Lifeboat Foundation

We combined a machine learning algorithm with knowledge gleaned from hundreds of biological experiments to develop a technique that allows biomedical researchers to figure out the functions of the proteins that turn genes on and off in cells, called transcription factors. This knowledge could make it easier to develop drugs for a wide range of diseases.

Early on during the COVID-19 pandemic, scientists who worked out the genetic code of the RNA molecules of cells in the lungs and intestines found that only a small group of cells in these organs were most vulnerable to being infected by the SARS-CoV-2 virus. That allowed researchers to focus on blocking the virus’s ability to enter these cells. Our technique could make it easier for researchers to find this kind of information.

The biological knowledge we work with comes from this kind of RNA sequencing, which gives researchers a snapshot of the hundreds of thousands of RNA molecules in a cell as they are being translated into proteins. A widely praised machine learning tool, the Seurat analysis platform, has helped researchers all across the world discover new cell populations in healthy and diseased organs. This machine learning tool processes data from single-cell RNA sequencing without any information ahead of time about how these genes function and relate to each other.

Researchers from the group of Hans Clevers (Hubrecht Institute) corrected mutations that cause cystic fibrosis in cultured human stem cells. In collaboration with the UMC Utrecht and Oncode Institute, they used a technique called prime editing to replace the ‘faulty’ piece of DNA with a healthy piece. The study, published in Life Science Alliance on August 9 shows that prime editing is safer than the conventional CRISPR/Cas9 technique. “We have for the first time demonstrated that this technique really works and can be safely applied in human stem cells to correct cystic fibrosis.”

Cystic fibrosis (CF) is one of the most prevalent genetic diseases worldwide and has grave consequences for the patient. The mucus in the lungs, throat and intestines is sticky and thick, which causes blockages in organs. Although treatments are available to dilute the mucus and prevent inflammations, CF is not yet curable. However, a new study from the group of Hans Clevers (Hubrecht Institute) in collaboration with the UMC Utrecht and Oncode Institute offers new hope.

Correcting CF mutations

Continue reading “New CRISPR/Cas9 technique corrects cystic fibrosis in cultured human stem cells” »

Since DNMT3A increases DNA methylation, the researchers used a natural product that donates methyl groups S-adenosylmethionine (SAMe) and to activate the retinoic acid receptor they treated the animals with vitamin A. They found that combined treatment with the methyl donor SAM and retinoic acid reversed PTSD-like behaviors.

Summary: Combining two natural products that modulate the epigenome, researchers believe they have identified a feasible approach to reversing symptoms of PTSD in animal models that could be effective in humans.

Source: Bar Ilan University

Continue reading “Nutritional Supplements Could Help Treat PTSD” »

ADS Codex translates binary data into nucleotides that can be sequenced in molecules as files for later retrieval, bringing potential cost savings and compact ‘cold storage.’

In support of a major collaborative project to store massive amounts of data in DNA

DNA, or deoxyribonucleic acid, is a molecule composed of two long strands of nucleotides that coil around each other to form a double helix. It is the hereditary material in humans and almost all other organisms that carries genetic instructions for development, functioning, growth, and reproduction. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).

Through a process known as RNA interference (RNAi), scientists have been able to modify the genetic make-up of the daddy long-legs arachnid so that its distinctive spindly limbs become twice as short.

This process – which uses a gene’s own DNA sequence and small fragments of RNA to turn the gene off – was applied to the Phalangium opilio species, one of the most common species of daddy long-legs in the world.

The result is effectively a daddy short-legs instead of a daddy long-legs. The team behind the work is hoping that the experiments can teach us more about how these elongated limbs evolved in the first place.

Gene-editing technique CRISPR may deliver new treatments for genetic diseases—and it’s already being tested on patients.

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In one of the first clinical applications of the technique, last month researchers reported in the New England Journal of Medicine that CRISPR had stopped a genetic disease called amyloidosis, which occurs when an abnormal protein accumulates in your organs. They’re not the only group moving toward using CRISPR on humans; recently, the FDA approved a human clinical trial that will use the technique to edit genes responsible for sickle cell disease.

A new tool helps researchers explore the types of cells that make up brain organoids — clusters of cells that can mimic the basic structure, function and development of different parts of the brain.

The software, detailed in Cell Stem Cell, maps information about when and where genes are expressed in brain organoids onto a reference atlas of the developing mouse brain. Scientists can use the resulting overlay to develop organoids that better recapitulate the developing brain, the team says, or to uncover the effects of gene mutations and other experimental perturbations.

Brain organoids derived from the cells of people with conditions such as autism have proved useful in capturing neuronal abnormalities. But the findings are muddied by methodological differences in how researchers develop these lab-grown blobs. Advanced techniques to profile gene expression in single cells have made it easier to identify the cell types in any given organoid. But it’s remained difficult to map those cell types onto different brain regions.

Three pioneering technologies have forever altered how researchers do their work and promise to revolutionize medicine, from correcting genetic disorders to treating degenerative brain diseases.

Some mutations that disable SCN2A, one of the genes most strongly linked to autism, can unexpectedly make neurons hyperexcitable, a study in mice shows. The findings may help explain why a sizeable proportion of autistic children with mutations in SCN2A experience epileptic seizures.

Deleterious mutations in an autism-associated gene can make neurons hyperexcitable, raising the risk of epileptic seizures.