genes

I was just going back for that lotion whitewax, orangeflower water

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DNA (deoxyribonucleic acid) is the main component of our genetic material. It is formed by combining four parts: A, C, G and T (adenine, cytosine, guanine and thymine), called bases of DNA combine in thousands of possible sequences to provide the genetic variability that enables the wealth of aspects and functions of living beings.

In the early 80s, to these four “classic” bases of DNA was added a fifth: the methyl-cytosine (mC) derived from cytosine. And it was in the late 90’s when mC was recognized as the main cause of epigenetic mechanisms: it is able to switch genes on or off depending on the physiological needs of each tissue.

In recent years, interest in this fifth DNA base has increased by showing that alterations in the methyl-cytosine contribute to the development of many human diseases, including cancer.

Today, an article published in Cell describes the possible existence of a sixth DNA base, the methyl-adenine (mA), which also help determine the epigenome and would therefore be key in the life of the cells.

{ ScienceDaily | Continue reading }

Et qui n’est, chaque fois, ni tout à fait la même, ni tout à fait une autre

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Prosecution is often dropped in cases largely reliant on DNA evidence when the suspect is an identical twin. The risk of convicting the wrong twin is too great.

The chance of a DNA match between two unrelated individuals is extraordinarily small — one in a billion. For siblings, the chance is 1 in 10,000. But identical twins have essentially the same DNA sequence, making the identification of the forensic evidence they leave behind extremely difficult.

But researchers at the University of Huddersfield recently developed a cost-effective and accurate method for differentiating between the genetic profiles of identical twins. The method looks at DNA methylation, a biochemical process that helps manage gene expression — turning genes on and off.

As identical twins age, different environmental factors affect their genomes, or the ways in which their genetic material is expressed. These differences can be seen in their corresponding DNA methylation. […]

The process isn’t perfect. Young twins with similar environments may not have developed significant differences in their DNA methylation. The technique also requires a large genetic sample, which may not be recoverable at every crime scene.

{ UPI | Continue reading }

related { FBI Admits Flaws in Hair Analysis Over Decades }

‘Anyone who speaks in the name of others is always an impostor.’ —Cioran

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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 }

The whool of the whaal in the wheel of the whorl

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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 }

What one refuses in a minute, no eternity will return

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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 }

‘Why are there beings at all, and why not rather nothing?’ –Heidegger

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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 }

Jerry, just remember, it’s not a lie if you believe it

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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) }

Your reputation precedes you

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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 }

Only the whole is true

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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 }

‘We live among ideas much more than we live in nature.’ —Saul Bellow

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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 }

‘To do nothing is sometimes a good remedy.’ –Hippocrates

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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 }

‘Two simple words in the English language: I forgot!’ –Steve Martin

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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 }