Lifeboat Foundation

“DNA, RNA and proteins are the key players to regulate all processes in the cells of our body,” Leiden Professor John van Noort explains. “To understand the (mis-)functioning of these molecules, it is essential to uncover how their 3D structure depends on their sequence and for this it is necessary to measure them one molecule at a time. However, single-molecule measurements are laborious and slow, and the number of possible sequence variations is massive.”

Now the team of scientists developed an innovative tool, called SPARXS (Single-molecule Parallel Analysis for Rapid eXploration of Sequence space), that allows for studying millions of DNA molecules simultaneously.

Continue reading “Revealing DNA behavior in record time (w/video)” »

CRISPR-Cas systems, defense systems in bacteria, have become a plentiful source of technologies for molecular diagnostics. Researchers at the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg have expanded this extensive toolbox. Their novel method, called PUMA, enables the detection of RNA with Cas12 nucleases, which naturally target DNA. PUMA promises a wide range of applications and high accuracy.

The team published its results in the journal Nature Communications (“TracrRNA reprogramming enables direct PAM-independent detection of RNA with diverse DNA-targeting Cas12 nucleases”).

Bacteria have developed special defense mechanisms to protect themselves against viruses, which by no means infect only humans. As part of these so-called CRISPR-Cas systems, a CRISPR ribonucleic acid (crRNA), which serves as a “guide RNA,” recognizes regions of a foreign genome, such as viral DNA. The CRISPR-associated (Cas) nuclease, directed by a crRNA, then renders it harmless by cutting it like a pair of scissors.

Researchers worldwide can now create highly realistic brain cortical organoids — essentially miniature artificial brains with functioning neural networks — thanks to a proprietary protocol released this month by researchers at the University of California San Diego.

The new technique, published in Nature Protocols (“Generation of ‘semi-guided’ cortical organoids with complex neural oscillations”), paves the way for scientists to perform more advanced research regarding autism, schizophrenia and other neurological disorders in which the brain’s structure is usually typical, but electrical activity is altered. That’s according to Alysson Muotri, Ph.D., corresponding author and director of the UC San Diego Sanford Stem Cell Institute (SSCI) Integrated Space Stem Cell Orbital Research Center. The SSCI is directed by Dr. Catriona Jamieson, a leading physician-scientist in cancer stem cell biology whose research explores the fundamental question of how space alters cancer progression.

The newly detailed method allows for the creation of tiny replicas of the human brain so realistic that they rival “the complexity of the fetal brain’s neural network,” according to Muotri, who is also a professor in the UC San Diego School of Medicine’s Departments of Pediatrics and Cellular and Molecular Medicine. His brain replicas have already traveled to the International Space Station (ISS), where their activity was studied under conditions of microgravity.

In a study published in Cell Reports Physical Science (“Electro-Active Polymer Hydrogels Exhibit Emergent Memory When Embodied in a Simulated Game-Environment”), a team led by Dr Yoshikatsu Hayashi demonstrated that a simple hydrogel — a type of soft, flexible material — can learn to play the simple 1970s computer game ‘Pong’. The hydrogel, interfaced with a computer simulation of the classic game via a custom-built multi-electrode array, showed improved performance over time.

Dr Hayashi, a biomedical engineer at the University of Reading’s School of Biological Sciences, said: Our research shows that even very simple materials can exhibit complex, adaptive behaviours typically associated with living systems or sophisticated AI.

This opens up exciting possibilities for developing new types of ‘smart’ materials that can learn and adapt to their environment.

A research team at the University of Virginia School of Engineering and Applied Science has developed what it believes could be the template for the first building blocks for human-compatible organs printed on demand.

Liheng Cai, an assistant professor of materials science and engineering and chemical engineering, and his Ph.D. student, Jinchang Zhu, have made biomaterials with controlled mechanical properties matching those of various human tissues.

“That’s a big leap compared to existing bioprinting technologies,” Zhu said.

Researchers from North Carolina State University and Johns Hopkins University have demonstrated a technology capable of a suite of data storage and computing functions – repeatedly storing, retrieving, computing, erasing or rewriting data – that uses DNA rather than conventional electronics. Previous DNA data storage and computing technologies could complete some but not all of these tasks.

“In conventional computing technologies, we take for granted that the ways data are stored and the way data are processed are compatible with each other,” says project leader Albert Keung, co-corresponding author of a paper on the work (Nature Nanotechnology, “A Primordial DNA Store and Compute Engine”). “But in reality, data storage and data processing are done in separate parts of the computer, and modern computers are a network of complex technologies,” Keung is an associate professor of chemical and biomolecular engineering and a Goodnight Distinguished Scholar at NC State.

“DNA computing has been grappling with the challenge of how to store, retrieve and compute when the data is being stored in the form of nucleic acids,” Keung says. “For electronic computing, the fact that all of a device’s components are compatible is one reason those technologies are attractive. But, to date, it’s been thought that while DNA data storage may be useful for long-term data storage, it would be difficult or impossible to develop a DNA technology that encompassed the full range of operations found in traditional electronic devices: storing and moving data; the ability to read, erase, rewrite, reload or compute specific data files; and doing all of these things in programmable and repeatable ways.

In the past decade, lab-grown blobs of human brain tissue began making news headlines, as they ushered in a new era of scientific discovery and raised a slew of ethical questions.

These blobs — scientifically known as brain organoids, but often called “minibrains” in the news — serve as miniature, simplified models of full-size human brains. These organoids can potentially be useful in basic research, drug development and even computer science.

Mitochondria in brain cells frequently insert their DNA into the nucleus, potentially impacting lifespan, as those with more insertions were found to die earlier. Stress appears to accelerate this process, suggesting a new way mitochondria influence health beyond energy production.

As direct descendants of ancient bacteria, mitochondria have always been a little alien. Now a study shows that mitochondria are possibly even stranger than we thought.

Mitochondria in our brain cells frequently fling their DNA into the nucleus, the study found, where the DNA becomes integrated into the cells’ chromosomes. And these insertions may be causing harm: Among the study’s nearly 1,200 participants, those with more mitochondrial DNA insertions in their brain cells were more likely to die earlier than those with fewer insertions.

There are different types of biotechnology protocols for genome/gene editing (GE), but the preferred one is the Clustered Regularly Interspaced Short Palynodromic Repeat (CRISPR) Cas9 system. Advantages include precision, the ability to design variants tailored to needs, and optimal operational cost and time.