bluuebunny/crossref_metadata_2025 huggingface dataset:
Ballistic phonon transport in ultra-thin silicon layers: Effects of confinement and orientation
Authors: Karamitaheri Hossein , Neophytou Neophytos , Kosina Hans
Published: June 2013

We investigate the effect of confinement and orientation on the phonon transport properties of ultra-thin silicon layers of thicknesses between 1 nm and 16 nm. We employ the modified valence force field method to model the lattice dynamics and the ballistic Landauer transport formalism to calculate the thermal conductance. We consider the major thin layer surface orientations {100}, {110}, {111}, and {112}. For every surface orientation, we study thermal conductance as a function of the transport direction within the corresponding surface plane. We find that the ballistic thermal conductance in the thin layers is anisotropic, with the {110}/⟨110⟩ channels exhibiting the highest and the {112}/⟨111⟩ channels the lowest thermal conductance with a ratio of about two. We find that in the case of the {110} and {112} surfaces, different transport orientations can result in ∼50% anisotropy in thermal conductance. The thermal conductance of different transport orientations in the {100} and {111} layers, on the other hand, is mostly isotropic. These observations are invariant under different temperatures and layer thicknesses. We show that this behavior originates from the differences in the phonon group velocities, whereas the phonon density of states is very similar for all the thin layers examined. We finally show how the phonon velocities can be understood from the phonon spectrum of each channel. Our findings could be useful in the design of the thermal properties of ultra-thin Si layers for thermoelectric and thermal management applications.
Carrier capture dynamics of single InGaAs/GaAs quantum-dot layers
Authors: Chauhan K. N. , Riffe D. M. , Everett E. A. , Kim D. J. , Yang H. , Shen F. K.
Published: June 2013

Using 800 nm, 25-fs pulses from a mode locked Ti:Al2O3 laser, we have measured the ultrafast optical reflectivity of MBE-grown, single-layer In0.4Ga0.6As/GaAs quantum-dot (QD) samples. The QDs are formed via two-stage Stranski-Krastanov growth: following initial InGaAs deposition at a relatively low temperature, self assembly of the QDs occurs during a subsequent higher temperature anneal. The capture times for free carriers excited in the surrounding GaAs (barrier layer) are as short as 140 fs, indicating capture efficiencies for the InGaAs quantum layer approaching 1. The capture rates are positively correlated with initial InGaAs thickness and annealing temperature. With increasing excited carrier density, the capture rate decreases; this slowing of the dynamics is attributed to Pauli state blocking within the InGaAs quantum layer.
Negative differential resistance induced by thermalization of two-dimensional electrons in terahertz quantum-well photodetectors
Authors: Guo X. G. , Gu L. L. , Dong M. , Cao J. C. , Liu H. C. , Guo F. M.
Published: June 2013

Negative differential resistance (NDR) behavior existing in dark current-voltage (IV) curves of terahertz quantum-well photodetectors (QWPs) is theoretically investigated. Due to electron-electron scattering, the localized two-dimensional (2D) electrons in terahertz QWPs are thermalized. In steady state, the effective temperature of the 2D electrons is found to be higher than that of lattice. A self-consistent model is used to simulate the dark IV curves of terahertz QWPs, taking into account the thermalization effect of the 2D electrons. The NDR behavior is qualitatively reproduced. The periodic structures of electric-field domain and 2D electron occupation are formed in the NDR regime. The improved self-consistent model is useful for further understanding of the electron transport properties and improving the performance of terahertz QWPs.
Benchmarking current density in staggered gap In0.53Ga0.47As/GaAs0.5Sb0.5 heterojunction Esaki tunnel diodes
Authors: Romanczyk B. , Thomas P. , Pawlik D. , Rommel S. L. , Loh W.-Y. , Wong M. H. , Majumdar K. , Wang W.-E. , Kirsch P. D.
Published: June 2013

The impact of dopant concentration on the current densities of In0.53Ga0.47As/GaAs0.5Sb0.5 heterojunction Esaki tunnel diodes is investigated. Increased doping density results in increased peak and Zener current densities. Two different structures were fabricated demonstrating peak current densities of 92 kA/cm2 and 572 kA/cm2, Zener current densities of 994 kA/cm2 and 5.1 MA/cm2 at a −0.5 V bias, and peak-to-valley current ratios of 6.0 and 5.4, respectively. The peak current scaled linearly with area down to a 70 nm diameter. The peak current densities were benchmarked against Esaki diodes from other material systems based on doping density and tunnel barrier height.
Surface plasmon enhanced light emission from AlGaN-based ultraviolet light-emitting diodes grown on Si (111)
Authors: Cho Chu-Young , Zhang Yinjun , Cicek Erdem , Rahnema Benjamin , Bai Yanbo , McClintock Ryan , Razeghi Manijeh
Published: June 2013

We report on the development of surface plasmon (SP) enhanced AlGaN-based multiple quantum wells (MQWs) ultraviolet (UV) light-emitting diodes (LEDs) grown on silicon (111) substrates. In order to generate SP-coupling with the radiating dipoles in MQWs, an aluminum layer is selectively deposited in holes etched in the top p-AlGaN to p-GaN layers. After flip-chip bonding and substrate removal, an optical output power of ∼1.2 mW is achieved at an emission wavelength of 346 nm; the output power of these UV LEDs with Al layer is increased by 45% compared to that of conventional UV LEDs without Al layer. This enhancement can be attributed to an increase in the spontaneous emission rate and improved internal quantum efficiency via resonance coupling between excitons in MQWs and SPs in the aluminum layer.
Giant intrinsic thermomagnetic effects in thin MgO magnetic tunnel junctions
Authors: Teixeira J. M. , Costa J. D. , Ventura J. , Fernandez-Garcia M. P. , Azevedo J. , Araujo J. P. , Sousa J. B. , Wisniowski P. , Cardoso S. , Freitas P. P.
Published: June 2013

An intrinsic spin-dependent Seebeck effect in the linear tunneling transport regime of magnetic tunneling junctions (MTJs) was discovered recently. This effect leads to a nonlinear correction of Ohm's law in the dc response. We analyze this intrinsic magneto-thermoelectrical effect for MTJs with different MgO barrier (tb=0.7−1.35 nm) thicknesses. We report strong intrinsic effects in MTJs with thin MgO barriers (1189%), upon reversal of the magnetization of the two CoFeB layers. Such large effects are promising for useful spin caloritronic devices, integrating charge, heat, and spin tunnel transport.
Space-station experiment measures arriving positrons with unprecedented precision
Authors: Blau Steven K.
Published: June 2013

The excess positrons above those produced by cosmic-ray collisions may result from dark-matter annihilation or from extreme astrophysical environments.
National Ignition Facility faces an uncertain future
Authors: Kramer David
Published: June 2013

As its budget declines, Lawrence Livermore’s $3.5 billion laser fusion facility is refocusing on experiments in support of nuclear weapons science.
An undergraduate alliance comes of age
Authors: Feller Steve , Sauncy Toni
Published: June 2013

Together, Sigma Pi Sigma and the Society of Physics Students establish a vital link between the physicists of tomorrow and those of today and yesterday.
Selective Kv1.3 channel blocker as therapeutic for obesity and insulin resistance
Authors: Upadhyay Sanjeev Kumar , Eckel-Mahan Kristin L. , Mirbolooki M. Reza , Tjong Indra , Griffey Stephen M. , Schmunk Galina , Koehne Amanda , Halbout Briac , Iadonato Shawn , Pedersen Brian , Borrelli Emiliana , Wang Ping H. , Mukherjee Jogeshwar , Sassone-Corsi Paolo , Chandy K. George
Published: June 2013

Significance

Obesity is a global epidemic in need of novel and safe therapeutics. We show that ShK-186, a selective blocker of the Kv1.3 potassium channel, has powerful antiobesity effects in a mouse model of diet-induced obesity. ShK-186 increases energy expenditure by activating brown adipose tissue, causes profound changes in liver metabolism and reduces obesity-induced inflammation of white adipose tissue. Our studies highlight the potential use of selective Kv1.3 blockers in the treatment of obesity and insulin resistance.
Simulating the pulling of stalled elongated peptide from the ribosome by the translocon
Authors: Rychkova Anna , Mukherjee Shayantani , Bora Ram Prasad , Warshel Arieh
Published: June 2013

The nature of the coupling between the stalling of the elongated nascent peptide chain in the ribosome and its insertion through the translocon is analyzed, focusing on the recently discovered biphasic force that overcomes the stalling barrier. The origin of this long-range coupling is explored by coarse-grained simulations that combine the translocon (TR) insertion profile and the effective chemical barrier for the extension of the nascent chain in the ribosome. Our simulation determined that the inserted H segment is unlikely to climb the TR barrier in parallel with the peptide synthesis chemical step and that the nascent chain should first overcome the chemical barriers and move into the ribosome–TR gap region before the insertion into the TR tunnel. Furthermore, the simulations indicate that the coupled TR-chemistry free energy profile accounts for the biphasic force. Apparently, although the overall elongation/insertion process can be depicted as a tug-of-war between the forces of the TR and the ribosome, it is actually a reflection of the combined free-energy landscape. Most importantly, the present study helps to relate the experimental observation of the biphasic force to crucial information about the elusive path and barriers of the TR insertion process.
Colonization of Steelhead in a Natal Stream after Barrier Removal
Authors: Weigel Dana E. , Connolly Patrick J. , Martens Kyle D. , Powell Madison S.
Published: June 2013

Colonization of vacant habitats is an important process for supporting the long‐term persistence of populations and species. We used a before–after experimental design to follow the process of colonization by steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) at six monitoring sites in a natal stream, Beaver Creek, after the modification or removal of numerous stream passage barriers. Juvenile O. mykiss were collected at monitoring sites by using a backpack electrofisher. Passive integrated transponder tags and instream tag reading stations were used in combination with 16 microsatellite markers to determine the source, extent, and success of migrant O. mykiss after implementation of the barrier removal projects. Steelhead migrated into the study area during the first spawning season after passage was established. Hatchery steelhead, although comprising more than 80% of the adult returns to the Methow River basin, constituted a small proportion (23%) of the adult O. mykiss colonizing the study area. Adult steelhead and fluvial Rainbow Trout entered the stream during the first spawning season after barrier removal and were passing the uppermost tag reader (12 km upstream from the mouth) 3–4 years later. Parr that were tagged in Beaver Creek returned as adults, indicating establishment of the anadromous life history in the study area. Population genetic measures at the lower two monitoring sites (lower 4 km of Beaver Creek) significantly changed within one generation (4–5 years). Colonization and expansion of steelhead occurred more slowly than expected due to the low number of adults migrating into the study area.
Efficacy of Spray Administration of Formalin-Killed Streptococcus agalactiae in Hybrid Red Tilapia
Authors: Noraini O. , Sabri M. Y. , Siti-Zahrah A.
Published: June 2013

An initial evaluation of spray vaccination was carried out with 60 hybrid Red Tilapia Oreochromis spp., divided into three groups that consisted of 10 fish per group with duplicates. The formalin-killed cells (FKCs) of Streptococcus agalactiae were administered once to group 1 by spray and once daily for five consecutive days to group 2. Group 3 remained as the untreated control group and was sprayed with normal saline. A booster was given twice to all the groups, once at the second week and again at the fourth week after the first vaccination. After this initial evaluation, a challenge study was conducted with 40 tilapia divided into two groups that consisted of 10 fish per group with duplicates. Group 1 was vaccinated with FKCs of S. agalactiae by a single spray administration while group 2 remained as the untreated control group. A booster was given twice using the same protocol as in the initial evaluation. After 6 weeks, fish from one of the duplicate tanks from each of groups 1 and 2 were challenged with pathogenic S. agalactiae by intraperitoneal (IP) injection, while fish in another tank were challenged through immersion. Based on the observations, serum immunoglobulin M (IgM) levels were significantly higher (P < 0.05) in the challenged fish than in the either the preexposed fish or the control group 1 week after the initial exposure. However, no significant differences (P > 0.05) were noted between challenged groups 1 and 2. In addition, no significant differences (P > 0.05) were observed between the frequencies of exposure. The mucus IgM level, however, remained high after each booster until the end of the 8-week study period. Meanwhile, serum IgM levels decreased after the challenge. A higher percentage of survival was noted for fish challenged through immersion (80%) compared with IP injection (70%). These results suggested that single spray exposure was able to induce IgM, which gave moderate to high protection during the challenge study.

Received October 9, 2012; accepted February 22, 2013
Dactylosporangium siamense sp. nov., isolated from soil
Authors: Thawai Chitti , Suriyachadkun Chanwit
Published: June 2013

A novel actinomycete strain, designed MW4-36T, was isolated from tropical forest soil in Nakhon Sawan Province, Thailand. Morphological and chemotaxonomic characteristics of this strain clearly demonstrated that it belongs to the genus

Dactylosporangium

. The strain formed finger-shaped sporangia on short sporangiophores that emerged directly from substrate hyphae. The cell-wall peptidoglycan contained glutamic acid, glycine, alanine and meso-diaminopimelic acid including 3-hydroxy-meso-diaminopimelic acid; arabinose, glucose, rhamnose, ribose and xylose were found as whole-cell sugars. The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol; no phosphatidylcholine was found. The predominant menaquinones were MK-9(H8) and MK-9(H6). Mycolic acids were not detected. The predominant cellular fatty acids were iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 72.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences also indicated that the strain should be classified in the genus

Dactylosporangium

and showed that the closest relative was

Dactylosporangium maewongense

JCM 15933T (99.4 % similarity). These taxonomic data revealed that strain MW4-36T could be readily distinguished from its phylogenetically closest relative. On the basis of these phenotypic and genotypic data, strain MW4-36T is considered to represent a novel species, for which the name Dactylosporangium siamense sp. nov. is proposed. The type strain is MW4-36T ( = BCC 34901T = NBRC 106093T).
Gemmobacter
lanyuensis sp. nov., isolated from a freshwater spring
Authors: Sheu Shih-Yi , Shiau Yu-Wen , Wei Yan-Ting , Chen Wen-Ming
Published: June 2013

A bacterial strain designated Orc-4T was isolated from a freshwater spring in Taiwan and characterized using the polyphasic taxonomic approach. Cells of strain Orc-4T were facultatively anaerobic, Gram-reaction-negative, poly-β-hydroxybutyrate-accumulating, non-motile rods surrounded by a thick capsule and forming cream–white colonies. Growth occurred at 15–40 °C (optimum, 25–30 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 0–1 % NaCl (optimum, 0–0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Orc-4T belonged to the genus

Gemmobacter

within the family

Rhodobacteraceae

of the class

Alphaproteobacteria

and its most closely related neighbour was

Gemmobacter fontiphilus

JS43T with sequence similarity of 97.8 %. Strain Orc-4T contained C18 : 1ω7c as the predominant fatty acid. The major respiratory quinone was Q-10. The DNA G+C content of the genomic DNA was 63.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one uncharacterized aminolipid and several uncharacterized phospholipids. The DNA–DNA relatedness of strain Orc-4T with respect to recognized species of the genus

Gemmobacter

was less than 48 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Orc-4T represents a novel species of the genus

Gemmobacter

, for which the name Gemmobacter
lanyuensis sp. nov. is proposed. The type strain is Orc-4T ( = BCRC 80378T = LMG 26667T = KCTC 23714T).
Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle
Authors: Gu Chun Tao , Li Chun Yan , Yang Li Jie , Huo Gui Cheng
Published: June 2013

A Gram-stain-positive bacterial strain, S4-3T, was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain S4-3T showed 97.9–98.7 % 16S rRNA gene sequence similarities, 84.4–94.1 % pheS gene sequence similarities and 94.4–96.9 % rpoA gene sequence similarities to the type strains of

Lactobacillus nantensis

,

Lactobacillus mindensis

,

Lactobacillus crustorum

,

Lactobacillus futsaii

,

Lactobacillus farciminis

and

Lactobacillus kimchiensis

. dnaK gene sequence similarities between S4-3T and

Lactobacillus nantensis

LMG 23510T,

Lactobacillus mindensis

LMG 21932T,

Lactobacillus crustorum

LMG 23699T,

Lactobacillus futsaii

JCM 17355T and

Lactobacillus farciminis

LMG 9200T were 95.4, 91.5, 90.4, 91.7 and 93.1 %, respectively. Based upon the data obtained in the present study, a novel species, Lactobacillus heilongjiangensis sp. nov., is proposed and the type strain is S4-3T ( = LMG 26166T = NCIMB 14701T).
GEE for Multinomial Responses Using a Local Odds Ratios Parameterization
Authors: Touloumis Anestis , Agresti Alan , Kateri Maria
Published: June 2013

In this article, we propose a generalized estimating equations (GEE) approach for correlated ordinal or nominal multinomial responses using a local odds ratios parameterization. Our motivation lies upon observing that: (i) modeling the dependence between correlated multinomial responses via the local odds ratios is meaningful both for ordinal and nominal response scales and (ii) ordinary GEE methods might not ensure the joint existence of the estimates of the marginal regression parameters and of the dependence structure. To avoid (ii), we treat the so‐called “working” association vector as a “nuisance” parameter vector that defines the local odds ratios structure at the marginalized contingency tables after tabulating the responses without a covariate adjustment at each time pair. To estimate and simultaneously approximate adequately possible underlying dependence structures, we employ the family of association models proposed by Goodman. In simulations, the parameter estimators with the proposed GEE method for a marginal cumulative probit model appear to be less biased and more efficient than those with the independence “working” model, especially for studies having time‐varying covariates and strong correlation.
Regional density of private dentists: empirical evidence from Austria
Authors: Gächter Martin , Schwazer Peter , Theurl Engelbert , Winner Hannes
Published: June 2013

Objectives

We investigated the determinants of disparities in the regional density of private dentists in Austria. Specifically, we focused on the relationship between the density of private dentists and their public counterparts, thereby controlling for other possible covariates of dentist density.

Methods

Dentist density was measured at the district level. We used panel data of dentist density from 121 Austrian districts over the years 2001–2008. We applied a Hausman–Taylor framework to cope with possible endogeneity and to control for cross‐district effects in the dentist density.

Results

A significant negative relationship was found between the density of private and public dentists, indicating a substitution effect between the two dentist groups. A significant positive spatial relationship also existed for private and public dentists in the neighboring regions. Dental capacities in public and private hospitals and dental laboratories run by the public health insurance system did not have a significant effect on private dentist density.

Conclusions

Although a strong negative relationship existed between private and public dentists within the districts, one should not draw the conclusion that private dentists in Austria are close substitutes for public dentists. Such a conclusion would require further empirical analysis on the utilization patterns of dental services and their relationships with financing mechanisms.
Developmental changes in memory encoding: insights from event‐related potentials
Authors: Rollins Leslie , Riggins Tracy
Published: June 2013

The aim of the present study was to investigate developmental changes in encoding processes between 6‐year‐old children and adults using event‐related potentials (ERPs). Although episodic memory (‘EM’) effects have been reported in both children and adults at retrieval and subsequent memory effects have been established in adults, no previous ERP studies have examined subsequent memory effects in children. This represents a critical gap in the literature because encoding processes, and changes in neural correlates supporting encoding, partially account for age‐related improvements in children's memory performance. Results revealed that subsequent memory effects differed between children and adults temporally, directionally, and topographically. These findings lend support to the hypothesis that encoding processes and their neural correlates are an important source of change in memory development.

A video abstract of this article can be viewed at http://youtu.be/sH83_qVimgc.
Soil nitrous oxide emissions following crop residue addition: a meta‐analysis
Authors: Chen Huaihai , Li Xuechao , Hu Feng , Shi Wei
Published: June 2013

Annual production of crop residues has reached nearly 4 billion metric tons globally. Retention of this large amount of residues on agricultural land can be beneficial to soil C sequestration. Such potential impacts, however, may be offset if residue retention substantially increases soil emissions of N2O, a potent greenhouse gas and ozone depletion substance. Residue effects on soil N2O emissions have gained considerable attention since early 1990s; yet, it is still a great challenge to predict the magnitude and direction of soil N2O emissions following residue amendment. Here, we used a meta‐analysis to assess residue impacts on soil N2O emissions in relation to soil and residue attributes, i.e., soil pH, soil texture, soil water content, residue C and N input, and residue C : N ratio. Residue effects were negatively associated with C : N ratios, but generally residue amendment could not reduce soil N2O emissions, even for C : N ratios well above ca. 30, the threshold for net N immobilization. Residue effects were also comparable to, if not greater than, those of synthetic N fertilizers. In addition, residue effects on soil N2O emissions were positively related to the amounts of residue C input as well as residue effects on soil CO2 respiration. Furthermore, most significant and stimulatory effects occurred at 60–90% soil water‐filled pore space and soil pH 7.1–7.8. Stimulatory effects were also present for all soil textures except sand or clay content ≤10%. However, inhibitory effects were found for soils with >90% water‐filled pore space. Altogether, our meta‐analysis suggests that crop residues played roles beyond N supply for N2O production. Perhaps, by stimulating microbial respiration, crop residues enhanced oxygen depletion and therefore promoted anaerobic conditions for denitrification and N2O production. Our meta‐analysis highlights the necessity to connect the quantity and quality of crop residues with soil properties for predicting soil N2O emissions.
Prosthetic Rehabilitation of a Cleidocranial Dysplasia Patient with Vertical Maxillofacial Deficiency: A Clinical Report
Authors: Noh Kwantae , Kwon Kung‐Rock , Ahn Hyowon , Paek Janghyun , Pae Ahran
Published: June 2013

Cleidocranial dysplasia (CCD) is a rare congenital disorder characterized by skeletal and dental anomalies. This clinical report describes the prosthodontic approach to treating a CCD patient who presented with decreased facial height and relative mandibular protrusion due to maxillary hypoplasia after orthodontic treatment. Functional and esthetic rehabilitation was achieved using telescopic detachable prostheses in the maxilla and osseointegrated implants and metal‐ceramic fixed dental prostheses in the mandible. These treatment approaches precluded the need for orthognathic surgical correction and presented a favorable prognosis during the 5‐year observation period.
The Effect of Different Restorative and Abutment Materials on Marginal and Internal Adaptation of Three‐Unit Cantilever Implant‐Supported Fixed Partial Dentures: An In Vitro Study
Authors: Kahramanoğlu Erkut , Kulak‐Özkan Yasemin
Published: June 2013

Purpose

Passive fit is generally assumed to be a significant prerequisite for long‐term implant success. The aim of this study was to evaluate the precision fit of three‐unit implant‐supported fixed partial dentures with different restorative and abutment materials on two implant systems: the Straumann and Astra Tech.

Materials and Methods

Two mandibular epoxy resin models (one for each implant system) were fabricated, and two implants were inserted at the first and second molar region. Poly(vinyl siloxane) impression material was used to make the dental impression. For each implant system, fifteen models were fabricated, and each group was divided into three subgroups (group 1: titanium abutment with metal framework, group 2: titanium abutment with zirconium framework, group 3: zirconium abutment with zirconium framework). The replica technique was used to examine the marginal and internal gap values. For each restoration, 20 measurements were performed, totaling 1200 measurements for all groups. Data were evaluated statistically using ANOVA and LSD post hoc test (p < 0.05).

Results

The highest values at internal adaptation measurements were found at the occlusal surface for all groups. When the mean values of the marginal measurements were assessed, the lowest measurements were found in group 3 (51.416 μm), and the highest values were found in group 1 (79.394 μm). There were statistically significant differences between subgroups for marginal measurements (p < 0.05).

Conclusions

As included in our study, marginal measurement values were found to be 46 to 87 μm. The marginal discrepancy of the tested materials could be considered clinically acceptable.
Characterization of the Genome of the Dairy Lactobacillus helveticus Bacteriophage ΦAQ113
Authors: Zago Miriam , Scaltriti Erika , Rossetti Lia , Guffanti Alessandro , Armiento Angelarita , Fornasari Maria Emanuela , Grolli Stefano , Carminati Domenico , Brini Elena , Pavan Paolo , Felsani Armando , D'Urzo Annalisa , Moles Anna , Claude Jean-Baptiste , Grandori Rita , Ramoni Roberto , Giraffa Giorgio
Published: June 2013

The complete genomic sequence of the dairy
Lactobacillus helveticus
bacteriophage ΦAQ113 was determined. Phage ΦAQ113 is a
Myoviridae
bacteriophage with an isometric capsid and a contractile tail. The final assembled consensus sequence revealed a linear, circularly permuted, double-stranded DNA genome with a size of 36,566 bp and a G+C content of 37%. Fifty-six open reading frames (ORFs) were predicted, and a putative function was assigned to approximately 90% of them. The ΦAQ113 genome shows functionally related genes clustered together in a genome structure composed of modules for DNA replication/regulation, DNA packaging, head and tail morphogenesis, cell lysis, and lysogeny. The identification of genes involved in the establishment of lysogeny indicates that it may have originated as a temperate phage, even if it was isolated from natural cheese whey starters as a virulent phage, because it is able to propagate in a sensitive host strain. Additionally, we discovered that the ΦAQ113 phage genome is closely related to
Lactobacillus gasseri
phage KC5a and
Lactobacillus johnsonii
phage Lj771 genomes. The phylogenetic similarities between
L. helveticus
phage ΦAQ113 and two phages that belong to gut species confirm a possible common ancestral origin and support the increasing consideration of
L. helveticus
as a health-promoting organism.
Increased Water Activity Reduces the Thermal Resistance of Salmonella enterica in Peanut Butter
Authors: He Yingshu , Li Ye , Salazar Joelle K. , Yang Jingyun , Tortorello Mary Lou , Zhang Wei
Published: June 2013

Increased water activity in peanut butter significantly (
P
< 0.05) reduced the heat resistance of desiccation-stressed
Salmonella enterica
serotypes treated at 90°C. The difference in thermal resistance was less notable when strains were treated at 126°C. Using scanning electron microscopy, we observed minor morphological changes of
S. enterica
cells resulting from desiccation and rehydration processes in peanut oil.
Mannitol and the Mannitol-Specific Enzyme IIB Subunit Activate Vibrio cholerae Biofilm Formation
Authors: Ymele-Leki Patrick , Houot Laetitia , Watnick Paula I.
Published: June 2013

Vibrio cholerae
is a halophilic, Gram-negative rod found in marine environments. Strains that produce cholera toxin cause the diarrheal disease cholera.
V. cholerae
use a highly conserved, multicomponent signal transduction cascade known as the phosphoenolpyruvate phosphotransferase system (PTS) to regulate carbohydrate uptake and biofilm formation. Regulation of biofilm formation by the PTS is complex, involving many different regulatory pathways that incorporate distinct PTS components. The PTS consists of the general components enzyme I (EI) and histidine protein (HPr) and carbohydrate-specific enzymes II. Mannitol transport by
V. cholerae
requires the mannitol-specific EII (EII
Mtl
), which is expressed only in the presence of mannitol. Here we show that mannitol activates
V. cholerae
biofilm formation and transcription of the
vps
biofilm matrix exopolysaccharide synthesis genes. This regulation is dependent on mannitol transport. However, we show that, in the absence of mannitol, ectopic expression of the B subunit of EII
Mtl
is sufficient to activate biofilm accumulation. Mannitol, a common compatible solute and osmoprotectant of marine organisms, is a main photosynthetic product of many algae and is secreted by algal mats. We propose that the ability of
V. cholerae
to respond to environmental mannitol by forming a biofilm may play an important role in habitat selection.
Lytic Infection of Lactococcus lactis by Bacteriophages Tuc2009 and c2 Triggers Alternative Transcriptional Host Responses
Authors: Ainsworth Stuart , Zomer Aldert , Mahony Jennifer , van Sinderen Douwe
Published: June 2013

Here we present an entire temporal transcriptional profile of
Lactococcus lactis
subsp.
cremoris
UC509.9 undergoing lytic infection with two distinct bacteriophages, Tuc2009 and c2. Furthermore, corresponding high-resolution whole-phage genome tiling arrays of both bacteriophages were performed throughout lytic infection. Whole-genome microarrays performed at various time points postinfection demonstrated a rather modest impact on host transcription. The majority of changes in the host transcriptome occur during late infection stages; few changes in host gene transcription occur during the immediate and early infection stages. Alterations in the
L. lactis
UC509.9 transcriptome during lytic infection appear to be phage specific, with relatively few differentially transcribed genes shared between cells infected with Tuc2009 and those infected with c2. Despite the apparent lack of a coordinated general phage response, three themes common to both infections were noted: alternative transcription of genes involved in catabolic flux and energy production, differential transcription of genes involved in cell wall modification, and differential transcription of genes involved in the conversion of ribonucleotides to deoxyribonucleotides. The transcriptional profiles of both bacteriophages during lytic infection generally correlated with the findings of previous studies and allowed the confirmation of previously predicted promoter sequences. In addition, the host transcriptional response to lysogenization with Tuc2009 was monitored along with tiling array analysis of Tuc2009 in the lysogenic state. Analysis identified 44 host genes with altered transcription during lysogeny, 36 of which displayed levels of transcription significantly reduced from those for uninfected cells.
Extracellular Electron Transfer to Fe(III) Oxides by the Hyperthermophilic Archaeon Geoglobus ahangari via a Direct Contact Mechanism
Authors: Manzella Michael P. , Reguera Gemma , Kashefi Kazem
Published: June 2013

The microbial reduction of Fe(III) plays an important role in the geochemistry of hydrothermal systems, yet it is poorly understood at the mechanistic level. Here we show that the obligate Fe(III)-reducing archaeon
Geoglobus ahangari
uses a direct-contact mechanism for the reduction of Fe(III) oxides to magnetite at 85°C. Alleviating the need to directly contact the mineral with the addition of a chelator or the electron shuttle anthraquinone-2,6-disulfonate (AQDS) stimulated Fe(III) reduction. In contrast, entrapment of the oxides within alginate beads to prevent cell contact with the electron acceptor prevented Fe(III) reduction and cell growth unless AQDS was provided. Furthermore, filtered culture supernatant fluids had no effect on Fe(III) reduction, ruling out the secretion of an endogenous mediator too large to permeate the alginate beads. Consistent with a direct contact mechanism, electron micrographs showed cells in intimate association with the Fe(III) mineral particles, which once dissolved revealed abundant curled appendages. The cells also produced several heme-containing proteins. Some of them were detected among proteins sheared from the cell's outer surface and were required for the reduction of insoluble Fe(III) oxides but not for the reduction of the soluble electron acceptor Fe(III) citrate. The results thus support a mechanism in which the cells directly attach and transfer electrons to the Fe(III) oxides using redox-active proteins exposed on the cell surface. This strategy confers on
G. ahangari
a competitive advantage for accessing and reducing Fe(III) oxides under the extreme physical and chemical conditions of hot ecosystems.
Fungus-Specific Sirtuin HstD Coordinates Secondary Metabolism and Development through Control of LaeA
Authors: Kawauchi Moriyuki , Nishiura Mika , Iwashita Kazuhiro
Published: June 2013

The sirtuins are members of the NAD
+
-dependent histone deacetylase family that contribute to various cellular functions that affect aging, disease, and cancer development in metazoans. However, the physiological roles of the fungus-specific sirtuin family are still poorly understood. Here, we determined a novel function of the fungus-specific sirtuin HstD/
Aspergillus oryzae
Hst4 (AoHst4), which is a homolog of Hst4 in
A. oryzae
yeast. The deletion of all histone deacetylases in
A. oryzae
demonstrated that the fungus-specific sirtuin HstD/AoHst4 is required for the coordination of fungal development and secondary metabolite production. We also show that the expression of the
laeA
gene, which is the most studied fungus-specific coordinator for the regulation of secondary metabolism and fungal development, was induced in a Δ
hstD
strain. Genetic interaction analysis of
hstD
/
Aohst4
and
laeA
clearly indicated that HstD/AoHst4 works upstream of LaeA to coordinate secondary metabolism and fungal development. The
hstD/Aohst4
and
laeA
genes are fungus specific but conserved in the vast family of filamentous fungi. Thus, we conclude that the fungus-specific sirtuin HstD/AoHst4 coordinates fungal development and secondary metabolism via the regulation of LaeA in filamentous fungi.
ADF/Cofilin Is Not Essential but Is Critically Important for Actin Activities during Phagocytosis in Tetrahymena thermophila
Authors: Shiozaki Nanami , Nakano Kentaro , Kushida Yasuharu , Noguchi Taro Q. P. , Uyeda Taro Q. P. , Wloga Dorota , Dave Drashti , Vasudevan Krishna Kumar , Gaertig Jacek , Numata Osamu
Published: June 2013

ADF/cofilin is a highly conserved actin-modulating protein. Reorganization of the actin cytoskeletonin vivothrough severing and depolymerizing of F-actin by this protein is essential for various cellular events, such as endocytosis, phagocytosis, cytokinesis, and cell migration. We show that in the ciliateTetrahymena thermophila, the ADF/cofilin homologue Adf73p associates with actin on nascent food vacuoles. Overexpression of Adf73p disrupted the proper localization of actin and inhibited the formation of food vacuoles.In vitro, recombinant Adf73p promoted the depolymerization of filaments made ofT. thermophilaactin (Act1p). Knockout cells lacking theADF73gene are viable but grow extremely slowly and have a severely decreased rate of food vacuole formation. Knockout cells have abnormal aggregates of actin in the cytoplasm. Surprisingly, unlike the case in animals and yeasts, inTetrahymena, ADF/cofilin is not required for cytokinesis. Thus, theTetrahymenamodel shows promise for future studies of the role of ADF/cofilinin vivo.
Importance and Determinants of Induction of Cold-Induced DEAD RNA Helicase in the Hyperthermophilic Archaeon Thermococcus kodakarensis
Authors: Nagaoka Eriko , Hidese Ryota , Imanaka Tadayuki , Fujiwara Shinsuke
Published: June 2013

Thermococcus kodakarensis
, which grows optimally at 85°C, expresses cold stress-inducible DEAD box RNA helicase (
Tk-deaD
) when shifted to 60°C. A DDA1 deletion (Δ
Tk-deaD
) mutant exhibited decreased cell growth, and cells underwent lysis at 60°C in nutrient broth in the absence of elemental sulfur. In contrast, cells in medium containing elemental sulfur at 60°C did not undergo lysis, suggesting that
Tk-deaD
is necessary for cell growth in sulfur-free medium. To identify the element responsible for the cold response, a pTKR expression probe plasmid was constructed using thermostable catalase from
Pyrobaculum calidifontis
as a reporter. The plasmid pTKRD, which contained the transcription factor B recognition element, TATA region, and Shine-Dalgarno (SD) region, including the initiation codon of the
Tk-deaD
gene, exhibited cold inducibility. We also constructed a series of deletion and chimeric constructs with the glutamate dehydrogenase (
gdh
) promoter, whose expression is constitutive independent of culture temperatures and catalase expression. Reporter assay experiments indicated that the regulatory element is located in the region between the SD region and the initiation codon (ATG). Nucleotide sequences in the upstream regions of
Tk-deaD
and
gdh
were compared and revealed a five-adenosine (AAAAA) sequence between SD and ATG of
Tk-deaD
that was not present in
gdh
. Replacement of the repeated adenosine sequence with other sequences revealed that the AAAAA sequence is important for cold induction. This sequence-specific mechanism is unique and is one that has not been identified in other known cold-inducible genes.
NO-Induced Biofilm Dispersion in Pseudomonas aeruginosa Is Mediated by an MHYT Domain-Coupled Phosphodiesterase
Authors: Li Yi , Heine Sabrina , Entian Michael , Sauer Karin , Frankenberg-Dinkel Nicole
Published: June 2013

Dispersion is a process used by bacteria to successfully transit from a biofilm to a planktonic growth state and to spawn novel communities in new locales. Alterations inbis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) levels have been shown to be associated with biofilm dispersal in a number of different bacteria. The signaling molecule nitric oxide (NO) is known to induce biofilm dispersion through stimulation of c-di-GMP-degrading phosphodiesterase (PDE) activity. However, no c-di-GMP modulating enzyme directly involved in NO-induced dispersion has yet been described in the opportunistic pathogenPseudomonas aeruginosa. Here, we characterized MucR (PA1727) and NbdA (PA3311,NO-inducedbiofilmdispersion locusA), two membrane-bound proteins with identical domain organization consisting of MHYT-GGDEF-EAL, with respect to their role in NO-induced dispersion. Inactivation ofmucRimpaired biofilm dispersion in response to NO and glutamate, whereas inactivation ofnbdAonly impaired biofilm dispersion upon exposure to NO. A specific role of NbdA in NO-induced dispersion was supported by increased PDE activity, resulting in decreased c-di-GMP levels in biofilms expressingnbdAupon exposure to NO, a response that was absent in the ΔnbdAstrain. Moreover, increased PDE activity was mainly due to a transcriptional activation ofnbdAupon addition of NO. Biochemical analyses of recombinant protein variants lacking the membrane-anchored MHYT domain support NbdA being an active PDE. In contrast, MucR displayed both diguanylate cyclase and PDE activityin vitro, which seemed regulated in a growth-dependent mannerin vivo. This is the first description of a PDE specifically involved in NO-induced biofilm dispersion inP. aeruginosa.
Peripapillary and macular retinoschisis in a patient with pseudoexfoliation glaucoma
Authors: Örnek Nurgül , Büyüktortop Nesrin , Örnek Kemal
Published: June 2013

A 55-year-old man was admitted with a 2-year history of pseudoexfoliation glaucoma. The best-corrected visual acuities were 10/10 in both eyes. Pseudoexfoliation material was noted on the iris and the lens capsule. Fundus examination evidenced cup-to-disc ratio of 0.7 OD and 0.9 OS with peripapillary atrophy. Gonioscopy revealed open angles. Optical coherence tomography demonstrated peripapillary retinoschisis extending to the nasal macula in the left eye and optic nerve head was almost fully excavated. Coexisting retinoschisis in a patient with glaucoma may interfere with the reliability of retinal nerve fibre layer and ganglion cell complex analysis and may change the treatment plan and follow-up intervals.
Idiopathic bilateral adrenal haemorrhage related to acute adrenal insufficiency
Authors: Ogino Jun , Toda Joe , Onitsuka Shiro , Hashimoto Naotake
Published: June 2013

A 54-year-old woman presented with sudden epigastralgia and left back pain. She had no significant history. Laboratory data showed mild inflammation and no liver or renal dysfunction. Abdominal CT showed left adrenal enlargement and haemorrhage. Hydrocortisone therapy was started to prevent adrenal insufficiency before laboratory findings for ACTH (adrenocorticotropic hormone) and cortisol levels. On the second hospital day, abdominal CT showed additional right adrenal enlargement and haemorrhage. The serum cortisol level suggested adrenal insufficiency. No specific findings were detected by bilateral adrenal angiography. 6 to 12 months later, abdominal CT showed decreased bilateral adrenal haemorrhage. This case illustrates the importance of prompt diagnosis and treatment of acute adrenal insufficiency, and shows sequential changes in the size of bilateral adrenal haemorrhage. Rapid corticosteroid replacement is important if acute adrenal insufficiency is suspected. In a case with unilateral adrenal haemorrhage, the possibility of additional adrenal haemorrhage on the opposite side should also be considered.
Recognising compartment syndrome in the upper limbs of a patient with central cord syndrome: getting out of pitfalls
Authors: Weerasuriya Thisara , Lally Victoria A , Thalava Ramesh
Published: June 2013

This is a case where limb threatening compartment syndrome of the hand was masked by co-existing central cord syndrome following trauma.
Cortisol: ACTH ratio to test for primary hypoadrenalism: a pilot study
Authors: Lee Mark K V , Vasikaran Samuel , Doery James C G , Wijeratne Nilika , Prentice David
Published: June 2013

Introduction

A standard short Synacthen test (SST) is the conventional diagnostic test for primary hypoadrenalism. Measuring simultaneous plasma cortisol and adrenocorticotrophin hormone (ACTH) and using the cortisol: ACTH ratio as a first-line test may be safer and more convenient than performing a SST.

Methods

A retrospective study of 349 patients who had a SST with simultaneous baseline plasma cortisol and ACTH performed between 2005 and 2010 in two separate Australian health centres. The plasma cortisol: ACTH ratio was calculated for each patient and their final diagnosis was determined based on their SST result and a review of their clinical notes.

Results

Eighteen patients had primary hypoadrenalism, 46 patients had secondary hypoadrenalism and 285 patients had normal adrenal function. All the patients with primary hypoadrenalism had a plasma cortisol: ACTH ratio <3, while none of the patients with normal adrenal function or secondary hypoadrenalism had a cortisol: ACTH ratio <3. Therefore, a cortisol: ACTH ratio <3 had a 100% sensitivity and specificity for the diagnosis of primary hypoadrenalism. Patients with secondary hypoadrenalism had a cortisol: ACTH ratio >3, while subjects with normal adrenal function had a cortisol: ACTH ratio >15. There was overlap in cortisol: ACTH ratios of patients with secondary hypoadrenalism and normal adrenal function.

Conclusions

Although the cortisol: ACTH ratio predicts primary hypoadrenalism, its value is limited to diagnosing primary hypoadrenalism as it does not distinguish secondary hypoadrenalism from normal adrenal function. Larger prospective studies that include patients with early primary hypoadrenalism are needed to confirm the reliability of plasma cortisol: ACTH ratio as a diagnostic test for primary hypoadrenalism.
Mitogen-Activated Protein Kinase Pathways in Osteoblasts
Authors: Greenblatt Matthew B. , Shim Jae-Hyuck , Glimcher Laurie H.
Published: June 2013

Mitogen-activated protein kinases (MAPKs) are ancient signal transducers well characterized as mediators of inflammation and neoplastic transformation. Recent work has expanded our understanding of their developmental functions, particularly in the regulation of bone mass via control of osteoblast differentiation. Here, we review the functions of MAPK pathways in osteoblasts, including a consideration of MAPK substrates. In particular, MAPKs function to regulate the key transcriptional mediators of osteoblast differentiation, with ERK and p38 MAPKs phosphorylating RUNX2, the master regulator of osteoblast differentiation. ERK also activates RSK2, which in turn phosphorylates ATF4, a transcriptional regulator of late-stage osteoblast synthetic functions. The MAP3Ks and MAP2Ks upstream of MAPKs have also been investigated, and significant differences have been found in the wiring of MAPK pathways in osteoblasts relative to other tissues. Thus, the investigation of MAPKs in osteoblasts has both revealed critical mechanisms for the maintenance of bone mass and added to our understanding of how the individual components of MAPK pathways function in concert in a complex in vivo system.