Lifeboat Foundation: Safeguarding Humanity
Toggle light / dark theme

Blog

Category: genetics – Page 293

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.

Read more | >

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.

By measuring the electrical activity in sections of tissue removed during surgery on epileptic patients and analysing their structure using fluorescent microscopy, the neurologists found individual cells in the cortex used not just the usual sodium ions to ‘fire’, but calcium as well.

Read more | >

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.

The research is published in Nature Communications in the paper, “Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis.”

“This work defies the genetic constraints of sexual reproduction that an offspring inherits 50% of their genetic materials from each parent,” said Yunde Zhao, PhD, professor of cell and developmental biology at the University of California, San Diego (UCSD). “This work enables inheritance of both copies of the desired genes from only a single parent. The findings can greatly reduce the generations needed for plant breeding.”

Read more | >

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.

Read more | >

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” can differentiate between and that are often intermingled in and around tumors, destroying only the targeted cells.

The natural killer cells’ ability to distinguish the , 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.

Read more | >

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.

Read more | >

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.

Read more | >

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.”

Read more | >

CRISPR gene editing already promises to fight diseases that were once thought unassailable, but techniques so far have required injecting the tools directly into affected cells. That’s not very practical for some conditions. However, there’s just been a breakthrough. NPR reports that researchers have published results showing that you can inject CRISPR-Cas9 into the bloodstream to make edits, opening the door to the use of gene editing for treating many common diseases.

The experimental treatment tackled a rare genetic disease, transthyretin amyloidosis. Scientists injected volunteers with CRISPR-loaded nanoparticles that were absorbed by the patients’ livers, editing a gene in the organ to disable production of a harmful protein. Levels of that protein plunged within weeks of the injection, saving patients from an illness that can rapidly destroy nerves and other tissues in their bodies.

The test involved just six people, and the research team still has to conduct long-term studies to check for possible negative effects. If this method proves viable on a large scale, though, it could be used to treat illnesses where existing CRISPR techniques aren’t practical, ranging from Alzheimer’s to heart disease.

Read more | >