genes

Where there’s a microscope, there’s always a slide

Back in the 1980s, when DNA forensic analysis was still in its infancy, crime labs needed a speck of bodily fluid—usually blood, semen, or spit—to generate a genetic profile.

That changed in 1997, when Australian forensic scientist Roland van Oorschot stunned the criminal justice world with a nine-paragraph paper titled “DNA Fingerprints from Fingerprints.” It revealed that DNA could be detected not just from bodily fluids but from traces left by a touch. Investigators across the globe began scouring crime scenes for anything—a doorknob, a countertop, a knife handle—that a perpetrator may have tainted with incriminating “touch” DNA.

But van Oorschot’s paper also contained a vital observation: Some people’s DNA appeared on things that they had never touched. […]

In one of his lab’s experiments, for instance, volunteers sat at a table and shared a jug of juice. After 20 minutes of chatting and sipping, swabs were deployed on their hands, the chairs, the table, the jug, and the juice glasses, then tested for genetic material. Although the volunteers never touched each other, 50 percent wound up with another’s DNA on their hand. A third of the glasses bore the DNA of volunteers who did not touch or drink from them.

Then there was the foreign DNA—profiles that didn’t match any of the juice drinkers. It turned up on about half of the chairs and glasses, and all over the participants’ hands and the table. The only explanation: The participants unwittingly brought with them alien genes, perhaps from the lover they kissed that morning, the stranger with whom they had shared a bus grip, or the barista who handed them an afternoon latte.

{ Wired | Continue reading }

related { The Hunt for the Golden State Killer and A New Way to Solve Murders }

About time!

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Nobel Prize in Chemistry awarded to American biochemist Jennifer A. Doudna (left) and French microbiologist Emmanuelle Charpentier who discovered gene-editing tool CRISPR […] Doudna and Charpentier have been considered top candidates for the prize for several years, but there’s an ongoing fight over patents for CRISPR and its use.

{ Axios | Continue reading }

Blood is a juice with curious properties

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…a girl with different-colored eyes and ambiguous genitals who appeared at a Seattle genetics clinic. Her ovaries proved to have only XX chromosomes—typical female—but her other tissues were mixtures of XX and XY. Further analysis showed that she had started out as opposite-sex twins. But early in development, the two embryos had fused, becoming a single, highly unusual child. Like a verse from the old Ray Stevens novelty song “I’m My Own Grandpa,” this girl was her own twin brother.

In pregnant women, fetal stem cells can cross the placenta to enter the mother’s bloodstream, where they may persist for years. If Mom gets pregnant again, the stem cells of her firstborn, still circulating in her blood, can cross the placenta in the other direction, commingling with those of the younger sibling. Heredity can thus flow “upstream,” from child to parent—and then over and down to future siblings.

Forget the notion that your genome is just the DNA in your chromosomes. We have another genome, small but vital, in our cells’ mitochondria—the tiny powerhouses that supply energy to the cell. Though the mitochondrial genes are few, damage to them can lead to disorders of the brain, muscles, internal organs, sensory systems, and more. At fertilization, an embryo receives both chromosomes and mitochondria from the egg, and only chromosomes from the sperm. Mitochondrial heredity thus flows strictly through the maternal line; every boy is an evolutionary dead end, as far as mitochondria are concerned.

{ The Atlantic | Continue reading }

The problem is all inside your head she said to me. The answer is easy if you take it logically.

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if being very smart was much, much better than being of average smarts, then everyone would [have] become very smart up to the physiological limit. […] The fact that being very intelligent is not evolutionarily clearly “good” seems ridiculousness to many people who think about these things. […]

let’s talk about another quantitative trait which is even more heritable than intelligence, and easier to measure: height. […] Though being a tall male seems in most circumstances to be better in terms of physical attractiveness than being a short male, circumstances vary, and being too tall increases one’s mortality and morbidity. Being larger is calorically expensive. Large people need to eat more because they have larger muscles. […]

let’s go back to intelligence. What could be the trade-offs? First, there are now results presented at conferences that very high general intelligence may exhibit a correlation with some mental pathologies. Though unpublished, this aligns with some prior intuitions. […] Additionally […] one could argue that being too deviated from the norm might make socialization and pair-bonding difficult.

{ GeneExpression | Continue reading }

photo { Linda Evangelista photographed by Philip Tracy for Vogue, January 1992 }

perhaps the same bird echoed through both of us

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identical twins […] bought home kits from AncestryDNA, MyHeritage, 23andMe, FamilyTreeDNA and Living DNA, and mailed samples of their DNA to each company for analysis. Despite having virtually identical DNA, the twins did not receive matching results from any of the companies. […]

An entire DNA sample is made up of about three billion parts, but companies that provide ancestry tests look at about 700,000 of those to spot genetic differences.

{ CBC | Continue reading }

Don’t keep doing what doesn’t work

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Two years ago a New Scientist headline announced the “world’s first baby born with new ‘3 parent’ technique.” Whereas an embryo is usually produced by one sperm and one egg, this technique uses genetic material from three separate people. First performed by a New York fertility clinic in Mexico to evade US legal restrictions, the procedure has now been replicated several times. […]

Two cases in the UK and Mexico involve a woman who carries a rare disease of her mitochondria, the cellular structures that produce energy in our cells. Mitochondria have their own DNA and can harbor their own genetic diseases. These are passed on solely through the maternal line, because mitochondria are found in eggs but not in sperm. One approach to blocking transmission of these illnesses involves inserting the DNA-filled nucleus from the egg of the woman into a donor egg full of healthy mitochondria but stripped of its own nucleus. Fertilize that hybrid egg with a sperm, and presto! A child could be born nine months later with DNA from three people and without a catastrophic mitochondrial disorder. […] Children conceived with a third person’s mitochondria are, it follows, the offspring of three parents. […]

Mitochondria, it turns out, were originally bacteria; their free-wheeling existence came to an end one day deep in evolutionary history when they entered another single-celled organism and started a new life inside. […]

This is not what we think of as Darwinian evolution, the transmission of genes and traits down the family line. DNA, it turns out, can also be passed laterally, between individuals, including those of different species. […] We may like to think of DNA as the neat bequest of our parents, the fusion of two unique, circumscribed human lineages.  Yet it is—and we are—something more: short strands within a vast interwoven genetic web, stretching back to the earth’s earliest days, linking all living things. 

{ New Republic | Continue reading }

‘The future enters into us long before it happens.’ –Rainer Maria Rilke

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[L]ife may have been seeded here on Earth by life-bearing comets as soon as conditions on Earth allowed it to flourish (about or just before 4.1 Billion years ago). […]

Evidence of the role of extraterrestrial viruses in affecting terrestrial evolution has recently been plausibly implied in the gene and transcriptome sequencing of Cephalopods. The genome of the Octopus shows a staggering level of complexity with 33,000 protein-coding genes more than is present in Homo sapiens. Octopus belongs to the coleoid sub-class of molluscs (Cephalopods) that have an evolutionary history that stretches back over 500 million years, although Cephalopod phylogenetics is highly inconsistent and confusing. Cephalopods are also very diverse, with the behaviourally complex coleoids, (Squid, Cuttlefish and Octopus) presumably arising under a pure terrestrial evolutionary model from the more primitive nautiloids. However the genetic divergence of Octopus from its ancestral coleoid sub-class is very great, akin to the extreme features seen across many genera and species noted in Eldridge-Gould punctuated equilibria patterns (below). Its large brain and sophisticated nervous system, camera-like eyes, flexible bodies, instantaneous camouflage via the ability to switch colour and shape are just a few of the striking features that appear suddenly on the evolutionary scene. The transformative genes leading from the consensus ancestral Nautilus to the common Cuttlefish to Squid to the common Octopus are not easily to be found in any pre-existing life form — it is plausible then to suggest they seem to be borrowed from a far distant “future” in terms of terrestrial evolution, or more realistically from the cosmos at large. Such an extraterrestrial origin as an explanation of emergence of course runs counter to the prevailing dominant paradigm. […]

One plausible explanation, in our view, is that the new genes are likely new extraterrestrial imports to Earth — most plausibly as an already coherent group of functioning genes within (say) cryopreserved and matrix protected fertilized Octopus eggs. […]

Hoyle and Wickramasinghe thus argued and predicted on the basis of the then available evidence that microorganisms and virus populations in the comets and related cosmic bolides appear to have regularly delivered living systems (organisms, viruses and seeds) to the Earth since its formation, and continue to do so. […]

Darwinian evolution and its various non-Darwinian terrestrial drivers are therefore most likely caused by the continuing supply of new virions and micro-organisms from space with their genetic impact events written all over our genomes. Indeed a strong case can be made for hominid evolution involving a long sequence of viral pandemics, each one of which was a close call to total extinction of an evolving line. The most crucial genes relevant to evolution of hominids, as indeed all species of plants and animals, seems likely in many instances to be of external origin, being transferred across the galaxy largely as information rich virions. In some cases it is possible to imagine multicellular life-forms that were established on an icy cometary or planetary body to be transferred as frozen eggs, embryos or seeds in large icy bolides that have been transported to the Earth in soft landings.

{ Progress in Biophysics and Molecular Biology | PDF }

photo { Ezra Stoller, Philip Morris headquarters, Richmond, 1972 }

My leaves have drifted from me

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In a study published in Nature Neuroscience on Jan. 21, neuroscientists and systems biologists from Harvard Medical School reveal just how inexorably interwoven nature and nurture are.

Using novel technologies developed at HMS, the team looked at how a single sensory experience affects gene expression in the brain by analyzing more than 114,000 individual cells in the mouse visual cortex before and after exposure to light.

Their findings revealed a dramatic and diverse landscape of gene expression changes across all cell types, involving 611 different genes, many linked to neural connectivity and the brain’s ability to rewire itself to learn and adapt.

The results offer insights into how bursts of neuronal activity that last only milliseconds trigger lasting changes in the brain, and open new fields of exploration for efforts to understand how the brain works.

{ Harvard Medical School | Continue reading }

art { Josef Albers, Hotel Staircase, Geneva, 1929/1932 }

I lie about my zodiac sign and watch people break down the person I’m not

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In what appears to be the first successful hack of a software program using DNA, researchers say malware they incorporated into a genetic molecule allowed them to take control of a computer used to analyze it. […]

To carry out the hack, researchers encoded malicious software in a short stretch of DNA they purchased online. They then used it to gain “full control” over a computer that tried to process the genetic data after it was read by a DNA sequencing machine.  

The researchers warn that hackers could one day use faked blood or spit samples to gain access to university computers, steal information from police forensics labs, or infect genome files shared by scientists.  

{ Technology Review | Continue reading }

Lift your head up high, and scream out to the world, I know I am someone

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The tendency of people to forge friendships with people of a similar appearance has been noted since the time of Plato. But now there is research suggesting that, to a striking degree, we tend to pick friends who are genetically similar to us in ways that go beyond superficial features.

For example, you and your friends are likely to share certain genes associated with the sense of smell.

Our friends are as similar to us genetically as you’d expect fourth cousins to be, according to the study published Monday in the Proceedings of the National Academy of Sciences. This means that the number of genetic markers shared by two friends is akin to what would be expected if they had the same great-great-great-grandparents. […]

The resemblance is slight, just about 1 percent of the genetic markers, but that has huge implications for evolutionary theory.

{ Washington Post | Continue reading }

polyvinyl chloride, colored with oil, mixed technique and accessories { Duane Hanson, Children Playing Game, 1979 }

The new What Went Wrong Foundation

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This study aims to investigate the frequency and amount of female DNA transferred to the penis and underwear of males following staged nonintimate social contact with females and to compare the findings with the amount of female DNA transferred to the penis and subsequently to the underwear of a male who had engaged in unprotected sexual intercourse with a female. […]

It was possible to demonstrate that DNA can occasionally transfer to the waistband and outside front of underwear worn by a male following staged nonintimate social contact.

{ Science & Justice | Continue reading }

An eye like Mars

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In 2012, a genetic analysis confirmed that Concetta’s enhanced color vision can be explained by a genetic quirk that causes her eyes to produce four types of cone cells, instead of the regular three which underpin colour vision in most humans. […]

Women with four cone types in their retinas are actually more common than we think. Researchers estimate that they represent as much as 12% of the female population. […] A woman has the potential to produce four cone types because she inherits two X-chromosomes. […]

The three cone types that most of us have in our retinas allow us to see millions of colours. Each cone’s membrane is packed with molecules, called opsins, which absorb lights of some wavelengths and cause the cone to send electrical signals to the brain. […]

Four cones don’t automatically grant you superior color vision. […] Only one of the seven women with four cones behaved as if she actually perceived differences between the colour mixtures that were invisible to everyone apart from her sons.

{ The Neurosphere | Continue reading }

They say any artist paying six dollars may exhibit

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Experts say fakes have become one of the most vexing problems in the art market. […]

Two years ago, the center, known for its work in bioengineering, encryption and nanotechnology, set about developing a way to infuse paintings, sculptures and other artworks with complex molecules of DNA created in the lab. […]

The new approach, in its formative stage, would implant synthetic DNA, not the personal DNA of the artists, because of privacy issues and because a person’s DNA could conceivably be stolen and embedded, thus undermining the authority of such a marking protocol.

The developers said the bioengineered DNA would be unique to each item and provide an encrypted link between the art and a database that would hold the consensus of authoritative information about the work. The DNA details could be read by a scanner available to anyone in the art industry wanting to verify an object.

{ NY Times | Continue reading }

installation { Yayoi Kusama, The obliteration room, 2002-present }

You try to scream, but terror takes the sound before you make it

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People with a certain type of gene are more deeply affected by their life experiences, a new study has revealed.

The findings challenge traditional thinking about depression, showing what might be considered a risk gene for depression in one context, may actually be beneficial in another.

Researchers at the University of Melbourne were interested in why some, but not all adults who have experienced sexual or physical abuse as children go on to develop long-term depression. […]

Those with the s/s genotype (23%) who had experienced sexual or physical abuse as a child were more likely to experience ongoing severe depressive symptoms in middle age. But, conversely, those with this same genotype but no history of abuse were happier than the rest of the population.

{ EurekAlert | Continue reading }

Fumbally’s lane that night: the tanyard smells.

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Most humans perceive a given odor similarly. But the genes for the molecular machinery that humans use to detect scents are about 30 percent different in any two people, says neuroscientist Noam Sobel. […] This variation means that nearly every person’s sense of smell is subtly different. [….]

Sobel and his colleagues designed a sensitive scent test they call the “olfactory fingerprint.” […] People with similar olfactory fingerprints showed similarity in their genes for immune system proteins linked to body odor and mate choice. […]

It has been shown that people can use smell to detect their genetic similarity to others and avoid inbreeding, says neuroscientist Joel Mainland of Monell Chemical Senses Center in Philadelphia.  

{ Science News | Continue reading }

photo { Juergen Teller, Octopussy, Rome, 2008 }

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 }