CRISPR Gene Editing

A DNA Time Capsule

For the first time, researchers have been able to extract DNA fragments from an ancient clay brick, demonstrating how these building blocks from times long past could be used to catalog flora found in the environment at the time.


When this brick was made some 2,900 years ago in what is now northern Iraq, the process would have involved mixing mud from the banks of the Tigris river, with materials such as chaff, straw, or animal dung.


Small plant particles amid the animal waste and straw can remain protected inside the brick for millennia – as has now been demonstrated by the team from the University of Oxford in the UK and the National Museum of Denmark and the University of Copenhagen in Denmark.


Having extracted a sample of the brick, the researchers used an analytical technique previously used on other forms of porous material, such as bone. This gave them the ability to sequence (or decode) the DNA in the plant matter, identifying 34 distinct taxonomic groups of plants.


"We were absolutely thrilled to discover that ancient DNA, effectively protected from contamination inside a mass of clay, can successfully be extracted from a 2,900-year-old brick," says biologist Sophie Lund Rasmussen from the University of Oxford.


The brick analyzed in this study was found in the palace of the Neo-Assyrian king Ashurnasirpal II, located in the ancient city of Kalhu. Dating it to some time between 879 and 869 BCE – the years the palace was under construction – was made easier by an inscription in the clay that specifically mentioned the palace.


Plant families with the most abundant DNA in the brick included Brassicaceae (the cabbage and mustard family) and Ericaceae (heather), while genetic material from Betulaceae (birch), Lauraceae (laurels), Selineae (the family containing carrots and parsley), and Triticeae (cultivated grasses) was also present.


"The brick serves as a biodiversity time capsule of information regarding a single site and its surroundings," says Assyriologist Troels Arbøll, from the University of Copenhagen.


"In this case, it provides researchers with a unique access to the ancient Assyrians."  READ MORE...

Quantum Memory Stores Information

Researchers at University of Oxford have recently created a quantum memory within a trapped-ion quantum network node. Their unique memory design, introduced in a paper in Physical Review Letters, has been found to be extremely robust, meaning that it could store information for long periods of time despite ongoing network activity.

"We are building a network of quantum computers, which use trapped ions to store and process quantum information," Peter Drmota, one of the researchers who carried out the study, told Phys.org. "To connect quantum processing devices, we use single photons emitted from a single atomic ion and utilize quantum entanglement between this ion and the photons."

Trapped ions, charged atomic particles that are confined in space using electromagnetic fields, are a commonly used platform for realizing quantum computations. Photons (i.e., the particles of light), on the other hand, are generally used to transmit quantum information between distant nodes. Drmota and his colleagues have been exploring the possibility of combining trapped ions with photons, to create more powerful quantum technologies.

"Until now, we have implemented a reliable way of interfacing strontium ions and photons, and used this to generate high-quality remote entanglement between two distant network nodes," Drmota said. "On the other hand, high-fidelity quantum logic and long-lasting memories have been developed for calcium ions. In this experiment, we combine these capabilities for the first time, and show that it is possible to create high-quality entanglement between a strontium ion and a photon and thereafter store this entanglement in a nearby calcium ion."

Integrating a quantum memory into a network node is a challenging task, as the criteria that need to be fulfilled for such a system to work are higher than those required for the creation of a standalone quantum processor. Most notably, the developed memory would need to be robust against concurrent network activity.   READ MORE...

Prehistoric Hunting in Desert

Aerial photo of a typical kite from eastern Jordan. Credit: APAAME

Archaeologists at the University of Oxford's School of Archaeology have used satellite imagery to identify and map more than 350 monumental hunting structures known as "kites" across northern Saudi Arabia and southern Iraq—most of which had never been previously documented.

Led by Dr. Michael Fradley, a team of researchers in the Endangered Archaeology in the Middle East and North Africa (EAMENA) project used a range of open-source satellite imagery to carefully study the region around the eastern Nafud desert, an area little studied in the past. The surprising results, published in the journal The Holocene, have the potential to change our understanding of prehistoric connections and climate change across the Middle East.

Termed kites by early aircraft pilots, these structures consist of low stone walls making up a head enclosure and a number of guiding walls, sometimes kilometers long. They are believed to have been used to guide game such as gazelles into an area where they could be captured or killed. There is evidence that these structures may date back as far as 8,000 BCE in the Neolithic period.

Kites cannot be observed easily from the ground, however the advent of commercial satellite imagery and platforms such as Google Earth have enabled recent discoveries of new distributions. While these structures were already well-known from eastern Jordan and adjoining areas in southern Syria, these latest results take the known distribution over 400km further east across northern Saudi Arabia, with some also identified in southern Iraq for the first time.  READ MORE...

Oldest Known Ingredients for Metal

RESEARCHERS HAVE IDENTIFIED THE INGREDIENTS IN FORMULAE FOR METAL FROM THE OLDEST KNOWN TECHNICAL ENCYCLOPAEDIA, THE KAOGONG JI.

The Kaogong ji, translated variously as the Record of Trades, Records of Examination of Craftsman, Book of Diverse Crafts or Artificers’ Record was written in China around the middle of the first millennium BC and is the oldest known technical encyclopaedia, detailing the methods used to make items such as swords and instruments, including six chemistry formulae for mixing bronze.

In a study published in the journal Antiquity, a team from the University of Oxford believe that they have identified Jin and Xi, previously thought to be copper and tin, two key components of bronze.

The study analysed the chemical composition of Chinese coins from the period the Kaogong ji was written, indicating that the coins were made by diluting copper with tin and lead to create the desired form of bronze by mixing two pre-prepared metal alloys: a copper-tin-lead alloy and a copper-lead alloy.

“These recipes were used in the largest bronze industry in Eurasia during this period,” said Dr Ruiliang Liu from the British Museum, “Attempts to reconstruct these processes have been made for more than a hundred years, but have failed.”

As well as shedding light on the enigmatic ancient recipe, this discovery also indicates ancient Chinese metallurgy was more complex than expected.  READ MORE...

Common Viruses and Alzheimer's

Varicella zoster virus (VZV), which commonly causes chickenpox and shingles, activates herpes simplex virus (HSV) from dormancy in neural tissue grown in vitro, which then leads to an increase in plaque deposits and decrease in neural signaling — hallmarks of Alzheimer’s disease. Credit: Tufts University

Shingles infection may awaken dormant neurological herpes viruses, causing inflammation and accumulation of Alzheimer’s associated proteins in the brain.

Alzheimer’s disease is the most common cause of dementia in older adults and the 7th leading cause of death in the United States, according to the National Institute on Aging. 

It is a debilitating progressive illness that slowly destroys cognitive function and memory.

It can begin almost imperceptibly, often masquerading in the early months or years as forgetfulness that is very common in older age. What causes Alzheimer’s disease remains largely a mystery.

But researchers using a three-dimensional human tissue culture model mimicking the brain, have shown that varicella zoster virus (VZV), which commonly causes chickenpox and shingles, may activate herpes simplex (HSV), another common virus, to set in motion the early stages of Alzheimer’s disease. 

The study was conducted by scientists at Tufts University and the University of Oxford.  READ MORE...

Math and Machine Learning

Machine learning makes it possible to generate more data than mathematician can in a lifetime

For the first time, mathematicians have partnered with artificial intelligence to suggest and prove new mathematical theorems. While computers have long been used to generate data for mathematicians, the task of identifying interesting patterns has relied mainly on the intuition of the mathematicians themselves. However, it’s now possible to generate more data than any mathematician can reasonably expect to study in a lifetime. Which is where machine learning comes in.

Two separate groups of mathematicians worked alongside DeepMind, a branch of Alphabet, Google’s parent company, dedicated to the development of advanced artificial intelligence systems. András Juhász and Marc Lackenby of the University of Oxford taught DeepMind’s machine learning models to look for patterns in geometric objects called knots. The models detected connections that Juhász and Lackenby elaborated to bridge two areas of knot theory that mathematicians had long speculated should be related. In separate work, Williamson used machine learning to refine an old conjecture that connects graphs and polynomials.

András Juhász and Marc Lackenby of the University of Oxford taught DeepMind’s machine learning models to look for patterns in geometric objects called knots. The models detected connections that Juhász and Lackenby elaborated to bridge two areas of knot theory that mathematicians had long speculated should be related. In separate work, Williamson used machine learning to refine an old conjecture that connects graphs and polynomials.

“The most amazing thing about this work and it really is a big breakthrough is the fact that all the pieces came together and that these people worked as a team,” said Radmila Sazdanovic of North Carolina State University.

Some observers, however, view the collaboration as less of a sea change in the way mathematical research is conducted. While the computers pointed the mathematicians toward a range of possible relationships, the mathematicians themselves needed to identify the ones worth exploring.

Our Brains and a Conscious Universe

As humans, we know we are conscious because we experience and feel things. Yet scientists and great thinkers are unable to explain what consciousness is and they are equally baffled about where it comes from.

"Consciousness — or better, conscious experience — is obviously a part of reality," said Johannes Kleiner, a mathematician and theoretical physicist at the Munich Center For Mathematical Philosophy, Germany. "We're all having it but without understanding how it relates to the known physics, our understanding of the universe is incomplete."

With that in mind, Kleiner is hoping math will enable him to precisely define consciousness. Working with colleague Sean Tull, a mathematician at the University of Oxford, U.K., the pair are being driven, to some degree, by a philosophical point of view called panpsychism.

This claims consciousness is inherent in even the tiniest pieces of matter — an idea that suggests the fundamental building blocks of reality have conscious experience. Crucially, it implies consciousness could be found throughout the universe.

If the researchers can answer how our brains give rise to subjective experience, there's a chance their mathematical model could extend to inanimate matter too, they said.

"A mathematical theory can be applied to many different systems, not just brains," Kleiner told All About Space via email. "If you develop a mathematical model of consciousness based on data obtained from brains, you can apply the model to other systems, for example, computers or thermostats, to see what it says about their conscious experience too."

Some prominent minds lend weight to the view of panpsychism, not least renowned Oxford physicist Sir Roger Penrose, who was among the first academics to propose we go beyond neuroscience when looking at consciousness.  TO READ MORE, CLICK HERE...