Researchers led by Prof. Wout Boerjan have discovered a way to control the amount of lignin in poplar by applying CRISPR/Cas9 tech. Lignin is one of the main structural substances in plants and it makes processing wood difficult. This study is an important breakthrough in the development of wood resources for the production of paper with a lower carbon footprint, biofuels, and other bio-based materials.

Introduction 

Today's fossil-based economy results in a net increase of CO2 in the Earth's atmosphere and is a major cause of global climate change. To counter this, a shift toward a circular and bio-based economy is essential. Woody biomass can play a crucial role in such a bio-based economy by serving as a renewable and carbon-neutral resource for the production of many chemicals. Unfortunately, the presence of lignin hinders the processing of wood into bio-based products.

Making the future easier

A field trial with poplars that were engineered to make wood containing less lignin. Most plants showed large improvements in processing efficiency. However, was that the reduction in lignin accomplished with the technology we used then—RNA interference—was unstable and the trees grew less tall. Then they employed the recent CRISPR/Cas9 technology in poplar to lower the lignin amount in a stable way, without causing a biomass yield penalty.

Trials and Tribulations

Poplar is a diploid species - every gene is present in two copies. Using CRISPR/Cas9, we introduced specific changes in both copies of a gene that is crucial for the biosynthesis of lignin. We inactivated one copy and only partially inactivated the other. The resulting poplar line had a stable 10% reduction in lignin amount while it grew normally in the greenhouse. Wood from the engineered trees had an up to 41% increase in processing efficiency. The mutations that were introduced by CRISPR/Cas9 are similar to those that arise naturally. The advantage of the CRISPR/Cas9 method is that the beneficial mutations can be directly introduced into the DNA in only a fraction of the time it used to take.

Methodology

The applications of this method are not only restricted to <a href="https://phys.org/tags/lignin/">lignin </a>but might also be useful to engineer other traits in crops, providing a versatile new breeding tool to improve agricultural productivity.

Moving on

CRISPRing trees for a climate-friendly economy

All athletes want to be at the top of their game when they compete, but some resort to nefarious approaches to achieve peak muscle growth, speed and agility. Recent developments in gene editing technology could tempt athletes to change their DNA to get an edge. Now, researchers reporting in ACS' Analytical Chemistry demonstrate first steps toward detecting this type of doping both in human plasma and in live mice.

Preemptive Approach

The gene editing method called CRISPR/Cas 9. The RNA molecule guides the protein to the appropriate DNA sequence, and then the protein cuts DNA, like a pair of scissors, to allow alterations. Despite the <a href="https://phys.org/tags/ethical+concerns/">ethical concerns </a>that have been raised about the method's potential application in humans, some athletes could ignore the risks and misuse it to alter their <a href="https://phys.org/tags/genes/">genes </a>.

Use and misuse

CRISPR/Cas changes DNA and is considered "gene doping" and is banned by the World Anti-Doping Agency, an independent international organization. A sufficient method to detect CRISPR/Cas gene editing needs to be developed, however. So, Mario Thevis and colleagues wanted to see whether they could identify the protein most likely to be used in this type of doping, Cas9 from the bacteria Streptococcus pyogenes (SpCas9), in <a href="https://phys.org/tags/human+plasma/">human plasma </a>samples and in mouse models.

Diagnostic Test

The team spiked the SpCas9 protein into human plasma, then isolated and cut it to analyse by <a href="https://phys.org/tags/mass+spectrometry/">mass spectrometry </a>. The researchers found that they could identify unique components of the SpCas9 <a href="https://phys.org/tags/protein/">protein </a>from the complex plasma matrix. In another experiment, inactivated SpCas9, which can regulate gene expression without altering DNA, was spiked into human plasma samples. With a slight modification, the method allowed the team to purify and detect the inactive form. Finally, the team injected mice with SpCas9 and showed that their concentrations peaked in circulating blood after 2 hours and could be detected up to 8 hours after administration into muscle tissue. The researchers say that although much work still needs to be done, this is an initial step toward a test to pinpoint athletes trying to gain an unfair advantage.

Experimenting

artificialintelligence

Artificial Intelligence

Detecting CRISPR/Cas gene doping

Results from a new study on mice have inspired hope for treating children born with progeria, a rare, fatal, genetic disease that causes symptoms much like early aging. In mice with a progeria-causing mutation, a cousin of the celebrated genome editor known as CRISPR corrected the DNA mistake, preventing the heart damage typical of the disease, a research team reports today in Nature . Treated mice lived about 500 days, more than twice as long as untreated animals.

Overview

Although the developers of the progeria therapy aim to improve it, they are also taking steps toward testing the current version in affected children, and some other scientists endorse a rush. The mouse results are “beyond anyone’s wildest expectations,” says Fyodor Urnov, a gene-editing researcher at the University of California, Berkeley. “The new data are an imperative to treat a child with progeria … and do so in the next 3 years.”

Moving Forward

About 400 people in the world are estimated to have Hutchinson-Gilford progeria syndrome - a single-base change in the gene for a protein called lamin A that helps support the membrane forming the nucleus in cells. The resulting abnormal protein progerin disrupts the nuclear membrane and is toxic to many cells. Toddlers soon become bald and have stunted growth, body fat loss, stiff joints, wrinkled skin, osteoporosis, and atherosclerosis. People with progeria die around the age 14 from a heart attack or stroke.

About the Condition

Researchers have used CRISPR to disrupt activity of the mutated gene for lamin A in progeria mice but their health improved only modestly, and disabling a person’s good copy of the gene could cause harm. So David Liu of Harvard University and the Broad Institute turned to base editing, a DNA-changing method originally inspired by CRISPR. Unlike CRISPR, which makes double-strand cuts in DNA, the base editor used in the progeria study nicks just one strand and swaps out a single base. Base editors have treated disorders in individual organs in mice, and Liu wanted to try one on an disease that involves multiple organs or tissues.

Base Editors Vs CRISPR

Teamed up with Vanderbilt University cardiologist Jonathan Brown and Francis Collins, director of the National Institutes of Health, whose group was one of two that identified the progeria mutation in 2003. The team first tested the base-editing approach in cultured cells from two progeria patients, finding that it corrected the mutation while making few unwanted changes elsewhere in the genome. They then packaged DNA encoding the base editor into adeno-associated viruses (AAVs), a standard delivery vehicle for gene therapies, and injected these into young mice with the progeria mutation.

Method

When the mice were examined 6 months later, <a href="https://www.nature.com/articles/s41586-020-03086-7">between 20% and 60% of their bone, skeletal muscle, liver, heart, and aorta carried the DNA fix </a>. Progerin levels fell and lamin A levels rose in several tissues. Even though the mice were already 2 weeks old when treated, age 5 in human years, their aortas months later bore virtually no signs of the fibrous tissue growth or loss of smooth muscle cells seen in mice and children with progeria.

Results 

Some of the rodents eventually developed liver tumors, a problem seen before in mice receiving high-dose AAV gene therapy. No people have been shown to have developed liver tumors as a result of such treatments. Still, lowering the AAV dose to improve safety “is a goal,” Liu says. He and Collins are evaluating more efficient base editors to that end.

Side Effects

Study co-author Leslie Gordon, a Brown University physician whose son died from progeria and who co-founded the Progeria Research Foundation, doesn’t want to wait for “the next iteration” before developing plans and raising money to test the treatment in children. Her foundation is talking to companies, including Beam Therapeutics, which Liu co-founded, in hopes of launching a clinical trial. “We will find a way to get this done for these kids,” Gordon says.

Looking Ahead

Gene therapy using “base editor” derived from CRISPR extends life span, preserved aortas in mice with progeria

‘Incredible’ gene-editing result in mice inspires plans to treat premature-aging syndrome in children

In 2018, a group of mostly European funders sent shock waves through the world of scientific publishing by proposing an unprecedented rule: The scientists they funded would be required to make journal articles developed with their support immediately free to read when published.

The Rule

The new requirement, which takes effect this month, seeks to upend tradition in scientific publishing, whereby scientists publish their research in journals for free and publishers profit by charging universities and other institutions for subscriptions. Advocates hope to destroy subscription paywalls and speed scientific progress by allowing findings to be shared more freely. It’s part of a larger shift in scientific communication that began more than 20 years ago and has recently picked up steam.

How?

Scientists have several ways to comply with Plan S, including by paying publishers a fee to make an article freely available on a journal website, or depositing the article in a free public repository where anyone can download it. The mandate is the first by an international <a href="https://www.coalition-s.org/organisations/">coalition </a>of funders, which now includes 17 agencies and six foundations, including the Wellcome Trust and Howard Hughes Medical Institute, two of the world’s largest funders of biomedical research.

In action

The group, which calls itself Coalition S, has fallen short of its initial aspiration to catalyze a truly international movement, however. Officials in three top producers of scientific papers—China, India, and the United States—have expressed general support for open access, but have not signed on to Plan S. Its <a href="https://www.coalition-s.org/addendum-to-the-coalition-s-guidance-on-the-implementation-of-plan-s/principles-and-implementation/">mandate </a>for immediate open access will apply to only about 6% of authors of the world’s papers in 2017, according to an <a href="https://clarivate.com/webofsciencegroup/campaigns/plan-s-footprint/">estimate </a>by the Clarivate analytics firm.

Not so global

Still, there’s reason to think Coalition S will make an outsize impact. In 2017, 35% of papers published in Nature and 31% of those in Science cited at least one coalition member as a funding source. “The people who get [Coalition S] funding are very prominent scientists,” Rooryck says. “We punch above our weight.” The Nature and Cell Press families of journals announced in recent weeks that they would allow authors to publish papers outside their paywall, for hefty fees.

Influence

As funders’ Plan S requirements begin, the open-access movement shows progress and faces questions

A new mandate highlights costs, benefits of making all scientific articles free to read

Last summer, doctors in Tennessee injected <a href="https://www.npr.org/sections/health-shots/2019/12/25/784395525/a-young-mississippi-womans-journey-through-a-pioneering-gene-editing-experiment">Victoria Gray—a 34-year-old sickle cell disease patient </a>—with billions of her own <a href="https://www.wired.com/tag/stem-cells/?intcid=inline_amp">stem cells </a>that scientists in Massachusetts had reprogrammed with Crispr to produce healthy blood cells. The hours-long infusion made her the first American with a heritable disease to be treated with the experimental gene-editing technology. And it appears to be working.

CRISPR & Sickle Cell

In December, a team that includes researchers from CRISPR Therapeutics and Vertex Pharmaceuticals published<a href="https://www.nejm.org/doi/10.1056/NEJMoa2031054"> promising results </a>from a clinical trial, which is also treating patients in Germany who suffer from a related disease called ß-thalassaemia. In both groups of patients, the treatment seems to be safe, and it so far has eliminated the need for regular blood transfusions. It’s still too soon to say how long the effects will last but the consequences could be huge. Sickle cell disease and ß-thalassaemia are among the most common genetic disorders caused by mutations to a single gene, affecting millions of people worldwide.

CRISPR & Thalassaemia

For thousands of years, humans have been modifying the DNA of our closest furry and feathered friends by breeding animals to produce the most desirable traits. With Crispr, one no longer has to wait generations to make significant genetic changes. This year, researchers 'created' <a href="https://www.technologyreview.com/2020/12/11/1013176/crispr-pigs-prrs-cd163-genus">pandemic-proof pigs </a>, whose cells have been edited to remove the molecular lock-and-key mechanism that a variety of respiratory viruses use to infect them, and <a href="https://www.pnas.org/content/117/4/2108">chickens Crispr’d to make them impervious </a>to a common bird disease caused by the avian leukosis virus.

CRISPR & Animals

It would be beneficial to develop commercial diagnostics without the need for expensive lab instruments by using Crispr’s programmable gene-seeking capabilities to pick up bits of foreign genetic material—from a virus, bacteria, or fungus—circulating in a sick person’s bodily fluids, and deliver those results via something that looks like a pregnancy test. Tests made with disposable paper strips are cheap and can go into the field or into people’s homes, greatly expanding their reach. This summer, the FDA authorized two Crispr-based tests, both for detecting SARS-CoV-2. Boston-based (Sherlock Biosciences, May, and the Bay Area’s Mammoth Biosciences, August). It marked the first time the FDA has allowed a Crispr-based diagnostic tool to be used on patients. The tests still need to be analyzed in a lab, but they are faster than <a href="https://www.wired.com/story/i-tested-positive-covid-19-what-that-mean/?intcid=inline_amp">the standard method </a>for detecting SARS-CoV-2, called PCR.

CRISPR & Diagnostics

Unlike chromosomes, which you inherit from both parents, mitochondrial DNA comes only from your maternal side. Mutations can cripple the cell’s ability to generate energy and lead to debilitating, <a href="https://www.umdf.org/what-is-mitochondrial-disease/types-of-mitochondrial-disease/">often fatal conditions </a>that affect about one in 6,500 people worldwide. Until now, scientists prevent mitochondrial disease by swapping out one egg’s mitochondria for another, a procedure commonly known <a href="https://www.wired.co.uk/article/what-is-three-person-ivf">as three-person IVF </a>. This summer, scientists in Seattle and Boston <a href="https://go.redirectingat.com/?id=100099x1570350&amp;xcust=amp&amp;url=https%3A%2F%2Fwww.nature.com%2Farticles%2Fd41586-020-02094-x&amp;sref=https%3A%2Fwww.wired.com%2Fstory%2F2020-was-a-breakout-year-for-crispr%2Famp">published a study </a>showing they had discovered a way to harness a strange enzyme found in biofilm-forming bacteria to make precise changes to mitochondrial DNA. The new system has not yet been tested in humans but the discovery opens up another promising avenue.

CRISPR & Mitochondria

The 2020 Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna (first women to win prizes in science together) for Crispr genome editing. It was both a stunning choice (as a DNA-altering tool, Crispr has only been around for 8 years) and a completely expected one. Crispr has completely revolutionized biological research <a href="https://www.wired.com/2015/07/crispr-dna-editing-2/?intcid=inline_amp">since its arrival in 2012 </a>; scientists have since published more than 300,000 studies using the tool to manipulate the genomes of organisms across every kingdom. It’s cheap, fast, and easy enough for almost anyone to use.

CRISPR ascends to Nobel 

scienceandnature

Science & Nature

2020 Was a Breakout Year for Crispr | WIRED

Using x-ray lasers, researchers at Stockholm University have been able to follow the transformation between two distinct different liquid states of water, both being made of H2O molecules. At around -63 Centigrade the two liquids exist at different pressure regimes with a density difference of 20%. By rapidly varying the pressure before the sample could freeze, it was possible to observe one liquid changing into the other in real time. Their findings are published in the journal Science .

Water, both common and necessary for life on Earth, behaves very strangely in comparison with other substances. How water’s properties such as density, specific heat, viscosity, and compressibility respond to changes in pressure and temperature is completely opposite to other liquids that we know. Consequently, water is often called “anomalous.” If water would have behaved as a “normal liquid” we would not exist, since marine life could not have developed. What causes these anomalies?

Weird and Wonderful Water

There have existed a number of explanations to the strange properties of water and one of them propose that water has the ability to exist as two different liquids at different pressures and at low temperatures. If we would be able to keep the two liquids in a glass they would separate with a clear interface in between, as for water and oil (see figure). Ordinary water at our ambient conditions is only one liquid and no interface would be seen in a glass – but on a molecular level, it fluctuates creating small local regions of similar density as the two liquids, causing water’s strange behavior. The challenge has been that no experiment has been possible at the temperatures where the two liquids would co-exist since ice would form almost instantaneously.

Hypothesis

“What was special was that we were able to X-ray unimaginably fast, before the water froze, and could observe how one liquid transformed to the other,” says Anders Nilsson, Professor of Chemical Physics at Stockholm University. “For decades, there has been speculations and different theories to explain these anomalous properties and why they get stronger when water becomes colder. Now we have found that the two liquid states are real and can explain the water strangeness.”“Maybe one of the liquid forms is more prominent for water in small pores inside membranes used to desalinate water,” says Marjorie Ladd Parada, Postdoc at Stockholm University. “I think the access to clean water will be one of the major challenges with climate change.”

Next up...

Two Distinct Different Liquid States of Water Exist, Both Made of H2O Molecules - SciTechDaily

Normally, the two photosystems are kept apart from each other to prevent a short-cut and allow efficient photosynthesis. In winter, the structure of the thylakoid membrane, where the two photosystems are located, is reorganized bringing the two photosystems in physical contact. The researchers showed that photosystem II donates energy directly to photosystem I and this short-cut mode protects the green chlorophyll and the needles when conditions become harsh.

More Efficient Pathways

All plants have safety valves to deal with the excess light energy which is either dissipated as heat or as fluorescence light. However, only conifers seem to have such powerful valves that they can keep the photosynthetic apparatus intact over the extreme boreal winter. The research team combined biochemistry and ultrafast fluorescence analysis. Like this, they could demonstrate how the pine needles deal with excess light energy to protect their sensitive photosynthetic apparatus from damage.

Adaptation Experimentation

In winter, light energy is absorbed by the green chlorophyll molecules but cannot be utilized by the downstream reactions as freezing temperatures stop most biochemical reactions. This is a problem in the early spring when temperatures can be very low, but sunlight is strong, and the excess light energy can damage the proteins of the photosynthetic machinery. The researchers showed that the photosynthetic apparatus is wired in a special way that allows pine needles to stay green all year long.