Nuclear weak interaction rates during stellar evolution and collapse

Nuclear weak interaction rates, including electron and positron emission rates, and continuum electron and positron capture rates , as well as the associated v and –/v energy loss rates are calculated on a detailed grid of temperature and density for the free nucleons and 226 nuclei with masses between A = 21 and 60. Gamow-Teller and Fermi discrete-state transition matrix element systematics and the Gamow-Teller T^< →/← T^> resonance transitions are discussed in depth and are implemented in the stellar rate calculations. Results of the calculations are presented on an abbreviated grid of temperature and density and comparison is made to terrestrial weak transition rates where possible. Neutron shell blocking of allowed electron capture on heavy nuclei during stellar core collapse is discussed along with several unblocking mechanisms operative at high temperature and density. The results of one-zone collapse calculations are presented which suggest that the effect of neutron shell blocking is to produce a larger core lepton fraction at neutrino trapping which leads to a larger inner-core mass and hence a stronger post-bounce shock.

Techniques for strength measurement at high pressures and strain-rates using transverse waves

The study of the strength of a material is relevant to a variety of applications including automobile collisions, armor penetration and inertial confinement fusion. Although dynamic behavior of materials at high pressures and strain-rates has been studied extensively using plate impact experiments, the results provide measurements in one direction only. Material behavior that is dependent on strength is unaccounted for. The research in this study proposes two novel configurations to mitigate this problem.

The first configuration introduced is the oblique wedge experiment, which is comprised of a driver material, an angled target of interest and a backing material used to measure in-situ velocities. Upon impact, a shock wave is generated in the driver material. As the shock encounters the angled target, it is reflected back into the driver and transmitted into the target. Due to the angle of obliquity of the incident wave, a transverse wave is generated that allows the target to be subjected to shear while being compressed by the initial longitudinal shock such that the material does not slip. Using numerical simulations, this study shows that a variety of oblique wedge configurations can be used to study the shear response of materials and this can be extended to strength measurement as well. Experiments were performed on an oblique wedge setup with a copper impactor, polymethylmethacrylate driver, aluminum 6061-t6 target, and a lithium fluoride window. Particle velocities were measured using laser interferometry and results agree well with the simulations.

The second novel configuration is the y-cut quartz sandwich design, which uses the anisotropic properties of y-cut quartz to generate a shear wave that is transmitted into a thin sample. By using an anvil material to back the thin sample, particle velocities measured at the rear surface of the backing plate can be implemented to calculate the shear stress in the material and subsequently the strength. Numerical simulations were conducted to show that this configuration has the ability to measure the strength for a variety of materials.

Gut microbiota promote hematopoiesis to control bacterial infection

The commensal microbiota impacts specific immune cell populations and their functions at peripheral sites, such as gut mucosal tissues. However, it remains unknown whether gut microbiota control immunity through regulation of hematopoiesis at primary immune sites. We reveal that germ-free mice display reduced proportions and differentiation potential of specific myeloid cell progenitors of both yolk sac and bone marrow origin. Homeostatic innate immune defects may lead to impaired early responses to pathogens. Indeed, following systemic infection with Listeria monocytogenes, germ-free and oral antibiotic-treated mice display increased pathogen burden and acute death. Recolonization of germ-free mice with a complex microbiota restores defects in myelopoiesis and resistance to Listeria. These findings reveal that gut bacteria direct innate immune cell development via promoting hematopoiesis, contributing to our appreciation of the deep evolutionary connection between mammals and their microbiota.

The Mechanical Genome in Regulation and Infection

Biological information storage and retrieval is a dynamic process that requires the genome to undergo dramatic structural rearrangements. Recent advances in single-molecule techniques have allowed precise quantification of the nano-mechanical properties of DNA [1, 2], and direct in vivo observation of molecules in action [3]. In this work, we will examine elasticity in protein-mediated DNA looping, whose structural rearrangement is essential for transcriptional regulation in both prokaryotes and eukaryotes. We will look at hydrodynamics in the process of viral DNA ejection, which mediates information transfer and exchange and has prominent implications in evolution. As in the case of Kepler's laws of planetary motion leading to Newton's gravitational theory, and the allometric scaling laws in biology revealing the organizing principles of complex networks [4], experimental data collapse in these biological phenomena has guided much of our studies and urged us to find the underlying physical principles.

Part I: The abortive infection of bacteriophage øx174 at low temperatures. Part II: The early stages in the process of infection by bacteriophage øx174

Part I

The infection of E. coli by ΦX174 at 15°C is abortive; the cells are killed by the infection but neither mature phage nor SS (single-stranded) DNA are synthesized. Parental RF (replicative form) is formed and subsequently replicated at 15°C. The RF made at 15°C shows normal infectivity and full competence to act as precursor to progeny SS DNA after an increase in temperature to 37°C. The investigations suggest that all of the proteins required for SS DNA synthesis and phage maturation are present in the abortive infection at 15°C.

Three possible causes are suggested for the abortive infection at 15°C: (a) A virus-coded protein whose role is essential to the infection is made at 15°C and assumes its native conformation, but its rate of activity is too low at this temperature to sustain the infection process. (b) Virus maturation may involve the formation of a DNA-protein complex and conformational changes which have an energy threshold infrequently reached at 15°C. (c) A host-coded protein present in uninfected cells, and whose activity is essential to the infection at all temperatures, but not to the host at 15°C, is inactive at 15°C. An hypothesis of this type is offered which proposes that the temperature-limiting factor in SS DNA synthesis in vivo may reflect a temperature-dependent property of the host DNA polymerase.

Part II

Three distinct stages are demonstrated in the process whereby ΦX174 invades its host: (1) Attachment: The phage attach to the cell in a manner that does not irreversibly alter the phage particle and which exhibits "single-hit" kinetics. The total charge on the phage particle is demonstrated to be important in determining the rate at which stable attachment is effected. The proteins specified by ΦX cistrons II, III and VII play roles, which may be indirect, in the attachment reaction. (2) Eclipse: 'The attached phage undergo a conformational change. Some of the altered phage particles spontaneously detach from the cell (in a non-infective form) while the remainder are more tightly bound to the cell. The altered phage particles detached (spontaneously or chemically) from such complexes have at least 40% of their DNA extruded from the phage coat. It is proposed that this particle is, or derives from, a direct intermediate in the penetration of the viral DNA.

The kinetics for the eclipse of attached phage particles are first-order with respect to phage concentration and biphasic; about 85% of the phage eclipse at one rate (k = 0.86 min^-1) and the remainder do so at a distinctly lesser rate (k = 0.21 min^-1).

The eclipse event is very temperature-dependent and has the relatively high Arrhenius activation energy of 36.6 kcal/mole, indicating the cooperative nature of the process. The temperature threshold for eclipse is 17 to 18°C.

At present no specific ΦX cistron is identified as affecting the eclipse process. (3) DNA penetration: A fraction of the attached, eclipsed phage particles corresponding in number to the plaque-forming units complete DNA penetration. The penetrated DNA is found in the cell as RF, and the empty phage protein coat remains firmly attached to the exterior of the cell. This step is inhibited by prior irradiation of the phage with relatively high doses of UV light and is insensitive to the presence of KCN and NaN₃. Temporally excluded superinfecting phages do not achieve DNA penetration.

Both eclipsed phage particles and empty phage protein coats may be dissociated from infected cells; some of their properties are described.