Posts tagged genetics
Articles and news from the latest research reports.
New genetic data shows humans and great apes diverged earlier than thought
To calculate when a species diverged, researchers look at the average age of members of the species when they give birth and mutation rates. The older the average age, the more time it takes for mutations to cause changes. Insects that produce offspring in a matter of months, for example, can adapt much more quickly to environmental changes than large animals that produce offspring many years after they themselves are born. To find such data for both chimps and gorillas, the research team worked with many groups in Africa that included studies of the animals that totaled 105 gorillas and 226 chimps. They also looked at fossilized excrement that contained DNA data. In so doing they found that the average age of giving birth for female chimps was 25 years old. They then divided the number of mutations found by the average age of birth to get the mutation rate. In so doing, they found it to be slower than humans, which meant that estimates based on it to calculate divergence times were likely off by as much as a million years.
The end result of the team’s research indicates that humans and chimps likely diverged some seven to eight million years ago, while the divergence of gorillas (which led to both humans and chimps) came approximately eight to nineteen million years ago. To put the numbers in perspective, humans and Neanderthals split just a half to three quarters of a million years ago.
The collapse of the Fukushima Dai-ichi Nuclear Power Plant caused a massive release of radioactive materials to the environment. A prompt and reliable system for evaluating the biological impacts of this accident on animals has not been available. Here we show that the accident caused physiological and genetic damage to the pale grass blue Zizeeria maha, a common lycaenid butterfly in Japan. We collected the first-voltine adults in the Fukushima area in May 2011, some of which showed relatively mild abnormalities. The F1 offspring from the first-voltine females showed more severe abnormalities, which were inherited by the F2 generation. Adult butterflies collected in September 2011 showed more severe abnormalities than those collected in May. Similar abnormalities were experimentally reproduced in individuals from a non-contaminated area by external and internal low-dose exposures. We conclude that artificial radionuclides from the Fukushima Nuclear Power Plant caused physiological and genetic damage to this species.
The UT Dallas “tag and track” method not only sheds light on how DNA loops form, but also might be adapted to screen drugs for effectiveness against certain viruses that shuffle genetic material, such as HIV.
Until now, scientists primarily had “snapshots” of the initial and final stages of DNA loop formation, with only limited information about what happens during the intermediate steps.
"Scientists have known for more than 30 years that DNA looping is an important part of molecular biology and gene regulation, but until our work, there have been few serious attempts to understand the basic biophysics of the process, … We estimate that using fluorescence-based methods such as this for drug screening could be as much as 10,000 times more efficient than methods that are currently used," -Dr. Stephen Levene, professor of bioengineering, molecular and cell biology, and phyiscs at UT Dallas.
Scientists have found a way of growing new blood vessels inside the body. They used cells derived from skin, that when injected into a damaged leg in massive numbers, moulded into the shape of a small blood vessel. This improved blood supply to withered muscles, giving them a new lease of life.
The technique, developed at King’s College London, could also be used to repair the damage done by heart attacks. Professor Qingbo Xu, who is funded by the British Heart Foundation, started by taking human skin cells. Using a cocktail of genes and chemicals, he turned them into early-stage blood vessel cells, programmed to form blood vessels.
He then injected half a million of these cells into the hind leg of a mouse whose foot muscles had been damaged due to poor circulation. These formed a small blood vessel that ferried blood to the damaged muscle, allowing it to repair itself, enabling the creature to put some weight on its foot, the journal Proceedings of the National Academy of Sciences reports.
The professor hopes that injected into the heart, the same cells could be used to heal damage done by heart attacks.
The Cosmological Foundations of Consciousness explores the cosmological foundations of subjective consciousness in the biological brain, from cosmic-symmetry-breaking, through biogenesis, evolutionary diversification and the emergence of metazoa, to humans, presenting a new evolutionary perspective on the potentialities of quantum interactions in consciousness, and the ultimate relationship of consciousness with cosmology.
Cosmic symmetry-breaking and its interactive fractal and chaotic effects leading to biogenesis.
(a) Life portrayed as the consummation of interactive complexity (Σ) resulting from symmetry-breaking of the fundamental force of nature in the big-bang (α), whatever ultimate fate is in store (Ω). Inset (i) possible fractal inflation , (ii) the distribution of dark energy and matter and the matter of stars and planets. (b) Logarithmic time scale of cosmological events showing life on earth existing for a third of the universe’s current lifetime. (c) Symmetry-breaking of the forces of nature results in the color and weak forces generating 100 atomic nuclei, while gravity and electromagnetism govern long-range structure determining biogenesis, from fractal chemical bonding, to solar systems capable of photosynthetic life in the goldilocks zone of liquid water. (d) Interactive effects of cosmic symmetry-breaking lead to hierarchical interaction of the forces, generating hadrons, atomic nuclei and molecules (i). Non-linear energetics of chemical bonding lead to a cascade of cooperative weak-bonding effects, which generate fractal molecular complexity, from the molecular orbitals of simple molecules (ii), through the 3D structures of complex proteins and nucleic acids (iii) to supra-molecular cell organelles (iv), cells (v), and tissues (vi) and organisms. (e) These fractal effects are complemented by the chaotic effects of gravity as a non-linear force, resulting in extreme variation of the planets, generating a diversity of potential conditions for biogenesis, similar to the dynamic variations surrounding the Mandelbrot set.
Cancer May Result From Wrong Number of Genes
When a young person develops cancer, doctors most often assume that genetics are the reason, because the patient hasn’t lived long enough to accumulate environmental damage. But it’s been hard to find the faulty DNA behind many tumors. Now, using new genomic technology, scientists have discovered a novel explanation for some testicular cancers, the most common cause of cancer in men under 35. Rather than being triggered by a single gene mutation, the tumors are caused by too many or too few copies of a gene in a person’s cells. These “copy number variations” have been linked to other conditions such as autism, but never before to cancer.
Do Ovaries Continue to Produce Eggs During Adulthood?
A compelling new genetic study tracing the origins of immature egg cells, or ‘oocytes’, from the embryonic period throughout adulthood adds new information to a growing controversy. The notion of a “biological clock” in women arises from the fact that oocytes progressively decline in number as females get older, along with a decades-old dogmatic view that oocytes cannot be renewed in mammals after birth.
After careful assessment of data from a recent study published in PLoS Genetics, scientists from Massachusetts General Hospital and the University of Edinburgh argue that the findings support formation of new eggs during adult life; a topic that has been historically controversial and has sparked considerable debate in recent years.
Chemical Makes Blind Mice See; Compound Holds Promise for Treating Humans
ScienceDaily (July 25, 2012) — A team of University of California, Berkeley, scientists in collaboration with researchers at the University of Munich and University of Washington, in Seattle, has discovered a chemical that temporarily restores some vision to blind mice, and is working on an improved compound that may someday allow people with degenerative blindness to see again.
Mice with a genetic disease that causes blindness regained some sight after injection with a chemical “photoswitch.” The eye of the untreated mouse on the left shows no response to light, while the pupil of the mouse on the right, which was injected with the chemical, contracts in light. (Credit: Image courtesy of University of California - Berkeley)
The approach could eventually help those with retinitis pigmentosa, a genetic disease that is the most common inherited form of blindness, as well as age-related macular degeneration, the most common cause of acquired blindness in the developed world. In both diseases, the light sensitive cells in the retina — the rods and cones — die, leaving the eye without functional photoreceptors.
The chemical, called AAQ, acts by making the remaining, normally “blind” cells in the retina sensitive to light, said lead researcher Richard Kramer, UC Berkeley professor of molecular and cell biology. AAQ is a photoswitch that binds to protein ion channels on the surface of retinal cells. When switched on by light, AAQ alters the flow of ions through the channels and activates these neurons much the way rods and cones are activated by light.
"This is similar to the way local anesthetics work: they embed themselves in ion channels and stick around for a long time, so that you stay numb for a long time," Kramer said. "Our molecule is different in that it’s light sensitive, so you can turn it on and off and turn on or off neural activity."
Because the chemical eventually wears off, it may offer a safer alternative to other experimental approaches for restoring sight, such as gene or stem cell therapies, which permanently change the retina. It is also less invasive than implanting light-sensitive electronic chips in the eye.
"The advantage of this approach is that it is a simple chemical, which means that you can change the dosage, you can use it in combination with other therapies, or you can discontinue the therapy if you don’t like the results. As improved chemicals become available, you could offer them to patients. You can’t do that when you surgically implant a chip or after you genetically modify somebody," Kramer said.
"This is a major advance in the field of vision restoration," said co-author Dr. Russell Van Gelder, an ophthalmologist and chair of the Department of Ophthalmology at the University of Washington, Seattle.
Kramer, Van Gelder, chemist Dirk Trauner and their colleagues at UC Berkeley, the University of Washington, Seattle, and the University of Munich will publish their findings on July 26, in the journal Neuron.
The blind mice in the experiment had genetic mutations that made their rods and cones die within months of birth and inactivated other photopigments in the eye. After injecting very small amounts of AAQ into the eyes of the blind mice, Kramer and his colleagues confirmed that they had restored light sensitivity because the mice’s pupils contracted in bright light, and the mice showed light avoidance, a typical rodent behavior impossible without the animals being able to see some light. Kramer is hoping to conduct more sophisticated vision tests in rodents injected with the next generation of the compound.
"The photoswitch approach offers real hope to patients with retinal degeneration," Van Gelder said. "We still need to show that these compounds are safe and will work in people the way they work in mice, but these results demonstrate that this class of compound restores light sensitivity to retinas blind from genetic disease."
From optogenetics to implanted chips
The current technologies being evaluated for restoring sight to people whose rods and cones have died include injection of stem cells to regenerate the rods and cones; “optogenetics,” that is, gene therapy to insert a photoreceptor gene into blind neurons to make them sensitive to light; and installation of electronic prosthetic devices, such as a small light-sensitive retinal chip with electrodes that stimulate blind neurons. Several dozen people already have retinal implants and have had rudimentary, low vision restored, Kramer said.
Eight years ago, Kramer, Trauner, a former UC Berkeley chemist now at the University of Munich, and their colleagues developed an optogenetic technique to chemically alter potassium ion channels in blind neurons so that a photoswitch could latch on. Potassium channels normally open to turn a cell off, but with the attached photoswitch, they were opened when hit by ultraviolet light and closed when hit by green light, thereby activating and deactivating the neurons.
Subsequently, Trauner synthesized AAQ (acrylamide-azobenzene-quaternary ammonium), a photoswitch that attaches to potassium channels without the need to genetically modify the channel. Tests of this compound are reported in the current Neuron paper.
New versions of AAQ now being tested are better, Kramer said. They activate neurons for days rather than hours using blue-green light of moderate intensity, and these photoswitches naturally deactivate in darkness, so that a second color of light is not needed to switch them off.
"This is what we are really excited about," he said.
Source: Science Daily
Gene Therapy Holds Promise for Reversing Congenital Hearing Loss
ScienceDaily (July 25, 2012) — A new gene therapy approach can reverse hearing loss caused by a genetic defect in a mouse model of congenital deafness, according to a preclinical study published by Cell Press in the July 26 issue of the journal Neuron. The findings present a promising therapeutic avenue for potentially treating individuals who are born deaf.
(Credit: © Vasiliy Koval / Fotolia)
"This is the first time that an inherited, genetic hearing loss has been successfully treated in laboratory mice, and as such represents an important milestone for treating genetic deafness in humans," says senior study author Lawrence Lustig of the University of California, San Francisco.
Hearing loss is one of the most common human sensory deficits, and it results from damage to hair cells in the inner ear. About half of the cases of congenital hearing loss are caused by genetic defects. However, the current treatment options — hearing amplification devices and cochlear implants — do not restore hearing to normal levels. Correcting the underlying genetic defects has the potential to fully restore hearing, but previous attempts to reverse hearing loss caused by genetic mutations have not been successful.
Addressing this challenge in the new study, Lustig and his team used mice with hereditary deafness caused by a mutation in a gene coding for a protein called vesicular glutamate transporter-3 (VGLUT3). This protein is crucial for inner hair cells to send signals that enable hearing. Two weeks after the researchers delivered the VGLUT3 gene into the inner ear through an injection, hearing was restored in all of the mice. This improvement lasted between seven weeks and one and a half years when adult mice were treated, and at least nine months when newborn mice received the treatment.
The therapy did not damage the inner ear, and it even corrected some structural defects in the inner hair cells. Because the specific gene delivery method used is safe and effective in animals, the findings hold promise for future human studies. “For years, scientists have been hinting at the possibility of gene therapy as a potential cure for deafness,” Lustig says. “In this study, we now provide a very real and big step towards that goal.”
Source: Science Daily
Californian biotech firm Life Technologies is the first team to register for the $10 million (£6.4m) Archon Genomics X Prize, which will be a race to sequence the genomes of 100 centenarians.
The prize was first announced in 2006, and is a joint effort between the X Prize Foundation and geneticist J Craig Venter. It’s supposed to stimulate the development of less expensive sequencing technologies, and establish a clinical standard for DNA research.
Interested parties have until May 2013 to register. Late that year, in September, each team will have 30 days to sequence the genomes of 100 people, at a cost of $1,000 (£643) or less.
The DNA has been donated by 100 100 year old people from all over the world, to make the competition “scientifically valuable and more meaningful to the general public”. That way, the prize can double up as medical research into the science of healthy aging and longevity.
Life Technologies’ secret weapon is the Ion Proton Sequencer, which it describes as a “semiconductor device that enables chemical signals to be directly translated into digital information for the first time” — a bit like the CMOS imager in an iPhone, which turns photons into electrons.
"It would have cost $100 million and taken 33 years to meet this challenge when the competition was announced in 2006," said Jonathan Rothberg, CEO and founder of Life Technology’s Ion Torrent brand. "The Ion Proton sequencer is designed to sequence a human genome for $1,000 in just a few hours."
Source: Wired