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 

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.

Transgenic Animals Are Animals Carrying Foreign Genes

Experimental advances in gene transfer techniques have made it possible to introduce genes into animals by transfection. Transfection is defined as the uptake or injection of plasmid DNA into recipient cells. Animals that have acquired new genetic information as a consequence of the introduction of foreign genes are termed transgenic. Plasmids carrying the gene of interest are injected into the nucleus of an oocyte or fertilized egg, and the egg is then implanted into a receptive female. The technique has been perfected for mice (see figure). In a small number of cases—10% or so—the mice that develop from the injected eggs carry the transfected gene integrated into a single chromosomal site. The gene is subsequently inherited by the progeny of the transfected animal as if it were a normal gene. Expression of the donor gene in the transgenic animals is variable because the gene is randomly integrated into the host genome and gene expression is often influenced by chromosomal location. Nevertheless, transfection of animals has produced some startling results, as in the case of the transfection of mice with the gene encoding the rat growth hormone (rGH). The transgenic mice grew to nearly twice the normal size. Growth hormone levels in these animals were several hundred times greater than normal. Similar results were obtained in transgenic mice transfected with the human growth hormone (hGH) gene. The biotechnology of transfection has been extended to farm animals, and transgenic chickens, cows, pigs, rabbits, sheep, and even fish have been produced. The first animal cloned from an adult cell, a sheep named Dolly, represented a milestone in cloning technology. Subsequent accomplishments include incorporation of the human gene encoding blood coagulation factor IX into sheep. Fetal sheep fibroblast cells were transfected with the human factor IX gene, nuclei from the transfected cells were transferred into sheep oocytes lacking nuclei, and these transgenic oocytes were placed in the uterus of receptive female sheep, which subsequently gave birth to transgenic lambs. The introduced factor IX transgene was specifically designed so that factor IX protein, a medically useful product for the treatment of hemophiliacs, would be expressed in the milk of the transgenic sheep. Similar successes in cows, which produce much more milk, has brought the potential for commercial production of virtually any protein into the realm of reality. Transfection technology also holds promise as a mechanism for “gene therapy” by replacing defective genes in animals with functional genes. Problems concerning delivery, integration and regulation of the transfected gene, including its appropriate expression in the right cells at the proper time during development and growth of the organism, must be brought under control before gene therapy becomes commonplace in humans.

                                       

Why Does DNA Contain Thymine and Not Uracil?

Given that both uracil and thymine base-pair with adenine, why does RNA contain uracil and DNA contain thymine? Scientists now believe that RNA was the original hereditary molecule, and that DNA developed later. If we compare the structure of uracil and thymine, the only difference is the presence of a methyl group at C-5 of thymine. This group is not on the side of the molecule involved in base pairing. Because carbon sources and energy are required to methylate a molecule, there must be a reason for DNA developing with a base that does the same thing as uracil but that requires more energy to produce. The answer is that thymine helps guarantee replication fidelity. One of the most common spontaneous mutations of bases is the natural deamination of cytosine.     

At any moment, a small but finite number of cytosines lose their amino groups to become uracil. Imagine that during replication, a C–G base pair separates. If at that moment the C deaminates to U, it would tend to base-pair to A instead of to G. If U were a natural base in DNA, the DNA polymerases would just line up an adenine across from the uracil, and there would be no way to know that the uracil was a mistake. This would lead to a much higher level of mutation during replication. Because uracil is an unnatural base in DNA, DNA polymerases can recognize it as a mistake and can replace it. Thus, the incorporation of thymine into DNA, though energetically more costly, helps ensure that the DNA is replicated faithfully.