Lifeboat Foundation

Most simply, the phrase “genome editing” represents tools and techniques that biotechnologists use to edit the genome — that is, the DNA or RNA of plants, animals, and bacteria. Though the earliest versions of genome editing technology have existed for decades, the introduction of CRISPR in 2013 “brought major improvements to the speed, cost, accuracy, and efficiency of genome editing.”

CRISPR, or Clustered Regularly Interspersed Short Palindromic Repeats, is actually an ancient mechanism used by bacteria to remove viruses from their DNA. In the lab, researchers have discovered they can replicate this process by creating a synthetic RNA strand that matches a target DNA sequence in an organism’s genome. The RNA strand, known as a “guide RNA,” is attached to an enzyme that can cut DNA. After the guide RNA locates the targeted DNA sequence, the enzyme cuts the genome at this location. DNA can then be removed, and new DNA can be added. CRISPR has quickly become a powerful tool for editing genomes, with research taking place in a broad range of plants and animals, including humans.

A significant percentage of genome editing research focuses on eliminating genetic diseases. However, with tools like CRISPR, it also becomes possible to alter a pathogen’s DNA to make it more virulent and more contagious. Other potential uses include the creation of “‘killer mosquitos,’ plagues that wipe out staple crops, or even a virus that snips at people’s DNA.”

A large team of researchers affiliated with multiple institutions in and around Hangzhou, China, has taken a very large step toward the creation of a comprehensive human single-cell atlas. In their paper published in the journal Nature, the group describes how they sequenced the RNA of over a half-million single cells donated by volunteers and processed the information to present it in a way that could be used in a single-cell atlas.

All of the cells in the human body carry the same basic genetic information—they differ in which genes are expressed. Those genes that are expressed define the function of a given cell. For some time, medical researchers have wanted an atlas that would describe which genes are expressed in cells in all parts of the body. Such an atlas would help scientists better understand the functions of cells and how they work together, in addition to saving time on new research efforts. Atlases have been created for some tissue types, but currently, there is no single atlas to cover all of the cell types in the human body. Creating such an atlas would require much time and effort over many years, as the human body has over 30 trillion cells, after all. In this new effort, the researchers have taken a large step toward that goal by providing gene expression information for over 500,000 cells from different parts of the body (and some from fetal tissue), including all of the major organs.

The work involved first obtaining the tissue samples and then processing them. To that end, the cells were first isolated by putting some in a centrifuge and using enzymes with others. Once isolated, each of the cells were sequenced using a special tool the team previously developed called Microwell-seq—it allows for fast sequencing of large numbers of cells. In all, the team sequenced cells from 60 types of tissue. The researchers then generated a map using a method they devised for classifying cell information. The map and its underlying data form the basis of what could become a full, comprehensive single-cell database.

:33333 could lead to future cures of muscular dystrophy.

Facioscapulohumeral muscular dystrophy (FSHD) is caused by altered expression of DUX4, a gene important during development that is not usually present in adult cells. In FSHD skeletal muscle, activation of DUX4 leads to apoptosis. To identify potential targets that mediate DUX4-induced cell death, Lek et al. performed an unbiased screen using CRISPR-Cas9. Hypoxia signaling emerged as a target, and treating patient cells and zebrafish models of FSHD with inhibitors of hypoxia signaling reduced cell death and expression of DUX4 target genes and improved structural defects and muscle function. Results demonstrate the utility of this CRISPR-Cas9 screen for identifying putative therapeutic targets for FSHD.

The emergence of CRISPR-Cas9 gene-editing technologies and genome-wide CRISPR-Cas9 libraries enables efficient unbiased genetic screening that can accelerate the process of therapeutic discovery for genetic disorders. Here, we demonstrate the utility of a genome-wide CRISPR-Cas9 loss-of-function library to identify therapeutic targets for facioscapulohumeral muscular dystrophy (FSHD), a genetically complex type of muscular dystrophy for which there is currently no treatment. In FSHD, both genetic and epigenetic changes lead to misexpression of DUX4, the FSHD causal gene that encodes the highly cytotoxic DUX4 protein. We performed a genome-wide CRISPR-Cas9 screen to identify genes whose loss-of-function conferred survival when DUX4 was expressed in muscle cells. Genes emerging from our screen illuminated a pathogenic link to the cellular hypoxia response, which was revealed to be the main driver of DUX4-induced cell death.

Scientists took conspiracy theories seriously and analyzed the coronavirus to reveal its natural origins.

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Unlocking the full potential of cannabis for agriculture and human health will require a co-ordinated scientific effort to assemble and map the cannabis genome, says a just-published international study led by University of Saskatchewan researchers.

In a major statistical analysis of existing data and studies published in the Annual Review of Plant Biology, the authors conclude there are large gaps in the scientific knowledge of this high-demand, multi-purpose crop.

Continue reading “Mapping the cannabis genome to improve crops and health” »

Researchers have developed the first computational model of a human cell and simulated its behavior for 15 minutes—the longest time achieved for a biological system of this complexity. In a new study, simulations reveal the effects of spatial organization within cells on some of the genetic processes that control the regulation and development of human traits and some human diseases.

The study, which produced a new computational platform that is available to any researcher, is published in the journal PLOS Computational Biology.

“This is the first program that allows researchers to set up a virtual human cell and change chemical reactions and geometries to observe cellular processes in real time,” said Zhaleh Ghaemi, a research scientist at the University of Illinois at Urbana-Champaign and lead author of the study.

The Curious Case of Sickle-Cell Anemia

Even those uninterested in biology have likely heard of the disorder. Sickle-cell anemia holds the crown as the first genetic disorder to be traced to its molecular roots nearly a hundred years ago.

The root of the disorder is a single genetic mutation that drastically changes the structure of the oxygen-carrying protein, beta-globin, in red blood cells. The result is that the cells, rather than forming their usual slick disc-shape, turn into jagged, sickle-shaped daggers that damage blood vessels or block them altogether. The symptoms aren’t always uniform; rather, they come in “crisis episodes” during which the pain becomes nearly intolerable.

The longfin inshore squid can edit the RNA inside its nerve cells, Wired reports, meaning that it can drastically alter the behavior of its biological machinery as needed — perhaps to help the animal rapidly adapt to new environments. It’s a bizarre discovery, and one that could potentially lead to better genetic treatments for humans.

Neat Trick

Researchers from the Marine Biological Laboratory found that the squid alters the RNA within its axons instead of the DNA within its nuclei, according to research published Monday in the journal Nucleic Acids Research. Thus far, it’s the only animal known to do so.

Researchers at Stanford University have demonstrated they can rejuvenate human cells, making them more like young cells again, by rewinding an epigenetic aging clock.