ALBERT

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e27205, doi:10.1371/journal.pone.0027205.

Description: Heat shock protein 70 (Hsp70) is a molecular chaperone providing tolerance to heat and other challenges at the cellular and organismal levels. We sequenced a genomic cluster containing three hsp70 family genes linked with major histocompatibility complex (MHC) class III region from an extremely heat tolerant animal, camel (Camelus dromedarius). Two hsp70 family genes comprising the cluster contain heat shock elements (HSEs), while the third gene lacks HSEs and should not be induced by heat shock. Comparison of the camel hsp70 cluster with the corresponding regions from several mammalian species revealed similar organization of genes forming the cluster. Specifically, the two heat inducible hsp70 genes are arranged in tandem, while the third constitutively expressed hsp70 family member is present in inverted orientation. Comparison of regulatory regions of hsp70 genes from camel and other mammals demonstrates that transcription factor matches with highest significance are located in the highly conserved 250-bp upstream region and correspond to HSEs followed by NF-Y and Sp1 binding sites. The high degree of sequence conservation leaves little room for putative camel-specific regulatory elements. Surprisingly, RT-PCR and 5′/3′-RACE analysis demonstrated that all three hsp70 genes are expressed in camel's muscle and blood cells not only after heat shock, but under normal physiological conditions as well, and may account for tolerance of camel cells to extreme environmental conditions. A high degree of evolutionary conservation observed for the hsp70 cluster always linked with MHC locus in mammals suggests an important role of such organization for coordinated functioning of these vital genes.

Description: This work was supported by the Russian Foundation for Basic Research, project 09-04-00643 and 09-04-00660, project from ‘‘Genofond dynamics’’ program, and Grant of the Program of Molecular and Cellular Biology RAN to Dr. Evgen’ev; and by the Ministry of Education and Science of Russian Federation (State contract 14.740.11.0757 and Russia President Grant to young scientists MK-1418.2010.4. The research was supported by State Contract N16.552.11.7034 of Ministry of Education and Science.

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e38249, doi:10.1371/journal.pone.0038249.

Description: Arsenic (As) exposure is a significant worldwide environmental health concern. Chronic exposure via contaminated drinking water has been associated with an increased incidence of a number of diseases, including reproductive and developmental effects. The goal of this study was to identify adverse outcomes in a mouse model of early life exposure to low-dose drinking water As (10 ppb, current U.S. EPA Maximum Contaminant Level). C57B6/J pups were exposed to 10 ppb As, via the dam in her drinking water, either in utero and/or during the postnatal period. Birth outcomes, the growth of the F1 offspring, and health of the dams were assessed by a variety of measurements. Birth outcomes including litter weight, number of pups, and gestational length were unaffected. However, exposure during the in utero and postnatal period resulted in significant growth deficits in the offspring after birth, which was principally a result of decreased nutrients in the dam's breast milk. Cross-fostering of the pups reversed the growth deficit. Arsenic exposed dams displayed altered liver and breast milk triglyceride levels and serum profiles during pregnancy and lactation. The growth deficits in the F1 offspring resolved following separation from the dam and cessation of exposure in male mice, but did not resolve in female mice up to six weeks of age. Exposure to As at the current U.S. drinking water standard during critical windows of development induces a number of adverse health outcomes for both the dam and offspring. Such effects may contribute to the increased disease risks observed in human populations.

Description: This work was supported by National Institute of Environmental Health Sciences at the National Institutes of Health grants 1F32 ES019070 (CDK-H) and P42 ES007373 (BPJ, JWH, RIE and CDK-H, Dartmouth Superfund Research Program Project Grant, Project 2 and Pilot Project).

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e42535, doi:10.1371/journal.pone.0042535.

Description: Some beaked whale species are susceptible to the detrimental effects of anthropogenic noise. Most studies have concentrated on the effects of military sonar, but other forms of acoustic disturbance (e.g. shipping noise) may disrupt behavior. An experiment involving the exposure of target whale groups to intense vessel-generated noise tested how these exposures influenced the foraging behavior of Blainville’s beaked whales (Mesoplodon densirostris) in the Tongue of the Ocean (Bahamas). A military array of bottom-mounted hydrophones was used to measure the response based upon changes in the spatial and temporal pattern of vocalizations. The archived acoustic data were used to compute metrics of the echolocation-based foraging behavior for 16 targeted groups, 10 groups further away on the range, and 26 nonexposed groups. The duration of foraging bouts was not significantly affected by the exposure. Changes in the hydrophone over which the group was most frequently detected occurred as the animals moved around within a foraging bout, and their number was significantly less the closer the whales were to the sound source. Non-exposed groups also had significantly more changes in the primary hydrophone than exposed groups irrespective of distance. Our results suggested that broadband ship noise caused a significant change in beaked whale behavior up to at least 5.2 kilometers away from the vessel. The observed change could potentially correspond to a restriction in the movement of groups, a period of more directional travel, a reduction in the number of individuals clicking within the group, or a response to changes in prey movement.

Description: The research reported here was financially supported by the United States (U.S.) Office of Naval Research (www.onr.navy.mil) grants N00014-07-10988, N00014-07-11023, N00014-08-10990; the U.S. Strategic Environmental Research and Development Program (www.serdp.org) grant SI-1539, the Environmental Readiness Division of the U.S. Navy (http://www.navy.mil/local/n45/), the U.S. Chief of Naval Operations Submarine Warfare Division (Undersea Surveillance), the U.S. National Oceanic and Atmospheric Administration (National Marine Fisheries Service, Office of Science and Technology) (http://www.st.nmfs.noaa.gov/), U.S. National Oceanic and Atmospheric Administration Ocean Acoustics Program (http://www.nmfs.noaa.gov/pr/acoustics/), and the Joint Industry Program on Sound and Marine Life of the International Association of Oil and Gas Producers (www.soundandmarinelife.org).

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 10 (2012): e1001234, doi:10.1371/journal.pbio.1001234.

Description: Since the first discovery of deep-sea hydrothermal vents along the Galápagos Rift in 1977, numerous vent sites and endemic faunal assemblages have been found along mid-ocean ridges and back-arc basins at low to mid latitudes. These discoveries have suggested the existence of separate biogeographic provinces in the Atlantic and the North West Pacific, the existence of a province including the South West Pacific and Indian Ocean, and a separation of the North East Pacific, North East Pacific Rise, and South East Pacific Rise. The Southern Ocean is known to be a region of high deep-sea species diversity and centre of origin for the global deep-sea fauna. It has also been proposed as a gateway connecting hydrothermal vents in different oceans but is little explored because of extreme conditions. Since 2009 we have explored two segments of the East Scotia Ridge (ESR) in the Southern Ocean using a remotely operated vehicle. In each segment we located deep-sea hydrothermal vents hosting high-temperature black smokers up to 382.8°C and diffuse venting. The chemosynthetic ecosystems hosted by these vents are dominated by a new yeti crab (Kiwa n. sp.), stalked barnacles, limpets, peltospiroid gastropods, anemones, and a predatory sea star. Taxa abundant in vent ecosystems in other oceans, including polychaete worms (Siboglinidae), bathymodiolid mussels, and alvinocaridid shrimps, are absent from the ESR vents. These groups, except the Siboglinidae, possess planktotrophic larvae, rare in Antarctic marine invertebrates, suggesting that the environmental conditions of the Southern Ocean may act as a dispersal filter for vent taxa. Evidence from the distinctive fauna, the unique community structure, and multivariate analyses suggest that the Antarctic vent ecosystems represent a new vent biogeographic province. However, multivariate analyses of species present at the ESR and at other deep-sea hydrothermal vents globally indicate that vent biogeography is more complex than previously recognised.

Description: The ChEsSo research programme was funded by a NERC Consortium Grant (NE/DO1249X/1) and supported by the Census of Marine Life and the Sloan Foundation, and the Total Foundation for Biodiversity (Abyss 2100)(SVTH) all of which are gratefully acknowledged. We also acknowledge NSF grant ANT-0739675 (CG and TS), NERC PhD studentships NE/D01429X/1(LH, LM, CNR), NE/H524922/1(JH) and NE/F010664/1 (WDKR), a Cusanuswerk doctoral fellowship, and a Lesley & Charles Hilton-Brown Scholarship, University of St. Andrews (PHBS).

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e44015, doi:10.1371/journal.pone.0044015.

Description: Taxonomists have been tasked with cataloguing and quantifying the Earth’s biodiversity. Their progress is measured in code-compliant species descriptions that include text, images, type material and molecular sequences. It is from this material that other researchers are to identify individuals of the same species in future observations. It has been estimated that 13% to 22% (depending on taxonomic group) of described species have only ever been observed once. Species that have only been observed at the time and place of their original description are referred to as oncers. Oncers are important to our current understanding of biodiversity. They may be validly described species that are members of a rare biosphere, or they may indicate endemism, or that these species are limited to very constrained niches. Alternatively, they may reflect that taxonomic practices are too poor to allow the organism to be re-identified or that the descriptions are unknown to other researchers. If the latter are true, our current tally of species will not be an accurate indication of what we know. In order to investigate this phenomenon and its potential causes, we examined the microbial eukaryote genus Gymnodinium. This genus contains 268 extant species, 103 (38%) of which have not been observed since their original description. We report traits of the original descriptions and interpret them in respect to the status of the species. We conclude that the majority of oncers were poorly described and their identity is ambiguous. As a result, we argue that the genus Gymnodinium contains only 234 identifiable species. Species that have been observed multiple times tend to have longer descriptions, written in English. The styles of individual authors have a major effect, with a few authors describing a disproportionate number of oncers. The information about the taxonomy of Gymnodinium that is available via the internet is incomplete, and reliance on it will not give access to all necessary knowledge. Six new names are presented – Gymnodinium campbelli for the homonymous name Gymnodinium translucens Campbell 1973, Gymnodinium antarcticum for the homonymous name Gymnodinium frigidum Balech 1965, Gymnodinium manchuriensis for the homonymous name Gymnodinium autumnale Skvortzov 1968, Gymnodinium christenum for the homonymous name Gymnodinium irregulare Christen 1959, Gymnodinium conkufferi for the homonymous name Gymnodinium irregulare Conrad & Kufferath 1954 and Gymnodinium chinensis for the homonymous name Gymnodinium frigidum Skvortzov 1968.

Description: This work was funded by grants from the John D and Catherine T MacArthur Foundation and the Alfred P Sloan Foundation to the Encyclopedia of Life and the National Science Foundation Data Net Program 0830976 and Global Names Project DBI-1062387.

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e42872, doi:10.1371/journal.pone.0042872.

Description: The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. Among its diverse ecosystems are deep-sea brine pools - water bodies characterized by a unique combination of extreme conditions. The ‘polyextremophiles’ that constitute the microbial assemblage of these deep hot brines have not been comprehensively studied. We report a comparative taxonomic analysis of the prokaryotic communities of the sediments directly below the Red Sea brine pools, namely, Atlantis II, Discovery, Chain Deep, and an adjacent brine-influenced site. Analyses of sediment samples and high-throughput pyrosequencing of PCR-amplified environmental 16S ribosomal RNA genes (16S rDNA) revealed that one sulfur (S)-rich Atlantis II and one nitrogen (N)-rich Discovery Deep section contained distinct microbial populations that differed from those found in the other sediment samples examined. Proteobacteria, Actinobacteria, Cyanobacteria, Deferribacteres, and Euryarchaeota were the most abundant bacterial and archaeal phyla in both the S- and N-rich sections. Relative abundance-based hierarchical clustering of the 16S rDNA pyrotags assigned to major taxonomic groups allowed us to categorize the archaeal and bacterial communities into three major and distinct groups; group I was unique to the S-rich Atlantis II section (ATII-1), group II was characteristic for the N-rich Discovery sample (DD-1), and group III reflected the composition of the remaining sediments. Many of the groups detected in the S-rich Atlantis II section are likely to play a dominant role in the cycling of methane and sulfur due to their phylogenetic affiliations with bacteria and archaea involved in anaerobic methane oxidation and sulfate reduction.

Description: This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program.

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e28353, doi:10.1371/journal.pone.0028353.

Description: Simultaneous high resolution sampling of predator behavior and habitat characteristics is often difficult to achieve despite its importance in understanding the foraging decisions and habitat use of predators. Here we tap into the biosonar system of Blainville's beaked whales, Mesoplodon densirostris, using sound and orientation recording tags to uncover prey-finding cues available to echolocating predators in the deep-sea. Echolocation sounds indicate where whales search and encounter prey, as well as the altitude of whales above the sea-floor and the density of organisms around them, providing a link between foraging activity and the bio-physical environment. Tagged whales (n = 9) hunted exclusively at depth, investing most of their search time either in the lower part of the deep scattering layer (DSL) or near the sea-floor with little diel change. At least 43% (420/974) of recorded prey-capture attempts were performed within the benthic boundary layer despite a wide range of dive depths, and many dives included both meso- and bentho-pelagic foraging. Blainville's beaked whales only initiate searching when already deep in the descent and encounter prey suitable for capture within 2 min of the start of echolocation, suggesting that these whales are accessing prey in reliable vertical strata. Moreover, these prey resources are sufficiently dense to feed the animals in what is effectively four hours of hunting per day enabling a strategy in which long dives to exploit numerous deep-prey with low nutritional value require protracted recovery periods (average 1.5 h) between dives. This apparent searching efficiency maybe aided by inhabiting steep undersea slopes with access to both the DSL and the sea-floor over small spatial scales. Aggregations of prey in these biotopes are located using biosonar-derived landmarks and represent stable and abundant resources for Blainville's beaked whales in the otherwise food-limited deep-ocean.

Description: The work was funded by the Office of Naval Research and the National Ocean Partnership Program (US), by a consortium consisting of the Canary Islands Government, the Spanish Ministry of Environment and the Spanish Ministry of Defense, and by the European environmental funding LIFE-INDEMARES program for the inventory and designation of the Natura 2000 network in marine areas of the Spanish territory, headed by Fundacion Biodiversidad, with additional support from the Cabildo Insular of El Hierro. PA is currently supported by the National Research Project: Cetacean, Oceanography and Biodiversity from La Palma and El Hierro (CGL2009-13112) of the Spanish Ministry of Science and NAS by a Marie Curie fellowship from the 7th European Frame Program. MJ was supported by grants from the Strategic Environmental Research Development Program and from the National Ocean Partnership Program. PTM was supported by frame grants from the National Danish Science Foundation.

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e28257, doi:10.1371/journal.pone.0028257.

Description: Cytochrome P450 1 (CYP1) genes are biomarkers for aryl hydrocarbon receptor (AHR) agonists and may be involved in some of their toxic effects. CYP1s other than the CYP1As are poorly studied in birds. Here we characterize avian CYP1B and CYP1C genes and the expression of the identified CYP1 genes and AHR1, comparing basal and induced levels in chicken and quail embryos. We cloned cDNAs of chicken CYP1C1 and quail CYP1B1 and AHR1. CYP1Cs occur in several bird genomes, but we found no CYP1C gene in quail. The CYP1C genomic region is highly conserved among vertebrates. This region also shares some synteny with the CYP1B region, consistent with CYP1B and CYP1C genes deriving from duplication of a common ancestor gene. Real-time RT-PCR analyses revealed similar tissue distribution patterns for CYP1A4, CYP1A5, CYP1B1, and AHR1 mRNA in chicken and quail embryos, with the highest basal expression of the CYP1As in liver, and of CYP1B1 in eye, brain, and heart. Chicken CYP1C1 mRNA levels were appreciable in eye and heart but relatively low in other organs. Basal transcript levels of the CYP1As were higher in quail than in chicken, while CYP1B1 levels were similar in the two species. 3,3′,4,5,5′-Pentachlorobiphenyl induced all CYP1s in chicken; in quail a 1000-fold higher dose induced the CYP1As, but not CYP1B1. The apparent absence of CYP1C1 in quail, and weak expression and induction of CYP1C1 in chicken suggest that CYP1Cs have diminishing roles in tetrapods; similar tissue expression suggests that such roles may be met by CYP1B1. Tissue distribution of CYP1B and CYP1C transcripts in birds resembles that previously found in zebrafish, suggesting that these genes serve similar functions in diverse vertebrates. Determining CYP1 catalytic functions in different species should indicate the evolving roles of these duplicated genes in physiological and toxicological processes.

Description: Funding to MEJ and BB was from the Carl Tryggers Stiftelse and The Swedish Research Council Formas. Funding for BRW and JJS was from the United States National Institutes of Health (National Institute of Environmental Health Sciences), grants R01ES015912 and P42ES007381 to JJS.

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e33768, doi:10.1371/journal.pone.0033768.

Description: Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem function in the ocean. Diatoms are an abundant class of marine phytoplankton that are responsible for significant amounts of primary production. With the control they exert on the oceanic carbon cycle, there have been a number of studies focused on how diatoms respond to limiting macro and micronutrients such as iron and nitrogen. However, diatom physiological responses to P deficiency are poorly understood. Here, we couple deep sequencing of transcript tags and quantitative proteomics to analyze the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. A total of 318 transcripts were differentially regulated with a false discovery rate of 〈0.05, and a total of 136 proteins were differentially abundant (p〈0.05). Significant changes in the abundance of transcripts and proteins were observed and coordinated for multiple biochemical pathways, including glycolysis and translation. Patterns in transcript and protein abundance were also linked to physiological changes in cellular P distributions, and enzyme activities. These data demonstrate that diatom P deficiency results in changes in cellular P allocation through polyphosphate production, increased P transport, a switch to utilization of dissolved organic P through increased production of metalloenzymes, and a remodeling of the cell surface through production of sulfolipids. Together, these findings reveal that T. pseudonana has evolved a sophisticated response to P deficiency involving multiple biochemical strategies that are likely critical to its ability to respond to variations in environmental P availability.

Description: This research was supported by the National Science Foundation (NSF) Environmental Genomics and NSF Biological Oceanography Program through grant OCE-0723667 to Dr. Dyhrman, Dr. Jenkins, Dr. Saito, and Dr. Rynearson, the NSF Chemical Oceanography Program through grant OCE-0549794 to Dr. Dyhrman and OCE-0526800 to Dr. Jenkins, the G. B. Moore Foundation and OCE-0752291 to Dr. Saito, NSF-EPSCoR (NSF-0554548 & NSF-1004057) to the University of Rhode Island, the Center for Microbial Oceanography: Research and Education, and the Joint Genome Institute/DOE Community Sequencing Program (CSP795793) to Dr. Jenkins, Dr. Dyhrman, Dr. Rynearson and Dr. Saito.

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e43039, doi:10.1371/journal.pone.0043039.

Description: The transition metal, copper (Cu), is an enzymatic cofactor required for a wide range of biochemical processes. Its essentiality is demonstrated by Menkes disease, an X-linked copper deficiency disorder characterized by defects in nervous-, cardiovascular- and skeletal systems, and is caused by mutations in the ATP7A copper transporter. Certain ATP7A mutations also cause X-linked Spinal Muscular Atrophy type 3 (SMAX3), which is characterized by neuromuscular defects absent an underlying systemic copper deficiency. While an understanding of these ATP7A-related disorders would clearly benefit from an animal model that permits tissue-specific deletion of the ATP7A gene, no such model currently exists. In this study, we generated a floxed mouse model allowing the conditional deletion of the Atp7a gene using Cre recombinase. Global deletion of Atp7a resulted in morphological and vascular defects in hemizygous male embryos and death in utero. Heterozygous deletion in females resulted in a 50% reduction in live births and a high postnatal lethality. These studies demonstrate the essential role of the Atp7a gene in mouse embryonic development and establish a powerful model for understanding the tissue-specific roles of ATP7A in copper metabolism and disease.

Description: This work was supported by National Institutes of Health Grants DK59893 and DK093386 to M.J.P., and DK44464 to J.D.G.

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e27693, doi:10.1371/journal.pone.0027693.

Description: Atlantic bluefin tuna (Thunnus thynnus) is considered to be overfished, but the status of its populations has been debated, partly because of uncertainties regarding the effects of mixing on fishing grounds. A better understanding of spatial structure and mixing may help fisheries managers to successfully rebuild populations to sustainable levels while maximizing catches. We formulate a new seasonally and spatially explicit fisheries model that is fitted to conventional and electronic tag data, historic catch-at-age reconstructions, and otolith microchemistry stock-composition data to improve the capacity to assess past, current, and future population sizes of Atlantic bluefin tuna. We apply the model to estimate spatial and temporal mixing of the eastern (Mediterranean) and western (Gulf of Mexico) populations, and to reconstruct abundances from 1950 to 2008. We show that western and eastern populations have been reduced to 17% and 33%, respectively, of 1950 spawning stock biomass levels. Overfishing to below the biomass that produces maximum sustainable yield occurred in the 1960s and the late 1990s for western and eastern populations, respectively. The model predicts that mixing depends on season, ontogeny, and location, and is highest in the western Atlantic. Assuming that future catches are zero, western and eastern populations are predicted to recover to levels at maximum sustainable yield by 2025 and 2015, respectively. However, the western population will not recover with catches of 1750 and 12,900 tonnes (the “rebuilding quotas”) in the western and eastern Atlantic, respectively, with or without closures in the Gulf of Mexico. If future catches are double the rebuilding quotas, then rebuilding of both populations will be compromised. If fishing were to continue in the eastern Atlantic at the unregulated levels of 2007, both stocks would continue to decline. Since populations mix on North Atlantic foraging grounds, successful rebuilding policies will benefit from trans-Atlantic cooperation.

Description: This work was supported by grants from the TAG A Giant Foundation, the Monterey Bay Aquarium Foundation, the Lenfest Ocean Program, Washington, DC, USA, the Canadian Fisheries and Oceans International Governance Strategies Fund and the National Oceanic and Atmospheric Administration (NOAA) of the United States.

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e28949, doi:10.1371/journal.pone.0028949.

Description: Shotgun mass spectrometry was used to detect proteins in the harmful alga, Aureococcus anophagefferens, and monitor their relative abundance across nutrient replete (control), phosphate-deficient (−P) and −P refed with phosphate (P-refed) conditions. Spectral counting techniques identified differentially abundant proteins and demonstrated that under phosphate deficiency, A. anophagefferens increases proteins involved in both inorganic and organic phosphorus (P) scavenging, including a phosphate transporter, 5′-nucleotidase, and alkaline phosphatase. Additionally, an increase in abundance of a sulfolipid biosynthesis protein was detected in −P and P-refed conditions. Analysis of the polar membrane lipids showed that cellular concentrations of the sulfolipid sulphoquinovosyldiacylglycerol (SQDG) were nearly two-fold greater in the −P condition versus the control condition, while cellular phospholipids were approximately 8-fold less. Transcript and protein abundances were more tightly coupled for gene products involved in P metabolism compared to those involved in a range of other metabolic functions. Comparison of protein abundances between the −P and P-refed conditions identified differences in the timing of protein degradation and turnover. This suggests that culture studies examining nutrient starvation responses will be valuable in interpreting protein abundance patterns for cellular nutritional status and history in metaproteomic datasets.

Description: Research for this work was supported by a National Oceanic and Atmospheric Administration ECOHAB grant (#NA09NOS4780206) and National Science Foundation grant (#OCE-0723667) and a STAR Research Assistance Agreement No. R-83041501-0 awarded by the U.S. Environmental Protection Agency. Further support came from the Woods Hole Coastal Ocean Institute. LLW was supported by a Environmental Protection Agency STAR Fellowship (#FP916901). EMB was supported by a National Science Foundation (NSF) Graduate Research Fellowship (#2007037200) and an Environmental Protection Agency STAR Fellowship (#F6E20324).

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Computational Biology 7 (2011): e1002318, doi:10.1371/journal.pcbi.1002318.

Description: Function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. However, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. Here, using the FGGY carbohydrate kinase family as an example, we built a confidently annotated reference set (CARS) of proteins by propagating experimentally verified functional assignments to a limited number of homologous proteins that are supported by their genomic and functional contexts. Then, we analyzed, on both the phylogenetic and the molecular levels, the evolution of different functional specificities in this family. The results show that the different functions (substrate specificities) encoded by FGGY kinases have emerged only once in the evolutionary history following an apparently simple divergent evolutionary model. At the same time, on the molecular level, one isofunctional group (L-ribulokinase, AraB) evolved at least two independent solutions that employed distinct specificity-determining residues for the recognition of a same substrate (L-ribulose). Our analysis provides a detailed model of the evolution of the FGGY kinase family. It also shows that only combined molecular and phylogenetic approaches can help reconstruct a full picture of functional diversifications in such diverse families.

Description: This study was funded by NIH and DOE grants.

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e29813, doi:10.1371/journal.pone.0029813.

Description: Melanopsin, the receptor molecule that underlies light sensitivity in mammalian ‘circadian’ receptors, is homologous to invertebrate rhodopsins and has been proposed to operate via a similar signaling pathway. Its downstream effectors, however, remain elusive. Melanopsin also expresses in two distinct light-sensitive cell types in the neural tube of amphioxus. This organism is the most basal extant chordate and can help outline the evolutionary history of different photoreceptor lineages and their transduction mechanisms; moreover, isolated amphioxus photoreceptors offer unique advantages, because they are unambiguously identifiable and amenable to single-cell physiological assays. In the present study whole-cell patch clamp recording, pharmacological manipulations, and immunodetection were utilized to investigate light transduction in amphioxus photoreceptors. A Gq was identified and selectively localized to the photosensitive microvillar membrane, while the pivotal role of phospholipase C was established pharmacologically. The photocurrent was profoundly depressed by IP3 receptor antagonists, highlighting the importance of IP3 receptors in light signaling. By contrast, surrogates of diacylglycerol (DAG), as well as poly-unsaturated fatty acids failed to activate a membrane conductance or to alter the light response. The results strengthen the notion that calcium released from the ER via IP3-sensitive channels may fulfill a key role in conveying - directly or indirectly - the melanopsin-initiated light signal to the photoconductance; moreover, they challenge the dogma that microvillar photoreceptors and phoshoinositide-based light transduction are a prerogative of invertebrate eyes.

Description: This work was supported by the National Science Foundation of the USA (grant 0918930).

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e45138, doi:10.1371/journal.pone.0045138.

Description: A common geographical pattern of genetic variation is the one-dimensional cline. Clines may be maintained by diversifying selection across a geographical gradient but can also reflect historical processes such as allopatry followed by secondary contact. To identify loci that may be undergoing diversifying selection, we examined the distribution of geographical variation patterns across the range of the killifish (Fundulus heteroclitus) in 310 loci, including microsatellites, allozymes, and single nucleotide polymorphisms. We employed two approaches to detect loci under strong diversifying selection. First, we developed an automated method to identify clinal variation on a per-locus basis and examined the distribution of clines to detect those that exhibited signifcantly steeper slopes. Second, we employed a classic -outlier method as a complementary approach. We also assessed performance of these techniques using simulations. Overall, latitudinal clines were detected in nearly half of all loci genotyped (i.e., all eight microsatellite loci, 12 of 16 allozyme loci and 44% of the 285 SNPs). With the exception of few outlier loci (notably mtDNA and malate dehydrogenase), the positions and slopes of Fundulus clines were statistically indistinguishable. The high frequency of latitudinal clines across the genome indicates that secondary contact plays a central role in the historical demography of this species. Our simulation results indicate that accurately detecting diversifying selection using genome scans is extremely difficult in species with a strong signal of secondary contact; neutral evolution under this history produces clines as steep as those expected under selection. Based on these results, we propose that demographic history can explain all clinal patterns observed in F. heteroclitus without invoking natural selection to either establish or maintain the pattern we observe today.

Description: This work was supported by the National Science Foundation (DEB-0919064 and IOS-1052262

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e29659, doi:10.1371/journal.pone.0029659.

Description: Evidence that infectious diseases cause wildlife population extirpation or extinction remains anecdotal and it is unclear whether the impacts of a pathogen at the individual level can scale up to population level so drastically. Here, we quantify the response of a Common eider colony to emerging epidemics of avian cholera, one of the most important infectious diseases affecting wild waterfowl. We show that avian cholera has the potential to drive colony extinction, even over a very short period. Extinction depends on disease severity (the impact of the disease on adult female survival) and disease frequency (the number of annual epidemics per decade). In case of epidemics of high severity (i.e., causing 〉30% mortality of breeding females), more than one outbreak per decade will be unsustainable for the colony and will likely lead to extinction within the next century; more than four outbreaks per decade will drive extinction to within 20 years. Such severity and frequency of avian cholera are already observed, and avian cholera might thus represent a significant threat to viability of breeding populations. However, this will depend on the mechanisms underlying avian cholera transmission, maintenance, and spread, which are currently only poorly known.

Description: The study was supported by the Canadian Wildlife Service-Environment Canada (http://www.ec.gc.ca/), Nunavut Wildlife Management Board (http:// www.nwmb.com/), Greenland Institute of Natural Resources (http://www.natur.gl/), Polar Continental Shelf Project (http://polar.nrcan.gc.ca/), Fonds Que´be´cois de la Recherche sur la Nature et les Technologies (http://www.fqrnt.gouv.qc.ca/), Canadian Network of Centres of Excellence ArcticNet (http://www.arcticnet.ulaval. ca/), Natural Sciences and Engineering Research Council of Canada (http://www.nserc-crsng.gc.ca/), and the Department of Indian Affairs and Northern Canada (http://www.ainc-inac.gc.ca/).

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e39971, doi:10.1371/journal.pone.0039971.

Description: Ornamental fishes are among the most popular and fastest growing categories of pets in the United States (U.S.). The global scope and scale of the ornamental fish trade and growing popularity of pet fish in the U.S. are strong indicators of the myriad economic and social benefits the pet industry provides. Relatively little is known about the microbial communities associated with these ornamental fishes or the aquarium water in which they are transported and housed. Using conventional molecular approaches and next generation high-throughput amplicon sequencing of 16S ribosomal RNA gene hypervariable regions, we characterized the bacterial community of aquarium water containing common goldfish (Carassius auratus) and Chinese algae eaters (Gyrinocheilus aymonieri) purchased from seven pet/aquarium shops in Rhode Island and identified the presence of potential pathogens. Our survey identified a total of 30 phyla, the most common being Proteobacteria (52%), Bacteroidetes (18%) and Planctomycetes (6%), with the top four phyla representing 〉80% of all sequences. Sequences from our water samples were most closely related to eleven bacterial species that have the potential to cause disease in fishes, humans and other species: Coxiella burnetii, Flavobacterium columnare, Legionella birminghamensis, L. pneumophila, Vibrio cholerae, V. mimicus. V. vulnificus, Aeromonas schubertii, A. veronii, A. hydrophila and Plesiomonas shigelloides. Our results, combined with evidence from the literature, suggest aquarium tank water harboring ornamental fish are an understudied source for novel microbial communities and pathogens that pose potential risks to the pet industry, fishes in trade, humans and other species.

Description: Steven D. Granz, Katayun Barmak, and Mark H. Kryder A comparison was made of FePt-B and FePt-B-Ag thin films having different volume contents of boron, which were RF sputtered with in-situ heating at 425575 degrees C onto Si substrates with 20 nm thick (002) MgO. By introducing boron into FePt and varying the sputtering conditions, films with grain ... [J. Appl. Phys. 111, 07B709 (2012)] published Thu Mar 8, 2012.

Description: M. S. Khalil, M. J. A. Stoutimore, F. C. Wellstood, and K. D. Osborn We examine the transmission through nonideal microwave resonant circuits. The general analytical resonance line shape is derived for both inductive and capacitive coupling with mismatched input and output transmission impedances, and it is found that, for certain non-ideal conditions, the line shape ... [J. Appl. Phys. 111, 054510 (2012)] published Thu Mar 8, 2012.

Description: Julia Wagner, Mark Gruber, Andreas Wilke, Yuya Tanaka, Katharina Topczak et al. We investigate different parameters influencing the occurrence of s-shaped current voltage (j-V) characteristics in planar heterojunction organic solar cells. It is shown how substrate modification, purity of the active organic material as well as variation of the top contact can affect the shape of ... [J. Appl. Phys. 111, 054509 (2012)] published Thu Mar 8, 2012.

Description: Q. An, W. Z. Han, S. N. Luo, T. C. Germann, D. L. Tonks et al. We investigate with molecular dynamics the dynamic response of Cu bicrystals with a special asymmetric grain boundary (GB), (111)//(112), and its dependence on the loading directions. Shock loading is applied along the GB normal either from the left or right to the GB. Due to the structure asymmetry ... [J. Appl. Phys. 111, 053525 (2012)] published Thu Mar 8, 2012.

Description: S. Y. Liu, C. M. Zhen, Y. Z. Li, C. F. Pan, H. J. Zhou et al. Room temperature ferromagnetism has been observed in hydrogenated N-doped amorphous carbon films (a-CN:H) prepared by plasma enhanced chemical vapor deposition. The magnetization of the films changed depending on the ratio (R) of the flow rate of nitrogen to that of methane during deposition and on ... [J. Appl. Phys. 111, 053922 (2012)] published Thu Mar 8, 2012.

Description: H. Xiang and K. Komvopoulos A contact-mode surface micromachine consisting of polycrystalline silicon was used to study the effect of repetitive impact loading on the evolution of adhesion at sidewall contact interfaces under different conditions of contact load, ambient pressure, and relative humidity. All micromachines demon ... [J. Appl. Phys. 111, 054507 (2012)] published Thu Mar 8, 2012.

Description: K. H. Matlack, J. J. Wall, J.-Y. Kim, J. Qu, L. J. Jacobs et al. Nonlinear ultrasound was used to monitor radiation damage in two reactor pressure vessel (RPV) steels. The microstructural changes associated with radiation damage include changes in dislocation density and the formation of precipitates, and nonlinear ultrasonic waves are known to be sensitive to su ... [J. Appl. Phys. 111, 054911 (2012)] published Thu Mar 8, 2012.

Description: Jin Fang, Yi Huang, Christopher M. Lew, Yushan Yan, and Laurent Pilon This paper reports the temperature dependent cross-plane thermal conductivity of pure silica zeolite (PSZ) MFI and MEL thin films measured using the 3omega method between 30 and 315 K. PSZ MFI thin films were b-oriented, fully crystalline, and had a 33% microporosity. PSZ MEL thin films consisted of ... [J. Appl. Phys. 111, 054910 (2012)] published Thu Mar 8, 2012.

Description: K. Ozdogan, M. Upadhyay Kahaly, S. R. Sarath Kumar, H. N. Alshareef, and U. Schwingenschlogl We study epitaxial SrTiO interfaced with Nb-doped SrTiNbO (x = 0, 0.125, 0.25, 0.375, and 0.5) by full-potential density functional theory. From the electronic band structures obtained by our ab-initio calculations we determine the dependence of the induced metallicity on the Nb concentration. We ob ... [J. Appl. Phys. 111, 054313 (2012)] published Thu Mar 8, 2012.

Description: Jianbo Hu, Kouhei Ichiyanagi, Hiroshi Takahashi, Hiroaki Koguchi, Takeaki Akasaka et al. The high-pressure phase stability of the metastable tetragonal zirconia is still under debate. The transition dynamics of shocked YO (3 mol. %) stabilized tetragonal zirconia ceramics under laser-shock compression has been directly studied using nanosecond time-resolved x-ray diffraction. The marten ... [J. Appl. Phys. 111, 053526 (2012)] published Thu Mar 8, 2012.

Description: P. R. Coxon, M. Newman, M. R. C. Hunt, N. O'Farrell, B. R. Horrocks et al. Silicon nanocrystals (SiNCs) modified with 18-mer DNA oligonucleotides have been studied by X-ray excited optical luminescence (XEOL) and X-ray absorption spectroscopy (XAS) in photoluminescence yield (PLY) and total electron yield (TEY) modes. Luminescence spectra from the DNA-modified SiNCs under ... [J. Appl. Phys. 111, 054311 (2012)] published Thu Mar 8, 2012.

Description: Jim Long Her, Yasuhiro H. Matsuda, Motohiro Nakano, Yasuhiro Niwa, and Yasuhiro Inada X-ray absorption near-edge structure (XANES) spectra of Mn in a spin-crossover compound, [Mn(taa)], was studied in pulsed high magnetic fields up to 37 T. The significant changes in the XANES spectra, related to the spin-crossover from the low-spin (LS) state to high-spin (HS) state, were found to b ... [J. Appl. Phys. 111, 053921 (2012)] published Thu Mar 8, 2012.

Description: B. Berini, A. Fouchet, E. Popova, J. Scola, Y. Dumont et al. Determining phase transitions has always been a great challenge in material science due to their important fundamental and technological aspects. Recently, iron-based perovskites (RFeO), exhibiting phase transitions at high temperatures, have attracted much interest for their functional properties a ... [J. Appl. Phys. 111, 053923 (2012)] published Thu Mar 8, 2012.

Description: C. Lazzaroni and P. Chabert A global (volume-averaged) model of the self-pulsing regime of micro-hollow cathode discharges working in argon gas is proposed. The power balance is done using an equivalent circuit model of the discharge that allows the current and voltage dynamics to be calculated. The fraction of the total power ... [J. Appl. Phys. 111, 053305 (2012)] published Thu Mar 8, 2012.

Description: M. Koubaa, T. Dammak, D. Garrot, M. Castro, E. Codjovi et al. The thermal properties of the perovskite slab alkylammonium lead iodide (FCHCHNH)[PbI] are investigated using spectroscopic ellipsometry, differential scanning calorimetry, photoluminescence, and Raman spectroscopy. The spectroscopic ellipsometry, performed in the heating mode, clearly evidenced the ... [J. Appl. Phys. 111, 053521 (2012)] published Thu Mar 8, 2012.

Description: X. M. Dou, B. Q. Sun, D. S. Jiang, H. Q. Ni, and Z. C. Niu The temperature-dependent electron spin relaxation of positively charged excitons in a single InAs quantum dot was measured by time-resolved photoluminescence spectroscopy at zero applied magnetic fields. The experimental results show that the electron-spin relaxation is clearly divided into two dif ... [J. Appl. Phys. 111, 053524 (2012)] published Thu Mar 8, 2012.

Description: Y. Zhang, N. Mattern, and J. Eckert We have studied the phase formation of CuZr liquids with x = 0, 0.5, 1, 2, 5, 10, and 25 using molecular dynamics simulations, respectively, in order to find a direct relationship between the atomic structures and the glass forming abilities (GFAs). The difference among the critical cooling rates ha ... [J. Appl. Phys. 111, 053520 (2012)] published Thu Mar 8, 2012.

Description: Antonio Faraone, Kunlun Hong, Larry R. Kneller, Michael Ohl, and John R. D. Copley The coherent dynamics of a typical fragile glass former, meta-toluidine, was investigated at the molecular level using quasielastic neutron scattering, with time-of-flight and neutron spin echo spectrometers. It is well known that the static structure factor of meta-toluidine shows a prepeak origina ... [J. Chem. Phys. 136, 104502 (2012)] published Thu Mar 8, 2012.

Description: Minglong Jiang, Qun Zeng, Tingting Zhang, Mingli Yang, and Koblar Alan Jackson The lowest-energy isomers of Cu clusters for N = 2030 are identified using an unbiased search algorithm and density functional theory calculations. The low-energy structures over this size range are dominated by those based on a 13-atom icosahedral (I) core and a 19-atom double icosahedron (DI) core ... [J. Chem. Phys. 136, 104501 (2012)] published Thu Mar 8, 2012.

Description: Kyousuke Yoshida, Koichi Iwata, Yoshio Nishiyama, Yoshifumi Kimura, and Hiro-o Hamaguchi Vibrational cooling rate of the first excited singlet (S) state of trans-stilbene and bulk thermal diffusivity are measured for seven room temperature ionic liquids, CmimTfN, CmimTfN, CmimPF, CmimTfN, CmimTfN, CmimTfN, and bmpyTfN. Vibrational cooling rate measured with picosecond time-resolved Rama ... [J. Chem. Phys. 136, 104504 (2012)] published Thu Mar 8, 2012.

Description: Ayse Arslanargin and Thomas L. Beck Free energy partitioning analysis is employed to explore the driving forces for ions interacting with the water liquid-vapor interface using recently optimized point charge models for the ions and SPC/E water. The Na and I ions are examined as an example kosmotrope/chaotrope pair. The absolute hydra ... [J. Chem. Phys. 136, 104503 (2012)] published Thu Mar 8, 2012.

Description: Taweetham Limpanuparb, Joshua W. Hollett, and Peter M. W. Gill We discuss the efficient computation of the auxiliary integrals that arise when resolutions of two-electron operators (specifically, the Coulomb operator [T. Limpanuparb, A. T. B. Gilbert, and P. M. W. Gill, J. Chem. Theory Comput. 7, 830 (2011)] and the long-range Ewald operator [T. Limpanuparb and ... [J. Chem. Phys. 136, 104102 (2012)] published Thu Mar 8, 2012.

Description: Sarom S. Leang, Federico Zahariev, and Mark S. Gordon The performance of 24 density functionals, including 14 meta-generalized gradient approximation (mGGA) functionals, is assessed for the calculation of vertical excitation energies against an experimental benchmark set comprising 14 small- to medium-sized compounds with 101 total excited states. The ... [J. Chem. Phys. 136, 104101 (2012)] published Thu Mar 8, 2012.

Description: Longjiu Cheng (程龙玖) Experiments revealed that small boron cluster anions and cations are (quasi-)planar. For neutral boron cluster, (quasi-)planar motifs are also suggested to be global minimum by many theoretical studies, and a structural transformation from quasi-planar to double-ring tubular structures occurs at B. ... [J. Chem. Phys. 136, 104301 (2012)] published Thu Mar 8, 2012.

Description: Paul Baird and Mohammad Wehbe Given a Riemannian 3-manifold (M, g) endowed with a unit vector field U that is tangent to a conformal foliation, we require that the pair extend to a space-time ([script M],[script G]) endowed with a space-like unit vector field U in such a way that U simultaneously generates null geodesics and is ... [J. Math. Phys. 53, 032504 (2012)] published Thu Mar 8, 2012.

Description: Ph. Traore and A. T. Perez Two-dimensional numerical simulations are carried out to examine the problem of transient electroconvection stability of dielectric liquids subjected to unipolar injection. The entire set of electrohydrodynamics equations associated with the electroconvective phenomena that occur in a layer of a die ... [Phys. Fluids 24, 037102 (2012)] published Thu Mar 8, 2012.

Description: Jianqiang Han, Xiaofei Wang, Tianhong Yan, Yan Li, and Meixuan Song Microcantilever with integrated piezoresistor has been applied to in situ surface stress measurement in the field of biochemical sensors. It is well known that piezoresistive cantilever-based sensors are sensitive to ambient temperature changing due to highly temperature-dependent piezoresistive eff ... [Rev. Sci. Instrum. 83, 035002 (2012)] published Thu Mar 8, 2012.

Description: Hong-xiang Sun, Shu-yi Zhang, and Xiu-ji Shui A model of acoustic diodes is realized by a thin brass plate with single-sided periodical grating structure immersed in water and studied both numerically and experimentally. The unidirectional transmission of acoustic waves is identified in two different frequency ranges, which can be systematicall ... [Appl. Phys. Lett. 100, 103507 (2012)] published Fri Mar 9, 2012.

Description: Xiaolei Wang, Kai Han, Wenwu Wang, Hong Yang, Jing Zhang et al. Band alignment of TiN/HfO interface of TiN/HfO/SiO/Si stack is investigated by x-ray photoelectron spectroscopy (XPS). The p-type Schottky barrier height (p-SBH) is found to increase with thicker HfO thickness. Since considering only the metal/dielectric interface cannot explain this phenomenon, ban ... [Appl. Phys. Lett. 100, 102906 (2012)] published Fri Mar 9, 2012.

Description: Wei Zou, Zhizhou Yu, C. X. Zhang, J. X. Zhong, and L. Z. Sun The transport properties of hybrid nanoribbons constructed by substituting zigzag graphane nanoribbons into zigzag graphene nanoribbons are investigated using the first-principles calculations and non-equilibrium Green's function. The transport properties of the hybrid systems are improved due to th ... [Appl. Phys. Lett. 100, 103109 (2012)] published Fri Mar 9, 2012.

Description: Brian E. Francisco, Christina M. Jones, Se-Hee Lee, and Conrad R. Stoldt While today's lithium-ion batteries offer acceptable energy storage capability, they lack the ability to be cycled repeatedly more than a couple thousand times. Electrochemical capacitors, i.e., supercapacitors, are being developed whose lifetimes exceed 1 x 10 cycles and power densities surpass t ... [Appl. Phys. Lett. 100, 103902 (2012)] published Fri Mar 9, 2012.

Description: Chun Cheng, Kai Liu, Bin Xiang, Joonki Suh, and Junqiao Wu Recently, it was discovered that single-crystalline VO nanostructures exhibit unique, single-domain metal-insulator phase transition. They enable a wide range of device applications as well as discoveries of oxide physics beyond those can be achieved with VO bulk or thin films. Previous syntheses of ... [Appl. Phys. Lett. 100, 103111 (2012)] published Fri Mar 9, 2012.

Description: Jing-Xin Yu, Yan Cheng, Stefano Sanvito, and Xiang-Rong Chen The bias-dependent oscillatory electron transport of monatomic sulfur chains sandwiched between gold electrodes is investigated with density functional theory and non-equilibrium Green's function method. At zero bias, in contrast to the typical odd-even oscillations observed in most metallic chains, ... [Appl. Phys. Lett. 100, 103110 (2012)] published Fri Mar 9, 2012.

Description: Jing Lou, Gerry N. Pellegrini, Ming Liu, Neil D. Mathur, and Nian X. Sun We demonstrate an equivalence between direct and converse magnetoelectric effects in two-phase systems comprising piezoelectric and magnetostrictive materials. This was achieved by recasting the Maxwell relation in terms of the effective electrical and magnetic dipole moments for the system and comp ... [Appl. Phys. Lett. 100, 102907 (2012)] published Fri Mar 9, 2012.

Description: Fei Ding, Yanxia Cui, Xiaochen Ge, Yi Jin, and Sailing He A microwave ultra-broadband polarization-independent metamaterial absorber is demonstrated. It is composed of a periodic array of metal-dielectric multilayered quadrangular frustum pyramids. These pyramids possess resonant absorption modes at multi-frequencies, of which the overlapping leads to the ... [Appl. Phys. Lett. 100, 103506 (2012)] published Fri Mar 9, 2012.

Description: Jie Su, Xiaomei Lu, Yaoyang Liu, Junting Zhang, Guorong Li et al. 0.7Pb(ZrTi)O-0.3Pb(NiNb)O (abbreviated as PZT-PNN) ceramics were prepared using the solid-state reaction method. The results reveal that ferroelectric and anti-ferromagnetic orderings coexist (multiferroicity) in PZT-PNN ceramics. Furthermore, the abnormal behavior of dielectric constant and loss ob ... [Appl. Phys. Lett. 100, 102905 (2012)] published Fri Mar 9, 2012.

Description: Yuan Tian, Hongliang Lu, Jifa Tian, Chen Li, Chao Hui et al. Magnesium-doped boron nanoswords were synthesized via a thermoreduction method. The as-prepared nanoswords are single crystalline and beta-rhombohedral (beta-rh) phase. Electrical transport measurements show that variable range hopping conductivity increases with temperature, and carrier mobility ha ... [Appl. Phys. Lett. 100, 103112 (2012)] published Fri Mar 9, 2012.

Description: Yohanna Seminovski, Pablo Palacios, Perla Wahnon, and Ricardo Grau-Crespo Based on theoretical arguments, we propose a possible route for controlling the band-gap in the promising photovoltaic material CdInS. Our ab initio calculations show that the experimental degree of inversion in this spinel (fraction of tetrahedral sites occupied by In) corresponds approximately to ... [Appl. Phys. Lett. 100, 102112 (2012)] published Fri Mar 9, 2012.

Description: Takao Shimizu, Desheng Fu, Hiroki Taniguchi, Tomoyasu Taniyama, and Mitsuru Itoh We perform a Raman scattering study to elucidate the mechanism of temperature independent dielectric response of BaCaTiO (BCTO-0.233) from a viewpoint of phonon dynamics. BCTO-0.233 remains tetragonal below T down to 3.5 K. Over-damped soft phonon observed in a pure BaTiO is found to become underdam ... [Appl. Phys. Lett. 100, 102908 (2012)] published Fri Mar 9, 2012.

Description: Levent Gutay, Alex Redinger, Rabie Djemour, and Susanne Siebentritt We present experimental proof for a narrow first conduction band in CuZnSnSe semiconductor films as it has been predicted by theoretical calculations. The optical absorption characteristics of CuZnSnSe thin films are analyzed by optical transmission spectroscopy. The experimental data show strong ev ... [Appl. Phys. Lett. 100, 102113 (2012)] published Fri Mar 9, 2012.

Description: Jibao Lu, Ying Dai, Meng Guo, Lin Yu, Kangrong Lai et al. The conflict of understandings on experimental results about chemical and optical properties of C-doped TiO, which has been overlooked for a long time but is essential for studies of the basic properties of this material, is unraveled. It is shown that in anatase TiO the doped C and O atoms can easi ... [Appl. Phys. Lett. 100, 102114 (2012)] published Fri Mar 9, 2012.

Description: Zhifeng Shi, Xiaochuan Xia, Wei Yin, Shikai Zhang, Hui Wang et al. Ultraviolet electroluminescence was demonstrated from a p-ZnO:As/n-SiC(6H) heterojunction light-emitting diode at room-temperature. The p-ZnO:As was fabricated by out-diffusion of arsenic atoms from a sandwiched GaAs interlayer on SiC substrate. The p-type doping was confirmed by both Hall and low-t ... [Appl. Phys. Lett. 100, 101112 (2012)] published Fri Mar 9, 2012.

Description: Saifeng Zhang, Wei Xie, Hongxing Dong, Liaoxin Sun, Yanjing Ling et al. A robust exciton-polariton effect in a ZnO whispering gallery microcavity well above room temperature is presented. The lower polariton branches are tuned by current induced thermal effect. The red shift can be as large as ~40 meV. It is found that the strong coupling can be preserved and the polari ... [Appl. Phys. Lett. 100, 101912 (2012)] published Fri Mar 9, 2012.

Description: J. A. Caraveo-Frescas, M. N. Hedhili, H. Wang, U. Schwingenschlogl, and H. N. Alshareef It is shown that the well-known negative flatband voltage (V) shift, induced by rare-earth oxide capping in metal gate stacks, can be completely reversed in the absence of the silicon overlayer. Using TaN metal gates and GdO-doped dielectric, we measure a ~350 mV negative shift with the Si overlayer ... [Appl. Phys. Lett. 100, 102111 (2012)] published Fri Mar 9, 2012.

Description: X. Y. Zhong, B. Kabius, D. K. Schreiber, J. A. Eastman, D. D. Fong et al. The protocol to calculate the chemical roughness from three-dimensional (3-D) data cube acquired by energy-filtered electron tomography has been developed and applied to analyze the 3-D Zr distribution at the arbitrarily shaped interfaces in the ZrO/InO multilayer films. The calculated root-mean-squ ... [Appl. Phys. Lett. 100, 101604 (2012)] published Fri Mar 9, 2012.

Description: Chunlei Wan, Yifeng Wang, Wataru Norimatsu, Michiko Kusunoki, and Kunihito Koumoto Layered metal sulfides (MS)(TiS) (M = Pb, Sn, Bi) with alternative stacking of MS layers and TiS layers (a natural superlattice) have been proposed as thermoelectric materials. In this paper, various nanoscale stacking faults have been found in these materials, including the translational disorder i ... [Appl. Phys. Lett. 100, 101913 (2012)] published Fri Mar 9, 2012.

Description: Mohammad Farazmand and George Haller Using the recently developed variational theory of hyperbolic Lagrangian coherent structures (LCSs), we introduce a computational approach that renders attracting and repelling LCSs as smooth, parametrized curves in two-dimensional flows. The curves are obtained as trajectories of an autonomous ordi ... [Chaos 22, 013128 (2012)] published Fri Mar 9, 2012.

Description: Lucas Illing, Alison M. Saunders, and Daniel Hahs We address the issue of multi-parameter estimation from scalar outputs of chaotic systems, using the dynamics of a Malkus water wheel and simulations of the corresponding Lorenz-equations model as an example. We discuss and compare two estimators: one is based on a globally convergent adaptive obser ... [Chaos 22, 013127 (2012)] published Fri Mar 9, 2012.

Description: A. A. Gonzalez-Fernandez, J. Juvert, Alfredo Morales-Sanchez, Jorge Barreto, M. Aceves-Mijares et al. This work presents electrical and electro-optical studies performed on light-emitting capacitors with silicon-rich silicon oxide fabricated by plasma-enhanced chemical vapor deposition and by the implantation of Si ions in thermally grown SiO. The influence of the fabrication technique and silicon c ... [J. Appl. Phys. 111, 053109 (2012)] published Thu Mar 8, 2012.

Description: Alvaro Valdes, Rita Prosmiti, and Gerardo Delgado-Barrio A full-dimensional quantum dynamics study is carried out for the highly fluxional H cation on a recent reference potential energy surface by using the multi configuration time-dependent Hartree method. With five equivalent light atoms and shallow barriers between various low-lying stationary points ... [J. Chem. Phys. 136, 104302 (2012)] published Thu Mar 8, 2012.

Description: M. H. Stockett and J. E. Lawler A novel absorption cell has been developed to enable a spectroscopic survey of a broad range of polycyclic aromatic hydrocarbons (PAH) under astrophysically relevant conditions and utilizing a synchrotron radiation continuum to test the still controversial hypothesis that these molecules or their io ... [Rev. Sci. Instrum. 83, 035104 (2012)] published Fri Mar 9, 2012.

Description: N. Tezuka, F. Mitsuhashi, and S. Sugimoto Tunnel magnetoresistance effect has been investigated for magnetic tunnel junctions with CoFeAlSi Heusler electrodes on a Cr-bufferd MgO (110) substrate. The grown CoFeAlSi has L2 structure for annealing above 500 degrees C. The TMR ratio of 73% at room temperature and 103% at 5 K were obtained for ... [J. Appl. Phys. 111, 07C718 (2012)] published Fri Mar 9, 2012.

Description: Manh Cuong Nguyen, Xin Zhao, Min Ji, Cai-Zhuang Wang, Bruce Harmon et al. Using genetic algorithm with first-principle calculations, we searched for low-energy crystal structures of FeCo alloys. We found that FeCo alloys are highly configurationally degenerate with many additional off-stoichiometric stable structures to the well-known B structure. The average magnetic mom ... [J. Appl. Phys. 111, 07E338 (2012)] published Fri Mar 9, 2012.

Description: Kazuhiko Okita, Kazushi Ishiyama, and Hideo Miura Magnetostriction constant of a magnetic thin film is conventionally measured by detecting the deformation of a coupon sample that consists of the magnetic film deposited on a thin glass substrate (e.g., cover glass of size 10 mm x 25 mm) under an applied field using a laser beam [A. C. Tam and H. ... [J. Appl. Phys. 111, 07E340 (2012)] published Fri Mar 9, 2012.

Description: Yuan-Feng Duan, Chung Ming Leung, Shengyao Zhang, Long Zhang, and Siu Wing Or A polymer-based magnetoelectric (ME) laminate was fabricated by sandwiching one layer of thickness-polarized, length-stretched polyvinylidene fluoride (PVDF) piezoelectric polymer between two layers of length-magnetized, epoxy-bonded TbDyFe (Terfenol-D) pseudo-13 magnetostrictive particulate composi ... [J. Appl. Phys. 111, 07C717 (2012)] published Fri Mar 9, 2012.

Description: Brooke L. Mesler, Kristen S. Buchanan, Mi-Young Im, and Peter Fischer We report experimental evidence of nonlinear gyrotropic vortex core motion. Using soft x-ray transmission microscopy we observed the time-averaged dynamic response of a magnetic vortex core in a 2 [mu]m diameter, 100 nm thick permalloy (NiFe) disk as a function of the amplitude and frequency of an a ... [J. Appl. Phys. 111, 07D311 (2012)] published Fri Mar 9, 2012.

Description: Sunjae Chung, Sangyeop Lee, Hakjoon Lee, Taehee Yoo, Sanghoon Lee et al. Two ferromagnetic semiconductor GaMnAs-based superlattices (SLs) were investigated by measuring the planar Hall effect (PHE) with the external magnetic field applied in the plane of the sample. The two GaMnAs/GaAs SLs differed only by the Be doping of the nonmagnetic GaAs spacer layers. Both SLs sho ... [J. Appl. Phys. 111, 07D310 (2012)] published Fri Mar 9, 2012.

Description: G. Consolo and E. Martinez In this paper a numerical investigation of the effects of disorder on the domain wall propagation along magnetic nanostrips induced by fields or currents is carried out. Such effects are included in the extended Landau-Lifshitz-Gilbert equation of motion by generalizing the classical viscous-type di ... [J. Appl. Phys. 111, 07D312 (2012)] published Fri Mar 9, 2012.

Description: Khabat Ebnabbasi, Yajie Chen, Anton Geiler, Vincent Harris, and Carmine Vittoria In this paper, magnetoelectric effects of Sr Z-type hexaferrite, SrFeCoO, at room temperature is measured. The change in remanence magnetization was measured by applying a DC voltage or electric field across a slab of hexaferrite. Changes of ~18% in remanence was observed in an electric field of 10 ... [J. Appl. Phys. 111, 07C719 (2012)] published Fri Mar 9, 2012.

Description: S. Narendra Babu, Seong-Gi Min, Amin Yourdkhani, Gabriel Caruntu, and Leszek Malkinski The present work is aimed at fabricating bi-layer aluminum nitride (AlN)/cobalt iron (CoFe) magnetoelectric (ME) thin films using reactive rf/dc magnetron sputtering. A systematic study on structural, morphological, piezoelectric, magnetic and magnetoelectric properties is undertaken. Except for AlN ... [J. Appl. Phys. 111, 07C720 (2012)] published Fri Mar 9, 2012.

Description: Tomoaki Inokuchi, Mizue Ishikawa, Hideyuki Sugiyama, Yoshiaki Saito, and Nobuki Tezuka Spin injection and detection properties in CoFe/AlO/SOI (Si on insulator) junctions were investigated by using Hanle effect measurements up to room temperature. Cross-sectional transmission electron microscope images and Fourier transform images of the CoFe/AlO/SOI junction, fabricated by using appr ... [J. Appl. Phys. 111, 07C316 (2012)] published Fri Mar 9, 2012.

Description: Hiroyuki Ohtori and Hiroshi Imamura This paper theoretically analyzes the Andreev reflection in normal-conductor/multi-band super-conductor junctions. We applied Bogoliubov-de Gennes equations to the case of superconductors with extended s-waves and calculated the respective point-contact Andreev reflection (PCAR) spectra. Our results ... [J. Appl. Phys. 111, 07C518 (2012)] published Fri Mar 9, 2012.

Description: W. M. Li, X. L. Huang, J. Z. Shi, Y. J. Chen, T. L. Huang et al. The motivation for this work is rooted in the reversal process that occurs in perpendicularly magnetic Co/Pd multilayered based bit-patterned media. In our work, temperature effect and angle dependence of critical fields (H) and switching field distribution (SFD) are studied by both experiment and s ... [J. Appl. Phys. 111, 07B917 (2012)] published Fri Mar 9, 2012.

Description: Youn Ho Park, Hyun Cheol Jang, Hyun Cheol Koo, Hyung-jun Kim, Joonyeon Chang et al. From the Shubnikov-de Haas oscillation, estimation of the spin[horizontal bar]orbit interaction parameter is possible only for very low temperature. An alternative method available for much wider temperature range is utilizing the ferromagnetic electrode which contacts the quantum well channel and r ... [J. Appl. Phys. 111, 07C317 (2012)] published Fri Mar 9, 2012.

Description: S. N. Piramanayagam, M. Ranjbar, H. K. Tan, W. C. Allen Poh, R. Sbiaa et al. Antidots of Co/Pd multilayers with 3-bilayers [(Co/Pd)] that were antiferromagnetically coupled(AFC) to (Co/Pd) were fabricated and their magnetic properties were investigated. The thickness of Co in (Co/Pd) was varied from 0.4 to 0.8 nm. Samples with a Co thickness of 0.8 nm in the bilayer showed a ... [J. Appl. Phys. 111, 07B916 (2012)] published Fri Mar 9, 2012.

Description: Seyong Choi, Jang-Hee Yoon, Byoung-Seob Lee, Mi-Sook Won, Jung-Woo Ok et al. We investigate the performance of a magnetic lens in very high magnetic fields exceeding 24 T. The magnetic lens is composed of Gd-Ba-Cu-O superconducting bulk materials. The unique configuration of the magnetic field amplifier, which consists of slits and electrical insulation in the bulk, allows t ... [J. Appl. Phys. 111, 07E728 (2012)] published Fri Mar 9, 2012.

Description: M. Godoy, A. J. Moreno, G. A. Jorge, H. J. Ferrari, P. S. Antonel et al. We report micrometric periodic assembly of live and dead magnetotactic bacteria, Magnetospirillum magneticum AMB-1, which synthesize chains of magnetic nanoparticles inside their bodies, and of superparamagnetic FeO and ferromagnetic CoFeO nanoparticles in aqueous suspensions using periodically magn ... [J. Appl. Phys. 111, 044905 (2012)] published Thu Feb 23, 2012.

Description: Mukannan Arivanandhan, Raira Gotoh, Tatsuro Watahiki, Kozo Fujiwara, Yasuhiro Hayakawa et al. The effect of Ge codoping on minority carrier lifetime in boron (B)-doped Czochralski-silicon (CZ-Si) crystals was investigated. The minority carrier lifetime increased from 110 to 176 [mu]s as Ge concentration was increased from zero to 1 x 10cm in B/Ge codoped CZ-Si crystals. Light-induced degra ... [J. Appl. Phys. 111, 043707 (2012)] published Thu Feb 23, 2012.

Description: S. S. Yakushkin, A. A. Dubrovskiy, D. A. Balaev, K. A. Shaykhutdinov, G. A. Bukhtiyarova et al. Magnetic properties of [eh]-FeO nanoparticles supported on silica with the average size of few nanometers, narrow size distribution and no admixture of any other iron oxide polymorphs are investigated. The investigation of the temperature behavior of magnetization within the temperature range from 4 ... [J. Appl. Phys. 111, 044312 (2012)] published Thu Feb 23, 2012.

Description: Biswadeep Saha, Meenakshisundaram Ramanathan, Chai Ren, and Sivaraman Guruswamy Dislocation arrays were introduced through controlled deformation of Fe20 at. % Ga alloy single crystal samples with and orientations. Alloy single crystals were obtained through vertical Bridgman growth process. Magnetostriction measurements show a large decrease in magnetostriction after deformi ... [J. Appl. Phys. 111, 043911 (2012)] published Thu Feb 23, 2012.

Description: Mudar A. Abdulsattar Infrared and Raman vibrational spectrum are calculated using ab initio density functional theory for SiGe superlattice nanocrystal of approximately 1.6 nm length. After obtaining the optimum positions of atoms via geometrical optimization using density functional theory, coupled perturbed Hartree-Fo ... [J. Appl. Phys. 111, 044306 (2012)] published Tue Feb 21, 2012.

Description: J. C. Lin, B. S. Wang, S. Lin, P. Tong, W. J. Lu et al. With increasing the substitution of Sn for Cu in CuSnMnNMn, the initial cubic-tetragonal structural phase transition disappears for the samples x 〉= 0.10 and is replaced by a discontinuous lattice expansion with a cubic structure which has been confirmed by the measurements of variable temperature x ... [J. Appl. Phys. 111, 043905 (2012)] published Tue Feb 21, 2012.

Description: Narihito Okada, Yoichi Yamada, and Kazuyuki Tadatomo Templates consisting of in-plane alternately arranged relaxed InGaN and GaN were obtained by (1122) facet growth and mass transport via metal-organic vapor phase epitaxy. InGaN/GaN multi-quantum wells (MQWs) were grown on the novel templates, and their optical and structural properties were investig ... [J. Appl. Phys. 111, 043508 (2012)] published Tue Feb 21, 2012.

Description: Yong Zhi Cheng, Ying Wang, Yan Nie, Rong Zhou Gong, Xuan Xiong et al. A broadband metamaterial absorber (MA) based on lumped elements is presented, which is composed of the dielectric substrate sandwiched with metal split-coin resonators (SCR) welded with lumped elements and continuous metal film. We simulated, fabricated, and measured the lumped elements MA. Compared ... [J. Appl. Phys. 111, 044902 (2012)] published Tue Feb 21, 2012.

Description: Jennifer T. Heath, Chun-Sheng Jiang, and Mowafak M. Al-Jassim We calibrate the secondary electron signal from a standard scanning electron microscope to voltage, yielding an image of the surface or near-surface potential. Data on both atomically abrupt heterojunction GaInP/GaAs and diffused homojunction Si solar cell devices clearly show the expected variation ... [J. Appl. Phys. 111, 046103 (2012)] published Tue Feb 21, 2012.

Description: Hui Zhang We have presented a theoretical model to describe the magnetoelectric coupling in TbDyFe/PZT laminate composite material. In this model, the stresses introduced by the magnetic field or electric field in the composite material are assumed to be the axial force. The magnetization of magnetostrictive ... [J. Appl. Phys. 111, 043906 (2012)] published Tue Feb 21, 2012.