Exons, introns and DNA thermodynamics

The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from the genomic DNA by removing all introns. A clear correspondence is observed between exons and melting domains. This finding may provide new insights in the physical mechanisms underlying the evolution of genes.Comment: 4 pages, 8 figures - Final version as published. See also Phys. Rev. Focus 15, story 1

Excavations at Natural Trap Cave

Among the more important questions addressed by students of earth history are those that relate to climatic change. This is especially true of change that has taken place during the last two million years of the Ice Age. It is not an accident that a great deal of effort has been directed towards the Late Pleistocene, and our knowledge of Late Pleistocene environmental parameters has increased markedly in the past few years. However, our knowledge of these changes is still incomplete, and we still have some uncertainty about the cause and nature of Late Pleistocene climatic change, its possible relationship to large mammal extinction, and the establishment of the modern distribution of fauna and flora in North America. Natural Trap Cave in the Big Horn Basin gives us an excellent opportunity to examine a record of these events extending from Late Pleistocene to Recent times

Troubles with Bayesianism: An introduction to the psychological immune system

A Bayesian mind is, at its core, a rational mind. Bayesianism is thus well-suited to predict and explain mental processes that best exemplify our ability to be rational. However, evidence from belief acquisition and change appears to show that we do not acquire and update information in a Bayesian way. Instead, the principles of belief acquisition and updating seem grounded in maintaining a psychological immune system rather than in approximating a Bayesian processor

Rapid coastal deoxygenation due to ocean circulation shift in the NW Atlantic.

Global observations show that the ocean lost approximately 2% of its oxygen inventory over the last five decades 1-3, with important implications for marine ecosystems 4, 5. The rate of change varies with northwest Atlantic coastal waters showing a long-term drop 6, 7 that vastly outpaces the global and North Atlantic basin mean deoxygenation rates 5, 8. However, past work has been unable to resolve mechanisms of large-scale climate forcing from local processes. Here, we use hydrographic evidence to show a Labrador Current retreat is playing a key role in the deoxygenation on the northwest Atlantic shelf. A high-resolution global coupled climate-biogeochemistry model 9 reproduces the observed decline of saturation oxygen concentrations in the region, driven by a retreat of the equatorward-flowing Labrador Current and an associated shift toward more oxygen-poor subtropical waters on the shelf. The dynamical changes underlying the shift in shelf water properties are correlated with a slowdown in the simulated Atlantic Meridional Overturning Circulation 10. Our results provide strong evidence that a major, centennial-scale change of the Labrador Current is underway, and highlight the potential for ocean dynamics to impact coastal deoxygenation over the coming century

Pathways for the Photoreduction of Fumarate on ZnS

Semiconductor mineral particles can act as photocatalysts for organic redox reactions that occur enzymatically in modern biological metabolic pathways. Semiconductor mineral-mediated photocatalysis may have contributed to the prebiotic synthesis of organic acids on the early Earth, but assessing the plausibility of this hypothesis is impeded by the lack of knowledge about the mechanisms for light-driven organic redox reactions on mineral surfaces. We selected one step in the reverse tricarboxylic acid (rTCA) cycle, the reduction of fumarate to succinate, that has been shown to be photocatalyzed by zinc sulfide (ZnS). Using static and time-resolved optical emission and absorption spectroscopy, we studied the adsorption of fumarate and the rates and pathways for charge transfer. We find that ZnS transfers photoexcited electrons to bound and dissolved fumarate on a wide range of time scales but not to succinate, supporting the concept that ZnS mediated photoreduction of fumarate could have operated in oceans of the early Earth. Optical transient absorption (TA) spectroscopy identified a signature tentatively attributed to the fumarate radical anion that is stable for at least 8 ns, providing evidence that fumarate photoreduction under solar illumination levels occurs by successive photoelectron transfer. The model for electronic excitation, relaxation, and interfacial charge-transfer processes in ZnS provided here will inform all future studies of the photochemical reactions of this mineral

Stimulated Raman adiabatic passage analogs in classical physics

Stimulated Raman adiabatic passage (STIRAP) is a well established technique for producing coherent population transfer in a three-state quantum system. We here exploit the resemblance between the Schrodinger equation for such a quantum system and the Newton equation of motion for a classical system undergoing torque to discuss several classical analogs of STIRAP, notably the motion of a moving charged particle subject to the Lorentz force of a quasistatic magnetic field, the orientation of a magnetic moment in a slowly varying magnetic field, the Coriolis effect and the inertial frame dragging effect. Like STIRAP, those phenomena occur for counterintuitively ordered field pulses and are robustly insensitive to small changes in the interaction properties

No safety without emotional safety

This Personal View highlights how emotional safety is required for a person to keep themselves physically safe. We explain how trying to control behaviour to increase physical safety in the short term can carry the unintended consequence of reducing emotional safety, which might in turn result in higher levels of stress and hopelessness. We use examples from institutions with psychiatric inpatients to describe these processes. We argue that emotional and physical safety cannot be separated, and therefore that the absence of emotional safety compromises basic care either in an acute crisis or in the long term. Staff who fear being criticised, and so feel driven to take autonomy and responsibility away from patients, unwittingly undermine patients' experience of being empathically understood and supported, adding to patients' sense of emotional turmoil and lack of safety. We suggest that a change in culture and regulatory reform is required to bring psychiatric care more in line with the psychological needs of patients to achieve both physical and emotional safety

Detecting brute-force attacks on cryptocurrency wallets

Blockchain is a distributed ledger, which is protected against malicious modifications by means of cryptographic tools, e.g. digital signatures and hash functions. One of the most prominent applications of blockchains is cryptocurrencies, such as Bitcoin. In this work, we consider a particular attack on wallets for collecting assets in a cryptocurrency network based on brute-force search attacks. Using Bitcoin as an example, we demonstrate that if the attack is implemented successfully, a legitimate user is able to prove that fact of this attack with a high probability. We also consider two options for modification of existing cryptocurrency protocols for dealing with this type of attacks. First, we discuss a modification that requires introducing changes in the Bitcoin protocol and allows diminishing the motivation to attack wallets. Second, an alternative option is the construction of special smart-contracts, which reward the users for providing evidence of the brute-force attack. The execution of this smart-contract can work as an automatic alarm that the employed cryptographic mechanisms, and (particularly) hash functions, have an evident vulnerability.Comment: 10 pages, 2 figures; published versio

Epigenetic Chromatin Silencing: Bistability and Front Propagation

The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms. We formulate a coarse-grained model of chromatin silencing in yeast and study the conditions under which the system becomes bistable, allowing for different epigenetic states. We also study the dynamics of the boundary between the two locally stable states of chromatin: silenced and unsilenced. The model could be of use in guiding the discussion on chromatin silencing in general. In the context of silencing in budding yeast, it helps us understand the phenotype of various mutants, some of which may be non-trivial to see without the help of a mathematical model. One such example is a mutation that reduces the rate of background acetylation of particular histone side-chains that competes with the deacetylation by Sir2p. The resulting negative feedback due to a Sir protein depletion effect gives rise to interesting counter-intuitive consequences. Our mathematical analysis brings forth the different dynamical behaviors possible within the same molecular model and guides the formulation of more refined hypotheses that could be addressed experimentally.Comment: 19 pages, 5 figure