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Mar 5, 2012

Int'l study finds new genetic loci associated with menopause onset

WASHINGTON, Jan. 23 -- An international team of researchers from the Boston University and other institutions has uncovered 13 genetic loci, linked to immune function and DNA repair, that are factors in the age of onset of menopause.

Menopause -- the cessation of reproductive function of the ovaries -- is a major hormonal change that affects most women when they are in their early 50s. Most prior studies of the age of onset of menopause have focused on genes from the estrogen-production pathway or vascular components.

In the new study, published online Jan. 22 in Nature Genetics, the research team identified 13 novel loci associated with menopause onset, while confirming four previously established loci. Most of the 17 loci are associated with genes related to DNA damage repair or auto-immune disease; others are linked to hormonal regulation.

The authors said they expected further research to identify "a substantial number of additional common variants" that impact age of menopause, and that many of them will be located in genes identified in their study. The study examined more than 50,000 women of European descent who had experienced menopause between the ages of 40 and 60.

The research team noted that a large-scale study of menopause onset in African-American women is underway, which will help to determine whether the genetic variations that affect menopause onset in African-American women are similar or substantially different for women of primarily European descent.

Colourful coral could pave way for cancer cure

The vividly fluorescent cluster was found in waters off Lord Howe Island, 600km east of the Australian mainland, with some displaying rich reds that were difficult to find and in high demand for studies of cancer cells.

Egg cells from stem cells can be applied in infertility treatment

Stem cells extracted from human ovaries can be used to generate egg cells to be applied in infertility treatment, said researchers at Massachusetts General Hospital as quoted by media reports Monday.

Lead researcher Dr. Jonathan Tilly said: "The discovery of oocyte precursor cells in adult human ovaries, coupled with the fact that these cells share the same characteristic features of their mouse counterparts that produce fully functional eggs, opens the door for development of unprecedented technologies to overcome infertility in women and perhaps even delay the timing of ovarian failure."

According to the research team, a rooted belief is that women are born with a complement of egg cells that must last throughout life.

The research was funded largely by the National Institutes of Health in U.S.

Tilly co-founded a company, OvaScience Inc., trying to develop the findings into fertility treatments.

Y chromosome not to become extinct

The Y sex chromosome of men will not become extinct, according to a study published on Wednesday in the journal Nature.

Researchers compared the chromosomes of humans to a Rhesus monkey, a species that separated from human ancestors 25 million years ago, and to chimpanzees, which separated 6 million years ago.

The data show that the genetic decay in the Y chromosome was quick at first, but then became minimal in recent history - there is no further gene lost within the past 6 million yeard.

"The Y is not going anywhere and gene loss has probably come to a halt. The genes (in Y chromosome) that remain on it have critical biological functions, and that means they are going to survive," said Jennifer Hughes from the Whitehead Institute in Cambridge, Massachusetts, the United States.

"We can't rule out the possibility it could happen another time, but the genes which are left on the Y are here to stay," she added.

The finding challenged the previous researches which suggested the Y chromosome may become extinct in five million years' time, based on the rate at which genes are disappearing from the chromosome.

UK animal-human hybrid embryos trigger controversy in world

News of animal-human hybrid embryos in UK has caused a stir all around the world, according to a report of British newspaper Daily Mail.

155 "admixed" embryos, containing both human and animal genetic material, have been created since the introduction of the 2008 Human Fertilisation Embryology Act, Daily Mail said.

Although the scientific sensation has drawn controversy around the UK, this kind of experiments are licensed in this country.

The 2008 Human Fertilisation and Embryology Act legalized the creation of a variety of hybrids, including the creation of "cybrids" in which a human nucleus is implanted into an animal cell.

Following are several stills from the U.S. movie "Splice" of 2009:

A still from the U.S. movie "Splice" of 2009 (Photo Source:Chinadaily.com)

A simple method for DNA extraction from formalin-fixed, paraffin embedded tissue blocks

Tissue preparation

  1. We used FFPE tissue blocks of Non-small cell lung cancer obtained from Pathology department of Kerman Medical University which were fixed from 2004 to 2006.
  2. Before outset of our examination, all plastic microtube (1.5ml and 0.5 ml) and pipette tips were autoclaved as well as sterile distilled water used.
  3. After delivering tissues from Pathology department, tissues were carved with a surgical blade into 1mm pieces and between 25 mg to 75 mg of the tissue was transferred into a microtube. The tissues were deparaffinized as follows.

Deparaffinization method

  1. Tissue sections were deparaffinized with 500 microliter 100% xylene under a fume hood. Then contents were vortexed for 1 minutes and left in a 65 ºC water bath for 15 minutes.
  2. The xylene solvent was decanted immediately and the procedure repeated two more times.

Xylene removal

To remove the residual xylene, the samples were washed five times with Ethanol as follows.

  1. 1ml of absolute ethanol was added and mixed by vortex for ten seconds and removed after 10 minutes.
  2. 1ml of absolute ethanol was added and mixed by vortex for ten seconds and removed after 30 minutes.
  3. 1ml of 90% ethanol was added and mixed by vortex for ten seconds and after 20 minutes, tube was centrifuged at 8000 RPM and then removed ethanol out.
  4. 1ml of 70% ethanol was added and mixed by vortex for ten seconds and after 20 minutes, tube was centrifuged at 8000 RPM and then removed ethanol out.
  5. 1ml of 50% ethanol was added and mixed by vortex for ten seconds and after 20 minutes, tube was centrifuged at 8000 RPM and then removed ethanol out.
The microtubes were then left in a 40 ºC oven to dry the tissues.

Tissue lysis

  1. After the tissues were dried, 500 microliter lysis solution was added to each microtubes (40 mM Tris, 1mM EDTA, 0.5% Tween-20, 0.5 µg/µl proteinase k, PH,8) the proteinase k was added after pH adjustment and the microtubes were left in a 60 ºC water bath and were inverted every 30 minutes until the tissue was completely lysed (temperatures over 60 will inactivate the enzyme rapidly.
  2. Then resulting cell lysate was heated at 95 ºC for 8 minutes to inactivate the proteinase k.

Phenol-cholorophorm method

For the DNA extraction from cell lysate, phenol-chloroform was used as following.

  1. An equal volume of Tris-saturated phenol (pH,8) was added the tubes were left on a rotating wheel for 10 minutes then centrifuged at 12000 for 2 minutes.
  2. Then 300 microliters of the upper phase was transferred to a new microtube and an equal volume of Phenol-Cholorophorm mixture (1:1) the tube contents were mixed on the rotating wheel for 10 minutes and were centrifuged at 12000g for 2 minutes.
  3. The upper phase transferred to new microtube and 2.5 volume of cold absolute ethanol was added and For DNA precipitation, microtube was left overnight at -20 ºC.
  4. Then tubes were centrifuged for 30 minutes at 4 and ethanol was decanted.
  5. The DNA pellet was washed gently two times with cold 70% ethanol and then the pellet was dried completely at room tempreture.
  6. The pellet was dissolved in 30 to 70 microliters of steril destilled water, depending on the size.
  7. To complete the solubilization the microtubes were put in 40 ºC water bath for one hour.
  8. To check the extracted DNA, 5 microliters of the solution was run on a 1% agarose gel. The extraction DNA is suitable for PCR.

References

  1. Cawkwell L, Quirke. Direct multiplex amplification of DNA from formalin fixed, paraffin wax embedded tissue section, J Clin Pathol: Mol Pathol 53, 51-52, 2000.
  2. Chan P K S, Chan D P C, To K-F, et al. Evaluation of extraction methods from paraffin wax embedded tissues for PCR amplification of human and viral DNA. Clin Pathol 54, 401-403, 2001.
  3. Jung K, Ha Y, Kim S-H, et al. Development of Polymerase Chain Reaction and comparison with In situ Hybridization for the detection of Haemophilus parasuis in formalin-fixed, Paraffin embedded tissues, J.vet. Med. Sci. 66(7), 841-845, 2004.
  4. Keohavong P, Gao W-M, Zheng K-C, et al. Detection of K-ras and p53 mutations in sputum samples of lung cancer patients using laser capture microdissection microscope and mutation analysis, Analytical Biochemistry 324, 92-99, 2004.
  5. Shi S-R, Cote R J, Wu L, et al. DNA extraction from archival formalin-fixed, Paraffin-embedded tissue sections based on the antigen retrieval principle: Heating under the influence of pH, The journal of Histochemistry & Cytochemistry 50, 1005-1011, 2002.

DNA reveals Neanderthal extinction clues

Neanderthal artist's impressionNeanderthals were close evolutionary cousins of our own species - Homo sapiens

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Neanderthals were already on the verge of extinction in Europe by the time modern humans arrived on the scene, a study suggests.

DNA analysis suggests most Neanderthals in western Europe died out as early as 50,000 years ago - thousands of years before our own species appeared.

A small group of Neanderthals then recolonised parts of Europe, surviving for 10,000 years before vanishing.

The work is published in the journal Molecular Biology and Evolution.

An international team of researchers studied the variation, or diversity, in mitochondrial DNA extracted from the bones of 13 Neanderthals.

This type of genetic information is passed down on the maternal line; because cells contain multiple copies of the mitochondrial genome, this DNA is easier to extract from ancient remains than the DNA found in the nuclei of cells.

The fossil specimens came from Europe and Asia and span a time period ranging from 100,000 years ago to about 35,000 years ago.

The scientists found that west European fossils with ages older than 48,000 years, along with Neanderthal specimens from Asia, showed considerable genetic variation.

But specimens from western Europe younger than 48,000 years showed much less genetic diversity (variation in the older remains and the Asian Neanderthals was six-fold greater than in the western examples).

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Neanderthals may have been more sensitive to the dramatic climate changes... than was previously thought”

Love DalenSwedish Museum of Natural History

In their scientific paper, the scientists propose that some event - possibly changes in the climate - caused Neanderthal populations in the West to crash around 50,000 years ago. But populations may have survived in warmer southern refuges, allowing the later re-expansion.

Low genetic variation can make a species less resilient to changes in its environment, and place it at increased risk of extinction.

"The fact that Neanderthals in Europe were nearly extinct, but then recovered, and that all this took place long before they came into contact with modern humans, came as a complete surprise," said lead author Love Dalen, from the Swedish Museum of Natural History in Stockholm.

"This indicates that the Neanderthals may have been more sensitive to the dramatic climate changes that took place in the last Ice Age than was previously thought."

Gibraltar NeanderthalThe last Neanderthals might have held out in southern Europe until 24,000 years ago

Neanderthals were close evolutionary cousins of modern humans, and once inhabited Europe, the Middle East and Central Asia. The reasons behind their demise remain the subject of debate.

The appearance of modern humans in Europe around the time of the Neanderthal extinction offers circumstantial evidence that Homo sapiens played a role. But changes in the climate and other factors may have been important contributors.

"The amount of genetic variation in geologically older Neanderthals as well as in Asian Neandertals was just as great as in modern humans as a species," said co-author Anders Gotherstrom, from Uppsala University.

Seal paintings, NerjaWere Neanderthals responsible for these cave paintings of seals at Nerja in southern Spain?

"The variation among later European Neanderthals was not even as high as that of modern humans in Iceland."

The researchers note that the loss of genetic diversity in west European Neanderthals coincided with a climatic episode known as Marine Isotope Stage Three, which was characterised by several brief periods of freezing temperatures.

These cold periods are thought to have been caused by a disturbance of oceanic currents in the North Atlantic, and it is possible that they had a particularly strong impact on the environment in western Europe, note the researchers.

Over the last few decades, research has shown that Neanderthals were undeserving of their brutish reputation.

(BBC)

Researchers recently announced that paintings of seals found in caves at Nerja, southern Spain, might date to 42,000 years - potentially making them the only known art created by Neanderthals. However, this interpretation remains controversial.