Diffusion pathways of hydrogen across the steps of a vicinal Si(001) surface

Hydrogen diffusion across DB steps on Si(001) surfaces is investigated by means of variable-temperature scanning tunneling microscopy and first-principles calculations. Experimentally, the hopping rate for diffusion from the step sites to the Si dimers of the upper terrace was found to be more than one order of magnitude higher than that for diffusion to the lower terrace. This clear preference, opposite to the trend for the respective binding energies, is explained by first-principles calculations that identify a metastable intermediate to be responsible for the unexpected lowering of the energy barrier for upward diffusion

A Pre-registered Meta-analysis Based on Three Empirical Studies Reveals No Association Between Prenatal (Amniotic) Cortisol Exposure and Fluctuating Asymmetry in Human Infants

Developmental instability (DI) reflects an organism’s inability to develop an ideal phenotype when challenged by genetic and environmental insults. DI can be estimated via the proxy measure of fluctuating asymmetry (FA), i.e., the small random deviations from perfect bilateral symmetry observed in the morphology of paired traits. The mechanisms involved in the genesis of FA in human populations are relatively unknown, though animal research indicates that hormonal processes may be involved. As maternal stress during pregnancy is detrimental to various developmental processes, elevated prenatal cortisol may represent a causal factor in the subsequent emergence of an asymmetrical phenotype. The main purpose of this pre-registered meta-analysis based on three empirical studies was to investigate whether mid-trimester amniotic cortisol levels predict subsequent FA in finger lengths of infants from Germany, Portugal, and the UK. No statistically significant relationships were observed, and meta-analytic combination of the effect size estimates yielded a null result. We did, however, detect significant positive correlations between the cortisol present in the amniotic fluid and maternal plasma in the Portuguese cohort, and observed that FA in the German cohort was significantly lower at 70-months than at either 9- or 20-months. Taken together, the current findings run contrary to animal research showing that elevated prenatal corticosterone exposure leads to increased FA. However, this may be because a single cortisol assay obtained via amniocentesis is an inadequate proxy for average gestational exposure, and/or that prenatal cortisol levels at an earlier (i.e., first rather than second trimester) stage of pregnancy is what explains variance in subsequent FA.publishersversionpublishe

Zinc Transporters YbtX and ZnuABC Are Required for the Virulence of \u3cem\u3eYersinia pestis\u3c/em\u3e in Bubonic and Pneumonic Plague in Mice

A number of bacterial pathogens require the ZnuABC Zinc (Zn2+) transporter and/or a second Zn2+ transport system to overcome Zn2+ sequestration by mammalian hosts. Previously we have shown that in addition to ZnuABC, Yersinia pestis possesses a second Zn2+ transporter that involves components of the yersiniabactin (Ybt), siderophore-dependent iron transport system. Synthesis of the Ybt siderophore and YbtX, a member of the major facilitator superfamily, are both critical components of the second Zn2+ transport system. Here we demonstrate that a ybtX znu double mutant is essentially avirulent in mouse models of bubonic and pneumonic plague while a ybtX mutant retains high virulence in both plague models. While sequestration of host Zn is a key nutritional immunity factor, excess Zn appears to have a significant antimicrobial role in controlling intracellular bacterial survival. Here, we demonstrate that ZntA, a Zn2+ exporter, plays a role in resistance to Zn toxicity in vitro, but that a zntA zur double mutant retains high virulence in both pneumonic and bubonic plague models and survival in macrophages. We also confirm that Ybt does not directly bind Zn2+in vitro under the conditions tested. However, we detect a significant increase in Zn2+-binding ability of filtered supernatants from a Ybt+ strain compared to those from a strain unable to produce the siderophore, supporting our previously published data that Ybt biosynthetic genes are involved in the production of a secreted Zn-binding molecule (zincophore). Our data suggest that Ybt or a modified Ybt participate in or promote Zn-binding activity in culture supernatants and is involved in Zn acquisition in Y. pestis

TMG 1 (2014): Pandemic Disease in the Medieval World: Rethinking the Black Death, ed. Monica Green

The plague organism (Yersinia pestis) killed an estimated 40% to 60% of all people when it spread rapidly through the Middle East, North Africa, and Europe in the fourteenth century: an event known as the Black Death. Previous research has shown, especially for Western Europe, how population losses then led to structural economic, political, and social changes. But why and how did the pandemic happen in the first place? When and where did it begin? How was it sustained? What was its full geographic extent? And when did it really end? Pandemic Disease in the Medieval World is the first book to synthesize the new evidence and research methods that are providing fresh answers to these crucial questions. It was only in 2011, thanks to ancient DNA recovered from remains unearthed in London’s East Smithfield cemetery, that the full genome of the plague pathogen was identified. This single-celled organism probably originated 3000-4000 years ago and has caused three pandemics in recorded history: the Justinianic (or First) Plague Pandemic, around 541-750; the Black Death (Second Plague Pandemic), conventionally dated to the 1340s; and the Third Plague Pandemic, usually dated from around 1894 to the 1930s. This ground-breaking book brings together scholars from the humanities and social and physical sci­ences to address the question of how recent work in genetics, zoology, and epi­de­miology can enable a rethinking of the Black Death\u27s global reach and its larger historical significance. It forms the inaugural double issue of The Medieval Globe, a new journal sponsored by the Program in Medieval Studies at the University of Illinois at Urbana-Champaign. This issue of The Medieval Globe is published with the support of the World History Center at the University of Pittsburgh.https://scholarworks.wmich.edu/medieval_globe/1000/thumbnail.jp

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations

Accelerated molecular dynamics (aMD) has been shown to enhance conformational space sampling relative to classical molecular dynamics; however, the exponential reweighting of aMD trajectories, which is necessary for the calculation of free energies relating to the classical system, is oftentimes problematic, especially for systems larger than small poly peptides. Here, we propose a method of accelerating only the degrees of freedom most pertinent to sampling, thereby reducing the total acceleration added to the system and improving the convergence of calculated ensemble averages, which we term selective aMD. Its application is highlighted in two biomolecular cases. First, the model system alanine dipeptide is simulated with classical MD, all-dihedral aMD, and selective aMD, and these results are compared to the infinite sampling limit as calculated with metadynamics. We show that both forms of aMD enhance the convergence of the underlying free energy landscape by 5-fold relative to classical MD; however, selective aMD can produce improved statistics over all-dihedral aMD due to the improved reweighting. Then we focus on the pharmaceutically relevant case of computing the free energy of the decoupling of oseltamivir in the active site of neuraminidase. Results show that selective aMD greatly reduces the cost of this alchemical free energy transformation, whereas all-dihedral aMD produces unreliable free energy estimates