Advancement in Stem Cell Alternative

Scientists reported yesterday that they have overcome a major obstacle to using a promising alternative to embryonic stem cells, bolstering prospects for bypassing the political and ethical tempest that has embroiled hopes for a new generation of medical treatments.

The researchers said they found a safe way to coax adult cells to regress into an embryonic state, alleviating what had been the most worrisome uncertainty about developing the cells into potential cures. "We have removed a major roadblock for translating this into a clinical setting," said Konrad Hochedlinger, a Harvard University stem cell researcher whose research was published online yesterday by the journal Science. "I think it's an important advance."

The development is the latest in the rapidly advancing and politically charged field of stem cell research. Embryonic stem cells are believed capable of becoming any type of cell in the body. Researchers hope to eventually use them to create replacement tissue and body parts tailored to individual patients. But the work has run into moral objections because the cells were originally obtained by destroying early-stage embryos.

Scientists last year shook up the scientific and political landscape by discovering how to manipulate the genes of adult cells to convert them into the equivalent of embryonic cells -- entities dubbed "induced pluripotent stem cells," or iPS cells -- which could then be transformed into any type of cell in the body. Subsequent work has found that the cells can alleviate symptoms of Parkinson's disease and sickle cell anemia in mice.

But the first iPS cells were created by ferrying four genes into the DNA of adult cells using retroviruses, which can cause cancer in animals. There was also concern because the viruses integrated their genes into the cells' DNA. In the new work, Hochedlinger and his colleagues used a different type of virus, known as an adenovirus, to carry the same four transformative genes into the DNA of mouse skin and liver cells. The adenovirus does not integrate its genes into a cell's DNA and therefore is believed to be harmless.

"The adenovirus will infect the cells but then will clear themselves from the cells. After a few cell divisions there are no traces of the virus in the cell," Hochedlinger said. "You can't tell the virus was ever there."

Rudolf Jaenisch, a professor of biology at the Whitehead Institute in Cambridge, Mass., praised the work but noted that the process is 100 times less efficient than using retroviruses. Hochedlinger said his team is working to streamline the conversion, perhaps by supplementing the introduced genes with chemicals that flip biological switches. Many researchers suspect they will eventually find ways to transform cells much more cleanly without transferring genes at all.

Critics of embryonic stem cell research said the work offered yet more evidence that research on embryonic cells is unnecessary. Last month, another Harvard team announced that it had converted adult cells directly into another type of adult cell, possibly offering another less contentious alternative.

But Hochedlinger and others said it is important to continue to work on embryonic stem cells as well as adult stem cells and reprogrammed adult cells, because it remains far from clear which will eventually prove most effective.
"We just don't know yet which ones will be useful for which types of treatment," said Mark A. Kay, a gene therapy researcher at Stanford University.

Source: Scientific American

Aging May Be Controlled by Brake and Accelerator Genes

Can we tweak certain genes to stave off the aging process—or, conversely, to speed it up? New research indicates that it may one day be possible. Scientists have discovered genetic switches in roundworms (Caenorhabditis elegans)—whose genetic makeup is remarkably similar to that of humans—that apparently cause the spineless critters to grow old when flicked on but, when off, may extend their lives.

"This is a new and potentially powerful circuit that has just been discovered," says Brown University biologist Marc Tatar, who was not involved in the study. "The take-home message is that aging can be slowed and managed by manipulating signaling circuits within cells.

"The new finding challenges the prevailing theory of aging, which is that our bodies wear out, or "rust," in much the same way as cars and other machines due to damage inflicted on our cellular DNA (genetic material) by factors such as smoking, disease, the sun's ultraviolet rays and chemically reactive molecules called free radicals, which are produced when our cells make energy. It suggests instead that a combination of factors is at play—that in addition to rusting, there are also certain genes that may carry instructions to start the aging process.

Stanford University School of Medicine biologist Stuart Kim, who co-authored the new study published in the journal Cell, says the results may explain different why species have different life spans: For example, worms can live up to two weeks, whereas humans stick around for an average of 66 years (78 in the U.S.) and tortoises can lumber along for 200 years. His hypothesis is that there are certain master genes tasked with directing and maintaining body functions. These genes make proteins called "transcription factors" that influence the activity of other genes by switching them on or off. According to Kim, these master genes are programmed to shift gears—that is to make either more or less of these transcription factors—which in turn changes the function of their charges, jump-starting the aging process.

Kim believes that it is possible to slow—or even reverse—senescence if scientists can figure out how to keep the master genes from changing course. "What we found was this developmental regulatory system (that keeps worms young) had become unbalanced in old age," Kim says.Kim studied the activity of all 20,000 genes in worms from the time they were about three days old (about 20 years in a human lifetime) until they were 18 days old (80 to 90 human years), which is when most of them died.

As the worms aged, researchers observed changes in the level of activity of more than 1,200 genes, with some turning on and others switching off. Most of these genes are controlled by a transcription factor made by the gene elt3, which is known to be involved in the development of roundworms' skin and intestines.Over time, elt3 began to shut down and its transcription factor production waned. According to Kim, elt3's shift was caused by the increased activity of two other genes: elt5 and elt6, also involved in skin and intestine development.

Kim likens elt5 and elt6 to brake pedals and elt3 to the accelerator in a car. As the brakes are applied and exert greater force, the car decelerates—and several genes that depend on the gas pedal for cues on how to behave stop functioning properly.When Kim and his team blocked both elt5 and elt6 in adult worms, they were able to keep elt3 from turning off in the animals. As a result, the worms lived up to a week longer than normal.

Kim believes the newly discovered process, along with DNA damage are responsible for aging, noting that the worms died when exposed to high levels of radiation, although there was no change in the elt genes or those that control them.

So the best way to prevent avoid it? Avoid factors known to cause DNA damage, manipulate the so-called master genes—and come up with a way to repair already hobbled cells. "It's partly rust and it's partly the gas pedal and brakes," he says, referring to the condition of a 10-year old car that has seen better days. "If I wanted to fix it up so I could keep driving it, I'd want to wax it to prevent rust and then I'd fix the gas pedal and the brakes, as well."

Source: Scientific American

HIV Replication 3D Medical Animation

microRNA Discovery

Scientists revealed factors involved in miRNA degradation in Arabidopsis

microRNAs (miRNAs) are now known to play regulatory functions in numerous developmental and metabolic processes in plants and animals. The biogenesis of miRNA is also well-established. But until now factors involved in miRNA degradation remain unknown. Ramachandran et al. now report (Science Vol. 321. no. 5895, pp. 1490 – 1492, 2008) a factor that is involved in the miRNA degradation in Arabidopsis plants (small flowering plants related to cabbage and mustard). Ramachandran et al. from University of California Riverside have shown that that a family of exoribonucleases (an exoribonuclease is an exonuclease ribonuclease, which are enzymes that degrade RNA by removing terminal nucleotides from either the 5' end or 3' end of the RNA molecule) encoded by the SMALL RNA DEGRADING NUCLEASE (SDN) genes degrades mature miRNAs in Arabidopsis. SDN1 acts specifically on single-stranded miRNAs in vitro. Ramachandran et al. also showed that knockdown of three SDN genes lead to an elevated miRNA levels and pleiotropic (pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits) developmental defects in Arabidopsis. This piece of information provided by this study is expected to shed more light in the understanding of pathways and factors involved in the degradation of miRNA in other plants and animals.

Week's Bioinformatic Term:

Contig

1. The term comes from a shortening of the word ‘contiguous’ and has several uses.
2. More often, the term ‘contig’ is used to refer to the product of a shotgun sequencing* which represents overlapping sequences of genes derived from single genome.
3. A ‘contig’ may refer to a map showing placement of a set of clones that completely, contiguously cover some segment of DNA in which you are interested. This is also called the ‘minimal tiling path’.

*In brief, Shotgun sequencing involves cloning of DNA fragments randomly generated from a genome. The DNA fragments are then sequenced and assembled to yield a continuous sequence without gaps.

Week's Molecular Biology Term:

Fosmid

1. Fosmids are similar to cosmids but utilizes the bacterial F-factor (The Fertility factor or F factor is a bacterial DNA sequence that allows a bacterium to produce a sex pilus necessary for conjugation).
2. Fosmid is capable of containing much larger pieces of DNA, up to 50 kilobase (kb) compared to about 10 kb in a plasmid vector.
3. Unlike plasmid vectors, E.coli can only ever contain one fosmid and therefore yields a much lower copy number when cloning. But low copy number offers higher stability than comparable high copy number cosmids.
4. Fosmid system may be useful for constructing stable libraries from complex genomes.

Micro RNA and Gene Regulation

Ribonucleic acid (RNA) is a polymer of nucleotides in which each nucleotide unit consists of a ribose sugar, a nitrogenous base and a phosphate group. There are four types of nitrogenous bases namely, Adenine (A), Thymine (T), Guanine (G) and Cytosine (C). The base composition of RNA is similar to the DNA but not identical. The Thymine base present in DNA is replaced by Uracil in RNA.Unlike DNA, RNA in the cell is single stranded and do not exist as a helical structure. The genetic information from DNA is first transcribed (copied) to RNA strand and then the RNA strand is used as a template for protein translation. Of many types of RNA, some are involved in protein translation while others function as regulatory element. Micro RNA (miRNA) is one of the recently identified RNA elements involved in gene regulation.

miRNA is a short (19-23 nucleotides), single stranded, non-coding RNA (not translated into protein) which is known to be present only in eukaryotic organisms (organisms whose nucleus is separated from cytoplasm by nuclear membrane), till date. miRNAs are transcribed as part of a long RNA molecule called primary miRNA (pre-miRNA). This pre-miRNA is double stranded and by the action of ribonuclease (dicer) is converted into single stranded mature miRNA. After maturation each miRNA is bound by a complex (which is similar to the RNA induced silencing complex or RISC). Recently, it has been identified that miRNA down regulate (lower or stop) the expression of many genes. A very little is known on the miRNA based gene expression. miRNA is known to mediate gene regulation at translational level. During translation RISC bound miRNA binds to its specific mRNA sequence through sequence complementarity. Binding of miRNA to mRNA resulted in translational inhibition and mRNA degradation. The choice between translational inhibition and mRNA destruction is governed by the degree of mismatch between the miRNA and its target mRNA, with degradation being the outcome for best-matched targets. As miRNAs can inhibit the translation of imperfectly matched targets, it is possible that each miRNA may target multiple genes, and that several miRNAs may regulate a given target.


At present miRNA is of immense scientific interest for its regulatory function, especially in the field of cancer cell research. It is well-known that cell multiplication in the body is controlled by certain genes and any disability of these genes leads to the uncontrolled proliferation of cells which finally resulted in tumor or cancer. Therefore, it is not surprising to assume that miRNA might play a key role in cancer development. One cluster of miRNAs, known as mir-17–92, has been shown to be a potential oncogene in an in vivo model of human B-cell lymphoma. In another study (He et al. and O’Donnell et al.), it has been shown that a cluster of miRNAs on human chromosome 13 are regulated by c-Myc (a cancer promoting gene) gene and over expression of 6 miRNAs are linked to increased expression of c-Myc that results in cancer. Lu et al. has shown that expression of miRNA varies dramatically across tumour types and defines the cancer type (such as gastric, colon and liver cancer) more accurately than mRNA expression profile. This allowed scientists to use miRNA as diagnosis and therapeutic basis. The miRNA research is expected to provide invaluable information in the future therapeutics development for many diseases including cancer.