Survival of polycyclic aromatic hydrocarbon knockout fragments in the interstellar medium

Laboratory studies play a crucial role in understanding the chemical nature of the interstellar medium (ISM), but the disconnect between experimental timescales and the timescales of reactions in space can make a direct comparison between observations, laboratory, and model results difficult. Here we study the survival of reactive fragments of the polycyclic aromatic hydrocarbon (PAH) coronene, where individual C atoms have been knocked out of the molecules in hard collisions with He atoms at stellar wind and supernova shockwave velocities. Ionic fragments are stored in the DESIREE cryogenic ion-beam storage ring where we investigate their decay for up to one second. After 10 ms the initially hot stored ions have cooled enough so that spontaneous dissociation no longer takes place at a measurable rate; a majority of the fragments remain intact and will continue to do so indefinitely in isolation. Our findings show that defective PAHs formed in energetic collisions with heavy particles may survive at thermal equilibrium in the interstellar medium indefinitely, and could play an important role in the chemistry in there, due to their increased reactivity compared to intact or photo-fragmented PAHs.

A Contextual Foundation for Mechanics, Thermodynamics, and Evolution v.5

The prevailing interpretations of physics are based on deeply entrenched assumptions, rooted in classical mechanics. Logical implications include: the denial of entropy and irreversible change as fundamental physical properties; the inability to explain random quantum measurements or nonlocality without untestable and implausible metaphysical implications; and the inability to define complexity or explain its evolution. We propose a conceptual model based on empirically justifiable assumptions. The WYSIWYG Conceptual Model (WCM) assumes no hidden properties: “What You can See Is What You Get.” The WCM defines a system’s state in the context of its actual ambient background, and it extends existing models of physical reality by defining entropy and exergy as objective contextual properties of state. The WCM establishes the irreversible production of entropy and the Second law of thermodynamics as a fundamental law of physics. It defines a dissipative system’s measurable rate of internal work as an objective measure of stability of its dissipative process. A dissipative system can follow either of two paths toward higher stability: it can 1) increase its rate of exergy supply (and maximize entropy production) or 2) utilize existing exergy supplies better to increase its internal work rate and functional complexity. These paths guide the evolution of both living and non-living systems.

A Contextual Foundation for Mechanics, Thermodynamics, and Evolution

The prevailing interpretations of physics are based on deeply entrenched assumptions, rooted in classical mechanics. Logical implications include: the denial of entropy and irreversible change as fundamental physical properties; the inability to explain random quantum measurements or nonlocality without untestable metaphysical implications; and the inability to define complexity or explain its evolution. We propose a conceptual model based on empirically justifiable assumptions. The WYSIWYG Conceptual Model (WCM) assumes no hidden properties: “What You can See Is What You Get.” The WCM defines a system’s state in the context of its actual ambient background, and it extends existing models of physical reality by defining entropy and exergy as objective contextual properties of state. The WCM establishes the irreversible production of entropy and the Second law of thermodynamics as a fundamental law of physics. It defines a dissipative system’s measurable rate of internal work as an objective measure of stability of its dissipative process. A dissipative system can follow either of two paths toward higher stability: it can 1) increase its rate of exergy supply or 2) utilize existing exergy supplies better to increase its internal work rate and functional complexity. These paths guide the evolution of both living and non-living systems.

A Contextual Foundation for Mechanics, Thermodynamics, and Evolution

The prevailing interpretations of physics are based on deeply entrenched assumptions, rooted in classical mechanics. Logical implications include: the denial of entropy and irreversible change as fundamental properties of state; the inability to explain random quantum measurements and nonlocality without unjustifiable assumptions and untestable metaphysical implications; and the inability to explain or even define the evolution of complexity. The dissipative conceptual model (DCM) is based on empirically justified assumptions. It generalizes mechanics’ definition of state by acknowledging the contextual relationship between a physical system and its positive-temperature ambient background, and it defines the DCM entropy as a fundamental contextual property of physical states. The irreversible production of entropy establishes the thermodynamic arrow of time and a system’s process of dissipation as fundamental. The DCM defines a system’s utilization by the measurable rate of internal work on its components and as an objective measure of stability for a dissipative process. The spontaneous transition of dissipative processes to higher utilization and stability defines two evolutionary paths. The evolution of life proceeded by both competition for resources and cooperation to evolve and sustain higher functional complexity. The DCM accommodates classical and quantum mechanics and thermodynamics as idealized non-contextual special cases.

A Contextual Foundation for Mechanics, Thermodynamics, and Evolution

The prevailing interpretations of physics are based on deeply entrenched assumptions, rooted in classical mechanics. Logical implications include: the denial of entropy and irreversible change as fundamental properties of state; the inability to explain random quantum measurements and nonlocality without implausible and empirically unjustified metaphysical implications; and the inability to explain or even define the evolution of complexity. The dissipative conceptual model (DCM) is based on empirically justified assumptions. It generalizes mechanics’ definition of state by acknowledging the contextual relationship between a physical system and its positive-temperature ambient background, and it defines the DCM entropy as a fundamental contextual property of physical states. The irreversible production of entropy establishes the thermodynamic arrow of time and a system’s process of dissipation as fundamental. The DCM defines a system’s utilization by the measurable rate of internal work on its components and as an objective measure of stability for a dissipative process. The spontaneous transition to dissipative processes of higher utilization and stability defines two evolutionary paths. The evolution of life proceeded by both competition for resources and cooperation to evolve and sustain higher functional complexity. The DCM accommodates classical and quantum mechanics and thermodynamics as idealized non-contextual special cases.

Experiments on and Numerical Modeling of the Capture and Concentration of Transcription-Translation Machinery inside Vesicles

Synthetic or semi-synthetic minimal cells are those cell-like artificial compartments that are based on the encapsulation of molecules inside lipid vesicles (liposomes). Synthetic cells are currently used as primitive cell models and are very promising tools for future biotechnology. Despite the recent experimental advancements and sophistication reached in this field, the complete elucidation of many fundamental physical aspects still poses experimental and theoretical challenges. The interplay between solute capture and vesicle formation is one of the most intriguing ones. In a series of studies, we have reported that when vesicles spontaneously form in a dilute solution of proteins, ribosomes, or ribo-peptidic complexes, then, contrary to statistical predictions, it is possible to find a small fraction of liposomes (<1%) that contain a very large number of solutes, so that their local (intravesicular) concentrations largely exceed the expected value. More recently, we have demonstrated that this effect (spontaneous crowding) operates also on multimolecular mixtures, and can drive the synthesis of proteins inside vesicles, whereas the same reaction does not proceed at a measurable rate in the external bulk phase. Here we firstly introduce and discuss these already published observations. Then, we present a computational investigation of the encapsulation of transcription-translation (TX-TL) machinery inside vesicles, based on a minimal protein synthesis model and on different solute partition functions. Results show that experimental data are compatible with an entrapment model that follows a power law rather than a Gaussian distribution. The results are discussed from the viewpoint of origin of life, highlighting open questions and possible future research directions.

Membrane fusion catalyzed by a Rab, SNAREs, and SNARE chaperones is accompanied by enhanced permeability to small molecules and by lysis

The fusion of sealed biological membranes joins their enclosed aqueous compartments while mixing their membrane bilayers. Reconstituted fusion reactions are commonly assayed by lipid mixing, which can result from either true fusion or from lysis and its attendant reannealing of membranes. Fusion is also frequently assayed by the mixing of lumenal aqueous compartments, using probes of low molecular weight. With several probes (biotin, methylumbelliferyl-N-acetyl-α-d-neuraminic acid, and dithionite), we find that yeast vacuolar SNAREs (SNAP [Soluble NSF attachment protein] Receptors) increase the permeability of membranes to small molecules and that this permeabilization is enhanced by homotypic fusion and vacuole protein sorting complex (HOPS) and Sec17p/Sec18p, the vacuolar tethering and SNARE chaperone proteins. We now report the development of a novel assay that allows the parallel assessment of lipid mixing, the mixing of intact lumenal compartments, any lysis that occurs, and the membrane permeation of small molecules. Applying this assay to an all-purified reconstituted system consisting of vacuolar lipids, the four vacuolar SNAREs, the SNARE disassembly chaperones Sec17p and Sec18p, the Rab Ypt7p, and the Rab effector/SM protein complex HOPS, we show that true fusion is accompanied by strongly enhanced membrane permeability to small molecules and a measurable rate of lysis.

Rearrangement mechanisms for azoxypyridines and azoxypyridine N-oxides in the 100% H2SO4 region — The Wallach rearrangement story comes full circle

Kinetic studies of the Wallach rearrangements of four azoxypyridines, four azoxypyridine N-oxides, and one azoxypyridine N-methiodide have been carried out in the 100% H2SO4 acidity region. For all of the β-isomers in the study the reactions proceeded at a spectrally measurable rate, and the log observed rate constants were found to be linear functions of the log H3SO4+ concentration, as previously found for azoxybenzene itself, suggesting that the reaction mechanism for these substrates is the same as that previously deduced for axozybenzene, i.e., a general-acid-catalysis A-SE2 process. For the α-azoxypyridines no reaction could be observed at all. The two α-azoxypyridine N-oxides in the study did react, albeit very slowly, but for these two compounds the log observed rate constants were not linear functions of the log H3SO4+ concentration, but were instead found to be linear in the H0 acidity function, which is known for the 100% H2SO4 acidity region. It follows that the reaction mechanism for these α-isomers is a different one, presumably an A1 process. This mechanism was proposed back in 1963 for azoxybenzene, but has never actually been observed for any substrate before the work reported in this study. Thus, the Wallach rearrangement story can be said to have come full circle.

Resting Ca2+ influx does not contribute to anoxia-induced cell death in adult rat cardiac myocytes

Calcium has been proposed as a primary influence on cell death during ischemic episodes in myocardial cells. One component of calcium entry into a cell is resting calcium influx. This basal movement of calcium is blocked by 100 µmol/L gadolinium chloride (GdCl3) in cardiac myocytes. Therefore, GdCl3 should be cardioprotective under anoxic conditions. To test this, cardiac myocytes isolated from adult male rats were subjected to anoxia (100% N2) in the presence or absence of 100 µmol/L GdCl3 in one of 2 ways. In the first method, cells were suspended in media and rendered anoxic for 0, 30, and 60 min, after which cell morphology and viability were scored. After 60 min of anoxia, rod-shaped cells accounted for 46% ± 4% of total cells (viability 81%); 10 min of reoxygenation markedly reduced rod-shaped cells to 27% (viability 72%). GdCl3 in the medium did not protect the cells (anoxic rods 49%, reoxygenated rods 30%, viability 77%). In the second method, cells were attached to a laminin substrate, rendered anoxic, and then videotaped for up to 6 h. In this system, cells maintained their shape for some time after the onset of anoxia, and then began to ‘die’ (i.e., to take on either a rigor form or hypercontracted form) at a measurable rate. Time to onset of ‘death’ (t0), time to 50% and 100% ‘death’ (t50 and t100), and rate of ‘death’ were used to measure anoxic damage. Without GdCl3, cells on average began to die 115 ± 32 min after the onset of anoxia (t0); they died at an average rate of 0.046 cells/min. t50 was achieved in 149 ± 42 min, t100 in 183 ± 54 min. Addition of 100 µmol/L GdCl3 did not affect any of these parameters. We concluded that GdCl3 was not cardioprotective for anoxic myocytes and that cell damage generated by anoxia could not be attributed to resting calcium influx.

Rational Design of Genetically Stable, Live-Attenuated Poliovirus Vaccines of All Three Serotypes: Relevance to Poliomyelitis Eradication

ABSTRACT The global eradication of poliomyelitis caused by wild-type virus is likely to be completed within the next few years, despite immense logistic and political difficulties, and may ultimately be followed by the cessation of vaccination. However, the existing live-attenuated vaccines have the potential to revert to virulence, causing occasional disease, and viruses can be shed by immunocompromised individuals for prolonged periods of time. Moreover, several outbreaks of poliomyelitis have been shown to be caused by viruses derived from the Sabin vaccine strains. The appearance of such strains depends on the prevailing circumstances but poses a severe obstacle to strategies for stopping vaccination. Vaccine strains that are incapable of reversion at a measurable rate would provide a possible solution. Here, we describe the constructions of strains of type 3 poliovirus that are stabilized by the introduction of four mutations in the 5′ noncoding region compared to the present vaccine. The strains are genetically and phenotypically stable under conditions where the present vaccine loses the attenuating mutation in the 5′ noncoding region completely. Type 1 and type 2 strains in which the entire 5′ noncoding regions of Sabin 1 and Sabin 2 were replaced exactly with that of one of the type 3 strains were also constructed. The genetic stability of 5′ noncoding regions of these viruses matched that of the type 3 strains, but significant phenotypic reversion occurred, illustrating the potential limitations of a rational approach to the genetic stabilization of live RNA virus vaccines.