Lifeboat Foundation

Big fan of long-read sequencing. It helped diagnose my rare disease when conventional sequencing failed.

What’s the Difference between Short-Read Sequencing and Long-Read Sequencing? Like their names suggest, short-read sequencing looks at DNA in short snippets (100−350 base pairs) while long-read sequencing measures long fragments of DNA (tens of thousands of base pairs). Why does that matter? Well, when trying to characterize a human genome that has two copies (one maternal and one paternal), each 3.2 billion base pairs in length — having longer snippets of DNA means you: Need fewer snippets to make up the length of the whole genome and have no gaps where the sequence is unknown Can more easily map how one region of the genome is connected to another region Have the ability to phase or determine which copy of a gene, maternal or paternal, a mutation occurs in.

PacBio long-read sequencing provides the most comprehensive view of genomes, transcriptomes, and epigenomes.

Scientists develop the first CRISPR-Cas9-based gene drive in plants which may breed crops better able to withstand drought and disease.

Scientists achieved a record level of visual detail with an imaging technique that could help develop future electronics and better batteries.

Scientists develop the first CRISPR-Cas9-based gene drive in plants which may breed crops better able to withstand drought and disease.

Scientists have discovered a unique form of cell messaging occurring in the human brain that’s not been seen before. Excitingly, the discovery hints that our brains might be even more powerful units of computation than we realized.

Early last year, researchers from institutes in Germany and Greece reported a mechanism in the brain’s outer cortical cells that produces a novel ‘graded’ signal all on its own, one that could provide individual neurons with another way to carry out their logical functions.

Continue reading “A Never-Before-Seen Type of Signal Has Been Detected in The Human Brain” »

For the first time, CRISPR-Cas9-based gene drive technology has been developed in plants. Enabling the inheritance of both copies of a target gene from a single parent could greatly reduce the generations needed for plant breeding. Establishing this genome editing technology in plants may allow for breeding resilient crops that are better able to withstand drought and disease.

#GenomeEditing #AgBio #CRISPR #Cas9

Gene drives have been established in insects, including fruit flies and mosquitoes, and mammals such as mice. Now, for the first time, the CRISPR-Cas9-based technology that disrupts Mendelian inheritance and allows for selective acquisition of target genes has been developed in plants. Establishing this genome editing technology in plants may allow for breeding resilient crops that are better able to withstand drought and disease.

Continue reading “First CRISPR-Based Gene Drive Developed in Plants” »

Changes in epigenetic age acceleration (EAA) were significant over time, with the biggest increase — 4.9 years — seen immediately after the completion of radiotherapy (PChanges in epigenetic age acceleration (EAA) were significant over time, with the biggest increase — 4.9 years — seen immediately after the completion of radiotherapy (P0.001), reported Canhua Xiao, RN, PhD, of Emory University School of Nursing in Atlanta, and colleagues.

The study also demonstrated that EAA was associated with greater inflammation and fatigue, even up to a year after treatment, they noted in Cancer.

While chronological age is a strong risk factor for chronic health problems, Xiao and colleagues said that it often differs from epigenetic age and may be a limited predictor of age-associated disorders. On the other hand, they noted that epigenetic clocks, based on blood DNA methylation measures, have become reliable aging biomarkers.

Researchers at McMaster University have developed a promising new cancer immunotherapy that uses cancer-killing cells genetically engineered outside the body to find and destroy malignant tumors.

The modified “natural killer” cells can differentiate between cancer cells and healthy cells that are often intermingled in and around tumors, destroying only the targeted cells.

The natural killer cells’ ability to distinguish the target cells, even from healthy cells that bear similar markers, brings new promise to this branch of immunotherapy, say members of the research team behind a paper published in the current issue of the journal iScience, newly posted on the PubMed database.

Caenorhabditis elegans is a nematode worm which is commonly utilised in longevity research due to their genetic similarity to humans and their extremely short lifespans (often no more than 4 weeks). Previous research into improving the lifespan of these worms has yielded several interesting results, with modifications to their insulin and rapamycin signalling pathways resulting in a 100% and 30% increase in lifespan respectively. These successes prompted the obvious question, what would happen if both of these pathways were modified at the same time?

Photograph of the Caenorhabditis elegans adult hermaphrodite. Scale bar, 100 μm. Credit: ResearchGate, Nobuyuki Hamada.

Humans perceive the world around them with five senses — vision, hearing, taste, smell and touch. Many other animals are also able to sense the Earth’s magnetic field. For some time, a collaboration of biologists, chemists and physicists centred at the Universities of Oldenburg (Germany) and Oxford (UK) have been gathering evidence suggesting that the magnetic sense of migratory birds such as European robins is based on a specific light-sensitive protein in the eye. In the current edition of the journal Nature, this team demonstrate that the protein cryptochrome 4, found in birds’ retinas, is sensitive to magnetic fields and could well be the long-sought magnetic sensor.

First author Jingjing Xu, a doctoral student in Henrik Mouritsen’s research group in Oldenburg, took a decisive step toward this success. After extracting the genetic code for the potentially magnetically sensitive cryptochrome 4 in night-migratory European robins, she was able, for the first time, to produce this photoactive molecule in large quantities using bacterial cell cultures. Christiane Timmel’s and Stuart Mackenzie’s groups in Oxford then used a wide range of magnetic resonance and novel optical spectroscopy techniques to study the protein and demonstrate its pronounced sensitivity to magnetic fields.

The team also deciphered the mechanism by which this sensitivity arises — another important advance. “Electrons that can move within the molecule after blue-light activation play a crucial role,” explains Mouritsen. Proteins like cryptochrome consist of chains of amino acids: robin cryptochrome 4 has 527 of them. Oxford’s Peter Hore and Oldenburg physicist Ilia Solov’yov performed quantum mechanical calculations supporting the idea that four of the 527 — known as tryptophans — are essential for the magnetic properties of the molecule. According to their calculations, electrons hop from one tryptophan to the next generating so-called radical pairs which are magnetically sensitive. To prove this experimentally, the team from Oldenburg produced slightly modified versions of the robin cryptochrome, in which each of the tryptophans in turn was replaced by a different amino acid to block the movement of electrons.

The new system streamlines the process of fermenting plant sugar to fuel by helping yeast survive industrial toxins.

More corn is grown in the United States than any other crop, but we only use a small part of the plant for food and fuel production; once people have harvested the kernels, the inedible leaves, stalks and cobs are left over. If this plant matter, called corn stover, could be efficiently fermented into ethanol the way corn kernels are, stover could be a large-scale, renewable source of fuel.

“Stover is produced in huge amounts, on the scale of petroleum,” said Whitehead Institute Member and Massachusetts Institute of Technology (MIT) biology professor Gerald Fink. “But there are enormous technical challenges to using them cheaply to create biofuels and other important chemicals.”