bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure and magnetic properties of low-temperature annealed Ni-Mn-Al alloys
Authors: Kim Yongdeok , Lee Seung Jae , Han Won Bae , Kim Hee-Soo , An Hyeun Hwan , Yoon Chong Seung
Published: March 2013

Off-stoichiometric Ni2Mn2−xAlx (x = 0.5–1.2) and Ni2+y(Mn1.3Al0.7)1−y/2, (y = 0.04–0.12) alloys were prepared to locate the composition range which is likely to form the ferromagnetic ordered L21 phase through low-temperature thermal annealing. In the Ni2Mn2−xAlx (x = 0.5–1.2) series, the alloy partially transformed to the ferromagnetic phase in the narrow composition range of x = 0.8–1.1. For the Ni-enriched composition series, Ni2+y(Mn1.3Al0.7)1−y/2, (y = 0.04–0.12), magnetic ordering was not observed and the magnetic susceptibility proportionally decreased with the Ni concentration. It was concluded that moving away from stoichiometric composition would likely increase the disordering of Mn and Al site occupation and is not conducive to achieving ferromagnetism in Ni2MnAl.
Oxygen monomers and dimers at gas-phase and Ag(111)-supported nanographenes: A density functional theory study
Authors: Nguyen Manh-Thuong
Published: March 2013

Density functional theory calculations are employed to examine the influence of Ag(111) on diffusion energy barriers of oxygen monomers and dimers at surface-supported nanographenes C24H12 (ℳ1) and C54H18(ℳ2). It is predicted that the underlying surface significantly reduces the activation energy barrier of single oxygen adatoms at ℳ1. Likewise, the barrier of a dimer oxygen adatom at ℳ2 is lowered. Energy barrier reduction is interpreted as a consequence of electronic and geometric modifications of molecular systems induced by the metal.
Temperature control of local magnetic anisotropy in multiferroic CoFe/BaTiO3
Authors: Lahtinen Tuomas H. E. , van Dijken Sebastiaan
Published: March 2013

This paper reports on the temperature evolution of local elastic interactions between ferromagnetic CoFe films and ferroelectric BaTiO3 substrates. Polarization microscopy measurements indicate that growth-induced stripe domains in the CoFe films are preserved and strengthened during cooling and heating through the structural phase transitions of BaTiO3. Moreover, rotation of the magnetic easy axes at the tertragonal-to-orthorhombic transition (T = 278 K) and at T ≈ 380 K simultaneously switches the local magnetization of both uniaxial domains by 90°. Irreversible changes in the ferromagnetic domain pattern are induced when the room-temperature ferroelectric domain structure is altered after temperature cycling.
Effects of magnetic field on anisotropic temperature relaxation
Authors: Dong Chao , Ren Haijun , Cai Huishan , Li Ding
Published: March 2013

In a strongly magnetized plasma, where the particles' thermal gyro-radii are smaller than the Debye length, the magnetic field greatly affects the plasma's relaxation processes. The expressions for the time rates of change of the electron and ion parallel and perpendicular temperatures are obtained and calculated analytically for small anisotropies through considering binary collisions between charged particles in the presence of a uniform magnetic field by using perturbation theory. Based on these expressions, the effects of the magnetic field on the relaxation of anisotropic electron and ion temperatures due to electron-electron collisions, ion-ion collisions, and electron-ion collisions are investigated. Consequently, the relaxation times of anisotropic electron and ion temperatures to isotropy are calculated. It is shown that electron-ion collisions can affect the relaxation of an anisotropic ion distribution in the strong magnetic field.
On the microscopic mechanism for the stabilization of structural and ferroic states in displacive multiferroics
Authors: Freitas V. F. , Bonadio T. G. M. , Dias G. S. , Protzek O. A. , Medina A. N. , Cótica L. F. , Santos I. A. , Garcia D. , Eiras J. A.
Published: March 2013

In this paper, the microscopic mechanism for structural, ferroelectric, and magnetic stabilities in displacive perovskite structured multiferroics is investigated by studying BiFeO3-PbTiO3 solid solutions. The results revealed that thermal stability and ferroic orders are intimately connected with the changes in A and B perovskite sites. The breakdown mechanism of the cycloidal magnetic network, which permits to observe the resulting macroscopic magnetization is reveled, compared, and presented for various compositions of the BiFeO3-PbTiO3 system. The delicate energetic balance that stabilizes the electrically polar structures in displacive perovskite multiferroics is proposed and it was showed that it is fully connected to the configuration (atomic occupancy and formal ionic charge) of each individual site of the perovskite unit cell.
Nature of magnetic domains in an exchange coupled BiFeO3/CoFe heterostructure
Authors: Qiu D. Y. , Ashraf K. , Salahuddin S.
Published: March 2013

We use the micromagnetic model to simulate magnetization in a multidomain BiFeO3(BFO)/CoFe bilayer. We show that CoFe couples to weak ferromagnetism on the BFO surface and breaks into domains that correspond exactly with BFO domains. Switching the direction of the BFO spins switches the corresponding CoFe domains and reverses the net magnetization. Since magnetization is coupled to polarization in BFO, this demonstrates a mechanism for controlling magnetization reversal with an electric field. Comparison with experimental values of BFO surface moment and hysteresis allows us to extract BFO/CoFe exchange and spin canting energies and predict behavior for domains of varying sizes.
Electric fields and dominant carrier transport mechanisms in CdTe Schottky detectors
Authors: Cola Adriano , Farella Isabella
Published: March 2013

CdTe Schottky diodes for X- and γ-ray detection exhibit excellent spectroscopic performance, even though these are not stable under operative voltages. Improvements require the comprehension of the main carrier transport mechanisms, presently unclear. We address this issue by correlating the internal electric field and the flowing current. Depending on the temperature and applied voltage, different mechanisms become dominant where the deep levels always play a central role. Indeed, the partial ionization of deep levels directly controls the electric field distribution. Transient measurements show how, under high voltages, the field at the contacts controls the current flowing through the detector.
Plasmon resonances and the plasmon-induced field enhancement in nanoring dimers
Authors: Yin Haifeng , Zhang Hong , Cheng Xin-Lu
Published: March 2013

Plasmon resonances and the plasmon-induced field enhancement (FE) in sodium nanoring dimers are investigated by time-dependent density functional theory. For larger separations, the optical absorption, the induced charge response and the frequency dependent current demonstrate that there are two capacitive coupling plasmon modes. One feature of FE is that, in the surface region of the nanoring, it has a very large maximum. Another feature of FE is that, along the perpendicular bisector of the line segment joining the two nanoring center points in the middle region of the nanoring dimers, it has maxima. With the decrease of the gap distance, because of the electrons tunneling across the dimer junction and screening, collective excitation modes are changed, and the charge transfer plasmon modes emerge in the nanoring dimers. FE induced by any plasmon modes decreases in the gap region. Moreover, corresponding to different gap distances, the high-energy plasmon resonance peak almost does not shift, because this plasmon mode is mainly the collective excitation as a result of interactions among degenerate individual electronic states.
Efficient organic-inorganic hybrid Schottky solar cell: The role of built-in potential
Authors: Zhu Yawen , Song Tao , Zhang Fute , Lee Shuit-Tong , Sun Baoquan
Published: March 2013

The organic-inorganic hybrid Schottky solar cells based on solution processed poly(3,4-ethlenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) in combination with silicon offer the merits of simple fabrication process and potential low cost. Here, we demonstrate that the work function (WF) of PEDOT:PSS films plays a critical role on the electronic output characteristics of the device. The WF of PEDOT:PSS is tuned by adding an aqueous solution of perfluorinated ionomer (PFI) due to its high electron affinity, which is compatible to fabricate the hybrid Si/PEDOT:PSS device. With an addition of 4% (weight) PFI into PEDOT:PSS, the device achieves a fill factor (FF) as high as 0.70 without sacrifice of open-circuit voltage and short-circuit current density, which improves 20% in comparison with the pristine PEDOT:PSS (0.58). The detailed electrical output measurements reveal that the high FF is ascribed to the enhanced built-in potential as well as suppression of charge recombination at organic-inorganic interface.
Using human-dimensions research to reduce implementation uncertainty for wildlife management: a case of moose (Alces alces) hunting in northern Ontario, Canada
Authors: Hunt Len M.
Published: March 2013

Context
Wildlife managers frequently use regulations to alter the preferred hunting strategies and outcomes of hunters. However, hunters can respond to changing social and resource conditions resulting from regulations in ways that can surprise wildlife managers.

Aims
The specific research questions were (1) how does the availability of licences (tags) required to harvest adult moose (Alces alces) relate to the success of hunters at filling these tags and (2) how do hunting pressure and the density of calf moose relate to the harvest rate of the calf population.

Methods
Information about hunters, harvest-related outcomes and moose abundance were estimated from social surveys and aerial inventories in 46 wildlife management units (WMUs) in northern Ontario, Canada. An information-theoretic approach was used to select regression models that predicted the average annual filling rate of tags for adult moose and for the average annual proportion of calf population harvested by hunters in the WMUs.

Key results
Tag filling rates were negatively and strongly associated with the availability of tags to hunters in the WMUs. The proportion of calf population harvested was positively related to hunting pressure and negatively related to the density of calf populations in the WMUs.

Conclusions
As tags became more scarce, hunters appeared to become more skilled at harvesting adult moose. As calf density declined, hunters harvested larger proportions of the population, indicating a possible inverse density-dependent relationship between abundance and harvest.

Implications
Understanding hunters and their actions and role within a larger social-ecological system are critical for helping to reduce the uncertainty of implementing regulations for managing wildlife. Without having this understanding, it is easy for managers to become trapped in situations where the intent of management actions is undermined by the abilities of hunters who respond to both changing social and resource conditions.
Sniffing out the stakes: hair-snares for wild cats in arid environments
Authors: Hanke Petra U. , Dickman Christopher R.
Published: March 2013

Context Wild cats (Felis spp.) are difficult to monitor because of their cryptic lifestyle and usually low numbers. Hair-snaring is a promising non-invasive method being used increasingly to estimate mammal populations. Aims Our aim was to carry out pilot trials of a simple hair-snare designed to capture hair from wild cats in arid environments. Methods Roughened wooden stakes were set at multiple sites on the crests of sand dunes and in swales in western Queensland, Australia, and in mostly sandy habitats of the Namib and Kalahari Deserts, Namibia. In Australia, stakes were sprayed with cat urine, extracts of catnip or valerian herbs as lures, or left untreated; in Namibia, alternate stakes were sprayed with a food lure of tuna emulsion oil. The stakes were checked for hair, usually daily, for 2–14 days, and the surrounding ground was inspected for tracks. Remote cameras also were used at some sites to confirm the identity of visitors to stakes. Key results In Australia, feral cats (Felis catus) were attracted to, and left hairs on, stakes sprayed with cat urine six times more frequently than to unsprayed stakes irrespective of whether snares were on dune crests or in swales, and showed no response to catnip or valerian. Tracks and photos showed that cats, dingoes or wild dogs (Canis lupus ssp.) and foxes (Vulpes vulpes) also approached and sniffed the stakes. In Namibia, F. catus, F. lybica and F. nigripes left hair on stakes, with deposition rates two and a half-fold higher at stakes with the food lure than without it. At least five other species of predators visited the hair-snare sites. Conclusions Simple wooden stakes provide a cheap and simple method of snaring hairs from wild cats, especially if used in conjunction with appropriate lures. Our results broadly support previous work, and extend the utility of the method to different Felis spp. in arid habitats. Implications Further research is needed on snares to investigate the seasonal efficiency of different lures. If DNA also is to be extracted to identify individuals, more work is needed to confirm that snares yield hair of sufficient quality to allow this.
China’s bullet trains facilitate market integration and mitigate the cost of megacity growth
Authors: Zheng Siqi , Kahn Matthew E.
Published: March 2013

Megacity growth in the developing world is fueled by a desire to access their large local labor markets. Growing megacities suffer from high levels of traffic congestion and pollution, which degrade local quality of life. Transportation technology that allows individuals to access the megacity without living within its boundaries offers potentially large social benefits, because individuals can enjoy the benefits of urban agglomeration while not paying megacity real estate rents and suffering from the city’s social costs. This paper presents evidence supporting the claim that China’s bullet trains are playing this role. The bullet train is regarded as one of the most significant technological breakthroughs in passenger transportation developed in the second half of the 20th century. Starting in 2007, China has introduced several new bullet trains that connect megacities such as Beijing, Shanghai, and Guangzhou with nearby cities. Through facilitating market integration, bullet trains will stimulate the development of second- and third-tier cities. By offering households and firms a larger menu of location alternatives, bullet trains help to protect the quality of life of the growing urban population. We document that this transport innovation is associated with rising real estate prices in the nearby secondary cities.
Projected Atlantic hurricane surge threat from rising temperatures
Authors: Grinsted Aslak , Moore John C. , Jevrejeva Svetlana
Published: March 2013

Detection and attribution of past changes in cyclone activity are hampered by biased cyclone records due to changes in observational capabilities. Here, we relate a homogeneous record of Atlantic tropical cyclone activity based on storm surge statistics from tide gauges to changes in global temperature patterns. We examine 10 competing hypotheses using nonstationary generalized extreme value analysis with different predictors (North Atlantic Oscillation, Southern Oscillation, Pacific Decadal Oscillation, Sahel rainfall, Quasi-Biennial Oscillation, radiative forcing, Main Development Region temperatures and its anomaly, global temperatures, and gridded temperatures). We find that gridded temperatures, Main Development Region, and global average temperature explain the observations best. The most extreme events are especially sensitive to temperature changes, and we estimate a doubling of Katrina magnitude events associated with the warming over the 20th century. The increased risk depends on the spatial distribution of the temperature rise with highest sensitivity from tropical Atlantic, Central America, and the Indian Ocean. Statistically downscaling 21st century warming patterns from six climate models results in a twofold to sevenfold increase in the frequency of Katrina magnitude events for a 1 °C rise in global temperature (using BNU-ESM, BCC-CSM-1.1, CanESM2, HadGEM2-ES, INM-CM4, and NorESM1-M).
Met synergizes with p53 loss to induce mammary tumors that possess features of claudin-low breast cancer
Authors: Knight Jennifer F. , Lesurf Robert , Zhao Hong , Pinnaduwage Dushanthi , Davis Ryan R. , Saleh Sadiq M. I. , Zuo Dongmei , Naujokas Monica A. , Chughtai Naila , Herschkowitz Jason I. , Prat Aleix , Mulligan Anna Marie , Muller William J. , Cardiff Robert D. , Gregg Jeff P. , Andrulis Irene L. , Hallett Michael T. , Park Morag
Published: March 2013

Significance

Triple-negative breast cancers lack targeted therapies and are subdivided into molecular subtypes, including basal and claudin-low. Preclinical models representing these subtypes are limited. We have developed a murine model in which mammary gland expression of a receptor tyrosine kinase (MET) and loss of tumor suppressor gene p53 (
Trp53
), synergize to promote tumors with pathological and molecular features of claudin-low breast cancer. These tumors require MET signaling for proliferation, as well as mesenchymal characteristics, which are key features of claudin-low biology. This work associates MET expression and p53 loss with claudin-low breast cancers and highly proliferative breast cancers of poor outcome.
Predicting free choices for abstract intentions
Authors: Soon Chun Siong , He Anna Hanxi , Bode Stefan , Haynes John-Dylan
Published: March 2013

Unconscious neural activity has been repeatedly shown to precede and potentially even influence subsequent free decisions. However, to date, such findings have been mostly restricted to simple motor choices, and despite considerable debate, there is no evidence that the outcome of more complex free decisions can be predicted from prior brain signals. Here, we show that the outcome of a free decision to either add or subtract numbers can already be decoded from neural activity in medial prefrontal and parietal cortex 4 s before the participant reports they are consciously making their choice. These choice-predictive signals co-occurred with the so-called default mode brain activity pattern that was still dominant at the time when the choice-predictive signals occurred. Our results suggest that unconscious preparation of free choices is not restricted to motor preparation. Instead, decisions at multiple scales of abstraction evolve from the dynamics of preceding brain activity.
Toward a unified physical model of nucleosome patterns flanking transcription start sites
Authors: Möbius Wolfram , Osberg Brendan , Tsankov Alexander M. , Rando Oliver J. , Gerland Ulrich
Published: March 2013

Recent genome-wide maps of nucleosome positions in different eukaryotes revealed patterns around transcription start sites featuring a nucleosome-free region flanked by a periodic modulation of the nucleosome density. For
Saccharomyces cerevisiae
, the average in vivo pattern was previously shown to be quantitatively described by a “nucleosome gas” model based on the statistical positioning mechanism. However, this simple physical description is challenged by the fact that the pattern differs quantitatively between species and by recent experiments that appear incompatible with statistical positioning, indicating important roles for chromatin remodelers. We undertake a data-driven search for a unified physical model to describe the nucleosome patterns of 12 yeast species and also consider an extension of the model to capture remodeling effects. We are led to a nucleosome gas that takes into account nucleosome breathing, i.e., transient unwrapping of nucleosomal DNA segments. This known biophysical property of nucleosomes rationalizes a “pressure”-induced dependence of the effective nucleosome size that is suggested by the data. By fitting this model to the data, we find an average energy cost for DNA unwrapping consistent with previous biophysical experiments. Although the available data are not sufficient to reconstruct chromatin remodeling mechanisms, a minimal model extension by one mechanism yields an “active nucleosome gas” that can rationalize the behavior of systems with reduced histone–DNA ratio and remodeler knockouts. We therefore establish a basis for a physical description of nucleosome patterns that can serve as a null model for sequence-specific effects at individual genes and in models of transcription regulation.
KIAA1199, a deafness gene of unknown function, is a new hyaluronan binding protein involved in hyaluronan depolymerization
Authors: Yoshida Hiroyuki , Nagaoka Aya , Kusaka-Kikushima Ayumi , Tobiishi Megumi , Kawabata Keigo , Sayo Tetsuya , Sakai Shingo , Sugiyama Yoshinori , Enomoto Hiroyuki , Okada Yasunori , Inoue Shintaro
Published: March 2013

Hyaluronan (HA) has an extraordinarily high turnover in physiological tissues, and HA degradation is accelerated in inflammatory and neoplastic diseases. CD44 (a cell surface receptor) and two hyaluronidases (HYAL1 and HYAL2) are thought to be responsible for HA binding and degradation; however, the role of these molecules in HA catabolism remains controversial. Here we show that KIAA1199, a deafness gene of unknown function, plays a central role in HA binding and depolymerization that is independent of CD44 and HYAL enzymes. The specific binding of KIAA1199 to HA was demonstrated in glycosaminoglycan-binding assays. We found that knockdown of KIAA1199 abolished HA degradation by human skin fibroblasts and that transfection of KIAA1199 cDNA into cells conferred the ability to catabolize HA in an endo-β-
N
-acetylglucosaminidase–dependent manner via the clathrin-coated pit pathway. Enhanced degradation of HA in synovial fibroblasts from patients with osteoarthritis or rheumatoid arthritis was correlated with increased levels of KIAA1199 expression and was abrogated by knockdown of KIAA1199. The level of KIAA1199 expression in uninflamed synovium was less than in osteoarthritic or rheumatoid synovium. These data suggest that KIAA1199 is a unique hyaladherin with a key role in HA catabolism in the dermis of the skin and arthritic synovium.
Dedicated olfactory neurons mediating attraction behavior to ammonia and amines in
Drosophila
Authors: Min Soohong , Ai Minrong , Shin Seul A , Suh Greg S. B.
Published: March 2013

Animals across various phyla exhibit odor-evoked innate attraction behavior that is developmentally programmed. The mechanism underlying such behavior remains unclear because the odorants that elicit robust attraction responses and the neuronal circuits that mediate this behavior have not been identified. Here, we describe a functionally segregated population of olfactory sensory neurons (OSNs) and projection neurons (PNs) in
Drosophila melanogaster
that are highly specific to ammonia and amines, which act as potent attractants. The OSNs express IR92a, a member of the chemosensory ionotropic receptor (IR) family and project to a pair of glomeruli in the antennal lobe, termed VM1. In vivo calcium-imaging experiments showed that the OSNs and PNs innervating VM1 were activated by ammonia and amines but not by nonamine odorants. Flies in which the IR92a
+
neurons or
IR92a
gene was inactivated had impaired amine-evoked physiological and behavioral responses. Tracing neuronal pathways to higher brain centers showed that VM1-PN axonal projections within the lateral horn are topographically segregated from those of V-PN and DC4-PN, which mediate innate avoidance behavior to carbon dioxide and acidity, respectively, suggesting that these sensory stimuli of opposing valence are represented in spatially distinct neuroanatomic loci within the lateral horn. These experiments identified the neurons and their cognate receptor for amine detection, and mapped amine attractive olfactory inputs to higher brain centers. This labeled-line mode of amine coding appears to be hardwired to attraction behavior.
Paleolithic human exploitation of plant foods during the last glacial maximum in North China
Authors: Liu Li , Bestel Sheahan , Shi Jinming , Song Yanhua , Chen Xingcan
Published: March 2013

Three grinding stones from Shizitan Locality 14 (
ca.
23,000–19,500 calendar years before present) in the middle Yellow River region were subjected to usewear and residue analyses to investigate human adaptation during the last glacial maximum (LGM) period, when resources were generally scarce and plant foods may have become increasingly important in the human diet. The results show that these tools were used to process various plants, including Triticeae and Paniceae grasses,
Vigna
beans,
Dioscorea opposita
yam, and
Trichosanthes kirilowii
snakegourd roots. Tubers were important food resources for Paleolithic hunter–gatherers, and Paniceae grasses were exploited about 12,000 y before their domestication. The long tradition of intensive exploitation of certain types of flora helped Paleolithic people understand the properties of these plants, including their medicinal uses, and eventually led to the plants' domestication. This study sheds light on the deep history of the broad spectrum subsistence strategy characteristic of late Pleistocene north China before the origins of agriculture in this region.
Defects in IRE1 enhance cell death and fail to degrade mRNAs encoding secretory pathway proteins in the
Arabidopsis
unfolded protein response
Authors: Mishiba Kei-ichiro , Nagashima Yukihiro , Suzuki Eiji , Hayashi Noriko , Ogata Yoshiyuki , Shimada Yukihisa , Koizumi Nozomu
Published: March 2013

The unfolded protein response (UPR) is a cellular response highly conserved in eukaryotes to obviate accumulation of misfolded proteins in the endoplasmic reticulum (ER). Inositol-requiring enzyme 1 (IRE1) catalyzes the cytoplasmic splicing of mRNA encoding bZIP transcription factors to activate the UPR signaling pathway.
Arabidopsis
IRE1 was recently shown to be involved in the cytoplasmic splicing of
bZIP60
mRNA. In the present study, we demonstrated that an
Arabidopsis
mutant with defects in two
IRE1
paralogs showed enhanced cell death upon ER stress compared with a mutant with defects in
bZIP60
and wild type, suggesting an alternative function of IRE1 in the UPR. Analysis of our previous microarray data and subsequent quantitative PCR indicated degradation of mRNAs encoding secretory pathway proteins by tunicamycin, DTT, and heat in an
IRE1
-dependent manner. The degradation of mRNAs localized to the ER during the UPR was considered analogous to a molecular mechanism referred to as the regulated IRE1-dependent decay of mRNAs reported in metazoans. Another microarray analysis conducted in the condition repressing transcription with actinomycin D and a subsequent Gene Set Enrichment Analysis revealed the regulated IRE1-dependent decay of mRNAs-mediated degradation of a significant portion of mRNAs encoding the secretory pathway proteins. In the mutant with defects in IRE1, genes involved in the cytosolic protein response such as heat shock factor A2 were up-regulated by tunicamycin, indicating the connection between the UPR and the cytosolic protein response.
Transient protonation changes in channelrhodopsin-2 and their relevance to channel gating
Authors: Lórenz-Fonfría Víctor A. , Resler Tom , Krause Nils , Nack Melanie , Gossing Michael , Fischer von Mollard Gabriele , Bamann Christian , Bamberg Ernst , Schlesinger Ramona , Heberle Joachim
Published: March 2013

Significance

It was always a dream to control cells and living animals by light. Discovery of channelrhodopsin turned the dream into reality because this light-activated cation channel is able to elicit action potentials with unprecedented spatial and temporal resolution. To unravel the underlying molecular mechanism, we have applied time-resolved IR spectroscopy, and we suggest how the observed proton transfer and the protein conformational changes lead to opening of the cation channel. Our results will not only contribute to the rational design of channelrhodopsin variants with improved properties, but also help to decipher the temporal sequence in the gating of ion channels.
Bacterial flagella explore microscale hummocks and hollows to increase adhesion
Authors: Friedlander Ronn S. , Vlamakis Hera , Kim Philseok , Khan Mughees , Kolter Roberto , Aizenberg Joanna
Published: March 2013

Biofilms, surface-bound communities of microbes, are economically and medically important due to their pathogenic and obstructive properties. Among the numerous strategies to prevent bacterial adhesion and subsequent biofilm formation, surface topography was recently proposed as a highly nonspecific method that does not rely on small-molecule antibacterial compounds, which promote resistance. Here, we provide a detailed investigation of how the introduction of submicrometer crevices to a surface affects attachment of
Escherichia coli
. These crevices reduce substrate surface area available to the cell body but increase overall surface area. We have found that, during the first 2 h, adhesion to topographic surfaces is significantly reduced compared with flat controls, but this behavior abruptly reverses to significantly increased adhesion at longer exposures. We show that this reversal coincides with bacterially induced wetting transitions and that flagellar filaments aid in adhesion to these wetted topographic surfaces. We demonstrate that flagella are able to reach into crevices, access additional surface area, and produce a dense, fibrous network. Mutants lacking flagella show comparatively reduced adhesion. By varying substrate crevice sizes, we determine the conditions under which having flagella is most advantageous for adhesion. These findings strongly indicate that, in addition to their role in swimming motility, flagella are involved in attachment and can furthermore act as structural elements, enabling bacteria to overcome unfavorable surface topographies. This work contributes insights for the future design of antifouling surfaces and for improved understanding of bacterial behavior in native, structured environments.
Additional pathway to translate the downstream
ndhK
cistron in partially overlapping
ndhC-ndhK
mRNAs in chloroplasts
Authors: Yukawa Maki , Sugiura Masahiro
Published: March 2013

The chloroplast
NAD(P)H dehydrogenase
(
NDH
)
C
(
ndhC
) and
ndhK
genes partially overlap and are cotranscribed in many plants. We previously reported that the tobacco
ndhC/K
genes are translationally coupled but produce NdhC and NdhK, subunits of the NDH complex, in similar amounts. Generally, translation of the downstream cistron in overlapping mRNAs is very low. Hence, these findings suggested that the
ndhK
cistron is translated not only from the
ndhC
5′UTR but also by an additional pathway. Using an in vitro translation system from tobacco chloroplasts, we report here that free ribosomes enter, with formylmethionyl-tRNA
fMet
, at an internal AUG start codon that is located in frame in the middle of the upstream
ndhC
cistron, translate the 3′ half of the
ndhC
cistron, reach the
ndhK
start codon, and that, at that point, some ribosomes resume
ndhK
translation. We detected a peptide corresponding to a 57-amino-acid product encoded by the sequence from the internal AUG to the
ndhC
stop codon. We propose a model in which the internal initiation site AUG is not designed for synthesizing a functional isoform but for delivering additional ribosomes to the
ndhK
cistron to produce NdhK in the amount required for the assembly of the NDH complex. This pathway is a unique type of translation to produce protein in the needed amount with the cost of peptide synthesis.
A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy
Authors: Jao Christine C. , Ragusa Michael J. , Stanley Robin E. , Hurley James H.
Published: March 2013

Autophagy-related 13 (Atg13) is a key early-acting factor in autophagy and the major locus for nutrient-dependent regulation of autophagy by Tor. The 2.3-Å resolution crystal structure of the N-terminal domain of Atg13 reveals a previously unidentified HORMA (Hop1p, Rev1p and Mad2) domain similar to that of the spindle checkpoint protein Mad2. Mad2 has two different stable conformations, O-Mad2 and C-Mad2, and the Atg13 HORMA structure corresponds to the C-Mad2 state. The Atg13 HORMA domain is required for autophagy and for recruitment of the phosphatidylinositol (PI) 3-kinase subunit Atg14 but is not required for Atg1 interaction or Atg13 recruitment to the preautophagosomal structure. The Atg13 HORMA structure reveals a pair of conserved Arg residues that constitute a putative phosphate sensor. One of the Arg residues is in the region corresponding to the “safety belt” conformational switch of Mad2, suggesting conformational regulation of phosphate binding. These two Arg residues are essential for autophagy, suggesting that the Atg13 HORMA domain could function as a phosphoregulated conformational switch.
Catalytic DNA with phosphatase activity
Authors: Chandrasekar Jagadeeswaran , Silverman Scott K.
Published: March 2013

Catalytic DNA sequences (deoxyribozymes, DNA enzymes, or DNAzymes) have been identified by in vitro selection for various catalytic activities. Expanding the limits of DNA catalysis is an important fundamental objective and may facilitate practical utility of catalysts that can be obtained from entirely unbiased (random) sequence populations. In this study, we show that DNA can catalyze Zn
2+
-dependent phosphomonoester hydrolysis of tyrosine and serine side chains (i.e., exhibit phosphatase activity). The best deoxyribozyme decreases the half-life for phosphoserine hydrolysis from as high as >10
10
y to <1 h. The phosphatase activity also occurs with nonpeptidic substrates but with reduced efficiency, indicating a preference for phosphopeptides. The newly identified deoxyribozymes can function with multiple turnover using free peptide substrates, have activity in the presence of human cell lysate or BSA, and catalyze dephosphorylation of a larger protein substrate, suggesting broader application of DNA catalysts as artificial phosphatases.
Cerebral hypoperfusion in multiple sclerosis is reversible and mediated by endothelin-1
Authors: D’haeseleer Miguel , Beelen Roel , Fierens Yves , Cambron Melissa , Vanbinst Anne-Marie , Verborgh Christian , Demey Johan , De Keyser Jacques
Published: March 2013

Decreased cerebral blood flow (CBF) may contribute to the pathology of multiple sclerosis (MS), but the underlying mechanism is unknown. We investigated whether the potent vasoconstrictor endothelin-1 (ET-1) is involved. We found that, compared with controls, plasma ET-1 levels in patients with MS were significantly elevated in blood drawn from the internal jugular vein and a peripheral vein. The jugular vein/peripheral vein ratio was 1.4 in patients with MS vs. 1.1 in control subjects, suggesting that, in MS, ET-1 is released from the brain to the cerebral circulation. Next, we performed ET-1 immunohistochemistry on postmortem white matter brain samples and found that the likely source of ET-1 release are reactive astrocytes in MS plaques. We then used arterial spin-labeling MRI to noninvasively measure CBF and assess the effect of the administration of the ET-1 antagonist bosentan. CBF was significantly lower in patients with MS than in control subjects and increased to control values after bosentan administration. These data demonstrate that reduced CBF in MS is mediated by ET-1, which is likely released in the cerebral circulation from reactive astrocytes in plaques. Restoring CBF by interfering with the ET-1 system warrants further investigation as a potential new therapeutic target for MS.
Stacking nonenzymatic circuits for high signal gain
Authors: Chen Xi , Briggs Neima , McLain Jeremy R. , Ellington Andrew D.
Published: March 2013

Signal amplification schemes that do not rely on protein enzymes show great potential in areas as abstruse as DNA computation and as applied as point-of-care molecular diagnostics. Toehold-mediated strand displacement, a programmable form of dynamic DNA hybridization, can be used to design powerful amplification cascades that can achieve polynomial or exponential amplification of input signals. However, experimental implementation of such amplification cascades has been severely hindered by circuit leakage due to catalyst-independent side reactions. In this study, we systematically analyzed the origins, characteristics, and outcomes of circuit leakage in amplification cascades and devised unique methods to obtain high-quality DNA circuits that exhibit minimal leakage. We successfully implemented a two-layer cascade that yielded 7,000-fold signal amplification and a two-stage, four-layer cascade that yielded upward of 600,000-fold signal amplification. Implementation of these unique methods and design principles should greatly empower molecular programming in general and DNA-based molecular diagnostics in particular.
Cortical response tracking the conscious experience of threshold duration visual stimuli indicates visual perception is all or none
Authors: Sekar Krithiga , Findley William M. , Poeppel David , Llinás Rodolfo R.
Published: March 2013

At perceptual threshold, some stimuli are available for conscious access whereas others are not. Such threshold inputs are useful tools for investigating the events that separate conscious awareness from unconscious stimulus processing. Here, viewing unmasked, threshold-duration images was combined with recording magnetoencephalography to quantify differences among perceptual states, ranging from no awareness to ambiguity to robust perception. A four-choice scale was used to assess awareness: “didn’t see” (no awareness), “couldn’t identify” (awareness without identification), “unsure” (awareness with low certainty identification), and “sure” (awareness with high certainty identification). Stimulus-evoked neuromagnetic signals were grouped according to behavioral response choices. Three main cortical responses were elicited. The earliest response, peaking at ∼100 ms after stimulus presentation, showed no significant correlation with stimulus perception. A late response (∼290 ms) showed moderate correlation with stimulus awareness but could not adequately differentiate conscious access from its absence. By contrast, an intermediate response peaking at ∼240 ms was observed only for trials in which stimuli were consciously detected. That this signal was similar for all conditions in which awareness was reported is consistent with the hypothesis that conscious visual access is relatively sharply demarcated.
Schrödinger equation revisited
Authors: Schleich Wolfgang P. , Greenberger Daniel M. , Kobe Donald H. , Scully Marlan O.
Published: March 2013

The time-dependent Schrödinger equation is a cornerstone of quantum physics and governs all phenomena of the microscopic world. However, despite its importance, its origin is still not widely appreciated and properly understood. We obtain the Schrödinger equation from a mathematical identity by a slight generalization of the formulation of classical statistical mechanics based on the Hamilton–Jacobi equation. This approach brings out most clearly the fact that the linearity of quantum mechanics is intimately connected to the strong coupling between the amplitude and phase of a quantum wave.
Molecular chaperone Hsp110 rescues a vesicle transport defect produced by an ALS-associated mutant SOD1 protein in squid axoplasm
Authors: Song Yuyu , Nagy Maria , Ni Weiming , Tyagi Navneet K. , Fenton Wayne A. , López-Giráldez Francesc , Overton John D. , Horwich Arthur L. , Brady Scott T.
Published: March 2013

Mutant human Cu/Zn superoxide dismutase 1 (SOD1) is associated with motor neuron toxicity and death in an inherited form of amyotrophic lateral sclerosis (ALS; Lou Gehrig disease). One aspect of toxicity in motor neurons involves diminished fast axonal transport, observed both in transgenic mice and, more recently, in axoplasm isolated from squid giant axons. The latter effect appears to be directly mediated by misfolded SOD1, whose addition activates phosphorylation of p38 MAPK and phosphorylation of kinesin. Here, we observe that several different oligomeric states of a fusion protein, comprising ALS-associated human G85R SOD1 joined with yellow fluorescent protein (G85R SOD1YFP), which produces ALS in transgenic mice, inhibited anterograde transport when added to squid axoplasm. Inhibition was blocked both by an apoptosis signal-regulating kinase 1 (ASK1; MAPKKK) inhibitor and by a p38 inhibitor, indicating the transport defect is mediated through the MAPK cascade. In further incubations, we observed that addition of the mammalian molecular chaperone Hsc70, abundantly associated with G85R SOD1YFP in spinal cord of transgenic mice, exerted partial correction of the transport defect, associated with diminished phosphorylation of p38. Most striking, the addition of the molecular chaperone Hsp110, in a concentration substoichiometric to the mutant SOD1 protein, completely rescued both the transport defect and the phosphorylation of p38. Hsp110 has been demonstrated to act as a nucleotide exchange factor for Hsc70 and, more recently, to be able to cooperate with it to mediate protein disaggregation. We speculate that it can cooperate with endogenous squid Hsp(c)70 to mediate binding and/or disaggregation of mutant SOD1 protein, abrogating toxicity.
Channel Catfish Hatchery Production Efficiency Using a Vertical-Lift Incubator (the See-Saw) at Various Egg Loading Rates
Authors: Torrans Les , Ott Brian , Jones Robert “Shorty” , Jones Robert
Published: March 2013

Channel Catfish Ictalurus punctatus spawns are typically incubated in 0.25-in-mesh baskets suspended in water that is agitated with paddles positioned between the baskets. We previously tested a vertical-lift incubator (the “See-Saw”) using Channel Catfish spawns. When loaded with spawns at rates higher than recommended for traditional paddle-type incubators, as often occurs during the peak of the spawning season, survival to the swim-up stage was significantly (2.3 times) higher with the See-Saw than with traditional incubators. This project examined the effect of spawn loading rate and added oxygen on fry production with the See-Saw. In study 1, See-Saws were loaded with 15.0 ± 0.1 lb (mean ± SE; 219,825 eggs), 30.1 ± 0.1 lb (446,055 eggs), 45.1 ± 0.1 lb (668,206 eggs), or 60.1 ± 0.1 lb (891,157 eggs) of spawns per trough. Water flow averaged 2.1 gal/min—roughly 40% of the rate recommended for paddle-type incubators. Swim-up fry production increased in proportion to egg loading density up to 45 lb/trough, with the 15-, 30-, and 45-lb loading rate treatments producing 132,658, 263,828, and 429,422 swim-up fry, respectively. However, the 60-lb treatment produced only 417,237 swim-up fry. Survival to the swim-up stage in the 15-, 30-, and 45-lb treatments averaged 60 ± 9, 59 ± 6, and 64 ± 4%, respectively, but survival to swim-up in the 60-lb treatment averaged only 46 ± 8%. In study 2, the addition of purified oxygen to See-Saw incubators loaded with 36 spawns/trough (∼45 lb/trough) increased the DO concentration by 4.0 ppm (to 125% air saturation) but had no effect on survival to swim-up. The See-Saw incubator can effectively incubate up to 45 lb of spawns (670,000 eggs)—up to three times as many eggs as traditional paddle-type incubators—while using less than half the water; thus, the See-Saw incubator can provide significant savings in space, water, and energy use.
Decreased Hatchery Rearing Density Improves Poststocking Harvest and Return to Spawning of Landlocked Fall Chinook Salmon
Authors: Barnes Michael E , Wipf Matthew M , Domenici Nola R , Kummer Wendy M , Hanten Robert P
Published: March 2013

Juvenile landlocked fall Chinook Salmon Oncorhynchus tshawytscha were coded-wire-tagged and reared in 1.8-m-diameter circular tanks at a low or high density for up to 52 d prior to stocking in Lake Oahe, South Dakota, during late May of 1999, 2003, and 2004. Final hatchery rearing densities ranged from 7.29 to 11.72 kg/m3 for the low-density tanks and from 15.02 to 25.22 kg/m3 for the high-density tanks, with the higher densities being at least double the lower densities in each year. Flows were adjusted to maintain similar loadings (kg·L−1·min−1) between the treatments each year. The fish used in this study came from spawns collected during the October prior to stocking; TL at the end of hatchery rearing ranged from 103 mm in 1999 to 124 mm in 2004. In each year-class, the percentage of fish that were harvested by anglers or that returned to spawn was significantly greater for the lower-density treatment than for the higher-density treatment. Angler harvest primarily consisted of age-3 fish, with a small number of age-4 fish harvested as well. Feed conversion ratios were significantly improved in the lower-density tanks relative to the higher-density tanks in 1999 and 2003, and fish from the lower-density tanks were also significantly longer just prior to stocking in 1999 and heavier prior to stocking in 2003. To maximize poststocking survival for landlocked fall Chinook Salmon, lower rearing densities are recommended.
Veii
Authors: Nagy Helen
Published: March 2013

The ancient city of Veii (in Italian, Veio) lies seventeen kilometers northwest of Rome and occupies a plateau of approximately 350 hectares, bounded by the rivers Valchetta (ancient Cremera) on the north and east and Piodoro on the west and south. The city had ample water and was naturally defensible, but sections of tufa walls remain, indicating that it was also fortified. Several major roads crossed the city and led toward other centers, such as Rome, Cerveteri, Tarquinia, Vulci, and Capena, via fortified gates. Impressive Etruscan-made drainage tunnels (cuniculi) flank and traverse the plateau. There is sporadic evidence of late Bronze Age settlements in the area, but it was during the Villanovan period, 9th and 8th centuries bce, that villages appeared on the plateau and on the citadel of Piazza d’Armi. A significant growth in population during the late 8th and 7th centuries bce resulted in urbanization. The strength and wealth of the city reached their peak in the 6th century bce, but by the late 5th century bce, conflicts with Rome weakened Veii, and it was finally taken after a ten-year siege in 396 bce by M. Fulvius Camillus. The triumph was sealed by the transfer of the principal cult of Juno Regina to Rome. Although Veii declined sharply after the Roman victory, some of the old popular sanctuaries continued to be frequented by the local population. In 2 bce the status of municipium was conferred on Veii by Augustus. By this time the city was falling into decay, although a small part of the Etruscan site continued to be inhabited, as evidenced by architectural fragments, sculptures (including one of Tiberius now in the Vatican Museum), and inscriptions. Once considered the richest city of the Etruscan League, Veii declined and was abandoned by the end of the 4th century ce. The plateau today is covered by fields, trees, and remnants of ancient structures. Principal among these is the archaeological site of the extra-urban Portonaccio Sanctuary. Etruscan necropolises and a few Roman tombs surround the city. Archaeological surveys continue to yield results such as the 2006 discovery of the early-7th-century Tomb of the Roaring Lions in the Grotta Gramiccia necropolis. In 1997, the Regional National Park of Veii (37,030 acres) was established to ensure the protection of the ancient city and its surroundings from the ravages of urban sprawl and illegal construction.