The DNA of a Eukaryotic chromosome has the shape of a fractal helix with six levels of coiling. The fractal shape allows for all sizes of the chromosome to be unpacked and transcribed efficiently, from individual genes to long sections of DNA with thousands of co-dependent genes and regulatory sequences. It has been hypothesized that DNA can act as a fractal antenna which responds to electromagnetic waves in the environment by packing or unpacking its helicies.
Video Credit: Drew Barry
Asymmetric distribution of mRNA is observed in diverse cell types and considered to be an important mechanism to generate cell polarity. Localization of mRNA allows protein synthesis to be regulated at high spatial and temporal resolution. Live-cell imaging reveals that β-actin mRNA localization is highly dynamic and correlated with the cell protrusion and migration.
Movie: Real-time dynamics of β-actin mRNA in a migrating cell. The MS2-GFP labeling technique was used to visualize the endogenous β-actin mRNA. The color map shows the fluorescence intensity of NLS-MCP-GFP divided by the intensity of cytoplasmic dye, representing the concentration of β-actin mRNA. Find out more in Park et al., Cell Reports 1(2):179–184 (2012) and Lionnet et al., Nat Methods 8(2):165–170 (2011).
It turns out that cultures with a history of dairy farming and milk drinking have a much higher frequency of lactose tolerance – and its associated gene – than those who don’t. Drinking milk is just one of example of the way that traditions and cultural practices can influence the path of our evolution. Culture and genetics are traditionally thought of as two separate processes, but researchers are increasingly realizing that they are intimately connected, each influencing the natural progression of the other. Scientists call it “gene-culture co-evolution.” Why does it matter? If we can pin down how culture influences our genetic makeup – and how the same processes apply to other creatures too – then we can be better understand how the way we act as a society today could influence our future.
Filed under: Tabs I keep open in my browser. Source
Interesting info. on survival rates for bone marrow transplant recipients from 1988–2003, with ALL, AML, CML, and MDS. Reblogging for those who have been following Amit’s story.
Also, Here is a link to more info on HLA typing from the Seattle Cancer Care Alliance.
Register to be a bone marrow donor with Be the Match online.
What’s the secret to staying young? A UCLA scientist may have uncovered it
A new U.S. study on the aging of tissues reveals that some areas of the body age faster than others, and this DNA-based research has possible applications for diseases, such as breast cancer treatments, stem cell work, and even on forensics. Is the fountain of youth here yet? No, but it could be getting closer, researchers say.
[Mohammed Abed/AFP/Getty Images]
A service that digitally weaves together the DNA of prospective parents to check for potential disease in thousands of “virtual babies” is set to launch in the US by December.
New York start-up Genepeeks will initially focus on donor sperm, simulating before pregnancy how the genetic sequence of a female client might combine with those of different males. Donors that more often produce “digital children” with a higher risk of inherited disorders will be filtered out, leaving those who are better genetic matches.
Everything happens in a computer, but experts have raised ethical questions.
"We are just in the business right now of giving prospective mothers, who are using donor sperm to conceive, a filtered catalogue of donors based on their own underlying genetic profile. We are filtering out the donor matches with an elevated risk of rare recessive paediatric conditions" Genepeeks co-founder Anne Morriss told BBC News.
She was motivated in part by her own experience of starting a family. Her son was conceived with a sperm donor who happened to share with Morriss the gene for an inherited disorder called MCADD. MCADD (medium-chain acyl-CoA dehydrogenase deficiency) prevents those affected from converting fats to sugar. It can be fatal if it is not diagnosed early. Luckily, in Ms Morriss’s case, the condition was picked up in newborn screening tests.
"My son has a pretty normal life" Ms Morriss said, "but about 30% of children with rare genetic diseases don’t make it past the age of five."
Genepeeks has formalised a partnership with a sperm bank - the Manhattan Cryobank - and has a patent pending on the DNA screening technology. The start-up benefits from the rapid pace of change in genetic technology. Indeed, six months ago, Genepeeks’ founders decided it was able to use a superior system for DNA analysis (called “targeted exon sequencing”) than the one originally envisaged - a result, says Anne Morriss, of falling costs and increased flexibility.
For couples planning babies, other companies already screen one or both partners for genes that could cause disease if combined with a similar variant - so-called “carrier screening”.
One academic who studies the use of genetic technology commented: “This is like that, but ramped up 100,000 times.”
Ms Morriss’s business partner, Prof Lee Silver, a geneticist and expert on bioethics at Princeton University, New Jersey, told BBC News: “We get the DNA sequence from two prospective parents. We simulate the process of reproduction, forming virtual sperm and virtual eggs. We put them together to form a hypothetical child genome. Then we can look at that hypothetical genome and - with all the tools of modern genetics - determine the risk that the genome will result in a child with disease. We’re looking directly for disease and not carrier status. For each pair of people that we’re going to analyse, we make 10,000 hypothetical children.”
The process will be run for the client and each potential donor one by one, scanning for some 600 known single-gene recessive conditions. In this way, the highest-risk pairings can be filtered out.
Anne Morriss added: “At this stage our clients won’t be receiving any genetic information back. We’re very much focused on the practical utility of helping prospective parents who want to protect their future kids, giving them the option of additional analysis to what is currently being offered in the industry.”
But the company’s founders have plans to expand the screening beyond single-gene recessive disorders to more complex conditions in which multiple genes play a part. Indeed, going to the trouble of simulating thousands of digital children deliberately lays the ground for this: “[It’s] impossible to get towards an accurate risk calculation in any other way” said Anne Morriss.
And in a video produced by the company, Prof Silver says: “My hope for the future is that any people who want to have a baby can use this technology to greatly reduce the risk of disease being expressed in their child.”
To some, such a prospect might appear like a step towards designer babies - until now the preserve of science fiction literature and films such as Gattaca, which envisaged a future of genetic “haves” and “have-nots”.
Bio-ethicists approached by the BBC said Genepeeks was a logical outcome of the increasing demand for more information when making reproductive decisions. However, some raised potential concerns about risk communication and the expansion of screening beyond rare single-gene disorders. But they suggested there were few, if any, regulatory barriers.
One ethicist told BBC News: “The biggest question for me, just from the outset, is the understanding of uncertainty. Even people who have been doing genomics for years still have a hard time figuring out exactly what a risk for a particular genetic predisposition really means for a family. Gene-environment interactions can lead to people either having disease or not having disease.”
Dr Ewan Birney, associate director of the European Bioinformatics Institute in Hinxton, UK, echoed the point: “It’s good that they’re focusing on the carrier status of these rare Mendelian disorders where it’s potentially more clear-cut. That said, these things are more complex than they first seem. I’m sure the scientists appreciate that complexity. But when transmitting that complexity to everyday people, these things can sound more absolute than they really are. The thing I would want to stress here is just how complex this is. It’s great that people are thinking of using this technology in lots of different ways, but our knowledge gap is very large.”
Risk communication to clients was, said Anne Morriss, “absolutely critical to anyone in this industry”. ”We have to be crystal clear about what we’re testing for, what risks we’re helping to reduce; that there’s no guarantee you won’t give birth to a sick child” she said.
Prof Mildred Cho, associate director of the Stanford Center for Biomedical Ethics in California, raised questions over whether the sperm donor should also receive information about their genome gleaned from the screening process. ”Unlike hair colour, occupation or family history - those are things the donor already knows - the thing that’s different about this that I see is it could create information that the donor doesn’t already have. It also has implications for the donor’s other biological family members.”
This week it also emerged that California-based consumer genetics company 23andMe had submitted the patent on a DNA analysis tool for planning a child.
Karyotypes describe the number of chromosomes, and what they look like under a light microscope. Attention is paid to their length, the position of the centromeres, banding pattern, any differences between the sex chromosomes, and any other physical characteristics. The study of whole sets of chromosomes is sometimes known as karyology. The chromosomes are depicted (by rearranging a microphotograph) in a standard format known as a karyogram or idiogram: in pairs, ordered by size and position of centromere for chromosomes of the same size. The basic number of chromosomes in the somatic cells of an individual or a species is called the somatic number and is designated 2n. Thus, in humans 2n = 46. In the germ-line (the sex cells) the chromosome number is n (humans: n = 23).
Almost every man alive can trace his origins to one man who lived about 135,000 years ago, new research suggests. And that ancient man likely shared the planet with the mother of all women. The findings, detailed Thursday, Aug. 1, in the journal Science, come from the most complete analysis of the male sex chromosome, or the Y chromosome, to date. The results overturn earlier research, which suggested that men’s most recent common ancestor lived just 50,000 to 60,000 years ago.
Despite their overlap in time, ancient “Adam” and ancient “Eve” probably didn’t even live near each other, let alone mate. “Those two people didn’t know each other,” said Melissa Wilson Sayres, a geneticist at the University of California, Berkeley, who was not involved in the study.
Researchers believe that modern humans left Africa between 60,000 and 200,000 years ago, and that the mother of all women likely emerged from East Africa. But beyond that, the details get fuzzy. The Y chromosome is passed down identically from father to son, so mutations, or point changes, in the male sex chromosome can trace the male line back to the father of all humans. By contrast, DNA from the mitochondria, the energy powerhouse of the cell, is carried inside the egg, so only women pass it on to their children. The DNA hidden inside mitochondria, therefore, can reveal the maternal lineage to an ancient Eve. But over time, the male chromosome gets bloated with duplicated, jumbled-up stretches of DNA, said study co-author Carlos Bustamante, a geneticist at Stanford University in California. As a result, piecing together fragments of DNA from gene sequencing was like trying to assemble a puzzle without the image on the box top, making thorough analysis difficult.
Bustamante and his colleagues assembled a much bigger piece of the puzzle by sequencing the entire genome of the Y chromosome for 69 men from seven global populations, from African San Bushmen to the Yakut of Siberia. By assuming a mutation rate anchored to archaeological events (such as the migration of people across the Bering Strait), the team concluded that all males in their global sample shared a single male ancestor in Africa roughly 125,000 to 156,000 years ago. In addition, mitochondrial DNA from the men, as well as similar samples from 24 women, revealed that all women on the planet trace back to a mitochondrial Eve, who lived in Africa between 99,000 and 148,000 years ago almost the same time period during which the Y-chromosome Adam lived.
More ancient Adam
But the results, though fascinating, are just part of the story, said Michael Hammer, an evolutionary geneticist at the University of Arizona who was not involved in the study. A separate study in the same issue of the journal Science found that men shared a common ancestor between 180,000 and 200,000 years ago. And in a study detailed in March in the American Journal of Human Genetics, Hammer’s group showed that several men in Africa have unique, divergent Y chromosomes that trace back to an even more ancient man who lived between 237,000 and 581,000 years ago. “It doesn’t even fit on the family tree that the Bustamante lab has constructed. It’s older,” Hammer told LiveScience. Gene studies always rely on a sample of DNA and, therefore, provide an incomplete picture of human history. For instance, Hammer’s group sampled a different group of men than Bustamante’s lab did, leading to different estimates of how old common ancestors really are.
Adam and Eve?
These primeval people aren’t parallel to the biblical Adam and Eve. They weren’t the first modern humans on the planet, but instead just the two out of thousands of people alive at the time with unbroken male or female lineages that continue on today. The rest of the human genome contains tiny snippets of DNA from many other ancestors they just don’t show up in mitochondrial or Y-chromosome DNA, Hammer said. (For instance, if an ancient woman had only sons, then her mitochondrial DNA would disappear, even though the son would pass on a quarter of her DNA via the rest of his genome.) As a follow-up, Bustamante’s lab is sequencing Y chromosomes from nearly 2,000 other men. Those data could help pinpoint precisely where in Africa these ancient humans lived. “It’s very exciting,” Wilson Sayres told LiveScience. “As we get more populations across the world, we can start to understand exactly where we came from physically.”
Key step in molecular ‘dance’ that duplicates DNA deciphered
Building on earlier work exploring the complex choreography by which intricate cellular proteins interact with and copy DNA prior to cell division, scientists at the U.S. Department of Energy’s Brookhaven National Laboratory and collaborators have captured a key step-molecular images showing how the enzyme that unwinds the DNA double helix gets drawn to and wrapped around its target. Details of the research, published in the journal Nature Structural & Molecular Biology, enhance understanding of an essential biological process and may suggest ways for stopping cell division when it goes awry.
"This was truly collaborative work where molecular biology expertise from Christian Speck’s lab at Imperial College, London, Bruce Stillman’s group at Cold Spring Harbor Laboratory, and the cryo-electron microscopy expertise at Brookhaven were all essential," said Huilin Li, a biologist at Brookhaven Lab and Stony Brook University and a lead author on the paper.
Getting the message to the proper place at the proper time can be just as important as the message itself. This is true at all scales of life. The ability to observe individual mRNA molecules in a live cell allows one to understand the importance of different cellular transport processes in post-transcriptional regulation and translation.
Movie: Individual mRNA granules are shown undergoing microtubule-dependent, intermittent processive motion interspersed between periods of passive motion. β-actin mRNA granules (yellow) are shown overlaid on a standard deviation map (red). Standard deviation maps show the paths of moving mRNA granules over the time-course of the movie. Find out more in Lifland et al., Traffic, 12(8):1000–11, 2011.
A nice video showing the transcription of DNA to mRNA by RNA-polymerase. A messenger RNA transcript then exists the nucleus to find a ribosome. Their is it translated into a primary structure polynucleotide. Chaperonin fold proteins with the use of ATP into secondary and tertiary structures. Once realised from the chaperonin the protein may be complete or join part of a quaternary structure.