Lifeboat Foundation

The Y chromosome is the smallest chromosome, and holds the least amount of genes, but scientists are still learning about all of its biological functions. Research has shown that many men start to lose Y chromosomes in blood cells as they get older, and this phenomenon has been linked to some disorders including heart disease and now, cancer. Some studies have suggested that the loss of the Y chromosome may help explain why men tend to die at slightly younger ages compared to women, or why there are sex differences in some types of cancer… Two new studies reported in Nature have explored the link between cancer and the loss of the Y chromosome.

One study used a mouse model to show that a specific gene on the Y chromosome known as KDM5D increases the chance that some types of colorectal cancer will metastasize. The other research report showed that when some cells lose the Y chromosome, bladder tumors are better at evading the immune system, and the risk of aggressive bladder cancer increases.

People who owned black-and-white television sets until the 1980s didn’t know what they were missing until they got a color TV. A similar switch could happen in the world of genomics as researchers at the Berlin Institute of Medical Systems Biology of the Max Delbrück Center (MDC-BIMSB) have developed a technique called Genome Architecture Mapping (“GAM”) to peer into the genome and see it in glorious technicolor. GAM reveals information about the genome’s spatial architecture that is invisible to scientists using solely Hi-C, a workhorse tool developed in 2009 to study DNA interactions, reports a new study in Nature Methods by the Pombo lab.

“With a black-and-white TV, you can see the shapes but everything looks gray,” says Professor Ana Pombo, a molecular biologist and head of the Epigenetic Regulation and Chromatin Architecture lab. “But if you have a color TV and look at flowers, you realize that they are red, yellow and white and we were unaware of it. Similarly, there’s also information in the way the genome is folded in three-dimensions that we have not been aware of.”

Understanding DNA organization can reveal the basis of health and disease. Our cells pack a 2-meter-long genome into a roughly 10 micrometer-diameter nucleus. The packaging is done precisely so that regulatory DNA comes in contact with the right genes at the right times and turns them on and off. Changes to the three-dimensional configuration can disrupt this process and cause disease.

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Insects, with their remarkable ability to undergo complete metamorphosis, have long fascinated scientists seeking to understand the underlying genetic mechanisms governing this transformative process.

Now, a recent study conducted by the Institute for Evolutionary Biology (IBE, CSIC-UPF) and the IRB Barcelona has shed light on the crucial role of three genes – Chinmo, Br-C and E93 – in orchestrating the stages of insect development. Published in eLife, this research provides valuable insights into the evolutionary origins of metamorphosis and sheds new light on the role of these genes in growth, development and cancer regulation [1].

Longevity. Technology: Chinmo might sound like a Pokémon character, but the truth is much more interesting. Conserved throughout the evolution of insects, scientists think it, and the more conventionally-named Br-C and E93, could play a key role in the evolution of metamorphosis, acting as the hands of the biological clock in insects. A maggot is radically different from the fly into which it changes – could understanding and leveraging the biology involved one day allow us to change cultured skin cells into replacement organs or to stop tumors in their early stages of formation? No, Dr Seth Brundle, you can buzz off.

Aleksandra Radenovic, head of the Laboratory of Nanoscale Biology in the School of Engineering, has worked for years to improve nanopore technology, which involves passing a molecule like DNA through a tiny pore in a membrane to measure an ionic current. Scientists can determine DNA’s sequence of nucleotides—which encodes genetic information—by analyzing how each one perturbs this current as it passes through. The research has been published in Nature Nanotechnology.

Currently, the passage of molecules through a nanopore and the timing of their analysis are influenced by random physical forces, and the rapid movement of molecules makes achieving high analytical accuracy challenging. Radenovic has previously addressed these issues with optical tweezers and viscous liquids. Now, a collaboration with Georg Fantner and his team in the Laboratory for Bio-and Nano-Instrumentation at EPFL has yielded the advancement she’s been looking for—with results that could go far beyond DNA.

Continue reading “Extreme DNA resolution: Spatially multiplexed single-molecule translocations through a nanopore at controlled speeds” »

By modifying the blueprint of life, researchers are endowing proteins with chemistries they’ve never had before.

At least, from a genetic point of view | Science & technology.

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A human cell harbors roughly 2 meters of DNA, encompassing the essential genetic information of an individual. If one were to unwind and stretch out all the DNA contained within a single person, it would span a staggering distance—enough to reach the sun and back 60 times over. In order to manage such an astounding volume of biological information, the cell compacts its DNA into tightly packed chromosomes.

“Imagine DNA as a piece of paper upon which all our genetic information is written,” says Minke A.D. Nijenhuis, co-corresponding author. “The paper is folded into a very tight structure in order to fit all of that information into a small cell nucleus. To read the information, however, parts of the paper have to be unfolded and then refolded. This spatial organization of our genetic code is a central mechanism of life. We therefore wanted to create a methodology that allows researchers to engineer and study the compaction of double-stranded DNA.”

Natural DNA is often double-stranded: one strand to encode the genes and one backup strand, intertwined in a double helix. The double helix is stabilized by Watson-Crick interactions, which allow the two strands to recognize and pair with one another. Yet there exists another, lesser-known class of interactions between DNA. These so-called normal or reverse Hoogsteen interactions allow a third strand to join in, forming a beautiful triple helix (Figure 1).