DNA can’t explain all inherited biological traits, research shows

Characteristics passed between generations are not decided solely by DNA, but can be brought about by other material in cells, new research shows. Scientists studied proteins found in cells, known as histones, which are not part of the genetic code, but act as spools around which DNA is wound. Histones are known to control whether or not genes are switched on.

{ Science Daily | Continue reading }

related { New Discovery Moves Gene Editing Closer to Use in Humans }

cgi { Rizon Parein }

A group of leading biologists called for a worldwide moratorium on use of a new genome-editing technique that would alter human DNA in a way that can be inherited.

The biologists fear that the new technique is so effective and easy to use that some physicians may push ahead before its safety can be assessed. They also want the public to understand the ethical issues surrounding the technique, [which holds the power to repair or enhance any human gene, and] could be used to cure genetic diseases, but also to enhance qualities like beauty or intelligence.

{ NY Times | Continue reading }

Genome-editing technologies may offer a powerful approach to treat many human diseases, including HIV/AIDS, haemophilia, sickle-cell anaemia and several forms of cancer. All techniques currently in various stages of clinical development focus on modifying the genetic material of somatic cells, such as T cells (a type of white blood cell). These are not designed to affect sperm or eggs. […]

The newest addition to the genome-editing arsenal is CRISPR/Cas9, a bacteria-derived system that uses RNA molecules that recognize specific human DNA sequences. The RNAs act as guides, matching the nuclease to corresponding locations in the human genome.

{ Nature | Continue reading }

photo { Darren Holmes }

related { Genetic Origins of Economic Development }

8,000 Years Ago, 17 Women Reproduced for Every One Man

[A] member of the research team, a biological anthropologist, hypothesizes that somehow, only a few men accumulated lots of wealth and power, leaving nothing for others. These men could then pass their wealth on to their sons, perpetuating this pattern of elitist reproductive success. Then, as more thousands of years passed, the numbers of men reproducing, compared to women, rose again. “Maybe more and more people started being successful,” Wilson Sayres says. In more recent history, as a global average, about four or five women reproduced for every one man.

{ Pacific Standard | Continue reading }

Imagine a virus wipes out everyone on the planet except [a man]. […] He finds the last woman on Earth. […] Can they repopulate the Earth? To do so, their children would have to mate with one another, or mom and dad, in order to rebuild the human race. All the incestuous taboos aside, is this even genetically possible?

Inbreeding has unfortunate genetic consequences due to the increased inheritance of recessive genes, which can result in neonatal death. Inbred children that survive are at increased risk of congenital birth defects, reduced fertility, smaller size, immune deficiencies, cystic fibrosis, and more. These defects are also likely to be passed on to their children as well. […]

Some real-life examples of the consequences of inbreeding can be found in places where there are restricted breeding opportunities — for example, within monarchies, islanders, or closed societies. Hemophilia was notoriously prevalent in European royal families. Some Amish societies have a larger number of children born with extra digits on their hands or feet. Jews of Eastern European descent tend to have higher rates of a number of genetic diseases, including cystic fibrosis. […]

The net result of inbreeding is that the resulting population loses a diverse genetic portfolio, which means they are less resistant to rare diseases and deformities. The smaller the gene pool, the faster it gets dirty. Such individuals would also have less diverse immune systems, making it much easier for a single germ to wipe them all out. […]

In addition to the genetic landmines, the family would likely have a very difficult time overcoming the innate resistance most species have against inbreeding. Evolution knows that inbreeding is not good for the species, so it engineered a built-in “incest taboo” that creates a strong aversion to such behavior. A devil’s advocate, however, could argue that the biological barrier to familial sex could be overcome through artificial insemination.

What about using a sperm bank? Sperm is stored in liquid nitrogen, so it would stay frozen for a short time after the power goes out. However, you’d have to act fast because no one is around to monitor the storage tanks and top off the liquid nitrogen as it evaporates.

There are practical concerns to consider as well. The last man and woman, as well as their kids, would need to have large numbers of children and, unless one of the founders happens to be a doctor, it is hard to imagine many of these babies surviving in such a world. Even if they (and mom) survive childbirth, there are countless opportunities for them to perish in this type of environment before reaching childrearing age.

{ The Scope | Continue reading }

art { Hilo Chen, Beach 166, 2010 }

Over the past twenty years, DNA analysis has revolutionized forensic science, and has become a dominant tool in law enforcement. Today, DNA evidence is key to the conviction or exoneration of suspects of various types of crime, from theft to rape and murder. However, the disturbing possibility that DNA evidence can be faked has been overlooked. It turns out that standard molecular biology techniques such as PCR, molecular cloning, and recently developed whole genome amplification (WGA), enable anyone with basic equipment and know-how to produce practically unlimited amounts of in vitro synthesized (artificial) DNA with any desired genetic profile. This artificial DNA can then be applied to surfaces of objects or incorporated into genuine human tissues and planted in crime scenes.

Here we show that the current forensic procedure fails to distinguish between such samples of blood, saliva, and touched surfaces with artificial DNA, and corresponding samples with in vivo generated (natural) DNA. Furthermore, genotyping of both artificial and natural samples with Profiler Plus1 yielded full profiles with no anomalies. In order to effectively deal with this problem, we developed an authentication assay, which distinguishes between natural and artificial DNA based on methylation analysis of a set of genomic loci: in natural DNA, some loci are methylated and others are unmethylated, while in artificial DNA all loci are unmethylated.

{ Forensic Science International: Genetics | PDF (2009) }

The idea of two sexes is simplistic. Biologists now think there is a wider spectrum than that.

The presence or absence of a Y chromosome is what counts: with it, you are male, and without it, you are female. But doctors have long known that some people straddle the boundary — their sex chromosomes say one thing, but their gonads (ovaries or testes) or sexual anatomy say another. Parents of children with these kinds of conditions — known as intersex conditions, or differences or disorders of sex development (DSDs) — often face difficult decisions about whether to bring up their child as a boy or a girl. Some researchers now say that as many as 1 person in 100 has some form of DSD. […]

That the two sexes are physically different is obvious, but at the start of life, it is not. Five weeks into development, a human embryo has the potential to form both male and female anatomy. Next to the developing kidneys, two bulges known as the gonadal ridges emerge alongside two pairs of ducts, one of which can form the uterus and Fallopian tubes, and the other the male internal genital plumbing: the epididymes, vas deferentia and seminal vesicles. At six weeks, the gonad switches on the developmental pathway to become an ovary or a testis. If a testis develops, it secretes testosterone, which supports the development of the male ducts. It also makes other hormones that force the presumptive uterus and Fallopian tubes to shrink away. If the gonad becomes an ovary, it makes oestrogen, and the lack of testosterone causes the male plumbing to wither. The sex hormones also dictate the development of the external genitalia, and they come into play once more at puberty, triggering the development of secondary sexual characteristics such as breasts or facial hair. […]

For many years, scientists believed that female development was the default programme, and that male development was actively switched on by the presence of a particular gene on the Y chromosome. In 1990, researchers made headlines when they uncovered the identity of this gene, which they called SRY. Just by itself, this gene can switch the gonad from ovarian to testicular development. For example, XX individuals who carry a fragment of the Y chromosome that contains SRY develop as males.

{ Nature | Continue reading }

Monozygotic twins are considered being genetically identical, therefore they cannot be differentiated using standard forensic DNA testing. Here we describe how identification of extremely rare mutations by ultra-deep next generation sequencing can solve such cases. We sequenced DNA from sperm samples of two twins and from a blood sample of the child of one twin. Bioinformatics analysis revealed five single nucleotide polymorphisms (SNPs) present in the twin father and the child, but not in the twin uncle.

Our results give experimental evidence for the hypothesis that rare mutations will occur early after the human blastocyst has split into two, the origin of twins, and that such mutations will be carried on into somatic tissue and the germline. The method provides a solution to solve paternity and forensic cases involving monozygotic twins as alleged fathers or originators of DNA traces.

{ FSI Genetics }

DNA is generally regarded as the basic building block of life itself. In the most fundamental sense, DNA is nothing more than a chemical compound, albeit a very complex and peculiar one. DNA is an information-carrying molecule. The specific sequence of base pairs contained in a DNA molecule carries with it genetic information, and encodes for the creation of particular proteins. When taken as a whole, the DNA contained in a single human cell is a complete blueprint and instruction manual for the creation of that human being.

In this article we discuss myriad current and developing ways in which people are utilizing DNA to store or convey information of all kinds. For example, researchers have encoded the contents of a whole book in DNA, demonstrating the potential of DNA as a way of storing and transmitting information. In a different vein, some artists have begun to create living organisms with altered DNA as works of art. Hence, DNA is a medium for the communication of ideas. Because of the ability of DNA to store and convey information, its regulation must necessarily raise concerns associated with the First Amendment’s prohibition against the abridgment of freedom of speech.

New and developing technologies, and the contemporary and future social practices they will engender, necessitate the renewal of an approach towards First Amendment coverage that takes into account the purposes and values incarnated in the Free Speech Clause of the Constitution.

{ Charleston School of Law | Continue reading }

photo { Bruce Davidson }

We all know that exercise can make us fitter and reduce our risk for illnesses such as diabetes and heart disease. But just how, from start to finish, a run or a bike ride might translate into a healthier life has remained baffling.

Now new research reports that the answer may lie, in part, in our DNA. Exercise, a new study finds, changes the shape and functioning of our genes, an important stop on the way to improved health and fitness. […]

Epigenetics [is] a process by which the operation of genes is changed, but not the DNA itself. Epigenetic changes occur on the outside of the gene, mainly through a process called methylation. In methylation, clusters of atoms, called methyl groups, attach to the outside of a gene like microscopic mollusks and make the gene more or less able to receive and respond to biochemical signals from the body.

Scientists know that methylation patterns change in response to lifestyle. Eating certain diets or being exposed to pollutants, for instance, can change methylation patterns on some of the genes in our DNA and affect what proteins those genes express. Depending on which genes are involved, it may also affect our health and risk for disease. […]

The volunteers pedaled one-legged at a moderate pace for 45 minutes, four times per week for three months. […] More than 5,000 sites on the genome of muscle cells from the exercised leg now featured new methylation patterns. Some showed more methyl groups; some fewer. […]

Most of the genes in question are known to play a role in energy metabolism, insulin response and inflammation within muscles. In other words, they affect how healthy and fit our muscles — and bodies — become.

They were not changed in the unexercised leg.

{ NY Times | Continue reading }

photo { David Hasselhoff, The SpongeBob Squarepants Movie, 2004 }

related { Phobias may be memories passed down in genes from ancestors }

In December last year, researchers Brian Dias and Kerry Ressler made a splash with a paper seeming to show that memories can be inherited.

This article, published in Nature Neuroscience, reported that if adult mice are taught to be afraid of a particular smell, then their children will also fear it. Which is pretty wild. Epigenetics was proposed as the mechanism.

Now, however, psychologist Gregory Francis says that the data Dias and Ressler published are just too good to be true.

{ Neuroskeptic | Continue reading }

Memories may be passed down through generations in DNA in a process that may be the underlying cause of phobias.

{ Telegraph | Continue reading }

photo { Guy Sargent }

{ DNA tests prove your close friends are probably distant relatives }

images { 1 | 2 }

For all those brunettes wishing they were naturally blond, a small genetic change could have made all the difference. Scientists have found that replacing one of DNA’s four letters at a key spot in the genome shifts a particular gene’s activity and leads to fairer hair. Not only does the work provide a molecular basis for flaxen locks, but it also demonstrates how changes in segments of DNA that control genes, not just changes in genes themselves, are important to what an organism looks like. […]

Over the past 6 years, studies of genetic variation in thousands of people have linked at least eight DNA regions to blondness based on the fact that a certain DNA letter, or base, was found in people with that hair color but not in people with other hair colors. Some of those base changes, or single-nucleotide polymorphisms (SNPs), were in genes involved in the production of pigments, such as melanin. Mutations in these genes typically change skin and hair color. Other SNPs lay outside genes but could be part of the regulatory DNA that helps control the function of genes nearby. Changes in that regulatory DNA could result in hair color but not skin color change, or vice versa, because regulatory DNA can change gene activity in just certain parts of the body.

{ Science | Continue reading }

related { Smokers with gene defect have one in four chance of developing lung cancer }

The average person misplaces up to nine items a day, and one-third of respondents in a poll said they spend an average of 15 minutes each day searching for items—cellphones, keys and paperwork top the list, according to an online survey of 3,000 people published in 2012 by a British insurance company. […]

In a recent study, researchers in Germany found that the majority of people surveyed about forgetfulness and distraction had a variation in the so-called dopamine D2 receptor gene (DRD2), leading to a higher incidence of forgetfulness. According to the study, 75% of people carry a variation that makes them more prone to forgetfulness.

{ WSJ | Continue reading }

related { Processing new information during sleep compromises memory }

photo { Daniel Bejar, The Visual Topography of a Generation Gap (Brooklyn, NY, #1), 2011 }

Now there is hope in the form of new genome-engineering tools, particularly one called CRISPR. This technology could allow researchers to perform microsurgery on genes, precisely and easily changing a DNA sequence at exact locations on a chromosome. Along with a technique called TALENs, invented several years ago, and a slightly older predecessor based on molecules called zinc finger nucleases, CRISPR could make gene therapies more broadly applicable, providing remedies for simple genetic disorders like sickle-cell anemia and eventually even leading to cures for more complex diseases involving multiple genes.

{ Technology Review | Continue reading }

Amoebas are puny, stupid blobs, so scientists were surprised to learn that they contain 200 times more DNA than Einstein did. Because amoebas are made of just one cell, researchers assumed they would be simpler than humans genetically. Plus, amoebas date back farther in time than humans, and simplicity is considered an attribute of primitive beings. It just didn’t make sense. […]

Before the advent of rapid, accurate, and inexpensive DNA sequencing technology in the early 2000s, biologists guessed that genes would provide more evidence for increasing complexity in evolution. Simple, early organisms would have fewer genes than complex ones, they predicted. […] Instead, their assumptions of increasing complexity began to fall apart. […]

Then molecular analyses did something else. They rearranged the order of branches on evolutionary trees. Biologists pushed aside trees based on how similar organisms looked to one another, and made new ones based on similarities in DNA and protein sequences. The results suggested that complex body parts evolved multiple times and had also been lost. One study found that winged stick insects evolved from wingless stick insects who had winged ancestors. […]

Perhaps the fact that people are stunned whenever organisms become simpler says more about how the human mind organizes the world than about evolutionary processes. People are more comfortable envisioning increasing complexity through time instead of reversals or stasis.

{ Nautilus | Continue reading }

design { Sam Winston }

We have identified a Y-chromosomal lineage with several unusual features. It was found in 16 populations throughout a large region of Asia, stretching from the Pacific to the Caspian Sea, and was present at high frequency: ~8% of the men in this region carry it, and it thus makes up ~0.5% of the world total. The pattern of variation within the lineage suggested that it originated in Mongolia ~1,000 years ago. Such a rapid spread cannot have occurred by chance; it must have been a result of selection. The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior.

{ National Institutes of Health }

An international group of geneticists studying Y-chromosome data have found that nearly 8 percent of the men living in the region of the former Mongol empire carry y-chromosomes that are nearly identical. That translates to 0.5 percent of the male population in the world, or roughly 16 million descendants living today. […]

To have such a startling impact on a population required a special set of circumstances, all of which are met by Genghis Khan and his male relatives, the authors note in the study.

[Genghis Khan lived from 1162-1227 and raped and pillaged from Mongolia to the gates of Vienna. Once he captured a village or town, he would essentially kill all the men and rape the women.]

The Y-chromosome is passed on as a chunk of DNA from father to son, basically unchanged through generations except for random mutations.

These random mutations, which happen naturally and are usually harmless, are called markers. Once the markers have been identified, geneticists can go back in time and trace them to the point at which they first occurred, defining a unique lineage of descent.

In this particular instance, the lineage originated 1,000 years ago. The authors aren’t saying that the genetic mutations defining the lineage originated with Khan, who was born around 1162; they are more likely to have been passed on to him by a great great grandfather.

[…]

The connection to Genghis Khan will never be a certainty unless his grave is found and his DNA could be extracted.

{ National Geographic | Continue reading | Audio: Radio Lab, Genghis Khan Episode }

The location of the tomb of Genghis Khan has been the object of much speculation and research. The site remains undiscovered. […] According to one legend, the funeral escort killed anyone and anything that crossed their path, in order to conceal where he was finally buried. After the tomb was completed, the slaves who built it were massacred, and then the soldiers who killed them were also killed.

{ Wikipedia | Continue reading }

Everyone grows older, but scientists don’t really understand why. Now a UCLA study has uncovered a biological clock embedded in our genomes that may shed light on why our bodies age and how we can slow the process. […]

While earlier clocks have been linked to saliva, hormones and telomeres, the new research is the first to identify an internal timepiece able to accurately gauge the age of diverse human organs, tissues and cell types. Unexpectedly, the clock also found that some parts of the anatomy, like a woman’s breast tissue, age faster than the rest of the body.

{ EurekAlert | Continue reading }

photo { Ray Metzker }

From biology class to “C.S.I.,” we are told again and again that our genome is at the heart of our identity. Read the sequences in the chromosomes of a single cell, and learn everything about a person’s genetic information.

But scientists are discovering that […] it’s quite common for an individual to have multiple genomes. Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people. […]

In 1953, a British woman donated a pint of blood. It turned out that some of her blood was Type O and some was Type A. The scientists who studied her concluded that she had acquired some of her blood from her twin brother in the womb, including his genomes in his blood cells.

Chimerism, as such conditions came to be known, seemed for many years to be a rarity. But “it can be commoner than we realized,” said Dr. Linda Randolph, a pediatrician at Children’s Hospital in Los Angeles.

Twins can end up with a mixed supply of blood when they get nutrients in the womb through the same set of blood vessels. In other cases, two fertilized eggs may fuse together. […] Women can also gain genomes from their children. After a baby is born, it may leave some fetal cells behind in its mother’s body, where they can travel to different organs and be absorbed into those tissues. […] In 2012, Canadian scientists performed autopsies on the brains of 59 women. They found neurons with Y chromosomes in 63 percent of them. The neurons likely developed from cells originating in their sons. […]

Medical researchers aren’t the only scientists interested in our multitudes of personal genomes. […] Last year, for example, forensic scientists at the Washington State Patrol Crime Laboratory Division described how a saliva sample and a sperm sample from the same suspect in a sexual assault case didn’t match.

{ NY Times | Continue reading }

First Genetic Evidence That Humans Choose Friends With Similar DNA

The discovery that friends are as genetically similar as fourth cousins has huge implications for our understanding of human evolution, say biologists.

{ The Physics arXiv Blog | Continue reading }