Studies on the Mechanisms of Microbial Adaptation to the Physical Environment

The environmental factors which affect humans and other animals also influence the microorganisms which are such an important part of our ecology. Some of the microorganisms are very closely associated with animals, living in the digestive tract and synthesizing essential nutrients for the host. For these microbes, most external physical changes are of little consequence, because they are well shielded by the animals' homeostatic systems. The vast majority of microorganisms, however, live free in nature, especially in the soil and oceans. It has been estimated that the upper 15 cm of a fertile soil may contain over 4000 kg of bacteria and fungi per hectare. These organisms are responsible for degrading the complex molecules of plants and animals when they die, eventually producing simple organics, carbon dioxide, and inorganics, which are then used for the next cycle of plant growth. It is believed that over 90 % of the biologically produced carbon dioxide results from the metabolic activity of bacteria and fungi. In addition to recycling plant nutrients, soil bacteria also provide new nutrients through 'fixation' of atmospheric nitrogen into ammonia and nitrate, the forms which can be used by plants. Microorganisms so have an enormous capacity for detoxifying both natural and man-made poisons. All of these functions of microorganisms are essential to the operation of the material cycles on Earth. This is true of all locations on the planet, regardless of the climate or other environmental factors. In fact, one of the most impressive attributes of microorganisms is their ability to adapt to every stable environment on Earth. These include such extremes as polar regions, hot springs, water saturated with salt, mountain tops, ocean depths, acid and alkaline waters, deserts, intense radioactivity, soil and water contaminated with toxic chemicals or petroleum, and areas devoid of oxygen

Novel multi-marker proteomics in phenotypically matched patients with ST-segment myocardial infarction:association with clinical outcomes

Early prediction of significant morbidity or mortality in patients with acute ST-segment elevation myocardial infarction (STEMI) represents an unmet clinical need. In phenotypically matched population of 139 STEMI patients (72 cases, 67 controls) treated with primary percutaneous coronary intervention, we explored associations between a 24-h relative change from baseline in the concentration of 91 novel biomarkers and the composite outcome of death, heart failure, or shock within 90 days. Additionally, we used random forest models to predict the 90-day outcomes. After adjustment for false discovery rate, the 90-day composite was significantly associated with concentration changes in 14 biomarkers involved in various pathophysiologic processes including: myocardial fibrosis/remodeling (collagen alpha-1, cathepsin Z, metalloproteinase inhibitor 4, protein tyrosine phosphatase subunits), inflammation, angiogenesis and signaling (interleukin 1 and 2 subunits, growth differentiation factor 15, galectin 4, trefoil factor 3), bone/mineral metabolism (osteoprotegerin, matrix extracellular phosphoglycoprotein and tartrate-resistant acid phosphatase), thrombosis (tissue factor pathway inhibitor) and cholesterol metabolism (LDL-receptor). Random forest models suggested an independent association when inflammatory markers are included in models predicting the outcomes within 90 days. Substantial heterogeneity is apparent in the early proteomic responses among patients with acutely reperfused STEMI patients who develop death, heart failure or shock within 90 days. These findings suggest the need to consider synergistic multi-biomarker strategies for risk stratification and to inform future development of novel post-myocardial infarction therapies

Low-Energy Electron Microscopy Studies of Interlayer Mass Transport Kinetics on TiN(111)

In situ low-energy electron microscopy was used to study interlayer mass transport kinetics during annealing of three-dimensional (3D) TiN(111) mounds, consisting of stacked 2D islands, at temperatures T between 1550 and 1700 K. At each T, the islands decay at a constant rate, irrespective of their initial position in the mounds, indicating that mass is not conserved locally. From temperature-dependent island decay rates, we obtain an activation energy of 2.8+/-0.3 eV. This is consistent with the detachment-limited decay of 2D TiN islands on atomically-flat TiN(111) terraces [Phys. Rev. Lett. 89 (2002) 176102], but significantly smaller than the value, 4.5+/-0.2 eV, obtained for bulk-diffusion-limited spiral step growth [Nature 429, 49 (2004)]. We model the process based upon step flow, while accounting for step-step interactions, step permeability, and bulk mass transport. The results show that TiN(111) steps are highly permeable and exhibit strong repulsive temperature-dependent step-step interactions that vary between 0.003 and 0.076 eV-nm. The rate-limiting process controlling TiN(111) mound decay is surface, rather than bulk, diffusion in the detachment-limited regime.Comment: 26 pages, 5 figure

Point defects, ferromagnetism and transport in calcium hexaboride

The formation energy and local magnetic moment of a series of point defects in CaB$_6$ are computed using a supercell approach within the generalized gradient approximation to density functional theory. Based on these results, speculations are made as to the influence of these defects on electrical transport. It is found that the substitution of Ca by La does not lead to the formation of a local moment, while a neutral B$_6$ vacancy carries a moment of 2.4 Bohr magnetons, mostly distributed over the six nearest-neighbour B atoms. A plausible mechanism for the ferromagnetic ordering of these moments is suggested. Since the same broken B-B bonds appear on the preferred (100) cleavage planes of the CaB$_6$ structure, it is argued that internal surfaces in polycrystals as well as external surfaces in general will make a large contribution to the observed magnetization.Comment: Calculated defect formation energies had to be corrected, due to the use of a wrong reference energy for the perfect crystal in the original pape

Fossils, fish and tropical forests: prehistoric human adaptations on the island frontiers of Oceania

Oceania is a key region for studying human dispersals, adaptations and interactions with other hominin populations. Although archaeological evidence now reveals occupation of the region by approximately 65–45 000 years ago, its human fossil record, which has the best potential to provide direct insights into ecological adaptations and population relationships, has remained much more elusive. Here, we apply radiocarbon dating and stable isotope approaches to the earliest human remains so far excavated on the islands of Near and Remote Oceania to explore the chronology and diets of the first preserved human individuals to step across these Pacific frontiers. We demonstrate that the oldest human (or indeed hominin) fossil outside of the mainland New Guinea-Aru area dates to approximately 11 800 years ago. Furthermore, although these early sea-faring populations have been associated with a specialized coastal adaptation, we show that Late Pleistocene–Holocene humans living on islands in the Bismarck Archipelago and in Vanuatu display a persistent reliance on interior tropical forest resources. We argue that local tropical habitats, rather than purely coasts or, later, arriving domesticates, should be emphasized in discussions of human diets and cultural practices from the onset of our species' arrival in this part of the world.1. Introduction 2. Background (a) Human colonization of near and remote Oceania (b) Stable isotope analysis and past human adaptations in the tropics 3. Methods (a) Radiocarbon dating (b) Stable isotope analysis (c) Phytolith analysis of dental calculus 4. Results (a) Radiocarbon dating and Bayesian modelling (b) Stable isotope analysis (c) Phytolith analysis of dental calculus 5. Discussion and conclusio

Electronic Structure of Calcium Hexaboride within the Weighted Density Approximation

We report calculations of the electronic structure of CaB$_6$ using the weighted density approximation (WDA) to density functional theory. We find a semiconducting band structure with a sizable gap, in contrast to local density approximation (LDA) results, but in accord with recent experimental data. In particular, we find an $X$-point band gap of 0.8 eV. The WDA correction of the LDA error in describing the electronic structure of CaB$_6$ is discussed in terms of the orbital character of the bands and the better cancelation of self-interactions within the WDA.Comment: 1 figur

CaB_6: a new semiconducting material for spin electronics

Ferromagnetism was recently observed at unexpectedly high temperatures in La-doped CaB_6. The starting point of all theoretical proposals to explain this observation is a semimetallic electronic structure calculated for CaB_6 within the local density approximation. Here we report the results of parameter-free quasiparticle calculations of the single-particle excitation spectrum which show that CaB_6 is not a semimetal but a semiconductor with a band gap of 0.8 eV. Magnetism in La_xCa_{1-x}B_6 occurs just on the metallic side of a Mott transition in the La-induced impurity band.Comment: 4 pages, 1 postscript figur