are needed to make one virion).
NS encodes two distinct non-structural proteins (NS1 and NEP) also by using different reading frames from the same RNA segment.
PA encodes an RNA polymerase.
PB1 encodes an RNA polymerase and PB1-F2 protein (induces apoptosis) by using different reading frames from the same RNA segment.
PB2 encodes an RNA polymerase.

The genome is a composite of avian flu, human flu Type A, human flu Type B, Asian swine flu, and European swine flu. A strange combination having less than 0.1% chance of being a natural event. Most of the genes, including the hemagglutinin (HA) gene, are of the same family as seen in US pigs in the last decade, but the neuraminidase (NA) and matrix (M) protein genes are more like swine flu viruses seen in Eurasia. Other chunks of the genome came from influenza viruses carried by birds and humans. Novel swine flu isolates are resistant to the older antiviral adamantane class of drugs (M2 inhibitors), but sensitive to the adamantanes. Two anti-viral drugs on the market – Tamiflu and Relenza –can lessen the symptoms of swine flu.

Take a look at the BLAST results of 8 NA sequences coding for the protein targeted by drugs oseltamivir (Tamiflu) and zanamivir (Relenza). Perfect alignment to european swine flu sequences, minimal variations. The bird viruses come second best. Taking into account that bird flu easily developed resistance to the above mentioned drugs, and that vaccine development will be a challenge, this does not sound too good.

Flu viruses are growing resistant to key weapon Tamiflu This year, Tamiflu resistance in that class of viruses has reached almost 100%, turning the tables on a drug designed to defeat resistance. A CDC team tested 1,155 A/H1N1 viruses from 45 states. They found that 142 viruses from 24 states were resistant to Tamiflu, or 12.3%. Earlier this year, 264 of 268 viruses tested were Tamiflu-resistant, or 98.5%, reported in The Journal of the American Medical Association.

CDC expects we will see more deaths. From a historical perspective, this is, indeed, scary: Asian Flu pandemic of 1957 and the Hong Kong Flu pandemic of 1968 occurred as a result of influenza mutated by antigenic shift, recombination similar to the one observed for current swine flu outbreak. Missense mutations account for other milder epidemics (1962, 1964, etc). The human swine flu outbreak continues to grow in the United States and internationally. So is it going to be a Worldwide Pandemic or a Case of the Sniffles? Let’s hope for the best, but prepare for the worst.

Swine Flu Unlikely to Affect the Economy (time.com)
Swine Flu: Facts, Myths and Whether to Worry (abcnews.go.com)
Swine Flu: What You Need to Know (abcnews.go.com)
Resistance to Tamiflu Growing (nlm.nih.gov)
Swine Flu: Is this the Big One? (grantlawrence.blogspot.com)
Questions, answers about swine flu (seattletimes.nwsource.com)
Why the hullabaloo about Swine Flu? (thegenesherpa.blogspot.com)
CDC Readies Swine Flu Vaccine (time.com)

Ilaria Capua: La scienza open source

paoblog — Tue, 31 Mar 2009 07:00:02 +0000

Allora. Parliamone. Ho vinto nel 2007 il premio SciAm50 per la leadership in science policy e nel 2008 sono stata inclusa fra le cinque “Revolutionary Minds” dell’anno dalla rivista americana Seed. Parliamone, per cercare di comprendere i meccanismi dietro questo riconoscimento formale a livello internazionale e in che cosa ciò si può tradurre. Nel 2006, in piena emergenza mediatica da H5N1, cioè l’aviaria, il laboratorio che dirigo è il primo a caratterizzare il primo H5N1 africano.

Come laboratorio che si occupa di sanità pubblica veterinaria, ci rendiamo conto che l’introduzione di questo virus nel continente africano si tradurrà in grave malattia e morte per alcune persone, milioni di animali morti e riduzione della principale fonte di proteine nobili alle popolazioni più in difficoltà. Lo sapevate che il pollo è l’unica carne che non ha barriere religiose e viene consumata in tutto il mondo? È la prima volta che un virus influenzale con le caratteristiche dell’H5N1 raggiunge l’Africa e la comunità scientifica non può perdere tempo. Ricevo una telefonata da un funzionario dell’Oms, l’Organizzazione mondiale della sanità, che mi invita a depositare in un database ad accesso limitato (solo 15 laboratori) il codice genetico (l’impronta digitale) del virus; in cambio avrei avuto accesso tramite password al suddetto database. Mi trovo di fronte a un bivio: entrare a far parte degli auto-eletti depositari della scienza, oppure mettere a disposizione della comunità scientifica i nostri dati.

Così abbiamo fatto e la sequenza è stata scaricata mille volte da GenBank in una settimana, scatenando un dibattito internazionale sull’accessibilità ai dati scientifi ci in tempo reale che sconfi na nell’etica della ricerca. Dove si traccia la linea fra quelli che possono essere considerati dati di un ricercatore o di un gruppo e quelli invece della comunità scientifica intera?

Nell’era della comunicazione globale, a fronte di un rischio (reale o percepito) per la salute pubblica, è eticamente accettabile tenersi delle informazioni che possono aiutarci a comprendere meglio l’evolversi di un’epidemia? Non me la sono sentita e ho rotto gli schemi. Sono fi nita in un uragano di consensi ed è arrivata anche qualche dolorosa critica. Le testate internazionali come il Wall Street Journal, il New York Times, il Washington Post e ovviamente Nature e Science hanno cercato di scuotere la comunità scientifica, sorpresi e increduli che potessero anche solo esistere problematiche di questo tipo.

Quello che mi ha insegnato l’esperienza è che, se hai cose da dire e il tuo lavoro è solido, bisogna avere il coraggio di andare controcorrente e di sfidare le consuetudini. Certo, è rischioso, si ha paura di fare una figuraccia, di rimanere isolati, ma è solo attraverso un confronto alla pari che possiamo fare il salto di qualità. Ed è giusto che chi lo può fare lo faccia e assuma ruoli rilevanti nella comunità scientifica internazionale. Tutto ciò mi porta a un’ultima riflessione: «Ma tanto qui non cambia niente».

Ecco. Questo non è vero. Se io, veterinario che lavora presso una struttura pubblica del Servizio sanitario nazionale sono stata in grado di accendere un dibattito internazionale che ha toccato l’Assemblea mondiale della sanità, ha fatto criticare aspramente un sistema poco trasparente (che di fatto rallentava la ricerca) a favore di una raccolta dati e di analisi degli stessi aperta e soprattutto inter-disciplinare, sono sicura che in altre discipline ci sono colleghi preparatissimi, con idee innovative, che possono rompere gli argini e far prendere alla ricerca una direzione che ci porti a essere partner e leader della scienza che conta.

Fonte: www.wired.it

The Vertebrate Bias

myrmecos — Fri, 12 Dec 2008 04:24:21 +0000

The above pie chart shows the relative proportions of described species in various groups of organisms. As we can see, most species are invertebrate animals. Things like snails, flatworms, spiders, sponges, and insects.

Now compare that slice of pie to the proportion of GenBank sequences that represent invertebrates:

Yes, that thin blue wedge is all we’ve got. While most mammal species have had at least a gene or two sequenced, the vast majority of non-vertebrate species have yet to meet a pipettor. Entire families of insects haven’t received even a cursory genetic study.

Of course, we make great progress with the efficiency of focusing our efforts on a small number of model organisms. But surely there’s an opportunity cost of putting all our eggs in the mammal basket. What about the rest of life?

Bir Genin İnsiliko Ortamda İncelenmesi

biyoinformatik — Sun, 23 Nov 2008 12:22:50 +0000

Biyoinformatik araçlarını internet ortamnda kullanmak günümüzde moleküler biyoloji ,tıbbi genetik,kanser genetiği gibi konularda çalışma yapan birçok bilim adamı için ve tıp sektöründe gün geçtikçe önem kazanmaktadır.Genome dizileme yarışı gün geçtikçe daha önem kazanmakta.Yapılan çalışmaların ve genome dizileme merkezlerinin büyük bir hızla artması birden fazla veri tabanını arayan yeni multi-base veritabanlarının oluşmasıyla gün geçtikçe biyoinformatik araçalrının kullanımını artırmaktadır.

Dünya çapında yada ulusal ölçekli merkezlerden tutunda yerel ölçekli akademik veya özel girişimlere kadar birçok farklı yer ve ölçekte çalışmalar yapılmakta.Genome dizileme çalışmaları Sağlık,Ziraat,Medikal ve benzeri sekörler için gerçekten önemli.Biyolojik proseslerin incelenmesi ve kararlı sentez mekanizmalarının ortaya çıkarılması gelecekte hayatımızda birçok yeniliğin ortaya çıkmasına neden olacağı açık.

Bu haftaki özel konumuzda dünya çapında kabül görmüş Amerikan sağlık bakanlığının kurmuş olduğu National center of Bioinformatics (NCBI) yada diğer bir değişle akademik ortamlarda PUBMED olarak da bilinen uygulamalı biyoinformatik araçlarının kullanımına ve insiliko ortamda araştırma yapmaya imkan veren web portalını incelemeye aldık.

Yazının devamı yakında…

Bio.Ali İsmet ÇAPHAN

a.caphan@gmail.com

Who’s your Ur-mama?

Ron Pavellas — Wed, 17 Sep 2008 06:35:00 +0000

In his book The Seven Daughters of Eve, scientist-author Bryan Sykes presents “the classification of all modern Europeans into seven groups, the mitochondrial haplogroups. Each haplogroup is defined by set of characteristic mutations on the mitochondrial genome, and can be traced along a person’s maternal line to a specific prehistoric woman” (Wikipedia, reference link above). The seven “clan mothers” mentioned by Sykes each correspond to a human mitochondrial haplogroup.

Ursula: Haplogroup U;Xenia: Haplogroup X
Helena: Haplogroup H; Velda:Haplogroup V
Tara: Haplogroup T; Jasmine: Haplogroup J

And, my Ur-mother* is Katrine, corresponding to Haplogroup K, who hypothetically lived around 12,000 years ago in northern Italy, near the Austrian border. (*The prefix ‘Ur-’ is “a combining form meaning ‘earliest, original,’ used in words denoting the primal stage of a historical or cultural entity or phenomenon” according to Dictionary.com Unabridged (v 1.1)).

Please click on the image to see the detail

How do I know this? Let me explain …

I have long been interested in the genealogy of my family. Upon a recommendation, I read Sykes’s book and found his science and imaginative hypotheses fascinating. I believe there was reference in his book to places where a person’s DNA could be analyzed in order to see which ur-mother could be assigned to him or her, assuming that the person was of consistent European ancestry on his or her mother’s matrilineal side.

I decided to pay for a DNA analysis from Family Tree DNA, based in Houston, Texas, founded in March of 2000. “It is the world leader and foremost organization in the field of Genetic Genealogy that has been constantly developing the science that enables thousands of genealogists around the world to advance their families’ research. With over 100,000 DNA records, it has the largest YDNA and mtDNA databases in the world, and processes a wide array of genealogy related tests. It also provides the DNA testing for the National Geographic’s Genographic Project.” (Source).

Helen Diakakis, my maternal grandmother, whose ur-mother was in northern Italy; she was born in Astros, The Peloponnesus, Greece

I received from Houston a kit to capture some of my tissue from which my DNA could be extracted. This tissue is the epithelial lining of my cheeks. I used the two swabs provided in the kit (a precautionary redundancy) to scrape the inside of my cheeks, then inserted them into two tubes containing some preserving liquid. I mailed them back in the special envelope Family Tree DNA provided, along with the paperwork. In due course I received results that were specific for my mother’s side (mtDNA) and my father’s patrilineal side (Y-DNA). There is no way to determine one’s “Ur-father” for reasons which are beyond the scope of this blog, but are detailed in some of the links underlying the text.

My Patrilineal great-grandfather, Greek Orthodox priest Konstantinos Alexander Pavellas

Over several years, and as the science and technology advanced, I paid for additional tests on the same tissue I submitted, which was held in storage, and now have the all the information currently available for my matrilineal and patrilineal ancestors. On my father’s side, I am descended from the Y-DNA haplogroup J2, originating probably in Anatolia 5,000-12,000 years ago. My paternal line is further identified as a subclade of haplogroup J2, namely J2b2.

Now that I know all this, and more not presented here, about my matrilineal and patrilineal ancestors, what about all the other hundreds of ancestors not in these lines, for instance: the ancestors of my mother’s father and the ancestors of my father’s mother? When I started mentally calculating the number of all the ancestors I needed to have in order to be me (it would be more than all the people currently on Earth), my brain locked up. I put the problem to my son Alexander J. Pavellas, a mathematics guru. Here is part of his response:

Alexander J. Pavellas and his dad some years ago.

“Your calculation assumes that your/our lineage is a simple binary tree. What it neglects is the possible common ancestry of a given mother and father. When populations were small, inbreeding occurred frequently simply because there was not a genetically diverse population around (i.e. “My sister is the only girl in town.”) This has the effect of “pruning the family tree.” In reality, if you were to draw a graph representing your ancestry dating back in time, you would not see a continuously branching tree with more and more ancestors per generation, but lots of crisscrossing lines with lineages constantly splitting and merging. I would guess that the number of ancestors per generation would increase geometrically until it hit some critical value, at which point the total number of ancestors in a particular generation would remain relatively constant, possibly oscillating depending on more global variables such as the size of local populations, wars, plagues and whatever else might affect it.”

In the end, for me, this is all interesting but not vital to know. For some, there are questions to answer such as determining true paternal parentage, whether one has Native American or Family Cohen (Jewish) DNA and to what degree, and many others, such as relationships among persons of the same surname. Testing of other persons presumably or questionably related to oneself is necessary for some of these determinations.

Map of Human Migration. Please click on the image to see more detail (numbers indicate thousands of year ago)

As of April 13, 2008, Family Tree DNA achieved a data base of 188,022 records, the largest DNA databases in the field of Genetic Genealogy, including: 4,747 surname projects, 74,997 unique surnames, 123,062 Y-DNA records and 64,960 mtDNA records in the database. I have volunteered to be in several study projects, one relating to my Greek DNA heritage on my paternal side. I have also given my DNA information to GenBank of the US National Institutes of Health; and to the Genographic Project of the National Geographic magazine.

I started out on this quest to satisfy my curiosity and ended up as an active participant in the quest for more and better knowledge about the human condition.

And, now, I also know who my Ur-mama is: Katrine. Nice name.

ADDENDUM

All of this information, including that provided by volunteers such as myself, will lead to more knowledge of human DNA mutations and migrations, and to the application of this knowledge to human variations in disease and immunity patterns.

As a good book about the whole human genome, readable by non-scientists, I recommend Genome by Matt Ridley. The book has 23 chapters, each featuring the most recently discovered gene on each of our 23 chromosomes.

Although Ridley doesn’t mention this particular gene, there is one in chromosome 11 that determines whether or not a person will have normal red blood cells, or will have a mutation that makes the person anemic, to a greater or lesser degree depending on whether the mutation manifests itself recessively or dominantly. I have such a mutation in chromosome 11, the result of which is called Alpha Thalassemia, a relatively benign condition. There are serious effects when one has the genetically dominant, or “beta” form, called Mediterranean Anemia or Cooley’s Anemia. This will occur in 25% of instances, on average, where both parents have the alpha form of the mutation. I didn’t know this until all five of my children were born but I was lucky to have had mates who did not carry the alpha mutation in chromosome 11. But this is a cautionary for my children to investigate the possibility in their respective matings.

Geographic Distribution of Alpha Thalassemia