Unusual HIV-Vaccine perplexes Scientists
Scared from the escalating HIV pandemia with 25 million dead people since 1981? Here’s a flicker of hope: a HIV vaccine phase III study performed in Thailand this year is yielding promising results while reducing the infection rate with 31% effectiveness.
31 percent, that’s not rip-roaring, but at least it’s a beginning. Rather stunning, however, is the scientific approach behind this unusual trial that is performed under the code “RV 144”(a joint venture between the U.S. and Thai governments). It combines two more or less ineffective vaccines to create an effective one, Vaxgen’s AIDSVAX vaccine with Aventis Pasteur’s Alvac-HIV canarypox vector, also known as “vCP1521”.
AIDSVAX, targeting the gp120 glycoprotein that is exposed on the surface of HIV, failed in North America as well in Thailand in 2003, supplying “not a statistically significant reduction of HIV infection within the study population”.
On the other hand, the Aventis Pasteur vaccine, Alvac-HIV – a therapeutic vaccine designed to slow or halt disease progression in people who are already infected – induced just weak immunogenicity.
The current trial that cost $119 million involved 16,400 participants. 8,200 of them were given an experimental vaccine consisting of AIDSVAX / Alvac-HIV, while the remaining 8,200 were given a placebo. The participants were tested for HIV every six months. After 3 years, those given the vaccine had HIV infection rates reduced by 31% compared with those who had been given the placebo (51 newly HIV infected persons vs. 74 in the placebo group).
The US/Thai study is the only phase III trial of a HIV vaccine that currently is being performed. In addition, it’s the first successful HIV vaccine trial in history.
It’s too early to jubilate, however. These results could still be due to chance, and the whole thing has yet to undergo peer review.
Unicorn to be sequenced with 30x coverage
Man, mouse, Methanopyrus… and still counting the nucleotides. The genomes of 960 species have been sequenced by the end of July (as you can see on the relevant NCBI web page).
Out of all reason, however, the genomes of some relevant species were so far ignored by the scientific community. Just think of Crisensus bavaricus, of the common garden gnome or of the rarely sighted North American Bigfoot.
Another rare animal is to reveal its secrets soon. After its existence has been confirmed by serious sources, a renowned (but undisclosed) research institute has launched concrete plans to sequence the whole genome of the unicorn.
There’s just a tiny problem: there’s a serious lack of DNA sources.
Probably the researchers should try a near Arctic relative first. Could be more promising, your Mr Gene is sure.
Anthropologist stumbles over faked skulls
An incredible affair of faked skulls has found its inglorious end at a district court in Frankfurt, Germany. Reiner Protsch von Zieten, a previous highly respected professor of anthropology, was given an 18-month suspended sentence. Protsch had been debunked some years ago of systematically falsifying the dates of numerous major stone-age relics (see the Guardian and the Spiegel).
Protsch, a professor at the University of Frankfurt and widely recognized expert in carbon data, alleged in the 1980s and 1990s that the “woman from Binshof-Speyer” was 21,300 years old (although her real age emerged as only 3,000 years). In a similar case a 240-year-old skull, the “Paderborn-Sande man”, grew old to a faked-by-Protsch age of 27,400 years. Even the “oldest Hamburgian”, the “Neanderthal from Hahnöfersand” (who, according to Protsch, was aged 36,300), is not a quarter as old. Latest radiocarbon datings taken by the independent Oxford Radiocarbon Accelerator Unit measured that the skull has only 7,500 years under his belt.
The University of Frankfurt stated in 2005 that Protsch had fabricated data and plagiarized the works of his colleagues: “[…] Prof. Protsch has forged and manipulated scientific facts over the past 30 years”. Protsch, who had headed the Frankfurt University’s institute of anthropology since 1973, persistently defended any allegations even though a former assistant said that Protsch did not know how to handle his own institute’s radiocarbon dating equipment.
Protsch’s work had been cited as evidence that Neanderthal men had once lived in Northern Europe. Now, human prehistory must be written again. “Protsch’s work appeared to prove that anatomically modern humans and Neanderthals had co-existed, and perhaps even had children together”, said one of the archaeologists who had unmasked the scandal, adding that “this now appears to be rubbish. It’s a dating desaster.”
Protsch’s title was faked, too. As the Spiegel reported the Professor “Dr. Dr. Protsch von Zieten” emerged as an ordinary Doctor in the year 2000. His second “Dr.” wasn’t genuine. Thus, Protsch was condemned for title swindle and had to pay a penalty of the equivalent of €14,000.
Even Protsch’s last name (“Reiner Protsch von Zieten”) is arguable. The Spiegel claims that the “von Zieten” title is false, too.
It wasn’t professor Protsch’s misconduct for decades, however, that finally broke his neck. It was his attempt to sell the university’s chimpanzee skull collection to an American collector for $70,000. The lion’s share of the Frankfurt district court’s verdict results from this attempted theft.
How to win a piece of the moon??
Space aficionados around the world are electrified by an announcement made by the New Scientist. On the front cover of the print copy’s issue from June 13th, 2009 the weekly science magazine attracts its readers with the following promise calling attention in a screaming yellow circle:
>> WIN! This piece of the moon <<
Wow! A real piece of Earth’s companion! What an opportunity! Dozens of questions immediately arise in your Mr. Gene’s brain, such as “Where has the stone been found?”, “How big is it?”, and, most important, “What must a reader do to enter (and win!) this competition?”
Tons of questions, however, not a single answer. There’s no additional information provided neither on the magazine’s cover nor in the contents section or on the following 64 pages. Well, has your Mr. Gene read it over? Did the postman grab a potentially enclosed advice card?
There’s only a cover story about gravity(!) on pages 28 to 32, but neither a whiff of a hint inside the whole print magazine nor any clue to the New Scientist’s starting website (your Mr. Gene checked it up on the 29th of June and only found two articles, the first on “misty ice caverns on a Saturn moon”, the second on the DNA component adenine that “has been created in a lab experiment modelling Saturn’s moon Titan”).
Since your Mr. Gene cannot believe that the New Scientist is kidding its readers he hopes that YOU can enlighten this strange affair.
Please, let me know how to win a piece of the moon!
(I’m sorry, but this link is not the right one and these “certified pieces of the moon” are too pricy…)
Get your clone uncontaminated
It’s not unusual for a paternity test to reveal unpleasant truths about the kiddy (and its genitor).
The outcome of a Texas paternity test in May, however, wasn’t only unusual - it was crazy. Here’s the story.
A mother and her fiancé decided to take a paternity test due to the puzzling different facial features of their 11-month-old children (a pair of twins). When confronted with the test’s results they cannot believe the unbelievable truth:
The mother has given birth to twins, but they are by different fathers. They have completely different DNA.
One child is the biological son of the mother’s fiancé, the second one is the outcome of an affair with another man she had at the time the twins were conceived. Uuups!
However, is this odd story possible at all?
It is, even though there are only a handful of documented cases of bipaternal twins in the world. The rare phenomenon is known as heteropaternal superfecundation (published for the first time in 1994 in the Journal of Forensic Sciences by a Chinese(!) group).
The biological mechanism is simple: a woman can release more than one egg during ovulation and if she has sexual intercourse with more than one partner at that time, sperm from different partners can fertilize different eggs.
While there are only a few cases known, studies published by the NIH and other sources suggest that approximately 2 to 8 percent of fraternal twin sets are bi-paternal.
Look out for the unexpected, if you are thinking about a paternity test!
Lousy DNA analysis fools German police
The mysterious phantom killer the German police was searching after for years has finally been identified: it is a cotton swab. The photo below shows the wrongdoer after its arrest by a police investigator.
The search was extensive and sometimes extremely dangerous as you can see on this top secret snapshot taken by accident in 2004 (showing two brave cops hunting the dangerous phantom, doing their very best). Unfortunately, they grabbed the wrong person at that time.
Now, however, after DNA traces of the phantom (pointing at an unknown, criminal woman) have been found at 40 crime scenes, the police was successful. After spending millions of Euros and spinning the wheels of a 100-person investigation unit searching for “The Woman Without a Face” - who had been linked to six murders as well as to summerhouse burglaries - the German police revealed that they have been chasing after the DNA of a factory worker who handled the cotton swabs used by police lab workers.
In other words: the mystical person, often described as “the country’s most dangerous woman”, doesn’t exist a bit (or, more precisely, is a contamination on cotton swabs).
Ouch!!
The investigators suspect that certain batches of cotton swabs were contaminated before delivery. Although cotton swabs are sterilised before being used in investigations, they are often contaminated by human DNA from skin or sweat. Every forensic scientist who is in his right mind knows that and uses DNA-free swabs (to get more information on contamination problems, read, for example, this review from 2005: “Identifying and Preventing DNA Contamination in a DNA-Typing Laboratory”).
To quote this review: “[…] It is often easier, less time-consuming and more reassuring to simply discard all solutions that have come into contact with samples that demonstrate contamination.” and “For equipment that cannot be treated with bleach, exposure to ultraviolet light can eliminate DNA contaminants.”
The German police’s experts didn’t heed these advices. They rather put a €300,000 reward on their phantom and continued fishing in murky waters.
Now, many forensic scientists wonder about the simple-mindedness of their police colleagues at the German LKAs (the State Offices of Criminal Investigation where DNA traces from crime scenes are analysed). Are such lousy DNA analyses more exception than rule there, or vice versa?
Brenner’s kidding
South African biologist Sydney Brenner is a scientific icon of the “Golden Age” of molecular biology. The 2002 Nobel prize laureate was one of the first people to see the Watson-Crick model of the structure of DNA in 1953 (he was working at the nearby Oxford University’s Chemistry Department at that time). In the course of time, Brenner became one of the greatest biologists of the 20th century.
The man with the impressive eyebrows has made several epoch-making contributions to the emerging molecular biology in the 1960s (including the identification of mRNA, helping to elucidate the triplet nature of the genetic code regarding protein translation and frame shift mutations and establishing the soil roundworm Caenorhabditis elegans as a model organism for the investigation of animal development).
However, he is not only a leading researcher. Brenner is a humorous person, too (some even say he is a hopeless joker).
From January 1994 to December 2000 Brenner wrote a column for Current Biology, initially called Loose Ends
(renamed False Starts in 1998, when the column was moved from the back of the journal to the front). The entire set of Brenner’s pieces is available free via http://www.cell.com/current-biology/Brenner.
If you prefer the “living” Brenner, watch this interview from 23rd August 2007 with a good-humoured Brenner talking about why he had only dreamt of food for two years after he had come to the UK, how Watson & Crick killed all his joy and how science works like a medieval guild with journeyman and apprentices.
And if you are a synthetic biology aficionado, you should indulge in the following YouTube video, recorded in Oct 2008 at the Synthetic Biology 4.0 Conference at Hong Kong University (arranged by the BioBricks Foundation). It lasts 36 minutes but it’s worth it. Brenner is perpetually kidding the listening synthetic biology community (while philosophising on the reproduction of centaurs, on dragons and cookies, on the ‘Biofool’ industry, on human biofuel walking around on two legs etc.). - Enjoy!
Cool youtube movies #1
Tired of everyday’s boring lab routine? Let’s change the channel and take a look at YouTube where really cool stuff can be found, such as …
… the Large Hadron Rap (referring to CERN’s Large Hadron Collider) whose backup-dancers, ha-ha, prefer anonymity, according to the credits (and I know why they prefer it!).
A more comical clip is the Creation Science 101 song by Californian satirical singer-songwriter and guitarist Roy Zimmerman. Enjoy!
Also screamingly funny are these Ali G classics on science (“…would it be possible to multiply nine-nine-nine-nine-nine-nine-nine-nine-nine…”) and medical ethics (“…you are a homophobic doctor!?” – “No, no, I’m a homeopathic doctor!”).
More serious stuff desired? Well, just watch computer-game-hero Will Wright talking about The Science behind Spore – even though seriousness doesn’t seem to be Wright’s middle name (just pay attention to the label “Composed of matter, anti-matter AND it doesn’t matter” behind him…!!).
Here are two legerdemains for your next party…
- the nail trick (how to balance ten nails on the head of one),
- the water and pepper trick (nice visualisation of surface tension),
… the ultimate YouTube short film, however, is the cool real-life μ-Tetris under a microscope (by optically trapping 42 glass microspheres with 1 μm diameter, weighting 1 picogram each of them, in a 25 μm x 20 μm sized area under a microscope).
Wow!!!
The most useful genome for committing a crime
What is the optimal qualification to get out of a tight spot after you have committed a crime? Coolness? Unscrupulousness? Brutality? Exceptional intelligence? Or stupid constables (LOL)?
The unexpected answer is that the optimal qualification for a thug to get away without punishment is to have the adequate, well, genome. No, dude, I am not speaking of a cryptic “crime gene” or something like that.
You need a… well, it’s a really bizarre story.
Did you notice the jewellery robbery in Berlin in January? It was a spectacular coup, just as in the 1964 heist film Topkapi – three people had abseiled through a skylight into the German shopping mall KaDeWe with a rope-ladder and had stolen jewels amounting to €5 million (the masked men were filmed by a security camera). Two of the Berlin bandits were caught by the police soon after the theft while the third one still is on the run.
There is a startling detail around this robbery: while forensic scientists have found (and successfully analysed) the burglars’ DNA, they cannot use this DNA as evidence anyway.
Yes, you can believe me! It’s impossible to convict the two burglars that are arrested on remand by genetic fingerprinting (at least for the German justice). Why?
Quite simply, the suspects are monozygotic twins. They have identical DNA, so it is not possible to distinguish one from another (at least for the German authorities who are only allowed to analyse eight VNTR loci in criminal cases).
Before the court “twin A” would lay the blame on “twin B” and “twin B” would lay the blame on “twin A”. Hence the judge would be unable to convict any of them.
Are the German police a dead duck in this special case? It seems so.
However, if the police were allowed to check and compare the twins’ V(D)J regions (in B cells), the situation would change dramatically. These V(D)J regions contain genes that play important roles in the immune system. They are different, even in monozygotic twins.
The web’s most popular genes
Recently, your Mr. Gene was crouching in front of his good old computer when, all of a sudden, it crossed his mind to google the word, well, “gene”.
Having performed this, Mr. Gene proudly presents the ultimate Gene Ranking, powered by Google:
1) Placed 1st is Gene, Elsevier’s International Journal of Functional and Evolutionary Genomics. If you wish to chat with Gene’s Editor-in-Chief, Dr Batzer, please address to the Department of Biological Sciences at Louisiana State University, Baton Rouge, Louisiana. And if you wish to publish your next paper in Gene you should have top-quality results. Gene has an impact factor of 2.871.
2) On the 2nd position the Wikipedia headword “gene” is ranked (how on earth did Elsevier’s Gene manage to be ranked higher than Wikipedia’s???). – Anyway, the Wikipedia “gene” entry contains plethora of genetic material – more than 6,000 words on history, structure and concept of, well, genes (the equivalent of nearly 20 book pages!)
3) The genetic bronze medal goes to the US National Center for Biotechnology Information (NCBI), the well-known resource for molecular biology information established in 1988. Is anybody unaware of this exhaustible gateway to literature and molecular databases as well as tools and useful software? I don’t think so.
However, there are many more interesting or even bizarre “gene” websites at Google’s first 20 positionings, such as…
… the Movie Maze entry for actor Gene Hackman (rank 6!!!),
… the shareware genealogy database “Gene 4.3.4” for Macintosh computers (rank 9),
… and, surprisingly far from the podium, Genentech’s famous www.gene.com domain (rank 10).
Wondering where your Mr. Gene finishes?
Mr. Gene ranks 40th, that is not half bad considering the fact that the HUGO Gene Nomenclature Committee is ranked 56th; Encyclopaedia Britannica’s “gene” entry finishes as 70th – and Gene Kelly’s 4:36 minute YouTube appearance with I’m singing in the rain places at a poor 135th rank.
