Scientists Build ‘Mechanically Active’ DNA Material That Responds With Movement When Stimulated

Artificial muscles and self-propelled goo may be the stuff of Hollywood fiction, but for UC Santa Barbara scientists Omar Saleh and Deborah Fygenson, the reality of it is not that far away. By blending their areas of expertise, the pair have created a dynamic gel made of DNA that mechanically responds to stimuli in much the same way that cells do.

The results of their research were published online in the Proceedings of the National Academy of Sciences.

"This is a whole new kind of responsive gel, or what some might call a ‘smart’ material," said Saleh, associate professor of materials, affiliated with UCSB’s Biomolecular Science and Engineering program. "The gel has active mechanical capabilities in that it generates forces independently, leading to changes in elasticity or shape, when fed ATP molecules for energy — much like a living cell."

Their DNA gel, at only 10 microns in width, is roughly the size of a eukaryotic cell, the type of cell of which humans are made. The miniscule gel contains within it stiff DNA nanotubes linked together by longer, flexible DNA strands that serve as the substrate for molecular motors.

"DNA gives you a lot more design control," said Fygenson, associate professor of physics and also affiliated with UCSB’s BMSE program. "This system is exciting because we can build nano-scale filaments to specifications." Using DNA design, she said, they can control the stiffness of the nanotubes and the manner and extent of their cross-linking, which will determine how the gel responds to stimuli.

Complete mitochondrial DNA genome sequences from the first New Zealanders

The dispersal of modern humans across the globe began ∼65,000 y ago when people first left Africa and culminated with the settlement of East Polynesia, which occurred in the last 1,000 y. With the arrival of Polynesian canoes only 750 y ago, Aotearoa/New Zealand became the last major landmass to be permanently settled by humans. We present here complete mitochondrial genome sequences of the likely founding population of Aotearoa/New Zealand recovered from the archaeological site of Wairau Bar. These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia.

Neuroscientists propose a revolutionary DNA-based approach to map wiring of the whole brain

A team of neuroscientists have proposed a new and potentially revolutionary way of obtaining a neuronal connectivity map (the “connectome”) of the whole brain of the mouse. The details are set forth in an essay published October 23 in the open-access journal PLOS Biology.

The team, led by Professor Anthony Zador, Ph.D., of Cold Spring Harbor Laboratory, aims to provide a comprehensive account of neural connectivity. At present the only method for obtaining this information with high precision relies on examining individual cell-to-cell contacts (synapses) in electron microscopes. But such methods are slow, expensive and labor-intensive.

Zador and colleagues instead propose to exploit high-throughput DNA sequencing to probe the connectivity of neural circuits at the resolution of single neurons.

“Our method renders the connectivity problem in a format in which the data are readable by currently available high-throughput genome sequencing machines,” says Zador. “We propose to do this via a process we’re now developing, called BOINC: the barcoding of individual neuronal connections.”

The proposal comes at a time when a number of scientific teams in the U.S. are progressing in their efforts to map connections in the mammalian brain. These efforts use injections of tracer dyes or viruses to map neuronal connectivity at a “mesoscopic” scale—a mid-range resolution that makes it possible to follow neural fibers between brain regions.  Other groups are scaling up approaches based on electron microscopy.

Transgendered bellbird found in New Zealand

Biologists at the Zealandia eco-sanctuary in New Zealand have spotted a bellbird that exhibits features and behaviour of both male and female members of the species.

The bird hatched in early 2011, and DNA testing then showed it as female, but since then its development has been rather different to normal female korimakos.

Normally, female bellbirds have a white feather pattern but the chick bean to show signs of the dark plumage normally seen on male birds. It also began to behave in a masculine way, not flitting between flowers like a female bellbird but instead moving with purpose, ready to defend its territory.

The bird’s calls are unusual too. It makes both male calls and the distinctive “chup chup” normally heard from females, but the latter are louder and more frequent that is normal.

Zealandia conservation officer Erin Jeneway told the Dominion Post: “There’s something we can’t pin down. We haven’t seen anything like this before”. Victoria University biologist Ben Bell added: “It could be due to a hormonal imbalance or it could be a reaction to shock or an incomplete moult — given the appearance and behaviour, any of those would be unusual though.”

The Date of Interbreeding between Neandertals and Modern Humans

Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa. However, it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa. We measure the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.

Male DNA in women’s brains could protect against Alzheimer’s

Researchers found that up to two thirds of women carry male DNA in their brain, which was most likely passed on to them while pregnant with sons.

The exact medical consequences of the transfer from foetus to mother remains unclear but a study showed it was less common in women who suffered from Alzheimer’s, suggesting that it could offer protection against the condition.

Previous studies insicate that similar processes of DNA transfer could raise the risk of some cancers, such as breast cancer, and lower the risk of others including cancer of the colon.

The new study of brain tissue taken from 59 women who died aged 32 to 101 found male DNA in 63 per cent of specimens.

The findings, published in the Public Library of Science ONE journal, also showed that the male DNA was less common in the parts of the brain most severely damaged by Alzheimer’s.

But the researchers, from the Fred Hutchinson Cancer Research Centre in Seattle, emphsaised that the small scale of the study and the lack of data on the women’s pregnancy history meant the evidence was not conclusive.

Dr William Chan, who led the project, said: “Currently, the biological significance of harbouring male DNA and male cells in the human brain requires further investigation.”

The zebrafish is a major player in the study of vertebrate biology and human disease. Its transparent, externally fertilized eggs, short reproductive cycle and fast growth mean that its embryonic development can be studied closely while the animal is alive, and the fish is a useful model for studying gene behaviour and function.

Now, researchers led by Stephen Ekker, a molecular biologist at the Mayo Clinic in Rochester, Minnesota, have for the first time made custom changes to parts of the zebrafish (Danio rerio) genome, using artificial enzymes to cut portions of DNA out of targeted positions in a gene sequence, and replace them with synthetic DNA.

According to ENCODE’s analysis, 80 percent of the genome has a “biochemical function”. More on exactly what this means later, but the key point is: It’s not “junk”.

Scientists have long recognised that some non-coding DNA has a function, and more and more solid examples have come to light [edited for clarity - Ed]. But, many maintained that much of these sequences were, indeed, junk. ENCODE says otherwise. “Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more,” says Tom Gingeras, one of the study’s many senior scientists.

And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”

That the genome is complex will come as no surprise to scientists, but ENCODE does two fresh things: it catalogues the DNA elements for scientists to pore over; and it reveals just how many there are. “The genome is no longer an empty vastness – it is densely packed with peaks and wiggles of biochemical activity,” says Shyam Prabhakar from the Genome Institute of Singapore. “There are nuggets for everyone here. No matter which piece of the genome we happen to be studying in any particular project, we will benefit from looking up the corresponding ENCODE tracks.”

High quality Denisovan genome sheds light on human evolution: Sequencing our extinct relatives let us know how we differ from chimps.

The discovery that a second branch of the human family shared Asia with our ancestors and the Neanderthals was a real shock, but the Denisovans have continued to surprise many. All we have of them is a bit of a finger and some molars, but those few fragments have yielded a wealth of DNA, and with it the knowledge that the Denisovans interbred with the ancestors of some modern human populations. Now, with the help of a new approach to sequencing ancient DNA, we actually know more about the Denisovans’ genome than we do about Neanderthals’. In the process, we’ve discovered some of the changes that are distinct to modern humans.

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Expectant mothers are used to fuzzy images on ultrasound monitors and blood tests to screen for potential health problems in their unborn babies. But what if one of those blood tests came back with a readout of the baby’s entire genome? What if a simple test gave parents every nuance of a baby’s genetic makeup before birth?

Recent studies show that it’s possible to decode an entire fetal genome from a sample of the mother’s blood. In the future, doctors may be able to divine a wealth of information about genetic diseases or other characteristics of a fetus from the pregnant mother’s blood. Such tests will raise ethical questions about how to act on such information. But they could also lead to research on treating diseases before birth, and leave parents and their doctors better prepared to care for babies after birth.

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