Tag Archives: dna

Pap tests could one day tell women if they have breast or ovarian cancer

Experts have identified changes in a woman’s cervix that can help detect tumors elsewhere in the body. These tests involve scraping cells from the cervix to detect any abnormalities that could cause cervical cancer. But researchers from Innsbruck University and gynecological cancer research charity The Eve Appeal found the cells from this test can also give clues and alerts for other types of cancers. With development, they state that the method used could one day predict the risk of developing ovarian, breast, womb, and cervical cancers from a straightforward smear pap test.

They developed their system using a process known as DNA methylation — epigenetic modifications to DNA that don’t alter the genetic sequence but do determine whether a gene expresses or stifles its function: in this case, forming or preventing cancer in the body. These modifications leave ‘methylation markers or signatures’ on genomic regions that scientists can read to determine what has occurred within a person’s body throughout their lifetime. Akin to the rings of a tree, this method can provide chronological clues as to what has happened in our biological life.

Researchers created the test, dubbed WID (Women’s Risk Identification), to analyze markers left by cancerous activity in the DNA of cervical cells. By calculating a woman’s WID, they hope to identify those with a high risk of developing ovarian, breast, womb, or cervical cancers: providing an early-warning system for medical teams to increase treatment outcomes.

The team was able to spot these modifications because they matched DNA markers found in diseased cervical, breast, ovarian, and womb biopsy tissue (a highly invasive procedure) to those found in the easier to access cells of the cervix — whose similar biological structures undergo the same hormonal changes as the tissues these cancers flourish in.

Finding cancer through the cervix

The first study examined cervical cell samples collected from 242 women with ovarian cancer and 869 healthy controls. To develop the WID risk scale, the scientists measured 14,000 epigenetic changes to identify ovarian cancer’s unique DNA signature to spot the presence of the disease in epithelial tissue scraped from the cervix.

They then validated the signature in an additional cohort of 47 women who had ovarian cancer and 227 healthy subjects. Results identified 71% of women under 50 and roughly 55% of the volunteers older than 50 who had previously tested positive for the disease — giving the tests an overall specificity of 75%. A test’s specificity is its ability to correctly identify people without the disease.

Professor Martin Widschwendter of the University of Innsbruck and UCL, heading up the research, said the findings suggest their WID index is picking up cancer predisposition, adding that the results were similar to a study on women with cancer of the womb. He is adamant their test cannot predict ovarian, with more studies needed.

A possible screening method for an undetectable cancer 

In the second study, the same team analyzed epigenetic changes in cervical cell samples provided by 329 women with breast cancer against those from the same 869 healthy volunteers in the first study. Using the WID index, they were able to identify women with breast cancer based on a unique epigenetic signature. The group once again confirmed these markers in a smaller consort of 113 breast cancer patients and 225 women without this condition.

The researchers also used the patterns to predict whether patients had breast cancer-but they didn’t say exactly how accurate the tests were. Instead, they stressed that further trials are needed-with the hope that clinicians could use their WID as a regular test for women in the future-specifically for those under fifty years of age who do not have access to screening for this disease.

“This research is incredibly exciting,” said Liz O’Riordan, a breast cancer surgeon who was also diagnosed with this disease. “At the moment, there is no screening test for breast cancer in women under the age of 50. If this test can help pick up women with a high risk of developing breast, ovarian, cervical, and uterine cancer at a younger age, it could be a game-changer.”

The team adds that these findings are also crucial for ovarian cancer, whose symptoms can be as benign as a bloated abdomen. The biggest killer of women out of gynecological-based tumors, this disease is diagnosed late by clinicians in an alarming 3 out of four cases.

But for now, Widschwendter says, the findings suggest that the molecular signatures in cervical cells may detect the predisposition to other women-specific cancers rather than providing a solid prediction of the disease.

Because of the pandemic, women have stopped taking pap tests

A pap smear test detects abnormal cells on the cervix, which is the entrance to the uterus from the vagina. Removing these cells can prevent cervical cancer, which most commonly affects sexually-active women aged between 30 and 45. In most cases, the human papillomavirus causes this cancer after being acquired through unprotected sex or skin-to-skin contact. To summarise, the whole point of these tests is to detect women at risk of developing cancer and encourage them to carry further health check-ups, not to find those displaying cancer symptoms.

Around the world, the number of women taking smear tests has dropped substantially during the pandemic. In England, for instance, one of the countries with the highest testing rates, just 7 out of 10 eligible women got a cervical check-up — and conditions are expected to worsen due to a new policy brought in by the UK government at the start of 2022, which saw all eligible women in Wales have their wait times increased from three to five years in between tests. The government expects to roll out the policy in England this year after the pandemic caused the delay of its initial release. Experts insisted the move was safe, but campaigners hit back at the plans, arguing it would cause preventable deaths by delaying the detection of cancer or pre-cancerous issues.

In a statement to the Guardian, the UK’s Secretary for Patient Safety and Primary Care says it’s “great to see how this new research could help alert women who are at higher risk to help prevent breast, ovarian, womb, and cervical cancer before it starts.” Until this time, cancer screening remained vital and urged all women aged 25 and above to attend their appointments when invited. The secretary did not remark on the new government policy.

An ovarian cancer specialist urged caution in interpreting the data: They show a “moderate association” between the methylation signature and ovarian cancer, said Dr. Rebecca Stone, the Kelly Gynecologic Oncology Service director at Johns Hopkins Hospital. “They are not showing that it’s predictive or diagnostic,” Stone stressed. Clarifying that to see whether the cervical cell signature predicts cancer, a study would have to observe a large group of women over a long period.

Filling the gap in screening options for women

In contrast, Athena Lamnisos, CEO of the Eve Appeal, emphasizes the importance of a new screening tool:

“Creating a new screening tool for the four most prevalent cancers that affect women and people with gynae organs, particularly the ones which are currently most difficult to detect at an early stage, from a single test could be revolutionary.”

The Eve Appeal goes on that women could get separate risk scores for each of the four cancers in the future where medical teams could offer those with high scores more active monitoring, regular mammograms, risk-reducing surgery, or therapeutics.

Ultimately, it’s better to prevent than to treat, and this method could offer women worldwide access to proper screening services that could save lives through the application of early intervention and preventative medicine.

World’s tiniest antenna is made from DNA

Illustration of the fluorescent-based DNA antennae. Credit: Caitlin Monney.

Chemists at the Université de Montréal have devised a nano-scale antenna using synthetic DNA to monitor structural changes in proteins in real-time. It receives light in one color and, depending on the interaction with the protein it senses, transmits light back in a different color, which can be detected. The technology could prove useful in drug discovery and the development of new nanotechnologies.

DNA contains all the instructions needed for an organism to develop, survive, and reproduce. The blueprint of life is also extremely versatile thanks to the self-assembly of DNA building blocks.

Using short, synthetic strands of DNA that work like interlocking Lego bricks, scientists can make all sorts of nano-structures for more sophisticated applications than ever possible before. These include “smart” medical devices that target drugs selectively to disease sites, programmable imaging probes, templates for precisely arranging inorganic materials in the manufacturing of next-generation computer circuits, and more.

Inspired by these properties, the Canadian researchers led by chemistry professor Alexis Vallée-Bélisle have devised a DNA-based fluorescent nanoantenna that can characterize the function of proteins.

“Like a two-way radio that can both receive and transmit radio waves, the fluorescent nanoantenna receives light in one color, or wavelength, and depending on the protein movement it senses, then transmits light back in another color, which we can detect,” said Professor Vallée-Bélisle.

The receiver of the nanoantenna reacts chemically with molecules on the surface of the target proteins. The 5-nanometer-long antenna produces a distinct signal when the protein is performing a certain biological function, which can be detected based on the light released by the DNA structure.

“For example, we were able to detect, in real-time and for the first time, the function of the enzyme alkaline phosphatase with a variety of biological molecules and drugs,” said Harroun. “This enzyme has been implicated in many diseases, including various cancers and intestinal inflammation.”

These nanoantennas can be easily tweaked to optimize their function and size for a range of functions. For instance, it’s possible to attach a fluorescent molecule to the synthesized DNA and then attach the entire setup to an enzyme, allowing you to probe its biological function. Furthermore, these crafty DNA-based machines are ready-to-use for virtually any research lab across the world. Vallée-Bélisle is now working on setting up a startup to bring this product to the market.

“Perhaps what we are most excited by is the realization that many labs around the world, equipped with a conventional spectrofluorometer, could readily employ these nanoantennas to study their favorite protein, such as to identify new drugs or to develop new nanotechnologies,” said Vallée-Bélisle.

The findings appeared in the journal Nature Methods.

New breakthrough gets us closer to using DNA as data storage

The world is facing an unexpected problem: the speed at which we produce data is largely outpacing our ability to store said data. But help could be on the way — and not the help you’re probably expecting. Two groups of researchers have recently taken important steps towards using DNA as storage, one coming up with a new microchip and another one finding a way to write data faster in DNA format. 

Image credit: Flickr / Tom Woodward.

There’s a 20.4% growth every year in demand for data storage, which could reach nine zettabytes by 2024 — 1,000,000,000,000 gigabytes. This is more problematic than it seems at first glance because current methods of storage are having a difficult time keeping up with such demand. This is where synthetic DNA enters as a tiny storer of information.

DNA could help to reduce the amount of space and material needed for data storage needs in the future. It has a clear advantage over current storage media and could be a potential solution to challenges in data needs. It can be very durable, lasting thousands of years, and even have lower greenhouse gas emissions. A win-win deal — if we can get it to work.

Despite its advantages, there are still many barriers preventing DNA storage from becoming a reality, including the speed and current costs to synthesize DNA. Now, a research group at Microsoft has found a new way to write DNA with a chip that is 1000 times faster than before – allowing a higher write throughout and consequently lowering the costs associated to writing. 

The team at Microsoft worked with the University of Washington at the Molecular Information Laboratory (MISL) on the new chip, “demonstrating the ability to pack DNA-synthesis spots three orders of magnitude more tightly than before” and “shows that much higher DNA writing throughput can be achieved,” they wrote. 

For Microsoft, one of the main players in cloud storage, this kind of development would be a big plus amid a growing demand for data. To put this into numbers, about three billion personal computers are estimated to have been shipped around the world since 2011. And that number could keep on growing in the near future. 

A high-speed microchip

Alongside the research team from Microsoft, a team at the Georgia Tech Research Institute (GTRI) has recently taken another big step to store information as molecules of DNA. They have developed a working prototype of a microchip at their lab that they argue would improve on existing technology for DNA storage by a factor of 100. 

The record for writing DNA currently stands at 200MB per day, which means the new chip would increase that to 20GB per day – equivalent to 8GB per hour. In comparison, LTO-9, the most recent tape technology, reaches up to 1440GB per hour. Still, DNA storage is barely taking its first steps, with no commercially products available yet. The speed isn’t there yet, but it’s progressing quickly.

The microchip is about 2,5 centimeters (or one inch) square and comes with multiple microwells — microwells being the structures that allow DNA strands to be synthesized simultaneously. But as it’s only a prototype, and there’s plenty of work to be done.

However, the researchers have already partnered up with two companies to explore how to bring down the costs of the chip and make it robust enough to be used practically..

The study from Microsoft can be accessed here, while the study from GTRI was published in the journal Science Advances.

Scientists may have finally sequenced the entire human genome

In 2003, after nearly $3 billion in funding and 13 years of painstaking research, scientists with the Human Genome Project (HGP) announced they had finally mapped the first human genome sequence. This was a momentous breakthrough in science that would revolutionize genomics. However, the initial draft and updates of the human genome sequence that followed were not 100% complete. But now, scientists with the  Telomere-to-Telomere (T2T) Consortium claim they’ve addressed the remaining 8% of the human genome that was missing.

“The Telomere-to-Telomere (T2T) Consortium has finished the first truly complete 3.055 billion base pair (bp) sequence of a human genome, representing the largest improvement to the human reference genome since its initial release,” wrote the scientists in a paper published in the pre-print server bioRxiv, meaning it has yet to be peer-reviewed.

The first truly complete genome of a vertebrate

The genome is the sum of all the DNA and mitochondrial DNA (mtDNA) sequences in the cell. It contains all the instructions a living being needs to survive and replicate, consisting of chemical building blocks or “bases” (G, A, T, and C), whose order encodes biological information.

In diploid organisms, such as humans, the size of the genome is considered to be the total number of bases in one copy of its nuclear DNA. Humans and other mammals contain duplicate copies of almost all of their DNA. For instance, we have pairs of chromosomes, with one chromosome of each pair inherited from each parent. But scientists are only interested in sequencing the sum of the bases of one copy of each chromosome pair. A person’s actual genome is roughly six billion bases in size, but a single “representative” copy of the human genome is about three billion bases in size.

Because the human genome is so large, its bases cannot be read in order end-to-end in one single step. What HGP scientists did to sequence the genome was to first break down the DNA into smaller pieces, with each piece then subjected to various chemical reactions that allowed the identity and order of its bases to be deduced. These bits and pieces were then put back together to deduce the sequence of the starting genome.

Although genome sequencing technology has advanced a lot since the HGP announced the first draft of the human genome in 2001, a complete sequence of the entire genome was never achieved. Around 8% of the genome was missing, which corresponds to areas where DNA sequences are made up of long repeating patterns. Some of these repeating patterns, such as those found in the centromeres of chromosomes (the ‘knot’ that ties chromosomes together), play important biological roles, but standard technology hasn’t been able to decode them properly.

Using revolutionary new technology, scientists affiliated with T2T now claim that they’ve filled these gaps.

“You’re just trying to dig into this final unknown of the human genome,” Karen Miga, a researcher at the University of California, Santa Cruz, who co-led the international consortium, told STAT News. “It’s just never been done before and the reason it hasn’t been done before is because it’s hard.”

According to Miga and colleagues, the genome breakthrough was made possible thanks to new DNA sequencing technologies developed by Pacific Biosciences in California and Oxford Nanopore in the UK. These technologies do not cut the DNA into tiny pieces for later assembly, which can result in errors. Instead, Oxford Nanopore tech runs the DNA molecule through a nanoscopic hole, resulting in a long sequence. Meanwhile, lasers developed by Pacific Biosciences read the same DNA sequence again and again, which makes the readout far more accurate than previous technology.

Both technologies complemented each other to reveal the missing parts of the genome that have been eluding scientists for almost two decades. According to TNT, the number of DNA bases has been increased from 2.92 billion to 3.05 billion, marking a 4.5% improvement. However, the number of genes only increased by 0.4%, to 19.1969 — that’s because the vast majority of DNA sequences do not code for proteins but rather regulate the expression and activity of these genes.

“The complete, telomere-to-telomere assembly of a human genome marks a new era of genomics where no region of the genome is beyond reach. Prior updates to the human reference genome have been incremental and the high cost of switching to a new assembly has outweighed the marginal gains for many researchers. In contrast, the T2T-CHM13 assembly presented here includes five entirely new chromosome arms and is the single largest addition of new content to the human genome in the past 20 years,” wrote the researchers.

“This 8% of the genome has not been overlooked due to its lack of importance, but rather due to technological limitations. High accuracy long-read sequencing has finally removed this technological barrier, enabling comprehensive studies of genomic variation across the entire human genome. Such studies will necessarily require a complete and accurate human reference genome, ultimately driving adoption of the T2T-CHM13 assembly presented here,” they added.

The genome that the researchers sequenced didn’t come from a person but rather from a hydatidiform mole, a rare mass or growth that forms inside the womb (​uterus) at the beginning of a pregnancy. This tissue forms when sperm fertilizes an egg with no nucleus, so it contains only 23 chromosomes, just like a gamete (sperm or egg), rather than 46 found in the DNA of a human’s cell. These cells make the computational effort simpler but may constitute a limitation.

We will find out more once the paper is peer-reviewed and properly scrutinized by the international scientific community. If the findings hold water, they may mark a new age of genomics — one where no nook or cranny of DNA is left unexplored. 

What is DNA: the blueprint of life

Credit: Pixabay.

Deoxyribonucleic acid (DNA) is a long molecule that contains the hereditary genetic code required to build and maintain an organism. DNA sequences (the instructions inside the code) are converted into molecular messages that can be used to produce proteins. The DNA molecule is easily recognizable due to its double helix shape, consisting of two strands that wind around one another.

Ever wondered how to build a human? Like a cookbook, DNA contains all the necessary instructions in order to assemble a new organism. Although there are over a trillion cells that compose the human body, with varying degrees of complexity from neurons to immune cells, almost every one of these cells contains the same 3 billion DNA base pairs that make up the human genome.

Every species has a unique DNA sequence, and every individual also has slightly different DNA from the rest of the population (as long as they’re not clones that reproduce asexually).

What is DNA made of?

Each of the two DNA strands has a backbone made of alternating sugar (deoxyribose) and phosphate groups. Attached to each sugar is one of four types of nitrogen bases: adenine (A), thymine (T), guanine (G), and cytosine (C). These three parts together — a phosphate group, a sugar group, and a nitrogen base — are known as nucleotides.

The DNA double helix can be pictured as a sort of chemical ladder where the sides of the ladder are strands of alternating sugar and phosphate groups while the”rungs” are made up of two nitrogen bases, paired together by hydrogen bonds.

Base A always pairs with base T, and likewise C with G. Together, these units are called base pairs.

The sequence of nitrogen bases matters a lot. It can mean the difference between blue eyes or brown, tall or short, healthy or afflicted by a hereditary disease.

Overall, the complete instructions for a human contain three billion bases and about 20,000 genes found on 23 pairs of chromosomes, all wrapped inside a single molecule just six microns across located inside the nucleus of virtually every cell in the body.

Additionally, a small amount of DNA is present in the mitochondria, the structures within the cells that are responsible for converting the energy in food into a form that the cell can use — it’s called mitochondrial DNA (mtDNA). Together, the sum of all the DNA and mtDNA sequences in the cell is known as the genome.

If you uncoiled and stretched the DNA in one cell all the way out, it would be about two meters long. But what’s truly mind-boggling is that all the DNA in all your cells put together would stretch over a distance about twice the diameter of the solar system.

What does DNA do?

DNA sequences are used to make proteins in a two-step process. Enzymes first read the instructions in the DNA molecules in order to transcribe them into an intermediary molecule called messenger ribonucleic acid (mRNA). Pfizer’s and Moderna’s vaccines are based on mRNA, if that sounds familiar.

Next, the sequences in the mRNA molecules are translated into instructions that ribosomes, the small cellular structures responsible for making proteins, can ‘understand’. The protein-making machinery follows these instructions to the letter to link specific amino acids (protein building blocks) in the precise order required to produce a specific protein. The amino acids involved and the way they are linked to form the protein are what allow it to carry out its very specific tasks.

When a cell divides, so does DNA. Each strand of DNA in the double helix can serve as a pattern for duplicating the sequence of bases, so it can replicate and make exact copies of itself in the new cell. This copying process isn’t always perfect. Sometimes there is an alteration in the nucleotide sequence of the genome, called a mutation.

Each DNA sequence that contains the instructions for the production of a certain protein is known as a gene. Depending on how complex these instructions are, the size of a gene can vary from as little as 1,000 bases to one million bases in humans.

After the Human Genome Project was completed in 2003, scientists found that there were around 20,000 genes within the genome, a number that some researchers had already predicted.

But despite their fame, genes only make up 1% of the genome. The other 99% are instructions that regulate when and how these proteins are made. Scientists call this non-coding DNA because these sequences do not code for proteins.

At face value, the small number of genes relative to the entire genome might seem odd. But it makes sense when you consider that each of the over 200 cell types in the human body interprets a set of identical instructions (the genome) very differently in order to perform equally different functions.

Besides, a large genome doesn’t mean much. Plants in the genus Allium, which includes onions and garlic, have genome sizes ranging from 10 to 20 billion base pairs, whereas the human genome is only 3 billion base pairs. Obviously, a human is much more complex than an onion. This suggests that perhaps much of the genome isn’t actually useful and the size of a genome says nothing about how complex the organism is.

How do we know about DNA?

Since ancient times, people were at least somewhat aware that there was some hereditary factor that is passed down from parents to offspring. But it wasn’t until Gregor Mendel, a 19th-century monk, laid out the fundamental laws of inheritance that this process was unraveled scientifically.

Mendel was the first to demonstrate using his now-famous pea plant experiments that “invisible factors” — now known as genes — predictably determined the traits of an organism. He also coined many of the concepts and terms used in the field to this day, such as “recessive” and “dominant”.

DNA was actually known during the time of Mendel. The molecule was first discovered by Swiss biochemist Frederich Miescher in the late 1800s inside the nuclei of human white blood cells, but no one suspected that it had a central role in biology.

In the early 1900s, Russian biochemist Phoebus Levene, the author of over 700 papers on the chemistry of biological molecules, made phenomenal contributions to the unraveling of DNA. He was the first to discover the order of the three major components of a single nucleotide (phosphate-sugar-base), the carbohydrate component of RNA (ribose), and the carbohydrate component of DNA (deoxyribose), as well as the first to correctly identify the way RNA and DNA molecules are put together.

Levene’s work was expanded by Erwin Chargaff, an Austrian biochemist, who made additional discoveries surrounding DNA. He made two important contributions. First, he noted that the nucleotide composition of DNA varies among species. Secondly, he found that in almost all DNA, regardless of the organism or tissue it comes from, the amount of adenine (A) is usually similar to the amount of thymine (T), and the amount of guanine (G) usually approximates the amount of cytosine (C) — this now known as Chargaff’s rule.

3-D structure of DNA. Credit: Wikimedia Commons.

These discoveries paved the way for the discovery of DNA’s double helix. In 1953, James Watson, Francis Crick, Maurice Wilkins, and Rosalind Franklin performed X-ray diffraction and built models showing the three-dimensional, double helix structure of DNA.

Watson and Crick used cardboard cutouts representing the individual chemical components of the four bases and other nucleotide subunits. The two scientists shifted the molecules around countless times, as though they were putting together a puzzle. However, the puzzle pieces never seemed to click until American scientist Jerry Donohue suggested that they make new cardboard cutouts for thymine and guanine. The different atomic configurations made all the difference and the two complementary bases finally fitted together perfectly. What’s more, the structure also reflected Chargaff’s rule.

Since then, the Watson and Crick model has suffered minor corrections, but its four main features remain the same to this day. These are:

  • DNA is a double-stranded helix, with the two strands connected by hydrogen bonds. A bases always pair with Ts, and Cs always pair with Gs, which is consistent with and accounts for Chargaff’s rule.
  • Most DNA double helices are right-handed, meaning the sugar-phosphate backbone curls around the axis of the helix counter-clockwise.
  • The DNA double helix is antiparallel, which refers to the fact that the head of one strand is always laid against the tail of the other strand of DNA.
  • Not only are the DNA base pairs connected via hydrogen bonding, but the outer edges of the nitrogen-containing bases are exposed and available for potential hydrogen bonding as well. These hydrogen bonds provide easy access to the DNA for other molecules, including the proteins that play vital roles in the replication and expression of DNA.

More recently, scientists have found that the precise geometries and dimensions of the double helix can vary. The most common configuration is the one outlined by Watson and Crick, known as B-DNA. But there is also A-DNA, a shorter and wider form that is usually found in dehydrated samples of DNA and rarely encountered under normal conditions. Lastly, there’s Z-DNA, which is a left-handed conformation and is a transient form of DNA that appears only during certain types of biological activity.

Scientists store information in DNA of living cells

The message ‘Hello world!’ was encoded in the DNA of the E. coli bacteria. Credit: Wikimedia Commons.

One milliliter droplet of DNA can theoretically store as much information as two Walmarts full of data servers. Naturally, many scientists see the blueprint of life as the ultimate medium for storing information — but that’s a bit easier said than done.

Previously, scientists encoded the entire book The Wizard of Oz, images, and even GIFs into the iconic double-helix “twisted ladder,” which they could then decode.

Now, a team at Columbia University in New York have taken things to the next level. Rather than storing information in DNA molecules isolated in the lab, the scientists used gene-editing tool CRISPR to encode and store information inside living bacteria.

DNA kept outside cells tends to degrade fast, which is exactly what you don’t want to happen to your precious data. Bacteria, on the other hand, are remarkably resilient in the face of harsh conditions and can adapt to changing environments. Essentially, the bacteria act as a buffer between the information stored in its DNA and the harsh environment.

The researchers inserted specific DNA sequences of the four bases — adenine (A), cytosine (C), thymine (T), and guanine (G) — that encode binary data (the 1s and 0s that computers use) into the cells of E. coli bacteria. Different arrangements of these four bases can be used, for instance, to encode different letters of the alphabet, which is how the scientists managed to store the 12-byte text message ‘Hello world!’ in the bacterial cells.

The message was read by extracting and sequencing the bacterial DNA. Obviously, this is all a much more laborious and prone to error process than encoding 1s and 0s on a flash or hard drive. However, DNA storage will probably never be meant for average digital users. Instead, it might see use when long-term storage of important information is required, such as archives, even for up to thousands of years.

“We demonstrate multiplex data encoding into barcoded cell populations to yield meaningful information storage and capacity up to 72 bits, which can be maintained over many generations in natural open environments. This work establishes a direct digital-to-biological data storage framework and advances our capacity for information exchange between silicon- and carbon-based entities,” the researcher wrote.

The findings appeared in the journal Nature Chemical Biology.

Not your sister’s art hobby: DNA origami can save lives

Increasingly, origami (the Japanese art of paper folding) is becoming less of an artistic concern and more of a scientific one. The California Institute of Technology made special news in 2006 about a way to weave DNA strands into any two-dimensional shape or figure. Caltech’s Paul Rothemund called it “DNA origami” — but that was just the start of it.

Image credits: Nikoline Arns.

Imagine strands of DNA folded back and forth, forming a scaffold that fills the outline of a desired shape. Then, imagine more DNA strands specially designed to bind to that scaffold.

Rothemund, the strand-weaver, explained why this was useful. Scientists would find it easy to create and study any complex nanostructures they might want. Quoted in a 2006 press release, in he said he came up with a half a dozen shapes, including square, triangle, five-pointed star, and smiley face.

“At this point, high-school students could use the design program to create whatever shape they desired,” Rothemund said at the time.

Nature News said the binders, DNA ‘staples,’ were short strands “that stop the viral strand from unraveling,” adding that the method could find use in molecular biology and electronics. “The technique could be used to build a flat scaffold to carry microscopic electronic components. Enzymes could also be attached, creating a tiny protein factory,” the article emphasized.

In 2016, Caltech shed new light on the discovery. “The publication of Paul Rothemund’s paper on DNA origami (Nature, March 16, 2006) marked a turning point in DNA nanotechnology, enabling unprecedented control over designed molecular structures.”

Step by step

DNA origami object from viral DNA visualized by electron tomography. Image credits: OrigamiMonkey / Wikipedia.

Well, it’s 2021 and better late than never. The latest news about DNA origami is that Jacob Majikes and Alex Liddle, researchers at the National Institute of Standards and Technology (NIST), having stayed with the topic of DNA origami for years, have compiled a detailed tutorial on the technique. “DNA Origami Design: A How-To Tutorial” has been published in the Journal of Research of the National Institute of Standards and Technology. Majikes and Liddle have provided a step-by-step guide on the design of DNA origami nanostructures, making it easier than ever to design and use this type of structure.

Over the years, the method had attracted hundreds of researchers, said NIST, and for various reasons: Some may be interested in order to detect and treat diseases, or, to assess pollutants’ impacts on the environment and other applications. The two guide authors explained what they did. Namely, they went for the ‘how.’

“We wanted to take all the tools that people have developed and put them all in one place, and to explain things that you can’t say in a traditional journal article,” said Majikes. “Review papers might tell you everything that everyone’s done, but they don’t tell you how the people did it.”

Their journal paper further stated what was needed:

While the design and assembly of DNA origami are straightforward, its relative novelty as a nanofabrication technique means that the tools and methods for designing new structures have not been codified as well as they have for more mature technologies, such as integrated circuits. While design approaches cannot be truly formalized until design-property relationships are fully understood, this document attempts to provide a step-by-step guide to designing DNA origami nanostructures using the tools available at the current state of the art.”

Many potential applications of DNA origami have been suggested in literature, including drug delivery systems and nanotechnological self-assembly of materials, so this is not just some ethereal approach, it has clinical use. For instance, Harvard University Wyss Institute researchers reported the self-assembling and self-destructing drug delivery vessels using the DNA origami in lab tests, and another team of researchers from China and the US created a DNA origami delivery vehicle for Doxorubicin, a commonly used anti-cancer drug. So when someone acts like origami is just cute art, tell them that’s not nearly the case — it could be a real lifesaver.

Our body clock is largely kept working by “junk DNA”

The so-called “junk” bits of our DNA is not, after all, quite junk. New research shows that these seemingly inactive genetic elements, micro RNAs (miRNAs), act as a genome-wide time-keeping mechanism, maintaining the function and accuracy of our body clocks. They also make you jet-lagged.

Image via Pixabay.

Until now, research into the origins of our circadian rhythm (body clock) focused on what are known as clock genes — these contain the data for proteins that keep the clock ticking. Judging by this rhythm, our body knows when it’s time to wake up or go to bed, when it’s time to eat, when it falls dark. It then prepares for each of these times, generally by releasing different hormones to prep your body up. Needless to say, this rhythm is a very important adaptation that allows organisms to sync in with their environment.

We’ve been studying its origins in the hope of developing new treatment options for diseases such as Alzheimer’s, cancer and diabetes, but progress has been slow. It may have been that we were looking in the wrong place all along, new research reports.

Clocks in unusual places

“We’ve seen how the function of these clock genes are really important in many different diseases,” said Steve Kay, Provost Professor of neurology, biomedical engineering, and quantitative computational biology at the Keck School of Medicine of the University of Southern California.

“But what we were blind to was a whole different funky kind of genes network that also is important for circadian regulation and this is the whole crazy world of what we call non-coding microRNA.”

Molecular circadian clocks exist in every cell in the body, the team reports. They are small bunches on non-coding nucleotides known as micro RNAS, which can affect the patterns of gene expression by preventing messenger RNA from being turned into proteins. In essence, their job is to stop the protein blueprints from being taken to the factory if it’s not the right time. Past research has hinted at this role of miRNAs, but determining which of the hundreds of such molecules in the genome actually influence the circadian rhythm was quite a challenge.

The team, led by Lili Zhou, a research associate in the Keck School’s Department of Neurology, worked with the Genomics Institute of the Novartis Research Foundation (GNF) in San Diego, which produces robots capable of high throughput experiments. Along with Zhou, they developed a new robot to test almost a thousand miRNAs individually. Each strand was transferred into a cell. These cells were engineered to glow on and off based on their internal clock, which allowed the team to monitor its function.

The next step was to inactivate certain miRNAs identified in the previous step in similar cells. This had an inverse effect on the cells’ behavior than activating the genes — suggesting that their activity is directly involved in maintaining the circadian rhythm, and the previous experiment wasn’t picking up on an unrelated mechanism.

“The collaboration with GNF made it possible for us to conduct the first cell-based, genome-wide screening approach to systematically identify which of the hundreds of miRNAs might be the ones modulating circadian rhythms,” said Zhou.

“Much to our surprise,” added Kay, “we discovered about 110 to 120 miRNAs that do this.”

As for their role on a greater level, the team also studied the physiological and behavioral impacts of miRNAs. They engineered mice with an inactivated miR 183/96/182 cluster, which interfered with their wheel-running behavior in the dark compared with control mice. Further examination of brain, retina, and lung tissue revealed different effects in every tissue — suggesting that the way miRNAs operate is different among tissues.

The findings, the team says, could present a solid launching board for new treatments or prevention avenues for specific diseases.

“In the brain we’re interested in connecting the clock to diseases like Alzheimer’s, in the lung we’re interested in connecting the clock to diseases like asthma,” said Kay.

“The next step I think for us to model disease states in animals and in cells and look at how these microRNAs are functioning in those disease states.”

The paper “A genome-wide microRNA screen identifies the microRNA-183/96/182 cluster as a modulator of circadian rhythms” has been published in the journal Proceedings of the National Academy of Sciences.

Resistance is futile: what viruses are, and why we’ll never ‘beat’ them

No other year in living memory has been as heavily influenced by a virus as 2020. But what exactly are viruses, what makes them tick, what about them made us all put our lives on hold?

Image via Pixabay.

The short of it is that viruses are biological machines, supremely well-adapted to a single survival strategy. And this strategy is quite simple — viruses find living cells, infect them, and hijack their biochemical machinery to reproduce. They’ve done away with (or perhaps never developed in the first place ) anything that doesn’t directly help them perform that task, all the way down to the most fundamental traits of living organisms: viruses aren’t really alive, but they’re not not-alive either.

Their simplicity works to make viruses easy to ‘build’ (so they’re plentiful) and hard to detect and destroy. In fact, we still have very few reliable medicines against viruses (they’re known as ‘antiviral’ compounds), and they often only work on particular kinds or lineages of viruses. We’ve managed to put a man on the moon and put stars inside a bomb, but for all our achievements, humanity’s best defense against these pathogens is still our own bodies and immune systems. This becomes a bit scary when you consider that viruses very definitely outnumber any and all living things on the planet.

But I’m getting ahead of myself. Let’s start from the beginning:

General viral structure

Viruses are acellular. This means they are not made from cells nor do they have a cellular structure. This also means that all those fancy components you may or may not have learned about in cellular bio 101 — organelles, plasma membranes, ribosomes, etc — have nothing to do with a virus. They’re also exceedingly tiny, typically around 20–300 nanometers in diameter, though a few are larger. To put things into perspective, if a bacterium was the size of a soccer field, a virus would be around the size of three soccer balls put side-by-side. An animal cell would be the town around it.

One such pathogen (an individual, fully-assembled virus is referred to as a ‘virion’) is about as simple a biological machine as you can make and still have it work. They include a core that houses their nucleic acid (genetic material), an outer coat of proteins or ‘capsid’, and that’s pretty much it. That’s all you need to make a working virion. However, some fancier models can have additional features, such as an outer membrane shamelessly stolen off a host cell, different proteins (or glycoproteins) that can help them infect targets, or other structural elements. Capsids are constructed from proteins known as capsomeres. Them, alongside any membrane viruses have, typically tend to be peppered with glycoproteins that serve as binding or access keys into certain cells.

These proteins form the distinctive corona-like (‘crown’) structure of the coronavirus. Image via Pixabay.

By and large, viruses are classified into one of four groups based on their structure: filamentous, isometric (or icosahedral), enveloped, and head and tail. We’ll be getting to them in a second. One interesting characteristic of viruses is that across all strains, their complexity seems to be in no way related to the complexity of their hosts. The most complex and intricate structures we’ve seen in viruses belong to bacteriophages, pathogens that infect bacteria (which are the simplest living organisms).

What shape a virion takes, as well as the presence or absence of an envelope, has little bearing on what species it can infect and what the symptoms would be, but they’re still very useful classification criteria because they’re relatively easy to check.

Viral morphology

The shape and size of viruses tends to be consistent among different lineages, and quite distinctive for each.

Filamentous viruses have long, cylindrical bodies; plant viruses often employ this shape, including the TMV (tobacco mosaic virus). Icosahedral or isometric viruses look pretty much like spheres, or spheres with flattened faces. They get their name from the icosahedron, a polygon with 20 faces (like the dice you use in Dungeons and Dragons), although they don’t necessarily have to have that exact shape. One icosahedral virus you may know personally is the rhinovirus (which causes the common cold). Enveloped viruses have a membrane that surrounds their capsid, which is produced from bits of a cell’s membrane modified with viral proteins. The HIV virus is an enveloped virus, as most animal viruses tend to be. Finally we have head and tail viruses, which have a ‘head’ similar to icosahedral viruses and a ‘tail’ that resembles filamentous ones — they often infect bacteria.

Filamentous viruses are also known as ‘helical’, as their capsomers are arranged around a coil of genetic material, forming a helix. Them, alongside icosahedral viruses are sometimes called ‘simple’ viruses, while head and tail ones (or other shapes) are known as ‘complex’ viruses.

Image credits ZMEScience.

The presence of a membrane can help facilitate infection and provide protection against the host’s immune system (as it’s made from pilfered parts of cells). Enveloped viruses tend to rely completely on their membrane for infection. Its glycoproteins exploit cells’ natural pathways through the membrane to allow infections. They act as ‘keys’ to the protein ‘locks’ that are typically employed to allow nutrients or other elements through the lipid layers of the membrane. But through this, they become vulnerable to inactivation by compounds that interact with fats, such as soap. This is the case for the coronavirus, for example, which is why handwashing is so effective against it.

All of this is very swell, to be sure, but why are viruses so interested in getting inside cells? So glad you asked — here’s why:

The viral life cycle

The central idea to keep in mind here is that viruses aren’t technically alive. They have some of the trappings of living things — genetic material, they’re made of organic matter — but they also lack most essential elements of life, most notably the ability to reproduce by themselves. But that’s all fine and dandy, as far as viruses are concerned, because everyone else can do it for them.

Think of viruses as weaponized USB sticks. For the most part, they’re inert. Viruses have no metabolism, they don’t expend energy, they don’t move on purpose and they don’t chase their prey. They just float around, and every infection begins with a random encounter between a virus and a host. Once they make contact with an appropriate cell, a six-step process unfolds: attachment, penetration, uncoating, replication, assembly, and release.

Attachment and penetration are pretty self-explanatory. They involve the virion coming into contact with and attaching to the host cell, and the subsequent penetration through its membrane. Attachment is governed by the type of binding proteins on the capsid and the transfer proteins on the cell wall — if they’re compatible, the process can unfold. Penetration involves the transfer of viral genetic material through the membrane, which leaves the capsid outside the cell; in this step, the virion basically injects its genetic data into the host cell. Note that some enveloped viruses use other tricks to get inside the cell, most notably by fusing their membranes with that of the cell or tricking it into eating the virus. Once inside, the capsid degrades and the genetic material is released, representing the Uncoating phase.

An example of an enveloped virus infecting a cell.

In regards to this genetic data, first know that it can be either DNA or RNA (some virions that carry RNA are known as ‘retroviruses’). Viruses can carry single or double strands of DNA (‘ssDNA’ or ‘dsDNA’ viruses respectively) or RNA (‘ssRNA’ or ‘dsRNA’). Single strands can be either sense or antisense. Sense strands are those used actively as instructions to create proteins (messenger RNA, or ‘mRNA’), while antisense RNA are their mirror complementaries and serve as a template to create strands of mRNA.

Now, the moment we’ve all been waiting for: what does this genetic material encode? Well, the complete information on how to build the virus, naturally! Once the viral material enters the cell, it will hijack its ‘code’ to make it produce more viral genetic material, capsid elements, and anything else that is needed to Replicate the original virus. DNA viruses typically use a cell’s biochemical machinery to create more DNA (for the new viruses) that is then transcribed into mRNA, and this mRNA is used to start protein synthesis. RNA viruses use their genetic code as a direct template for more RNA (for the new viruses) and mRNA that is consumed in protein synthesis. Retroviruses such as HIV contain RNA that must first be copy-pasted into the host’s DNA — but they also have the right protein, ‘reverse transcriptase’, for the job.

If a cell lacks the know-how required to build these various elements, the viral genome instructs it on what needs to be done. This is best exemplified by retroviruses. Reverse transcription or retrotranscription involves turning a strand of RNA into a double-strand of DNA which is then inserted into the host genome; in very broad lines, it’s reverse-engineering, like creating a full blueprint on how to build a car by just looking at the car. Very nifty. Bacteria and cells do use reverse transcription, but typically for what could be considered data maintenance work. It’s unclear whether this is a natural ability of all cells or if it was inherited from ancient viruses that grafted the needed genes into their hosts (which goes to show that viruses can be a driver of evolution).

The bits and pieces that the cell creates will spontaneously self-Assemble into new virions inside the cytoplasm. Finally, they Release (or ‘egress’) out of the cell. Exactly how this takes place varies from strain to strain. Some viruses (especially enveloped ones, including HIV) gradually exit the cell through budding — a process through which they also gain their membrane covering — which keeps the host cell alive. Most commonly, however, virions are released when the cell is so full of viruses that it bursts open (and dies in the process).

Lytic vs Lysogenic

Now, viruses may seem evil, but they’re not out to kill you. In fact, they will occasionally put in the effort to not hurt their host, especially during times when prey cells are rare and harder to find.

The process of a cell ripping apart, the breaking down of its membrane, is known as ‘lysis’. Under normal circumstances, virions follow the lytic cycle, which is the one described above that ends in the death of the cell. Such an event sees several hundred virions released from the dying cell, around 100 to 200 individual particles, as a rule of thumb.

The lysogenic cycle is a bit more covert — it produces something known as a ‘temperate’ or ‘non-virulent’ infection. Through the lysogenic cycle, a virion lies dormant and hidden inside the host cell genome, waiting for the right time to strike. During this time, it uses inhibitor genes so that the host cell doesn’t read the viral information, leaving it free to hang around unimpeded. The cell also profits by gaining immunity from reinfection with the same virus.

But when the cell experiences some kind of stressor (such as exposure to UV light or chemical agents) that weaken these inhibitors, its automatic DNA-repair systems detect the intruder, activate, and cut it out of the genome. After this point, the viral genetic material activates and the steps of replication, assembly, and release resumes as per normal conditions, and the infection spreads.

Why are viruses a thing?

We don’t really know. They’re too simple for us to reliably extract information on their evolutionary history from them. They’re not exactly alive, but they can and do evolve and mutate when reproducing in cells. They also have an annoying habit of copy-pasting genes from and onto their hosts, which further muddies the waters.

What we do know is that they are the single most successful group on the planet. A paper published in the journal Nature in 2011 puts their immense scale into perspective. Although it cautions that these estimates are “mostly based on ‘back of the envelope’ calculations and should therefore be viewed as they were intended: ballpark figures aiming to inspire”, they’re still no less impressive.

“If all the 1 × 1031 viruses on earth were laid end to end, they would stretch for 100 million light years. Furthermore, there are 100 million times as many bacteria in the oceans (13 × 1028) as there are stars in the known universe. The rate of viral infection in the oceans stands at 1 × 1023 infections per second, and these infections remove 20–40% of all bacterial cells each day.”

“There are about 200 megatonnes of carbon in viruses in the ocean, which is equal to about 75 million blue whales,” explains Curtis Suttle, a Distinguished University Scholar and Professor at the University of British Columbia in another paper. “In fact, in a litre of coastal seawater there are more viruses than there are people on the planet.”

“If aliens randomly sampled Earth they would see a planet dominated by microbial life, most of which would be viruses,” Suttle adds. “On average, there are about 10 million viruses and a million bacteria per litre of seawater or freshwater. If we compare the number of viruses in the oceans to the number of stars in the universe, there are about 1023 stars in the universe [and] about 10 million-fold more viruses in the ocean.”

These numbers showcase why humanity can never truly hope to ‘defeat’ viruses — it hasn’t ever been an option. But one of the best, and perhaps most chilling ways to illustrate this is the legacy viruses have left in us.

Viruses have, to the fullest extent of the word, become a part of us. It’s estimated that around 8% of the genome of modern humans is viral, meaning it has been passed from a virus into a cell, down through the generations, and we still carry that around. By contrast, only between 1% and 2% of our genome was inherited from the Neanderthals.

We are more ‘virus’ than we are our closest relatives.

There may be over a million genetic molecules — DNA is just one of them

Credit: Public Domain.

All living things on Earth store information in genetic molecules: either DNA or RNA. But why is it that organisms use only two molecules to store genetic information? What makes DNA and RNA so special? Did the earliest life on Earth actually use a different molecule consisting of different building blocks? These are all important but also very difficult to answer questions — which is where a new study may come in handy.

Researchers at the Tokyo Institute of Technology, the German Aerospace Center (DLR), and Emory University used advanced computational methods to simulate possible nucleic acid-like molecules. They came up with over a million possibilities.

Hereditary molecules

DNA and RNA are known as nucleic acids. These tiny biomolecules not only form the basis for all life on earth, but they’re also key to many treatments for viral diseases such as HIV.

Nucleic acids were first discovered in the 19th-century but it wasn’t until 1953, when Watson and Crick revealed DNA’s double-helical structure, that scientists became aware of their biological and evolutionary functions.

Scientists know about the existence of other nucleic acid-like polymers, but that doesn’t mean that they are capable of storing hereditary information.

“There are two kinds of nucleic acids in biology, and maybe 20 or 30 effective nucleic acid-binding nucleic acid analogues. We wanted to know if there is one more to be found or even a million more. The answer is, there seem to be many more than was expected,” says professor Jim Cleaves of the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology

Surprisingly, Cleaves and colleagues found over a million variants of nucleic acid analogs after using sophisticated computational methods that explored the “chemical neighborhood” of DNA and RNA. For instance, although they can have quite different functions, RNA and DNA are separated by the presence of a single atom substitution. There are many more molecules in a similar situation, apparently — with just a minor change, you could end up with a completely new genetic molecule on your hand.

The ultimate aim of this kind of research is to improve our understanding of how the very first life forms appeared on Earth. Most biologists believe that RNA appeared before DNA, however, RNA is also a complex molecule. It is quite possible that a much simple nucleic acid seeded the most primitive life forms. After it served its place and time, this hypothetical genetic molecule was replaced by RNA and then DNA, which became the go-to storage medium for life.

“It is truly exciting to consider the potential for alternate genetic systems based on these analogous nucleosides—that these might possibly have emerged and evolved in different environments, perhaps even on other planets or moons within our solar system. These alternate genetic systems might expand our conception of biology’s ‘central dogma’ into new evolutionary directions, in response and robust to increasingly challenging environments here on Earth,” Dr. Jay Goodwin, a chemist with Emory University and co-author of the new study, said in a statement.

Besides fundamental science, there may also be practical applications for the new investigation, such as new drugs.

Organisms with large genomes, like humans, employ a very complex cellular machinery to copy hereditary information. As such, when copying DNA, these organisms have mechanisms in place that avoid selecting the wrong precursor molecules — otherwise, there might be excessive mutations. Although they’re not technically alive, viruses also have a genome. It is very small, though, and it is far less selective. This fact is exploited by many antiviral drugs, which employ nucleotide analogues that inhibit the virus’ ability to copy its DNA and reproduce.

“Trying to understand the nature of heredity, and how else it might be embodied, is just about the most basic research one can do, but it also has some really important practical applications,” says co-author Chris Butch, formerly of ELSI and now a professor at Nanjing University.

The findings appeared in the Journal of Chemical Information and Modeling.

Researchers encode “The Wizard of Oz” in DNA with unprecedented accuracy and efficiency

Credit: The Wizard of Oz (1939).

DNA is ridiculously good at storing information. One milliliter droplet of DNA can theoretically store as much information as two Walmarts full of data servers. What’s more, DNA can be stored at room temperature for hundreds of thousands of years. If your gears are turning right now, you’re not alone.

However, using DNA to store information is not at all as straightforward as storing it on a flash drive. In fact, it can be a nightmare to encode and decode information from the blueprint of life — but science is making progress in strides.

In a new study, researchers at the University of Texas have employed a new technique for storing and reading information encoded in the iconic double-helix “twisted ladder”.

The researchers demonstrated their novel technique by encoding the entire book of “The Wizard of Oz”, translated into Esperanto, with unprecedented accuracy and efficiency.

“The key breakthrough is an encoding algorithm that allows accurate retrieval of the information even when the DNA strands are partially damaged during storage,” said Ilya Finkelstein, an associate professor of molecular biosciences and one of the authors of the study.

DNA: 5 million times more efficient than any storage medium employed today

Every cell in our bodies and even instincts are encoded in base sequences of adenine (A), thymine (T), guanine (G), and cytosine (C) — DNA’s four nucleotide bases. Ever since DNA was first discovered in the 1950s by James Watson and Francis Crick (and the largely uncredited Rosalind Franklin) scientists quickly realized that huge quantities of data could be stored at high density in only a few molecules.

Just one gram of DNA is enough to store the entirety of all human knowledge, which is why some are keen on using the blueprint of life as the ultimate time capsule.

Additionally, DNA can be stable for a long time as a recent study showed, when researchers recovered DNA from 430,000-year-old human ancestor found in a cave in Spain.

For years, scientists have been storing all sorts of information in DNA, particularly during the previous decade. In 2017, researchers at the New York Genome Center (NYGC) stored a full computer operating system, an 1895 French film, “Arrival of a train at La Ciotat,” a $50 Amazon gift card, a computer virus, a Pioneer plaque and a 1948 study by information theorist Claude Shannon into 72,000 DNA strands each 200 bases long.

However, we’re still a long way from using DNA as a reliable storage medium. For one, synthesizing and reading DNA is prohibitively expensive.

The biggest impediment, however, is the fact that DNA is highly prone to errors.

Unlike malfunctioning computer code, which tends to show up as blanks, errors in DNA sequences appear as insertions or deletions. This can cause a huge predicament since such errors shift the whole sequence, with no blank spaces to alert us.

In order to account for inherent errors in DNA, researchers had to repeat a piece of information 10 to 15 times. These repetitions can be compared to track insertions or deletions.

But due to the way the team at the University of Texas chose to store information, there is no need for repetitions.

“We found a way to build the information more like a lattice,” said Stephen Jones, a research scientist who collaborated on the project with Finkelstein. “Each piece of information reinforces other pieces of information. That way, it only needs to be read once.”

To demonstrate the reliability of their method, Finkelstein’s team of researchers encoded the Wizard of Oz into DNA, which they then subjected to high temperature and extreme humidity.

Naturally, the DNA strands became damaged, but all the information was read successfully. This marks a huge leap in the long road to DNA storage of information.

“We tried to tackle as many problems with the process as we could at the same time,” said John Hawkins, co-author of the new study and a Ph.D. alumnus of the Oden Institute for Computational Engineering and Sciences at the University of Texas.

“What we ended up with is pretty remarkable.”

The method was described in the Proceedings of the National Academy of Sciences.

Researchers obtain oldest-ever human DNA from ancient tooth

Researchers at the University of Copenhagen have successfully isolated the oldest human genetic material to date, from an 800,000-year-old human fossil.

The Homo antecessor tooth used in the study.
Image credits Frido Welker et al., (2020), Nature.

The study gives us insight into humanity’s past going back much farther than previously considered possible. It could also help us get a better understanding of the different (now extinct) branches in the human family and how they related to one another, the team adds.

Old relatives

“Ancient protein analysis provides evidence for a close relationship between Homo antecessor, us (Homo sapiens), Neanderthals, and Denisovans. Our results support the idea that Homo antecessor was a sister group to the group containing Homo sapiens, Neanderthals, and Denisovans,” says Frido Welker, Postdoctoral Research Fellow at the Globe Institute, University of Copenhagen, and first author on the paper.

The ancient DNA was harvested from an 800,000-year-old tooth belonging to the species Homo antecessor. It was discovered by palaeoanthropologist José María Bermúdez de Castro and his team in 1994 at the Gran Dolina cave site, Spain, a part of the larger Sierra de Atapuerca archeological site.

Through the use of a technique called mass spectrometry, the team was able to isolate proteins from the enamel of the tooth, allowing them to sequence its genetic information and discover where this species fits in the human family tree.

We know that humans and chimpanzees split, genetically speaking, about 9-7 million years ago, but we don’t have a very clear picture of how many different human species there were at the time and how they related to one another. The fact that all these other human lineages are now extinct doesn’t help either, nor does the fact that genetic material tends to break down over time. Much of what we know on the topic so far is based on DNA analysis of samples no older than around 400,000 years, or direct observations of the shape and structure of early human fossils.

“Now, the analysis of ancient proteins with mass spectrometry, an approach commonly known as palaeoproteomics, allow us to overcome these limits,” says says Enrico Cappellini, Associate Professor at the Globe Institute, University of Copenhagen and leading author on the paper.

The findings suggest that Homo antecessor isn’t, in fact, the last common ancestor for us and the Neanderthals, but rather a closely related relative of that ancestor.

“I am happy that the protein study provides evidence that the Homo antecessor species may be closely related to the last common ancestor of Homo sapiens, Neanderthals, and Denisovans. The features shared by Homo antecessor with these hominins clearly appeared much earlier than previously thought. Homo antecessor would therefore be a basal species of the emerging humanity formed by Neanderthals, Denisovans, and modern humans,” says José María Bermúdez de Castro, Scientific Co-director of the excavations in Atapuerca and co-corresponding author on the paper.

The current research was only made possible by a ten-year-long collaboration between experts in fields ranging from paleoanthropology to biochemistry, proteomics, and population genomics, which allowed the team to retrieve and read proteins of such incredibly old age.

The paper “The dental proteome of Homo antecessor” has been published in the journal Nature.

Study finds new genetic editing powers in squids

Usually described as elusive, squids are highly skillful animals. They have bilateral symmetry, gills that are used for breathing, and skin covered with chromatophores, pigment-containing and light-reflecting cells through which they can camouflage to the environment.

Credit Wikipedia Commons

Now, scientists have discovered another surprising feature of squids. Not only they can edit their RNA or genetic instructions within the nucleus of their neurons but also within the axon, which are the neural projections that transmit electrical impulses to other neurons.

DNA and RNA are the most important molecules in cell biology, responsible for the storage and reading of genetic information that underpins all life. While DNA replicates and stores genetic information, RNA converts the genetic information contained within DNA to a format used to build proteins.

Back in 2015, a group of researchers discovered that squids were able to change their RNA instructions, fine-tuning the type of proteins to be produced. Now, they were able to dig deeper into their work and observe the edits outside the nucleus of the cell of the squids.

“We thought all the RNA editing happened in the nucleus, and then the modified messenger RNAs are exported out to the cell,” says Rosenthal, senior author. “Now we are showing that squid can modify the RNAs out in the periphery of the cell. That means, theoretically, they can modify protein function to meet the localized demands of the cell.”

In the past, Rosenthal and his group of researchers also worked in cuttlefish and octopus, which they discovered also rely on the editing of RNA to diversify the proteins they produce in the nervous system. Alongside the squid, this group of animals is known for its sophisticated behavior.

The findings could have implications not only for squids but also for humans, as the axon dysfunction is associated with neurological disorders. Researchers hope the study will help biotech companies use the RNA editing process in humans for therapeutic benefits.

“The idea that genetic information can be differentially edited within a cell is novel and extends our ideas about how a single blueprint of genetic information can give rise to spatial complexity. Such a process could fine-tune protein function to help meet the specific physiological demands of the different cellular region,” the researchers wrote.

The paper was published in Nucleic Acids Research.

Giant extinct primate is directly related to orangutans

Gigantopithecus blacki mandible. Credit: Prof. Wei Wang.

An international team of researchers just demonstrated the massive potential of ancient protein sequencing by retrieving genetic information from a 1.9-million-year-old extinct primate. The researchers concluded that the 3-meter-tall primate is directly related to the orangutan. This kind of genetic reconstruction is unprecedented, which means this method might someday allow scientists to reconstruct the evolutionary relationship between our own species and extinct relatives farther back in time than ever before.

Meet King Kong

‘By sequencing proteins retrieved from dental enamel about two million years old, we showed it is possible to confidently reconstruct the evolutionary relationships of animal species that went extinct too far away in time for their DNA to survive till now. In this study, we can even conclude that the lineages of orangutan and Gigantopithecus split up about 12 million years ago’, says Enrico Cappellini.

The fossils of the giant primate, known as Gigantopithecus blacki, were first discovered in 1935 in a traditional medicine shop in Hong Kong, where they were sold as “dragon teeth.”

To this day, we only know of a few lower jaws and some teeth, which has led to many speculations regarding the physical appearance of this ancient creature. Scientists believe that that Gigantopithecus stood almost 3 meters tall and weighed twice as much as a gorilla. Now, armed with genetic information scientists have settled the debate: it’s the direct ancestor of the orangutan and might have also looked like one.

“Previous attempts to understand which could be the living organism most similar to Gigantopithecus could only be based on the comparison of the shape of the fossils with skeletal reference material from living great apes. Ancient DNA analysis was not an option, because Gigantopithecus went extinct approximately 300.000 years ago, and in the geographic area Gigantopithecus occupied no DNA older than approximately 10.000 years has been retrieved so far. Accordingly, we decided to sequence dental enamel proteins to reconstruct its evolutionary relation with living great apes, and we found that orangutan is Gigantopithecus‘ closest living relative’, says Enrico Cappellini, an associate professor at the University of Copenhagen’s Globe Institute at the Faculty of Health and Medical Science and lead author of the new study published in Nature.

Gigantopithecus blacki mandible top view. Credit: Wei Wang.

For context, the oldest genetic information retrieved from a human is no older than 400,000 years and, up until now, it has only been possible to read DNA data from up to 10,000-year-old fossils in warm, humid areas — the kind of environment where the Gigantopithecus blacki fossils were retrieved. By comparison, retrieving genetic information from nearly 2 million years ago is light-years away, which is why this new research is so exciting. Many ancient remains belonging to our supposed ancestors are mainly found in subtropical areas, for instance. Imagine if the same could be done for other fossils, allowing scientists to piece together the complex evolutionary tree to which Homo sapiens belongs.

We’re all familiar with DNA, but what about its lesser-known brother, RNA? Close in concept, but very different in purpose, these two types of nucleic acid areessential to our biology. So, what is RNA, or, Ribonucleic acid?

A visual representation of RNA coding. Credit: Thomas Splettstoesser on Wikimedia Commons

RNA’s Purpose

While DNA encodes your genes, RNA is important for how those genes get expressed. During the process of transcription, RNA is created by reading DNA with something called RNA polymerase.

The most important subtype of RNA is mRNA, which stands for messenger RNA. This type of mRNA carries the information from the DNA and goes over to ribosomes in order to create proteins. And proteins are the molecules that actually go forth and make changes in the body.

The central dogma of molecular biology. Credit: Madprime on Wikimedia Commons.

So, it’s sort of like DNA is a booklet containing all possible instructions for how to make things in the body, RNA are copies of only the relevant information for what the body needs right now, and proteins are the workers that go out and make it happen. This is known as the central dogma of molecular biology.

RNA vs DNA

A visual representation of the primary differences between RNA and DNA. Credit: Verwendete Bilder on Wikimedia Commons.

RNA and DNA have a surprising number of similarities. And it makes sense: RNA is literally copying itself from that main template.

For example, RNA and DNA both are made up of four nucleotide building blocks. DNA is made up of G, T, A, and C. RNA is similar, but substitutes the T (thymine) for U (uracil). Uracil actually looks just like thymine but lacks one methyl (CH3) group that thymine has.

DNA is double-stranded, but RNA is just one strand (it can form double strands but this isn’t RNA’s normal state). It’s easier to stay this way because it’s a much shorter strand of molecules. Why? In its single-stranded form, it’s genetically cheaper to make (half the material) while still containing all of the information (after all, if one always pairs with the other then you know exactly what that other strand had to be). Also, it’s easier to read. We actually have to unzip the DNA helix in places in order to access the code within, while RNA already comes in a form that’s open and easy to read.

Finally, they have different backbones. DNA is held together by deoxyribose, the sugar-phosphate backbone holding all of those nucleotides in order. RNA’s backbone is made up of ribose. Ribose is a lot like deoxyribose but has an additional hydroxyl (OH) group. So, deoxyribose is just de-oxygenated ribose, because it doesn’t have that oxygen.

Special Types of RNA

When most people think of RNA, they think of mRNA. But there are several additional subtypes of RNA that each have special functions.

The process of creating mRNA wouldn’t be possible without other forms of RNA. Transfer RNA (tRNA) is required to bring amino acids to the ribosome. In the ribosome, ribosomal RNA (rRNA) links together amino acids so they can create proteins. Taken together, tRNA, rRNA, and mRNA are referred to as coding RNAs because they all work together to encode proteins.

A visual depiction of translation machinery. Credit: NHS HEE Genomics Education Programme on Flickr.

Most noncoding RNA performs regulatory functions. The most popular of this category are microRNA (called miRNA or miR). These miRNAs can pair with single-stranded mRNA. When it does so, these mRNAs are tagged to be degraded. Therefore, miRNA can tag mRNA and shut down protein translation. So miRNA is usually used to control the amount of protein being produced from mRNA.

There’s also a very similar subtype called small interfering RNA (siRNA) which tags RNA for degradation right after transcription. It can be used to prevent any protein from being created. In addition, siRNA is often artificially used in labs to prevent certain proteins from being created and then see how this affects other biological processes.

siRNA mechanism of action. Credit: Singh135 on Wikimedia Commons.

Enhancer RNA (eRNA) was only first discovered in 2010. They are transcribed from “enhancer” regions of DNA – regulatory sites known to enhance gene expression. These eRNAs are also used to up-regulate the amount of mRNA produced from that DNA segment.

Small nucleolar RNA, called snoRNA, helps chemically modify other groups of RNA. They may help add either a methyl group (CH3), a process called methylation. Or they can turn one of the nucleotides into a uridine, a process called pseudouridylation.

Finally, there are long non-coding RNAs (lncRNAs). They are thought to silence long stretches of DNA. They also are thought to be involved in regulating stem cell division very early on in life.

What is RNA? Now You Know!

Now you’ve learned all about the mysteries of RNA. While not as widely known as DNA and not as flashy as protein function, it still remains one of the three cores of molecular biology. Life couldn’t exist without it. In fact, RNA is often thought to potentially be responsible for forming all life.

Chicken.

Researchers make chicken cells resist bird flu by snipping out a tiny bit of their DNA

Designer chicken cells grown in the lab at Imperial College London can resist the spread of bird flu.

Chicken.

Image credits Samet Uçaner.

Bird flu, as its name suggests, is mostly concerned with infecting birds. And it’s quite good at it: severe strains of bird flu can completely wipe out a whole flock. In rare cases, the virus can even mutate to infect humans, causing serious illness. As such, bird flu is a well-known and scary pathogen in the public’s eye.

Now, researchers from Imperial College London and the University of Edinburgh’s Roslin Institute have devised chicken cells that can resist infection with the bird flu virus. Their efforts pave the way towards effective control of the disease, safeguarding one of the most important domesticated animals of today.

Be-gone, flu

“We have long known that chickens are a reservoir for flu viruses that might spark the next pandemic. In this research, we have identified the smallest possible genetic change we can make to chickens that can help to stop the virus taking hold,” says Professor Wendy Barclay, Chair in Influenza Virology at Imperial College London and the paper’s corresponding author. “This has the potential to stop the next flu pandemic at its source.”

The findings could make it possible to immunize chickens to the virus using a simple genetic modification. No such chickens have been produced just yet, but the team is confident that their method will prove safe, effective, and palatable with the public in the long run.

The approach involves a specific molecule found in chicken cells, called ANP32A. Researchers at Imperial report that during a bird flu infection, viruses use this molecule to replicate (multiply) and continue attacking the host. The researchers from the University of Edinburgh’s Roslin Institute worked to gene-edit chicken cells to remove a portion of DNA that encodes the production of ANP32A.

With this little tweak, the team reports, the virus was no longer able to replicate inside the cells.

Members at The Roslin Institute have previously worked on something similar. Teaming up with researchers from Cambridge University at the time, they successfully produced gene-edited chickens that didn’t transmit bird flu to other chickens following infection. However, the approach they used at the time involved adding new genetic sequences into the birds’ DNA; while the proof-of-concept was very encouraging, the approach didn’t seem to stick, commercially.

“This is an important advance that suggests we may be able to use gene-editing techniques to produce chickens that are resistant to bird flu,” says Dr. Mike McGrew, of the University of Edinburgh’s Roslin Institute and a paper co-author.

“We haven’t produced any birds yet and we need to check if the DNA change has any other effects on the bird cells before we can take this next step.”

The paper “Species specific differences in use of ANP32 proteins by influenza A virus” has been published in the journal eLife.

Researchers create bacteria synthetic DNA

Researchers have produced E. coli bacteria with completely synthetic DNA. While the research was aimed at studying genetic redundancies, the potential applications are limitless.

E. coli. Image credits: NIAID.

Researchers at the University of Cambridge have rewritten the DNA of the bacteria Escherichia coli, a strain of bacteria that is normally found in soil and the human gut. Although the bacteria look a bit weird and have some issues reproducing, they are alive and seem to function relatively normally — running by a set of rules directed by the human-edited genome.

For all its diversity and variation, all life on Earth (with the exception of some viruses) is based on DNA. The two-stranded DNA molecule is the blueprint for life as we know it, and each strand is composed of molecules containing just four bases: adenine, cytosine, guanine, and thymine (or A, C, G and T). Think of it this way: a handful of chemical letters are used to made three-letter words, and these words are then passed out as biological orders to proteins.

The four letters can be strung into 64 combinations of three-letter words called codons. Nearly all life on Earth uses these 64 codons, and these codons join to form virtually all proteins that can be found in nature — with the mention that three codons are used as punctuation marks, separating individual codons from one another.

However, there is a lot of redundancy within these combinations. Many combinations do the same thing, so they can theoretically be removed — but where do you stop? In order to study this, Jason Chin, an expert in synthetic biology who led the project, conducted a genetic “word swap”. He went through the bacteria’s DNA, and whenever he came across a particular codon (TCG, a codon that makes an amino acid called serine), he rewrote it as another one (AGC, which does the same job). He did this for three sets of codons, but the resulting genome was too long and complicated to brute-force in a cell — so instead, researchers split it into small segments and swapped them piece by piece inside the E. coli genome. By the time they were done, there were no natural segments in the bacteria’s DNA; the whole thing was synthetic.

The team then watched the bacteria go about its life. The first good news came immediately: it lived. It grew slower and presumably weaker than its “normal” version, but it was very much alive.

It’s not the first time a bacteria has been created with a synthetic DNA, but this achievement is by far the most complex achievement. In 2010, researchers from the J. Craig Venter Institute in Maryland created the first cell with synthetic DNA. In 2017, researchers at the Scripps Institute unveiled the first stable, semi-synthetic organism. Researchers are slowly starting to experiment with nature’s lifeforms and moving towards Life 2.0. Knowing which codons we need and which can be dropped is essential for this, especially as other groups are working on creating synthetic DNA for even more complex creatures such as baker’s yeast. The potential applications are limitless.

In addition to shedding new light on the chemical intricacies of DNA, this type of designer bacteria can also come in handy in the medical industry. They could, for instance, stop viral infections, or deliver diabetes or other compounds for treating serious conditions such as cancer and heart disease. After a certain point, you could even use it for more frivolous purposes, such as creating tastier bread or beer.

There is, however, a very strong impediment to this type of study: costs. Producing and inserting synthetic DNA is still an extremely expensive pursuit. Now that we know it can be done, we also know that in theory, you can recode anything. Actually having the know-how and the resources to do that remains a different matter.

The study has been published in Nature.

Credit: Public Domain.

Hair claimed to belong to Leonardo da Vinci to undergo DNA testing

Credit: Public Domain.

Credit: Public Domain.

A pair of art historians claim that they now possess a lock of hair which belonged to Leonardo da Vinci. They plan on conducting DNA testing in order to confirm the identity of the hair’s owner — an announcement which coincides with the 500th anniversary of da Vinci’s death. Critics, however, claim that it will be impossible to confirm whether the hair came from the famous Renaissance inventor and artist since Leonardo’s original tomb was destroyed and there are no reliable living descendants to compare their DNA to that from the hair.

The Renaissance of Leonardo’s DNA

Leonardo da Vinci was born on April 15, 1452, in a farmhouse outside the village of Anchiano, in present-day Italy. Historians believe he was born out of wedlock to respected Florentine notary Ser Piero Fruosino di Antonio da Vinci and a young peasant woman named Caterina. At the age of five, he moved to his father’s family estate in nearby Vinci, the Tuscan town from which his surname derives. Leonardo da Vinci died of a probable stroke on May 2, 1519, at the age of 67, in the French town of Amboise.

Both Italian and French towns celebrated the 500th anniversary of da Vinci’s death with special events and exhibitions. As part of the celebration, Alessandro Vessozi, the director of the “Museo Ideale Leonardo da Vinci,” and Agnese Sabato, the president of the Leonardo da Vinci Heritage Foundation, announced that they have come under the possession of a lock of hair belonging to Leonardo da Vinci. According to Vessozi, the hair had remained hidden in a private American collection.

“We found, across the Atlantic, a lock of hair historically tagged ‘Les Cheveux de Leonardo da Vinci’”—French for “Leonardo da Vinci’s hair,” Sabato said in a statement.

Vezzosi adds, “This historical relic … has long remained hidden in an American collection. It will now be exposed for the first time, along with documents attesting [to] its ancient French provenance.”

The artist is believed to have been buried in the Chapel of Saint-Florentin, which was destroyed during the French revolution. In the late 19th century, French poet Arsène Houssaye discovered what he believed to be Leonardo’s bones while excavating the ruins of the chapel. The bones were placed at the Chapel of Saint-Hubert, also located at Château d’Amboise.

[panel style=”panel-default” title=”The Vitruvian Man” footer=””]Leonardo da Vinci is known for important artworks such as “The Last Supper” and “Vitruvian Man”, as well as his codex, notebooks, and many sketches which have fascinated millions for centuries. A real Renaissance man, da Vinci’s interests spanned art, architecture, music, mathematics, and science. For instance, he first dreamed of the designs for the parachute, bicycle, and helicopter. [/panel]

On May 2, da Vinci’s Sabato and Vessozi said in a statement that they want to perform DNA analysis on the hair and compare it to the presumed remains at the Amboise tomb. However, the seriousness of such an undertaking has been put into question by experts.

Firstly, there is no reliable way to link Leonardo’s hair to the bones at the Amboise tomb, which could belong to anyone given the original ransacking. Then there’s the question of extracting DNA from the hair itself, a process which isn’t as straightforward as it might sound — the original genetic material may be degraded or contaminated.

The historians have also proposed comparing genetic material from the lock of hair to that belonging to da Vinci’s living descendants. In 2016, Vezzosi and Sabata claimed to have identified 35 living relatives of Leonardo using historical documents. These individuals were linked to Leonardo’s father via the artist’s brother. Leonardo didn’t marry or have children.

However, there are only two types of DNA can be traced reliably over the centuries. One is mitochondrial DNA, which is inherited only from the mother’s side and is solely passed on only through an unbroken female line. Similarly, Y-chromosome DNA comes from the father and is passed on to the next generation only through an unbroken male line. The relatives identified by Vezzosi and Sabata don’t represent unbroken male or female lines, and as such cannot be used to reliably confirm whether the hair did, in fact, belong to Leonardo.

Elsewhere, researchers at the J. Craig Venter Institute are testing paintings, notebooks, and drawings which belonged to da Vinci looking for traces of his DNA such as fingerprints, skin flakes, and strands of hair. If it can ever be obtained, this DNA can then be compared to the newly announced lock of hair or any other similar remains.

The atomic model of an entire human gene. Credit: Los Alamos National Laboratory.

Scientists perform billion-atom simulation of a human gene

The atomic model of an entire human gene. Credit: Los Alamos National Laboratory.

The atomic model of an entire human gene. Credit: Los Alamos National Laboratory.

Researchers have simulated a billion atoms which make up an entire human gene for a split-second. This is the largest simulation of human DNA and an important milestone towards the ultimate goal of digitally reproducing the human genome. 

“It is important to understand DNA at this level of detail because we want to understand precisely how genes turn on and off,” said Karissa Sanbonmatsu, a structural biologist at Los Alamos. “Knowing how this happens could unlock the secrets to how many diseases occur.”

Sanbonmatsu and colleagues performed their study on the Los Alamos’ Trinity supercomputer, the sixth fastest in the world. But even for this behemoth, simulating the intricate complexities of DNA was a huge challenge that required all of its computing resources. The model is quite slow too, simulating just one nanosecond of molecular activity per day.

DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. This incredible molecule contains all the instructions an organism needs to develop, live, and reproduce. Its structure is so neatly compacted and precise that you could string together all the DNA in a human body to wrap around the earth 2.5 million times.

The reason why the blueprint for life is so compact has to do with the way the string-like molecule is wound up in a network of tiny spools. The various ways in which these spools wind and unwind turn genes on and off. In other words, when the DNA is more compacted, genes are turned off and when DNA expands, genes are turned on.

Researchers do not yet fully understand how all of this process pans out, which is why they’ve developed this atomistic model. Solving this mystery could one day lead to novel gene therapies and medical applications.

But before that happens, we need much faster computers. Modeling billions and billions of atoms all moving at the same time requires phenomenal resources. And, if we want to model an entire chromosome (or even the human genome), scientists will have to wait for the next generation of supercomputers, such as exascale computers, which will be many times faster than today’s machines.

Scientific reference: Jaewoon Jung et al. Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations, Journal of Computational Chemistry (2019). DOI: 10.1002/jcc.25840.

Scientists create artificial material capable of metabolism, self-assembly, movement, and organization — key traits of life

The new material is eerily life-like.

The DNA material is capable of metabolism, in addition to self-assembly and organization. Image credits: John Munson/Cornell University.

What makes something alive? Is it the fact that it has a metabolism, that it can organize itself into a coherent structure? If that’s all it takes, then researchers might have just created artificial life. A Cornell team took advantage of some of DNA’s unique properties to develop a life-like material that can self-organize, self-assemble, and even metabolize nutrients.

“We are introducing a brand-new, lifelike material concept powered by its very own artificial metabolism. We are not making something that’s alive, but we are creating materials that are much more lifelike than have ever been seen before,” said Dan Luo, professor of biological and environmental engineering in the College of Agriculture and Life Sciences.

DNA is the foundation of all life on Earth. It contains the instructions needed for an organism to survive and develop, producing new cells and sweeping old ones away in a hierarchical pattern. However, DNA is also a polymer, meaning it has some useful bio-construction properties that researchers can use.

In this study, Luo and colleagues used what they call DASH (DNA-based Assembly and Synthesis of Hierarchical) materials to create a biomaterial that can autonomously emerge from its nanoscale building blocks and arrange itself — first into simple polymers, then into more complex shapes.

They started from a sequence of 55 nucleotides (the building blocks of DNA and RNA) and from there, the DNA molecules were multiplied hundreds of thousands of times, creating chains of repeating DNA reaching a few millimetres in size. Then, this reaction was injected into a microfluidic device that the necessary energy and materials for biosynthesis.

As material gathered more and more resources, the DNA was able to synthesize new strands at the front end, while the tail end degraded to maintain an optimum balance. Using this mechanism, it was also able to move around, even against the flow — very similar to how slime molds move.

“The designs are still primitive, but they showed a new route to create dynamic machines from biomolecules. We are at a first step of building lifelike robots by artificial metabolism,” said Shogo Hamada, lecturer and research associate in the Luo lab, and lead and co-corresponding author of the paper. “Even from a simple design, we were able to create sophisticated behaviors like racing. Artificial metabolism could open a new frontier in robotics.”

If that wasn’t life-like enough, researchers are currently working on ways to improve longevity and self-replication.

“Dynamic biomaterials powered by artificial metabolism could provide a previously unexplored route to realize “artificial” biological systems with regenerating and self-sustaining characteristics,” the study concludes.

The goal is not to produce artificial life, but rather to use the system as a biosensor or as a dynamic template for making proteins without living cells.

The study was published in Science Robotics.