Lifeboat Foundation

Summary: A new study on aging reveals a surprising discovery about the connection between protein shape and mitochondrial health.

Source: Buck Institute.

Every cell in the body goes through thousands of chemical reactions each day, and each reaction involves tiny protein molecules folded into precise shapes to perform their functions. Misfolded proteins underlie some of the most common and devastating diseases of aging, like Alzheimer’s and Parkinson’s. A major focus of aging research is discovering ways to maintain protein shape and prevent misfolded proteins from wreaking havoc on cellular function.

Circa 2012

Quantum ground-state problems are computationally hard problems for general many-body Hamiltonians; there is no classical or quantum algorithm known to be able to solve them efficiently. Nevertheless, if a trial wavefunction approximating the ground state is available, as often happens for many problems in physics and chemistry, a quantum computer could employ this trial wavefunction to project the ground state by means of the phase estimation algorithm (PEA). We performed an experimental realization of this idea by implementing a variational-wavefunction approach to solve the ground-state problem of the Heisenberg spin model with an NMR quantum simulator. Our iterative phase estimation procedure yields a high accuracy for the eigenenergies (to the 10–5 decimal digit).

New photo-oxygenation catalyst targets amyloid structure, recruits brain immune system cells.

A small, light-activated molecule recently tested in mice represents a new approach to eliminating clumps of amyloid protein found in the brains of Alzheimer’s disease patients. If perfected in humans, the technique could be used as an alternative approach to immunotherapy and used to treat other diseases caused by similar amyloids.

Researchers injected the molecule directly into the brains of live mice with Alzheimer’s disease and then used a specialized probe to shine light into their brains for 30 minutes each day for one week. Chemical analysis of the mouse brain tissue showed that the treatment significantly reduced amyloid protein. Results from additional experiments using human brain samples donated by Alzheimer’s disease patients supported the possibility of future use in humans.

Circa 2000

A 1940 paper by Gamow and Mario Schoenberg was the first in a subject we now call particle astrophysics. The two authors presciently speculated that neutrinos could play a role in the cooling of massive collapsing stars. They named the neutrino reaction the Urca process, after a well known Rio de Janeiro casino. This name might seem a strange choice, but not to Gamow, a legendary prankster who once submitted a paper to Nature in which he suggested that the Coriolis force might account for his observation that cows chewed clockwise in the Northern Hemisphere and counterclockwise in the Southern Hemisphere.

In the 1940s Gamow began to attack, with his colleague Ralph Alpher, the problem of the origin of the chemical elements. Their first paper on the subject appeared in a 1948 issue of the Physical Review. At the last minute Gamow, liking the sound of ‘alpha, beta, gamma’, added his old friend Hans Bethe as middle author in absentia (Bethe went along with the joke, but the editors did not). Gamow and Alpher, with Robert Herman, then pursued the idea of an extremely hot neutron-dominated environment. They envisioned the neutrons decaying into protons, electrons and anti-neutrinos and, when the universe had cooled sufficiently, the neutrons and protons assembling heavier nuclei. They even estimated the photon background that would be necessary to account for nuclear abundances, suggesting a residual five-degree background radiation.

Continue reading “The Big Bang and the genetic code” »

Common medications can accumulate in gut bacteria, a new study has found, altering bacterial function and potentially reducing the effectiveness of the drug. These interactions—seen for a variety of medications, such as depression, diabetes, and asthma drugs—could help researchers to better understand individual differences in drug effectiveness and side-effects, according to the study published in Nature.

It is known that bacteria can chemically modify some drugs, a process known as biotransformation. This study, led by researchers from the Medical Research Council (MRC) Toxicology Unit at the University of Cambridge and the European Molecular Biology Laboratory (EMBL) in Germany, is the first to show that certain species of gut bacteria accumulate human drugs, altering the types of bacteria and their activity.

This could change the effectiveness of the drug both directly, as the accumulation could reduce the availability of the drug to the body, and indirectly, as altered bacterial function and composition could be linked to side-effects.

The groups also explained why in previous studies by other scientists, the chromatin appeared to fill the cell nuclei. “When scientists plate cells on a glass slide in order to study them under a microscope, they change their volume and physically flatten them. This may perturb some of the forces governing chromatin arrangement and reduce the distance between the upper part of the nucleus to its base,” Safran explains.

If you open a biology textbook and run through the images depicting how DNA is organized in the cell’s nucleus, chances are you’ll start feeling hungry; the chains of DNA would seem like a bowl of ramen: long strings floating in liquid. However, according to two new studies—one experimental and the other theoretical—that are the outcome of the collaboration between the groups of Prof. Talila Volk of the Molecular Genetics Department and Prof. Sam Safran of the Chemical and Biological Physics Department at the Weizmann Institute of Science, this image should be reconsidered. Clarifying it is essential since DNA’s spatial arrangement in the nucleus can affect the expression of genes contained within the DNA molecule, and hence the proteins found in the cell.

This story began when Volk was studying how mechanical forces influence cell nuclei in the muscle and found evidence that muscle contractions had an immediate effect on gene expression patterns. “We couldn’t explore this further because existing methods relied on imaging of chemically preserved cells, so they failed to capture what happens in the cell nuclei of an actual working muscle,” she says.

Continue reading “Novel imaging method reveals a surprising arrangement of DNA in the cell’s nucleus” »

A more general definition of entropy was proposed by Boltzmann (1877) as S = k ln W, where k is Boltzmann’s constant, and W is the number of possible states of a system, in the units J⋅K⁻¹, tying entropy to statistical mechanics. Szilard (1929) suggested that entropy is fundamentally a measure of the information content of a system. Shannon (1948) defined informational entropy as \(S=-\sum_{i}{p}_{i}{log}_{b}{p}_{i}\) where p_i is the probability of finding message number i in the defined message space, and b is the base of the logarithm used (typically 2 resulting in units of bits). Landauer (1961) proposed that informational entropy is interconvertible with thermodynamic entropy such that for a computational operation in which 1 bit of information is erased, the amount of thermodynamic entropy generated is at least k ln 2. This prediction has been recently experimentally verified in several independent studies (Bérut et al. 2012; Jun et al. 2014; Hong et al. 2016; Gaudenzi et al. 2018).

The equivalency of thermodynamic and informational entropy suggests that critical points of instability and subsequent self-organization observed in thermodynamic systems may be observable in computational systems as well. Indeed, this agrees with observations in cellular automata (e.g., Langton 1986; 1990) and neural networks (e.g., Wang et al. 1990; Inoue and Kashima 1994), which self-organize to maximize informational entropy production (e.g., Solé and Miramontes 1995). The source of additional information used for self-organization has been identified as bifurcation and deterministic chaos (Langton 1990; Inoue and Kashima 1994; Solé and Miramontes 1995; Bahi et al. 2012) as defined by Devaney (1986). This may provide an explanation for the phenomenon termed emergence, known since classical antiquity (Aristotle, c. 330 BCE) but lacking a satisfactory explanation (refer to Appendix A for discussion on deterministic chaos, and Appendix B for discussion on emergence). It is also in full agreement with extensive observations of deterministic chaos in chemical (e.g., Nicolis 1990; Györgyi and Field 1992), physical (e.g., Maurer and Libchaber 1979; Mandelbrot 1983; Shaw 1984; Barnsley et al. 1988) and biological (e.g., May 1975; Chay et al. 1995; Jia et al. 2012) dissipative structures and systems.

This theoretical framework establishes a deep fundamental connection between cybernetic^{Footnote 1} and biological systems, and implicitly predicts that as more work is put into cybernetic systems composed of hierarchical dissipative structures, their complexity increases, allowing for more possibilities of coupled feedback and emergence at increasingly higher levels. Such high-level self-organization is routinely exploited in machine learning, where artificial neural networks (ANNs) self-organize in response to inputs from the environment similarly to neurons in the brain (e.g., Lake et al. 2017; Fong et al. 2018). The recent development of a highly organized (low entropy) immutable information carrier, in conjunction with ANN-based artificial intelligence (AI) and distributed computing systems, presents new possibilities for self-organization and emergence.

High-energy cosmic rays have proven elusive… but we may have found their source.

Thanks to new research led by the University of Nagoya, scientists have quantified the number of cosmic rays produced in a supernova remnant for the first time. This research has helped resolve a 100-year mystery and is a major step towards determining precisely where cosmic rays come from.

While scientists theorize that cosmic rays originate from many sources — our Sun, supernovae, gamma-ray bursts (GRBs), and active galactic nuclei (sometimes called quasars) — their exact origin has been a mystery since they were first discovered in 1912. Similarly, astronomers have theorized that supernova remnants (the after-effects of supernova explosions) are responsible for accelerating them to nearly the speed of light.

Continue reading “We may finally know where high-energy cosmic rays come from” »

Earlier this year, researchers found a deposit of rare-earth minerals off the coast of Japan that could supply the world for centuries, according to a study.

The study, published in the journal Nature in April 2,018 says the deposit contains 16 million tons of the valuable metals.

Rare-earth minerals are used in everything from smartphone batteries to electric vehicles. By definition, these minerals contain one or more of 17 metallic rare-earth elements (for those familiar with the periodic table, those are on the second row from the bottom).

Continue reading “Japan Discovered a Rare-Earth Mineral Deposit That Can Supply The World For Centuries” »