ENCODE takes the human genome to the next level

On 5 September, an international team of researchers reveal that much of what has been called ‘junk DNA’ in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes. Without these switches, genes would not work – and mutations in these regions might lead to human disease. Discovered by hundreds of scientists working on the ENCODE Project, the new information is so comprehensive and complex that it has given rise to a new publishing model in which electronic documents and datasets are interconnected.

Just as the Human Genome Project revolutionised biomedical research, ENCODE will drive new understanding and open new avenues for bio-medical science. Led by the National Genome Research Institute (NHGRI) in the US and the EMBL-European Bioinformatics Institute (EMBL-EBI) in the UK, ENCODE now presents a detailed map of genome function that identifies 4 million gene ‘switches’. This essential reference will help researchers pinpoint very specific areas of research for human disease. The findings are published in 30 connected, open-access papers appearing in three science journals: Nature, Genome Biology and Genome Research.

“Our genome is simply alive with switches: millions of places that determine whether a gene is switched on or off,” says Ewan Birney of EMBL-EBI, lead analysis coordinator for ENCODE. “The Human Genome Project showed that only 2% of the genome contains genes, the instructions to make proteins. With ENCODE, we can see that around80% of the genome is actively doing something. We found that a much bigger part of the genome – a surprising amount, in fact – is involved in controlling when and where proteins are produced, than in simply manufacturing the building blocks.”

“ENCODE data can be used by any disease researcher, whatever pathology they may be interested in,” said Ian Dunham of EMBL-EBI, who played a key role in coordinating the analysis. “In many cases you may have a good idea of which genes are involved in your disease, but you might not know which switches are involved. Sometimes these switches are very surprising, because their location might seem more logically connected to a completely different disease. ENCODE gives us a set of very valuable leads to follow to discover key mechanisms at play in health and disease. Those can be exploited to create entirely new medicines, or to repurpose existing treatments.”

“ENCODE gives us the knowledge we need to look beyond the linear structure of the genome to how the whole network is connected,” commented Dr Michael Snyder, professor and chair at Stanford University and a principal investigator on ENCODE. “We are beginning to understand the information generated ingenome-wide association studies – not just where certain genes are located, but which sequences control them. Because of the complex, three-dimensional shape of our genome, those controls are sometimes far from the gene they regulate and looping around to make contact. Were it not for ENCODE, we might never have looked in those regions. This is a major step toward understanding the wiring diagram of a human being. ENCODE helps us look deeply into the regulatory circuit that tells us how all of the parts come together to make a complex being.”

Until recently, generating and storing large volumes of data has been a challenge in biomedical research. Now, with the falling cost and rising productivity of genome sequencing, the focus has shifted to analysis – making sense of the data produced in genome-wide association studies. ENCODE partners have beenworking systematically through the human genome, using the same computational and wet-lab methods and reagents in laboratories distributed throughout the world.

To give some sense of the scale of the project: ENCODE combined the efforts of 442 scientists in 32 labs in the UK, US, Spain, Singapore and Japan. They generated and analysed over 15 terabytes (15 trillion bytes) of raw data – all of which is now publicly available. The study used around 300 years’ worth of computer time studying 147 tissue types to determine what turns specific genes on and off, and how that ‘switch’ differs between cell types.

The articles published today represent hundreds of pages of research. But the digital publishing group atNature recognizes that ‘pages’ are a thing of the past. All of the published ENCODE content, in all three journals, is connected digitally through topical ‘threads’, so that readers can follow their area of interest between papers and all the way down to the original data.

“Getting the best people with the best expertise together is what this is all about,” said Ewan Birney. “ENCODE has really shown that leading life scientists are very good at collaborating closely on a large scale to produce excellent foundational resources that the whole community can use.”

“Until now, everyone’s been generating and publishing this data piecemeal and unintentionally trapping it in niche communities and static publications. How could anyone outside that community exploit that knowledge if they don’t know it’s there?” commented Roderic Guigo of the Centre de Regulació Genómica (CRG) in Barcelona, Spain. “We have now an interactive encyclopedia that everyone can refer to, and that will make a huge difference.”

#This press release is copied from http://www.ebi.ac.uk/

Bowel cancer 'could be fuelled by E coli stomach bug'

One of Britain’s most common cancers could be fuelled by the E coli stomach bug, scientists believe.

The breakthrough raises the prospect of a vaccine against bowel cancer, which claims 16,000 lives a year and is the second most common form of the disease in women after breast cancer and the third most diagnosed in men.

The elderly, who are most at risk of the bowel cancer, could also be screened for the ‘sticky’ strain of E coli that makes a DNA-damaging poison.

Tests showed Ecoli bacteria to be much more common in bowel cancer patients than in healthy people

Although the idea that a bug is involved in cancer might seem strange, it is not unheard of, with a virus being to blame for most cases of cervical cancer and a bacterium strongly linked to stomach cancer.

Now, tests on mice and people, carried out in the UK and US, have pointed to E coli being a strong suspect in bowel cancer.

The concern surrounds a version that sticks well to the inside of the lower bowel, or colon.  It also contains genes that make a poison which causes the type of damage to DNA usually seen in cancer.

Although we usually think of E coli as causing food poisoning, these strains had been thought to live in the bowel without causing any problems.

However, tests show them to be much more common in bowel cancer patients than in healthy people.

Two-thirds of the 21 samples taken from bowel cancer patients contained the bug, compared to just one in five of those taken from healthy people, the journal Science reports.

Experiments also showed that  mice inoculated with the bug are at very high odds of developing bowel cancer – as long as the E coli carries the poison-making ‘pks’ genes.

Liverpool University’s Dr Barry Campbell, a co-author of the study, said: ‘The research suggests that Ecoli has a much wider involvement in the development of colon cancer than previously thought.

‘It is important to build on these findings to understand why this type of bacteria, containing the pks genes, is present in some people and not in others.’

Professor Jonathan Rhodes said: ‘The bottom line message is that there seems to be a strong association between a type of E coli and the development of colon cancer.

‘And given that this type of E coli is specifically able to damage DNA and inflict the sort of damage you get in a cancer, it is very likely it has a causative role, at least in some patients.’

The scientists, who collaborated with scientists from the University of North Carolina, aren’t sure why some people who have the bug go onto develop cancer and others don’t.

But factors such as genes and diet are probably important.

Professor Rhodes said: ‘The literature on colon cancer taken as a whole suggests that having the right genes, taking exercise, possibly taking an aspirin a day, limiting red meat and eating plenty of leafy green vegetables all have a protective effect.’

If the link is confirmed, it could lead to tests for the rogue form of E coli being included in bowel cancer screening for the elderly.

In the long-term, a vaccine that stops the bug from taking root is also possible, added the professor.

There is a precedent for this – the HPV vaccine which is given to teenage girls wards off infection by the human papilloma virus - the bug behind the majority of cases of cervical cancer.

Henry Scowcroft, of Cancer Research UK, said: ‘This is an intriguing study in mice suggesting that the bacteria in our gut may play a role in the development of bowel cancer. 

‘This would make sense, as we know that being infected with bacteria called H pylori can increase the chances of developing stomach cancer. 

‘But since this study only involved mice and is still at an early stage, it’s not yet clear whether E coli is actually linked to bowel cancer in humans at all, let alone whether this knowledge could be used to help improve things for patients or people at risk.’

Source:

http://www.dailymail.co.uk

A bioinformatician and Bollywood, NOWAY ;-)

Her is some fun facts, If a Bioinformatician starts producing Hindi movies, names will be like this.

 

1. BLAST : Eak khoj
2. Munna Bhai Promoter
3. Gene se Genome tak.
4. Maine BLAST kiya.
5. NCBI wale Data le jayenge 
6. Raju ban gaya Genefinder.
7. Har Ligand jo dock karega.
8. Alignment to hona hi tha.
9. Mera sequence mera base.
10. Markov aapke hai kaun.
11. Algo Banya Apne.
12. MOTIF mil gaya.
13. BLASTana FASTAna.
14. Hamari Sequence aapke pass hai.
15. BLAST To Hona Hi Tha !!
16. Meri Gene Tumhare Paas Hai
17. Aao Database Search Kare
18. Bioinformatician No.1
19. Mera Naam Tool Developer
20. Hum Apke Genome Mein Rehte Hein 
21. Do Sequence Baarah Hit
22. Tera Ligand Chal Gaya
23. Har Din Jo Modeling Karega 
24. Genbank Ke Us Paar
25. Proteomics Koi Khel Nahi
26. Jish Desh Mein Day Hoff Rehta Hai
27. PDB Ek Numbari Structure Dus Numbari
28. GCG Karo Sajana
29. Naukar NCBI Ka
30. 1942 -- A KEGG Story
31. Algorithm Se Program Tak
32. Haan Maine Bhi ClustalW Kiya Hai
33. GeneScan Karke Dekho
34. Alignment Apna Sequence Parayi

Stem cells drive human creativity: Scientists

Cancer Stem Cells

Scientists claim to have discovered a new type of stem cells responsible for creative thinking and memories in humans.

Researchers at The Scripps Research Institute identified a stem cell population that may give birth to neurons which play a key role in abstract thought and creativity.

The finding also paves the way for production of these neurons in culture, a first step towards developing better treatments for cognitive disorders like schizophrenia and autism. 

The cells were found in embryonic mice, where they formed the upper layers of the brain's cerebral cortex. In humans, the same brain region allows abstract thinking, planning for the future and solving problems. Previously it was thought that all cortical neurons - upper and lower layers - arose from the same stem cells, called radial glial cells (RGCs).

The new research shows that the upper layer neurons develop from a distinct population of diverse stem cells. "Advanced functions like consciousness, thought and creativity require quite a lot of different neuronal cell types and a central question has been how all this diversity is produced in the cortex," Dr Santos Franco, member of the US team from the Scripps Research Institute said.

"Our study shows this diversity already exists in the progenitor cells." said Franco. In mammals, the cerebral cortex is built in onion-like layers of varying thickness.

The thinner inside layers host neurons that connect to the brain stem and spinal cord to regulate essential functions such as breathing and movement.

The larger upper layers, close to the brain's outer surface, contain neurons that integrate information from the senses and connect across the two halves of the brain.

Higher thinking functions are seated in the upper layers, which in evolutionary terms are the "newest" parts of the brain.

"The cerebral cortex is the seat of higher brain function, where information gets integrated and where we form memories and consciousness," said the study's senior author Ulrich Mueller. The new research is published in the journal 'Science'.

DNA of unborn baby mapped from just mother's blood, paving way for new genetic disease screening.

Scientists have mapped the complete DNA of an unborn baby - using just the mother's blood.

The breakthrough could allow doctors to test for a range of genetic diseases in future such as cystic fibrosis and Down's syndrome without the need of the father.

It follows a similar study reported last month which required which successfully sequenced a foetus' genome from the mother's blood, along with a sample of saliva from the father.

This time researchers at the University of Stanford in California managed the task using material only found circulating in the mother's blood.

Current techniques used to pick up genetic diseases in unborn babies require invasive sampling, which carries certain risks to the health of the mother and child.

But early diagnosis of such problems can allow doctors to pre-empt whether treatments are needed immediately after a baby is born.

A pregnant woman's plasma, a component of blood, contains a mixture of DNA from the mother and unborn child.

Dr Stephen Quake and colleagues applied a counting method used for detecting diseases such as Down's syndrome to identify individual pieces of parental DNA in chromosomes, or haplotypes, transmitted to the baby.

They can even determine which haplotype came from the father in the absence of additional paternal information, which may be useful if his DNA is not available.

This is a significant advantage when a child's true paternity may not be known - a situation estimated to affect as many as one in ten births in the US alone - or the father may be unavailable or unwilling to provide a sample.

The researchers said their findings published in Nature brings foetal genetic testing one step closer to routine clinical use.

Prof Stephen Quake said: 'We are interested in identifying conditions that can be treated before birth, or immediately after.

'Without such diagnoses, newborns with treatable metabolic or immune system disorders suffer until their symptoms become noticeable and the causes determined.'

As the cost of such technology continues to drop, the researchers believe it will become increasingly common to diagnose genetic diseases within the first three months of pregnancy.

They even showed mapping just the exome, the coding portion of the genome, can provide clinically relevant information.

In the new study they were able to use the whole genome and exome sequences they obtained to determine a fetus had DiGeorge syndrome, a condition caused by a short deletion of chromosome 22. 

Although the exact symptoms and their severity can vary among affected individuals, it is associated with heart and neuromuscular problems, as well as mental impairment.

Affected newborns can have significant feeding difficulties, heart defects and convulsions due to excessively low levels of calcium.

Paediatrician Prof Diana Bianchi, of Tufts University, Massachusetts, who was not involved in the research, said: 'The problem of distinguishing the mother's DNA from the foetus's DNA, especially in the setting where they share the same abnormality, has seriously challenged investigators working in prenatal diagnosis for many years.

'In this paper, Quake's group elegantly shows how sequencing of the exome can show that a foetus has inherited DiGeorge syndrome from its mother.'

For decades, women have undergone procedures known as amniocentesis or chorionic villus sampling in an attempt to learn whether their foetus carries genetic abnormalities.

These tests rely on obtaining cells or tissue from the fetus through a needle inserted in the womb, which can itself lead to miscarriage in about one in two hundred pregnancies. They also detect only a limited number of genetic conditions.

The new technique hinges on the fact pregnant women have DNA from both their cells and those of their unborn child circulating freely in their blood.

In fact, the amount of circulating foetal DNA increases steadily during pregnancy, and late in the final three months can be as high as 30 percent of the total.

Circulating foetal DNA contains genetic material from both the mother and the father. By comparing the relative levels in the mother's blood of regions of maternal and paternal DNA known as haplotypes, the researchers were able to identify fetal DNA and isolate it for sequencing.

The method differs from the University of Washington group's reported in June by inferring the father's genetic contribution, rather than sampling it directly through saliva.

The Stanford team tried its method in two pregnant women, one of whom with DiGeorge syndrome and the other healthy.

Their whole genome and exome sequencing showed the child of the woman with DiGeorge syndrome would also have the disorder.

A similar finding in a real clinical setting would likely prompt doctors to assess the baby's heart health and calcium levels shortly after birth.

Read more: http://www.dailymail.co.uk/health/article-2168804/DNA-unborn-baby-mapped-just-mothers-blood-paving-way-new-genetic-disease-screening.html#ixzz20CnZClph 

The Human Genome Project

WHAT IS THE HUMAN GENOME AND WHY DO WE NEED TO SEQUENCE IT?

The Human Genome project is one of the most ambitious and challenging quests ever undertaken by science. Its goal is to completely map and sequence all of the genetic material that makes us human. When it is done, we will have a new and profoundly powerful tool to help us to unravel the mysteries of how the human body grows and functions.

The cells in our bodies each contain a master program which controls how and when they develop and how they should function. This information is organised in units called genes, which are arrayed, one after the other along long polymers called chromosomes. We have 46 chromosomes, arranged in pairs kept in the nucleus of most cells. The chromosomes are made of deoxyribonucleic acid, or DNA. Chemically, DNA is one of the simplest molecules in the cell. It is comprised of just four building blocks, or residues, strung together in enormously long strings. The residues combine to make our genes, and our genes string together to make our chromosomes.

The sequence of the building blocks is not random. It is inherited from our parents who in turn inherited from their parents. The sequence has been moulded over many aeons of environmental influences and directs our responses to the environmental stimuli we face today. To some extent our genome dictates our future. It may hold versions of genes that predispose us to certain illnesses, or conversely to good health and perhaps longevity. Even the basis of our personality may owe some debt to our genome.

GENES ENCODE PROTEINS, THE "WORKERS" OF THE CELL

The order of the residues in our genes encodes the ultimate structure of the proteins in a cell. It also controls when particular proteins will be produced. All of these control functions are themselves switched on or off by the action of yet more proteins. A knowledge of these proteins, their physical structure and how and when they are turned on or off can help biologists decipher many of the secrets of cell development and regulation.

This in turn would lead to a better understanding of how our bodies function normally and therefore a better comprehension of the processes that lead to disease. It is also thought, in as yet a not completely crystallized manner, that new biological tools will spring from a knowledge of the sequence of the human genome. These tools would rely heavily on computer manipulation of the huge amounts of data emanating from the human genome project.

THE GENOME PROJECT EMPLOYS A "DIVIDE AND CONQUER" STRATEGY.

The human genome is comprised of about three billion building-blocks or residues. This is a lot of information. If each residue was the equivalent of one byte of computer memory, the sequence of the genome from just one person would fill a respectably large hard disk.

The sequence of the residues is not easy to work out. The order can only be generated after millions of chemical reactions which allow us to deduce the sequence. The laboratory methods for doing this are very small scale and still carried out with technology similar to that described by the English scientist, Fred Sanger in the 1970's.

The ideal approach would be to start sequencing at the beginning of a chromosome and stop once we reached the other end. Unfortunately this not possible. With existing technology, only strings of around 1000 residues in length can be sequenced at a time. This means that many such strings must be sequenced and then the final sequence assembled from millions of such smaller sequences. This task is akin to taking 10 copies of the complete Oxford English Dictionary, all 12 volumes, ripping each page into 300,000 minute pieces, placing all of the pieces in to a large barrel, thoroughly mixing them and then trying to put all the pieces back together again.

This is near impossible. However if we did it one page at a time, the task can been made much easier. And different teams can work on different pages at the same time, because the page numbers act as a type of scaffold which tells us where each page belongs.

A similar approach is being used to sequence the human genome. A scaffold has been built on which to place these millions of smaller sequences and to act as the template for breaking the huge task into many smaller tasks. This scaffold is the physical map of the chromosomes.

THE PHYSICAL MAP OF THE GENOME PROVIDES THE SCAFFOLD FOR THE SEQUENCING PROJECT.

The process of building the scaffold for the human genome sequencing effort has almost been completed. This process is called physical mapping. It involves making large scale maps of landmarks that lie along the landscape of the chromosomal DNA. The landmarks that have been used are short pieces of DNA that have already been sequenced. These sequences are then used as tags for their chromosomal environ, a little like one would use the name of a town on a map.

The order of these tags relative to all other tags on a chromosome is then deduced by another series of biochemical tricks. These tricks involve smashing chromosomes into small pieces, finding out which of our landmarks belong to which chromosomal fragment and then trying to reassemble the whole into some semblance of its former self. During this process, the order of the landmarks can be deduced. The whole process is analogous to taking several copies of an RACV strip-map of the Hume Highway connecting Sydney and Melbourne, cutting this into many pieces and then trying to reconstruct the original map from the fragments.

The best way to do this would be to find pieces of map containing a given town and overlapping these pieces. Let us take all pieces with Wangaratta, for example. Some of these pieces will also show Albury and others may well show Benalla. From this information it is possible to deduce the relative order of these three towns. Wangaratta must lie between Albury and Benalla. The orientation is not known yet, not is their actual proximity to either Sydney or Melbourne. As this algorithm is repeated over and over again, the original strip map will be reconstructed and the order of all towns along the Hume Highway can be deduced.

The same approach is used to map our chromosomal landmarks. These maps then become the basis for the scaffolding onto which will be pinned all the small pieces of sequenced DNA. It is no longer a biologic blind man's bluff, but an orderly progression of many labs performing small parts of this huge task and joining them together to form a whole based on a prior knowledge of the map of the human genome.

The way this works is analogous to our Oxford English Dictionary example, the correspondence to the page of the dictionary is a cloned, isolated fragment of genomic DNA. These fragments are some 100,000 residues in length, their position in the genome is known because their location on the scaffold has been found. These small clones are then fragmented into even smaller pieces that are sequenced. These smaller pieces of sequence can then be assembled to deduce the sequence of the original 100,000 residue genomic fragment. The sequence of the chromosome is then in turn deduced by overlapping the sequence from adjacent fragments.

PARTIAL SEQUENCING OF MANY GENES

Genes are the important functional units of our genome. There are somewhere between 60,000 and 100,000 genes in our genome, the actual number is not yet known (one benefit to be gained from the sequence of the entire genome). While the sequence of the genome will allow biologists to identify most of the genes, many people have been unwilling to wait the 5-7 years that it will take to sequence all our DNA. They have taken a shortcut.

Genes do not make protein directly. First a copy is made in another nucleic acid called ribonucleic acid, or RNA. This RNA is called messenger RNA because it takes the information encoded by the gene from its home in the cell nucleus to the machinery that translates it into protein in the cell cytoplasm. Messenger RNA can be captured and tamed by molecular biologists. They have been doing it for decades. It is a process called "cloning" and does not involve sheep.

Each molecule of messenger RNA is isolated into a single species of bacteria but now as a DNA molecule where it can be purified away from other molecules and amplified simply by letting the bacterium do what it does best, reproduce. These amplified, cloned copies of the messenger RNA can then be purified from the bacterium and the nucleotide sequence deduced. Part of the human genome project has been doing this on a grand scale and there are now several million partial RNA sequences available in databases.

There is a problem with this data as it has mostly been produced by a small number of companies that have seen a profit in the sale of such data. They therefore do not release their data to the general biological community. This has been partly overcome by Merck, a large multinational drug company which has been funding the Washington University Sequencing group to replicate this work and they have deposited some 600,000 partial messenger RNA sequences in public databases.

This is many times the number of actual genes but as there is no real way of telling how many genes there are, and, many genes produce vastly different levels of messenger RNA in various different cell types. This approach sequences the most common RNAs many times so as to be certain of seeing some of the more rare RNAs a small number of times. These RNA sequences initially came from genes, they are therefore "tags" for genes. Once sequenced they can also function as our biochemical signposts of the genome and can be integrated into the physical maps like the landmarks described above. The end result of this is that we now have many of the known genes placed onto the "scaffold" of the genome. This is important for geneticists who are looking for genes for diseases.

WHAT WILL HAPPEN WHEN WE HAVE THE SEQUENCE OF THE HUMAN GENOME?

This is what we thought in 1997 when this article was written: The sequencing of the human genome should be complete within five or six years. When it is complete, the availability of this immense amount of knowledge will spawn new areas of biology. The interface between computer science, statistics and biology will need to be greatly enhanced to cope with this amount of data. With a list of all genes in the cell and the knowledge of when these are turned on and off, computer scientists can begin to start modeling biological processes inside our cells. Biologists will be able to use the information in new applications. At the moment there is a small glimpse of how this will happen. A company in the United States, Affymetrix, has designed a silicon chip that has DNA synthesised onto its surface. This DNA can represent many hundreds of thousands of genes and can be used by biologists to test any cell or tissue about the genes that are turned on at a given time. Undoubtedly many more clever ideas will turn the information encoded within the genome into techniques that will tell us more about biology.

This article was written in 1997 by Dr. Simon who was a Wellcome Senior Australian Science fellow at the Walter and Eliza Hall Institute of Medical research.

Drug could attack ‘the root’ of cancer cells: study

The findings, published in the journal Cell, have yet to be proven in humans and clinical trials may reveal thioridazine is not effective at treating cancer. 

But the initial discovery is creating excitement among cancer experts who have been looking for ways to target cancer stem cells. 

Until the 1990s, scientists didn’t know such a thing as cancer stem cells existed. They assumed cancer arose from ordinary cells that have somehow mutated. 

But some scientists turned their attention to stem cells – which have the ability to become any tissue type and multiply infinitely. They postulated that abnormal stem cells are the real culprits behind the growth of many tumours. 

Researchers, including cancer stem cell pioneer and Toronto scientist John Dick, identified their presence in leukemia, breast cancer, brain cancer, lung cancer and other types of cancers. 

Those findings suggested that cancer stem cells are a subset of regular cancer cells that act as the “starter” agents that can cause tumours to grow and cancerous cells to propagate. Scientists believe they help explain why some patients don’t respond to chemotherapy or radiation; those treatments kill cancer cells, but don’t get to the source of the problem. 

Mick Bhatia, lead author of the new study and scientific director of the Stem Cell and Cancer Research Institute at McMaster University in Hamilton, Ont., likened it to cutting dandelions. 

“Unless you eliminate the root, it’s just going to come back,” he said. 

Dr. Bhatia and his colleagues decided to look for treatments that could target cancer stem cells. They developed a system to test dozens of drugs on cancer stem cells and normal, healthy cells. 

It was an extremely challenging task because it required the research team to figure out a way to properly isolate cancer stem cells and healthy stem cells and have them grow outside the body. They found that thioridazine worked at killing the cancer stem cells in leukemia and some types of breast cancer, but left the healthy cells unharmed. The researchers then took cancerous tissue from humans and transplanted it into mice. Once again, thioridazine was effective at targeting the cancer stem cells. 

The reason the drug seems to work is that it affects the dopamine receptor in cancer stem cells. Most cells don’t have a dopamine receptor, and Dr. Bhatia said it was surprising to find it in cancer stem cells. It’s possible that cancer stem cells evolved to develop a dopamine receptor pathway, allowing them to propagate without the body being able to stop them. 

Now, the next step is to test the drug in human clinical trials to determine how well it works. Researchers hope to test the drug on cancer patients who have not responded to traditional treatments such as standard chemotherapy. If it turns out to work, thioridazine might be used in a wider group of cancer patients. 

“If they do respond and we can increase quality of life and potentially even get rid of the cancer, I think it’s the best thing anyone can hope for,” Dr. Bhatia said. 

The research team will also continue to test more compounds – Dr. Bhatia hopes to look at thousands – to find more that are effective at fighting cancer stem cells. He said the research team has already identified about a dozen other compounds that could also attack cancer stem cells and leave healthy cells unharmed. 

Health Canada ordered thioridazine off the market in Canada in 2005 following reports it could increase the risk of rare, but potentially fatal, changes in heart rhythm. 

Dr. Bhatia noted that heart problems typically occur in patients taking thioridazine for a prolonged period; cancer patients would be on it for only a matter of days or weeks. But it’s important to study how the drug works in cancer patients, he said, in order to determine what side effects may occur.

Studying the human genome - A complete set of human genes

Introduction: Transcript

Studying the human genome - the complete set of human genes - is a way of studying fundamental details about ourselves. The three billion letters of the human genome are written using the four-letter alphabet of DNA. The DNA is divided among 23 pairs of chromosomes that are found in each of the trillions of cells in our bodies. In 2003, The Human Genome Project produced a complete representative sequence of the human genome. Of course, people are not identical, and DNA sequences do differ subtly between individuals. Currently, a number of separate projects are charting sequence variations found in human populations.

The representative sequence is a composite from several people who donated blood samples. Originally, close to 100 people volunteered to give a sample of their blood. Each person provided their informed consent, affirming that they agreed to the study of their DNA. No names were attached to the blood samples and ultimately scientists used only a few of them. These measures ensured that the DNA sequences remained anonymous; not even the donors knew whether their samples were actually used or not.

The main goal of The Human Genome Project was to read, letter by letter, the three billion bases of human DNA. Before starting to sequence the human genome, scientists built maps of the chromosomes and developed and refined techniques for analyzing DNA. With the tools in place, project scientists began large-scale DNA sequencing in 1999. In just one year, they had amassed sequence data covering more than 80 percent of the genome.

The human genome is a massive text. If the three billion letters (or bases) of the genome were printed in telephone books, they would require a stack of books nearly as tall as the Washington monument.

To accurately determine the sequence of every base in the genome, scientists needed to read the three billion bases not just once, but at least six to ten times. Individual sequencing reactions could only reveal the order of a few hundred bases of DNA at a time - amounting to a fraction of a page. This meant that to place in order all of the DNA bases, it was necessary to produce many thousands of overlapping segments of DNA sequence.

Mapping: Transcript

To begin the project, researchers built maps of the human genome. They identified thousands of DNA sequence landmarks that helped them navigate across the chromosomes.

Developing genome maps was necessary preparation for DNA sequencing. These same maps also served to orient geneticists who were hunting for disease genes.

With enough landmarks in place, project scientists created "libraries" of clones that spanned the genome. Each clone contained a manageably small fragment of human DNA that was stored in bacteria. Scientists used the landmarks to tell them what part of the human genome each fragment came from.

This clone-by-clone approach made it possible to double check the location of each DNA sequence. It also allowed participating laboratories from around the world to carve up the genome and coordinate their work.

Building Libraries: Transcript

Clone libraries offered the same advantage of real libraries: orderly access to information. In most clone libraries, the DNA fragments were stored in E. Coli. These are bacteria that normally live in our intestines. Each E. Coli cell stored a single segment of human DNA and represented a single book of the library. Clone libraries allowed each human fragment to be tracked and easily copied.

Subclones: Transcript

The clone libraries were prepared using bacterial artificial chromosomes, or BACs. Each BAC clone contained 100,000 to 200,000 bases of DNA sequence. The large BAC clones were used to establish the order of the DNA sequences. To sequence the DNA, smaller-sized clones were needed. Project scientists cut the large BAC clones into smaller fragments of about 2,000 bases. These smaller fragments were typically stored in viruses called phage that can 

infectE. coli cells.

E. Coli to Store and Copy DNA: Transcript

E. coli cells containing fragments of human DNA, or any other type of DNA, can be stored in freezers indefinitely. When scientists need to retrieve DNA from the library, they simply revive the cells by bringing them back up to 37 degrees Centigrade - gut temperature.

The E. coli cells act as copiers, producing many copies of the human DNA sequence that they contain. To prepare to sequence DNA, a clone of cells containing the same bit of human DNA is released into a rich, warm broth. The cells are shaken vigorously to provide them with air. This causes them to divide rapidly - about once every half hour. After incubating for just a single night, one third of a teaspoon of broth contains billions of E. coli cells and so, billions of copies of the particular fragment of human DNA they contained.

 

Preparing DNA for Sequencing Reactions: Transcript

The next morning, the E. coli cells are broken open to release their DNA. The human DNA is separated from the cell debris and washed clean.

Now there are enough copies of the human DNA fragment to set up a sequencing reaction.

 

Sequencing Reactions: Transcript

A DNA sequencing reaction includes four main ingredients, "Template" DNA copied by the E. coli; free bases, the building blocks of DNA that come in 4 types; short pieces of DNA called "primers"; and DNA polymerase, the enzyme that copies DNA.

The chemical reaction that makes DNA in a test tube is similar to what happens in a living cell: both rely on DNA polymerase and, in both cases, DNA strands have a head end, which is called the 5' end, and a tail end, which is called the 3' end. A DNA strand can grow only from its 3' end.

Making DNA in cells and sequencing DNA in test tubes both depend on complementary base pairing. The building blocks on opposite strands of DNA pair specifically - a C always pairs with a G, and an A always pairs with a T.

The primer sequence binds to its complementary sequence on the template DNA.

Free bases that match the template sequence can attach to the new strand's growing (3') end.

Among the free bases in the solution are a few that have a fluorescent dye attached to them. When a dye-bearing base attaches to the growing strand, it stops the new DNA strand from growing any further. A different colored dye is 

attached to each of the four kinds of bases.

Products of Sequencing Reactions: Transcript

A completed sequencing reaction contains an array of colored DNA fragments. The shortest fragments correspond to the length of the primer plus one dye-colored base. The longest fragments are usually between 500 and 800 bases long, depending on when the sequencing reaction ran out of steam.

The products of sequencing reactions are fed into an automated sequencing machine. Automated sequencers have become increasingly sophisticated during the past decade. They can run more samples, process them more quickly, and are easier to operate.

 

Separating the Sequencing Products: Transcript

The DNA molecules produced during the sequencing reaction are separated from each other by a process called electrophoresis. DNA molecules are negatively charged. The sequencing machine sets up an electric field; all the DNA moves through a porous gel toward the positive electrode. The gel acts like a sieve; shorter DNA fragments move more quickly through the holes of the gel than do larger DNA fragments.

 

Reading the Sequencing Products: Transcript

As each DNA fragment reaches the end of the gel, a laser excites its fluorescent dye. A camera detects the color of the emitted light and passes that information to a computer. One by one, the machine records the colors of the DNA fragments that pass through the gel.

A single sequencing reaction can reveal the order of several hundred DNA bases.

Assembling the Results: Transcript

A computer program integrates the data from individual sequencing reactions. It can spot where DNA fragments overlap and order them as they originally were on the chromosome.

Many overlapping sequences reads are needed to generate the uninterrupted sequence of the original stretch of DNA. During the Human Genome Project, every base pair of DNA was sequenced an average of nine times. Some stretches of DNA were easy to read and needed to be sequenced little less often, while other stretches were more difficult to read and had to be sequenced more often.

During the Human Genome Project scientists ran more than 50 million sequencing reactions. Some 2000 scientists from more than two dozen labs around the world, worked on the project.

Working Draft Sequence: Transcript

Whenever a stretch of DNA that spanned 2,000 or more bases was assembled, it was placed into public databases within 24 hours. Anyone with access to the Internet could see and analyze the sequence data.

After sequencing the 3 billion letters in the human genome an average of nine times, the Human Genome Project had released DNA sequence for 99 percent of the genome. This finished sequence was 99.99 percent accurate. The project had completed all of its goals ahead of schedule and under budget. 

Conclusion: Transcript

The Human Genome Project also produced other advances, not expected to be accomplished until much later. These included an advanced draft of the mouse genome and an initial draft of the rat genome.

Medical researchers did not wait to use data from the Human Genome Project. When the project began in 1990, fewer than 100 human disease genes had been identified. At the project's conclusion in 2003, the number of identified disease genes had risen to more than 1,400.

The Human Genome Project focused on the DNA sequence of an individual. The next step was to analyze DNA sequences from different populations. This catalog of human genetic variation was called the HapMap. Completed in 2005, the HapMap used single nucleotide polymorphisms called SNPs to identify large blocks of DNA sequence called haplotypes that tend to be inherited together. To use the data, researchers compare haplotypes between people with and without a disease. Haplotypes shared by people with the disease are then examined in detail to look for associated genes. Already, scientists have used its data to identify a gene associated with age-related macular degeneration, a disease responsible for blindness among the elderly. It is expected that the HapMap will play an important role in identifying many more disease genes in the future.

Researchers make alternatives to DNA and RNA

 

DNA and RNA molecules are the basis for all life on Earth, but they don't necessarily have to be the basis for all life everywhere, scientists have shown.

Researchers at the Medical Research Council in Cambridge, England, demonstrated that six synthetic molecules that are similar to — but not exactly like — DNA and RNA have the potential to exhibit "hallmarks of life" such as storing genetic information, passing it along and undergoing evolution. The man-made molecules are called "XNAs."

"DNA and RNA aren't the only answers," said Vitor Pinheiro, the postdoctoral researcher who led the study, which was published this week in the journal Science

It could also shed light on how life emerged on Earth, and on what living things might look like if they exist beyond our planet.

"Everyone wants to know what aliens would use for DNA," said Steven Benner, a biochemist at the Foundation for Applied Molecular Evolution in Gainesville, Fla., who has synthesized artificial DNA but was not involved in the new study. "Lab experiments tell you about the possibilities in the universe."

In natural life on Earth, the nucleic acids DNA and RNA are formed by sugar molecules — deoxyribose in DNA and ribose in RNA — that link to phosphates to form a backbone onto which the four nucleotide bases attach to form a chain.

Genetic information is stored in the order in which the bases — known by the chemical letters A, C, G and T — are strung along the chain.

DNA forms the template that holds all the information needed to create an organism. RNA takes that information and translates it into proteins, the basic building blocks of biology. (Viruses, which some scientists consider to be a life form, use only RNA.)

To build alternatives to DNA and RNA, scientists often fiddle with one component or another and see how the changes affect genetic function.

Pinheiro and his team worked with six molecules that use different sugars or sugar-like groups in place of deoxyribose and ribose. Something called CeNA, for instance, employs a ring-shaped structure called cyclohexene. Another variant called HNA used a group of atoms called anhydrohexitol.

Collectively, the scientists refer to the group as XNAs. The X stands for "xeno-," the Greek prefix meaning "strange," "foreign" or "alien."

The researchers started with molecules that were already synthesized in other labs or sold by companies. The new part was demonstrating that the molecules were capable of passing along their genetic code. To do this, they had to engineer a group of enzymes that could read information stored in XNAs and write it onto DNA. After making make a bunch of copies of that DNA, they then used the enzymes to write those copies back to XNAs.

The group then showed that HNA was capable of evolution by making lots of copies of it, selecting out the ones with desired characteristics — in this case, the ability to bind to certain proteins — creating more copies of those, selecting out the best ones again, and so on.

"It's domesticated breeding of molecules," said Dr. Gerald Joyce, a researcher at the Scripps Research Institute in La Jolla, Calif., who was not involved in the study.

Joyce, who wrote an editorial for Science about the research, said the techniques Pinheiro and his colleagues used could some day make it easier for scientists to build nucleic acid-based medicines and diagnostic tests.

Today such products rely on RNA or DNA — both of which degrade quickly when exposed to enzymes called nucleases.

"If you take RNA and put it in a dish and breathe heavy, the RNA is a goner," Joyce said.

With an XNA alternative, scientists could produce tests or therapies that are impervious to nucleases, potentially speeding the drug development process, Pinheiro said.

As for XNAs' possible role in the evolution of life, Joyce said that scientists believe life on Earth probably was RNA-based before it became DNA-based — and could have been based on an even simpler XNA, such as TNA (made with a sugar called threose), before that.

"Some molecules developed the ability to replicate their own information, then we were off to the Darwinian races," he said.