bluuebunny/crossref_metadata_2025 huggingface dataset:
METHYLENE BLUE SENSITIVITY 1 (MBS1) is required for acclimation of Arabidopsis to singlet oxygen and acts downstream of β‐cyclocitral
Authors: Shumbe Leonard , D'Alessandro Stefano , Shao Ning , Chevalier Anne , Ksas Brigitte , Bock Ralph , Havaux Michel
Published: November 2016

Singlet oxygen (1O2) signalling in plants is essential to trigger both acclimatory mechanisms and programmed cell death under high light stress. However, because of its chemical features, 1O2 requires mediators, and the players involved in this pathway are largely unknown. The β‐carotene oxidation product, β‐cyclocitral, is one such mediator. Produced in the chloroplast, β‐cyclocitral induces changes in nuclear gene expression leading to photoacclimation. Recently, the METHYLENE BLUE SENSITIVITY protein MBS has been identified as a key player in 1O2 signalling leading to tolerance to high light. Here, we provide evidence that MBS1 is essential for acclimation to 1O2 and cross‐talks with β‐cyclocitral to mediate transfer of the 1O2 signal to the nucleus, leading to photoacclimation. The presented results position MBS1 downstream of β‐cyclocitral in 1O2 signalling and suggest an additional role for MBS1 in the regulation of plant growth and development under chronic 1O2 production.
How Often are Pediatric Patients with Clinically Amyopathic Dermatomyositis Truly Amyopathic?
Authors: Oberle Edward J. , Bayer Michelle L. , Chiu Yvonne E. , Co Dominic O.
Published: November 2016

Background

Pediatric patients can present with skin manifestations of dermatomyositis without overt weakness (clinically amyopathic juvenile dermatomyositis [JDM]), but it is unclear how often this happens and how often they have subclinical muscle inflammation.

Objective

Our goal was to determine the frequency of clinically amyopathic JDM and the frequency with which a thorough evaluation uncovers subclinical myositis at a single institution.

Methods

A retrospective review was performed of 46 patients diagnosed with JDM at Children's Hospital of Wisconsin.

Results

Of 46 patients presenting with skin findings consistent with dermatomyositis, 10 patients (21.7%) did not have evidence of muscle involvement on history or exam, and these tended to be the younger patients. Of these 10, only 2 (4% of all the JDM patients) were truly amyopathic upon further evaluation (all five muscle enzymes [aspartate aminotransferase, alanine aminotransferase, lactate dehydrogenase, creatine kinase and aldolase], magnetic resonance imaging [MRI], muscle biopsy). In our series, muscle biopsy was not helpful in identifying subclinical myositis. In contrast, MRI did uncover subclinical muscle disease.

Conclusion

These data suggest that truly amyopathic JDM is rare and that a thorough workup that includes all five muscle enzymes and MRI may uncover occult myositis.
Help yourself by helping others: The joint impact of group member organizational citizenship behaviors and group cohesiveness on group member objective task performance change
Authors: Liu Dong , Chen Xiao‐Ping , Holley Erica
Published: November 2016

This paper examines how a group member's individual‐targeted citizenship behavior (OCBI) and organization‐targeted citizenship behavior (OCBO) interact with a salient group‐level contextual variable, group cohesiveness, to foster positive change for that group member, starting with job self‐efficacy change, and followed by objective task performance change. Over a span of 6 months, we engaged in multilevel, multisource, multistage data collection and surveyed 587 members in 83 work groups. Our results indicate that a group member's OCBI, in comparison with OCBO, is more positively related to his or her job self‐efficacy change. Group cohesiveness was found to attenuate the relationship between a group member's OCBI and job self‐efficacy change, and conversely, to accentuate the relationship between a group member's OCBO and job self‐efficacy change. Furthermore, a group member's job self‐efficacy change mediated the interactive effects of the group member's OCBI and group cohesiveness (as well as the group member's OCBO and group cohesiveness) on his or her objective task performance change.
Trace Class Markov Chains for Bayesian Inference with Generalized Double Pareto Shrinkage Priors
Authors: Pal Subahdip , Khare Kshitij , Hobert James P.
Published: November 2016

Bayesian shrinkage methods have generated a lot of interest in recent years, especially in the context of high‐dimensional linear regression. In recent work, a Bayesian shrinkage approach using generalized double Pareto priors has been proposed. Several useful properties of this approach, including the derivation of a tractable three‐block Gibbs sampler to sample from the resulting posterior density, have been established. We show that the Markov operator corresponding to this three‐block Gibbs sampler is not Hilbert–Schmidt. We propose a simpler two‐block Gibbs sampler and show that the corresponding Markov operator is trace class (and hence Hilbert–Schmidt). Establishing the trace class property for the proposed two‐block Gibbs sampler has several useful consequences. Firstly, it implies that the corresponding Markov chain is geometrically ergodic, thereby implying the existence of a Markov chain central limit theorem, which in turn enables computation of asymptotic standard errors for Markov chain‐based estimates of posterior quantities. Secondly, because the proposed Gibbs sampler uses two blocks, standard recipes in the literature can be used to construct a sandwich Markov chain (by inserting an appropriate extra step) to gain further efficiency and to achieve faster convergence. The trace class property for the two‐block sampler implies that the corresponding sandwich Markov chain is also trace class and thereby geometrically ergodic. Finally, it also guarantees that all eigenvalues of the sandwich chain are dominated by the corresponding eigenvalues of the Gibbs sampling chain (with at least one strict domination). Our results demonstrate that a minor change in the structure of a Markov chain can lead to fundamental changes in its theoretical properties. We illustrate the improvement in efficiency resulting from our proposed Markov chains using simulated and real examples.
Re‐enlivening the Indian Ocean through contemporary trade: East African traders searching for new markets in Jakarta
Authors: Verne Julia
Published: November 2016

While much has been written about the history of mobility and trade in the Indian Ocean, recent trading connections between Eastern Africa and Asia have so far only gained very little attention. However, in Zanzibar alone, hundreds of traders regularly embark on journeys reviving old routes and further develop them, in order to take advantage of the way the global economy works today. By providing an ethnographic account of such a journey undertaken by four Zanzibari traders to Jakarta, this article gives an insight into the organization, calculations and imaginations involved in contemporary Indian Ocean trading networks. Although this trade journey clearly marks a new form of translocal mobility among Zanzibari traders, this mobile ethnography highlights how the journey is at the same time closely linked to, evokes and enlivens very old processes of mobility across the Indian Ocean, thus highlighting the dialectics between old and new mobilities, and between familiarity and strangeness.
Temporalities of Victimhood: Time in the Study of Postconflict Societies
Authors: Mueller‐Hirth Natascha
Published: November 2016

Researchers in peace and conflict studies have rarely explicitly engaged with time and temporality. This article develops a temporal analysis of victimhood in a mature posttransition society, drawing on qualitative research with victims/survivors of gross human rights violations in South Africa. Two decades after the democratic transition, there is a prevalent understanding that it is finally time for victims to “move on.” In contrast to the supposed linear temporality of peace processes, however, the consequences of past violence continue to impact on interviewees’ lives and are exacerbated by contemporary experiences of victimization. I identify several areas of temporal conflicts that characterize postconflict societies: victimhood as temporary/victimhood as continuous; the pace of national reconciliation/the time(s) of individual healing; and the speed of a neoliberal economy/the pace of social transformation. I examine temporal hierarchies that reflect broader socioeconomic marginalization, such as being made to wait for compensation and social pressures of overcoming the past. This temporal analysis of victimhood thus not only highlights the mismatch between victims’ needs and political and cultural expectations of closure, but it also draws attention to the temporality of transitional processes and programs at different social and institutional levels.
Characterization of a PCR‐based lymphocyte clonality assay as a complementary tool for the diagnosis of feline lymphoma
Authors: Hammer S. E. , Groiss S. , Fuchs‐Baumgartinger A. , Nedorost N. , Gress V. , Luckschander‐Zeller N. , Saalmüller A. , Schwendenwein I. , Rütgen B. C.
Published: November 2016

Differentiation between resident mature lymphocyte populations and small cell lymphoma cannot be made by cytological review alone and remains challenging in histopathological review. These cases warrant application of complementary tools like PCR‐based immunoglobulin (IG) and T‐cell receptor (TCR) clonality testing for confirmation. In this prospective study, diagnostic sensitivity and specificity of different primer sets for routine diagnosis of feline TCR gamma (TCRG) and complete IG heavy chain (IGH) gene rearrangements were assessed. Fine needle aspirates from 20 feline lymphoma cases and lymph node material from 10 cats without hematopoietic neoplasia were subjected to clonality testing. Feline lymphoma cell lines and previously confirmed patient material served as positive control. Detection limits for clonal populations within a polyclonal background was 90% for B‐cells and 50% for T‐cells. Diagnostic sensitivity and specificity of the clonality assay were 70% and 90%. Overall diagnostic accuracy was 77%, positive predictive value 93% and negative predictive value 60%.
From weed biology to successful control: an example of successful management of Ludwigia grandiflora in Germany
Authors: Hussner A , Windhaus M , Starfinger U
Published: November 2016

Ludwigia grandiflora (water primrose), a native to the Americas, is one of the most important invasive alien aquatic plants in Europe. In Germany, a first population was found in an oxbow lake of the River Leda in Lower Saxony, north‐western Germany, in 2004. Ludwigia grandiflora formed both dense monospecific patches and mixed stands with native plants. A study on the biology of L. grandiflora documented that the plants regrow in spring from vegetative means only, even though viable seed production occurred. Hand weeding was successfully tested in different sampling sites as a sustainable management tool and subsequently used for the management of this species. Within 3 days, more than 99% of the biomass (25 tonnes of fresh mass) was harvested in 2013. Afterwards, a one‐day post‐treatment in the same year, two‐one‐day treatments in 2014 and one‐one‐day treatment in 2015 were made to harvest the regrown plants. After the first year, plant regrowth occurred only in one extremely muddy site, while in more than 99% of the water body, L. grandiflora was eradicated. Even though L. grandiflora was not completely eradicated from the water, a total eradication seems achievable within the next few years. The study documented the difficulties in the management of aquatic weeds, particularly in heterogeneous habitats with varying sediment structure. Management measures must be adapted to the infested habitat and species biology, which is mandatory for successful management of all aquatic weeds.
Effects of Sequential Cuts on White Layer Formation and Retained Austenite Content in Hard Turning of AISI52100 Steel
Authors: Zhang Xiao-Ming , Huang Xin-Da , Chen Li , Leopold Jürgen , Ding Han
Published: November 2016

This technical brief is the extension of our previous work developed by Zhang et al. (2016, “Effects of Process Parameters on White Layer Formation and Morphology in Hard Turning of AISI52100 Steel,” ASME J. Manuf. Sci. Eng., 138(7), p. 074502). We investigated the effects of sequential cuts on microstructure alteration in hard turning of AISI52100 steel. Samples undergone five sequential cuts are prepared with different radial feed rates and cutting speeds. Optical microscope and X-ray diffraction (XRD) are employed to analyze the microstructures of white layer and bulk materials after sequential cutting processes. Through the studies we first find out the increasing of white layer thickness in the sequential cuts. This trend in sequential cuts does work for different process parameters, belonging to the usually used ones in hard turning of AISI52100 steel. In addition, we find that the white layer thickness increases with the increasing of cutting speed, as recorded in the literature. To reveal the mechanism of white layer formation, XRD measurements of white layers generated in the sequential cuts are made. As a result retained austenite in white layers is identified, which states that the thermally driven phase transformations dominate the white layer formation, rather than the severe plastic deformation in cuts. Furthermore, retained austenite contents in sequential cuts with different process parameters are discussed. While using a smaller radial feed rate, the greater retained austenite content found in experiments is attributed to the generated compressive surface residual stresses, which possibly restricts the martensitic transformation.
Zero Curvature Method and Protection Criterion Against Plastic Collapse
Authors: Duan Cheng-Hong , Sun Yu , Lu Ming-Wan
Published: November 2016

A zero curvature method to estimate the limit load is introduced in detail, and a uniform computing process for computerization of the zero curvature method is presented. A new protection criterion against plastic collapse is proposed. A lot of examples are performed and discussed. The zero curvature load determined by the zero curvature method is a preferable definition of the limit load for perfectly plastic materials or the plastic load for strain strengthening materials. Both advantages of the ASME VIII-2 code and the EN-13445 standard are absorbed in the new protection criterion.
Pantograph/Catenary Contact Formulations
Authors: Kulkarni Shubhankar , Pappalardo Carmine M. , Shabana Ahmed A.
Published: November 2016

In this investigation, the pantograph/catenary contact is examined using two different formulations. The first is an elastic contact formulation that allows for the catenary/panhead separation and for the analysis of the effect of the aerodynamic forces, while the second approach is based on a constraint formulation that does not allow for such a separation by eliminating the freedom of relative translation in two directions at the catenary/panhead contact point. In this study, the catenary system, including the contact and messenger wires, is modeled using the nonlinear finite element (FE) absolute nodal coordinate formulation (ANCF) and flexible multibody system (MBS) algorithms. The generalized aerodynamic forces associated with the ANCF position and gradient coordinates and the pantograph reference coordinates are formulated. The new elastic contact formulation used in this investigation is derived from the constraint-based sliding joint formulation previously proposed by the authors. By using a unilateral penalty force approach, separation of the catenary and panhead is permitted, thereby allowing for better evaluating the response of the pantograph/catenary system to wind loading. In this elastic contact approach, the panhead is assumed to have six degrees-of-freedom with respect to the catenary. The coordinate system at the pantograph/catenary contact point is chosen such that the contact model developed in this study can be used with both the fully parameterized and gradient deficient ANCF elements. In order to develop a more realistic model, the MBS pantograph model is mounted on a detailed three-dimensional MBS rail-vehicle model. The wheel/rail contact is modeled using a nonlinear three-dimensional elastic contact formulation that accounts for the creep forces and spin moment. In order to examine the effect of the external aerodynamic forces on the pantograph/catenary interaction, two scenarios are considered in this investigation. In the first scenario, the crosswind loading is applied on the pantograph components only, while in the second scenario, the aerodynamic forces are applied on the pantograph components and also on the flexible catenary. For the configuration considered in this investigation, it was found that the crosswind assists the uplift force exerted on the pantograph mechanism, increasing the mean contact force value. Numerical results are presented in order to compare between the cases with and without the wind forces.
Modal Analysis Method for Blisks Based on Three-Dimensional Blade and Two-Dimensional Axisymmetric Disk Finite Element Model
Authors: Pan Wangbai , Tang Guoan , Zhang Meiyan
Published: November 2016

In this paper, a novel and efficient modal analysis method is raised to work on blisk structures based on mixed-dimension finite element model (MDFEM). The blade and the disk are modeled separately. The blade model is figured by 3D solid elements considering its complex configuration and its degrees-of-freedom (DOFs) are condensed by dynamic substructural method. Meanwhile, the disk is structured by 2D axisymmetric element developed specially in this paper. The DOFs of entire blisk are tremendously reduced by this modeling approach. The key idea of this method is derivation of displacement compatibility to different dimensional models. Mechanical energy equivalence and summation further contribute to the model synthesis and modal analysis of blade and disk. This method has been successfully applied on the modal analysis of blisk structures in turbine, which reveals its effectiveness and proves that this method reduces the computational time expenses while maintaining the precision performances of full 3D model. Though there is limitation that structure should have proper coverage of blades, this method is still feasible for most blisks in engineering practice.
Investigation of Dry Sliding Wear Behavior of Ni–SiC Microwave Cladding
Authors: Kaushal Sarbjeet , Gupta Dheeraj , Bhowmick Hiralal
Published: November 2016

In the present work, a wear-resistant composite cladding of Ni-based+10% SiC was developed on martensitic stainless steel (SS-420) through a recently developed process microwave hybrid heating (MHH) technique. In the current investigation, domestic microwave oven of frequency 2.45 GHz and 900 W power was used for the development of clads. The metallurgical and mechanical characterizations of developed clads were carried through scanning electron microscope (SEM), X-ray diffraction (XRD), and Vicker's microhardness. The developed clad is uniformly developed and it is metallurgically bonded with the substrate. The average Vicker's microhardness of the clad was 652 ± 90 HV. The tribological behavior of cladding has been investigated through pin-on-disk sliding method against an EN-31 (HRC-62). The clad surface showed good resistance to the sliding wear. It is observed that in case of the clad samples, wear occurs due to dislocation of particles, smearing off of tribofilm, and craters due to pullout of carbides from the matrix.
Investigation of CO2–CH4 Displacement and Transport in Shale for Enhanced Shale Gas Recovery and CO2 Sequestration
Authors: Du Xi-Dong , Gu Min , Duan Shuo , Xian Xue-Fu
Published: November 2016

To gain a better understanding of the enhanced shale gas recovery by CO2 gas injection (CO2-ESGR) technique, the dynamic displacement mechanism of CO2–CH4, the CO2 enhanced shale gas recovery (RCH4), and CO2 storage capacity (VCO2) were studied based on transport properties of CO2 and CH4. Experiments of CO2 injection into shale gas reservoir preadsorbed by CH4 were performed in a fixed bed. Breakthrough curves were obtained under different test conditions and simulated by one-dimension advection-dispersion (AD) model. It was found that dispersion coefficient (K1) rather than molecular diffusivity of CO2 dominated its transport in shale. K1 together with advection velocity (υ) of CO2 during CH4 displacement controls RCH4 and VCO2. When transporting in shale gas reservoir, CO2 had larger dynamic adsorption amount and υ, but smaller K1 than CH4. The competitive transport and adsorption behavior of CO2 and CH4 made it possible for CO2 to store in shale reservoir and to drive the in-place CH4 out of shale reservoir. The transfer zone of CO2–CH4 displacement (CCD) was very wide. High RCH4 and VCO2 were reached at low injection CO2 gas pressure and for small shale particles. Higher injection flow rates of CO2 and temperatures ranging from 298 K to 338 K had a little effect on RCH4 and VCO2. For field conditions, high CO2 injection pressure has to be used because the pore pressure of shale reservoir and adsorption amount of CH4 increase with the increase in depth of shale gas reservoir, but RCH4 is still not high.
Quantification of a Single Gas Bubble Growth in Solvent(s)–CO2–Heavy Oil Systems With Consideration of Multicomponent Diffusion Under Nonequilibrium Conditions
Authors: Shi Yu , Yang Daoyong
Published: November 2016

A mechanistic model has been developed and validated to quantify a single gas bubble growth with considering multicomponent gas diffusion in solvent(s)–CO2–heavy oil systems under nonequilibrium conditions. Experimentally, constant-composition expansion (CCE) experiments are conducted for C3H8–CO2–heavy oil systems under equilibrium and nonequilibrium conditions, respectively. Theoretically, the classic continuity equation, motion equation, diffusion–convection equation, real gas equation, and Peng–Robinson equation of state (PR EOS) are integrated into an equation matrix to dynamically predict gas bubble growth. Also, the viscous term of motion equation on the gas phase pressure is included due mainly to the viscous nature of heavy oil. The newly proposed model has been validated by using the experimentally measured gas bubble radius as a function of time with good accuracy. Combining with the experimental measurements, the critical nucleus radius and gas bubble growth are quantitatively predicted with the newly proposed model. Effects of mass transfer, supersaturation pressure, mole concentration of each component, liquid cell radius, and pressure decline rate on the gas bubble growth are examined and analyzed. In general, gas bubble growth rate is found to increase with an increase of each of the aforementioned five parameters though the contribution of individual component in a gas mixture to the bubble growth rate is different. A one-step pressure drop and the unlimited liquid volume surrounding a gas bubble are considered to be the necessary conditions to generate the linear relationship between gas bubble radius and the square root of time.
Simulation Model of Photovoltaic and Photovoltaic/Thermal Module/String Under Nonuniform Distribution of Irradiance and Temperature
Authors: Marco Tina Giuseppe
Published: November 2016

The modern concepts of sustainable cities and smart grids have caused an increase in the installation of solar systems in urban and suburban areas, where, due to the presence of many obstacles or design constraints, photovoltaic (PV) modules can operate in operating conditions that are very different from the optimal ones (e.g., standard test conditions, STC). Shading and reflection are the main phenomena that cause uneven distribution of irradiance on PV cells; in turn, they create a nonuniform distribution of PV cell temperatures. The latter problem can also be caused by different ventilation regimes in various parts of the PV array. On the other hand, due to the need to exploit different solar technologies (solar thermal and photovoltaic), problems related to the availability of a useful surface can arise. In this context, there is a technology that produces heat end electrical energy at the same time, such a technology is referred to as a solar hybrid photovoltaic/thermal (PV/T). Here, the uneven distribution of temperature is a design input and its effect depends on both path of the water flow and the PV cell connections. To study the electrical behavior of a PV array under mismatching conditions, a suitable matlab/simulink model has been developed. The model has been tested both numerically and experimentally. Finally, an application of this model in the electrical analysis of a PV/T module is reported, and the results are discussed.
An Exact and General Model Order Reduction Technique for the Finite Element Solution of Elastohydrodynamic Lubrication Problems
Authors: Habchi W. , Issa J. S.
Published: November 2016

This work presents an exact and general model order reduction (MOR) technique for a fast finite element resolution of elastohydrodynamic lubrication (EHL) problems. The reduction technique is based on the static condensation principle. As such, it is exact and it preserves the generality of the solution scheme while reducing the size of its corresponding model and, consequently, the associated computational overhead. The technique is complemented with a splitting algorithm to alleviate the hurdle of solving an arising semidense matrix system. The proposed reduced model offers computational time speed-ups compared to the full model ranging between a factor of at least three and at best 15 depending on operating conditions. The results also reveal the robustness of the proposed methodology which allows the resolution of very highly loaded contacts with Hertzian pressures reaching several GPa. Such cases are known to be a numerical challenge in the EHL literature.
An atom-by-atom assembler of defect-free arbitrary two-dimensional atomic arrays
Authors: Barredo Daniel , de Léséleuc Sylvain , Lienhard Vincent , Lahaye Thierry , Browaeys Antoine
Published: November 2016

Making perfect atomic arrays

Arrays of atoms can be a useful resource for quantum information. However, loading atoms into arrays is typically a stochastic process, which leads to imperfections. Two groups have now performed defect-free assembly of atoms into arrays (see the Perspective by Regal). The researchers first loaded the atoms stochastically and imaged the system. They then shuttled the atoms around to form perfect arrays. Barredo
et al.
worked with two-dimensional arrays, creating a variety of spatial configurations. Endres
et al.
manipulated atoms along a line. By further cooling down the atoms and generating interactions among them, the techniques may also find use in quantum simulation.

Science
, this issue p.
972
, p.
1021
; see also p.
1024
Genome Sequences of Eight Bacterial Species Found in Coculture with the HaptophyteChrysochromulina tobin
Authors: Fixen Kathryn R. , Starkenburg Shawn R. , Hovde Blake T. , Johnson Shannon L. , Deodato Chloe R. , Daligault Hajnalka E. , Davenport Karen W. , Harwood Caroline S. , Cattolico Rose Ann
Published: November 2016

The microalgal division Haptophyta uses a range of nutritional sourcing, including mixotrophy. The genome of a member of this taxon,Chrysochromulina tobin, suggests that interactions with its bacterial cohort are critical forC. tobinphysiology. Here, we report the genomes of eight bacterial species in coculture withC. tobin.
Genome Sequence of Clostridium paraputrificum 373-A1 Isolated in Chile from a Patient Infected with Clostridium difficile
Authors: Guerrero-Araya Enzo , Plaza-Garrido Angela , Díaz-Yañez Fernando , Pizaro-Guajardo Marjorie , Valenzuela Sandro L. , Meneses Claudio , Gil Fernando , Castro-Nallar Eduardo , Paredes-Sabja Daniel
Published: November 2016

Clostridium paraputrificum
is a gut microbiota member reported in several cases of bacteremia and coinfections. So far, only one genome sequence of a
C. paraputrificum
(AGR2156) isolate is available. Here, we present the draft genome of
C. paraputrificum
strain 373-A1, isolated from stools from a patient with
C. difficile
infection.
Complete, Closed Genome Sequences of 10 Salmonella enterica subsp.
enterica
Serovar Typhimurium Strains Isolated from Human and Bovine Sources
Authors: Nguyen Scott V. , Harhay Dayna M. , Bono James L. , Smith Timothy P. L. , Fields Patricia I. , Dinsmore Blake A. , Santovenia Monica , Kelley Christy M. , Wang Rong , Bosilevac Joseph M. , Harhay Gregory P.
Published: November 2016

Salmonella enterica
is a leading cause of enterocolitis for humans and animals.
S. enterica
subsp.
enterica
serovar Typhimurium infects a broad range of hosts. To facilitate genomic comparisons among isolates from different sources, we present the complete genome sequences of 10
S
. Typhimurium strains, 5 each isolated from human and bovine sources.
Complete Whole-Genome Sequence of Salmonella enterica subsp.
enterica
Serovar Java NCTC5706
Authors: Fazal Mohammed-Abbas , Alexander Sarah , Burnett Edward , Deheer-Graham Ana , Oliver Karen , Holroyd Nancy , Parkhill Julian , Russell Julie E.
Published: November 2016

Salmonellae are a significant cause of morbidity and mortality globally. Here, we report the first complete genome sequence for
Salmonella enterica
subsp.
enterica
serovar Java strain NCTC5706. This strain is of historical significance, having been isolated in the pre-antibiotic era and was deposited into the National Collection of Type Cultures in 1939.
Draft Genome Sequence of a Novel
Luteimonas
sp. Strain from Coral Mucus, Hawai‘i
Authors: Wan Xuehua , Miller James M. , Rowley Sonia J. , Hou Shaobin , Donachie Stuart P.
Published: November 2016

Luteimonas
sp. strain JM171 was cultivated from mucus collected around the coral
Porites lobata
. The JM171 draft genome of 2,992,353 bp contains 2,672 protein-coding open reading frames, 45 tRNA coding regions, and encodes a putative globin-coupled diguanylate cyclase,
Jm
GReg.
Draft Genome Sequences of Lactobacillus animalis Strain P38 and Lactobacillus reuteri Strain P43 Isolated from Chicken Cecum
Authors: Rezvani Morvarid , Mendoza Mary , Koci Matthew D. , Daron Caitlyn , Levy Josh , Hassan Hosni M.
Published: November 2016

Here, we present the genome sequence of
Lactobacillus animalis
strain P38 and
Lactobacillus reuteri
strain P43, both isolated from the cecum content of a 4-week old chicken fed a diet supplemented with the prebiotic β(1-4)galacto-oligosaccharide (GOS). These indigenous
Lactobacillus
isolates are potential probiotic organisms for poultry.
Draft Genome Sequence of the Oleaginous Yeast
Cryptococcus curvatus
ATCC 20509
Authors: Close Dan , Ojumu John
Published: November 2016

Cryptococcus curvatus
ATCC 20509 is a commonly used nonmodel oleaginous yeast capable of converting a variety of carbon sources into fatty acids. Here, we present the draft genome sequence of this popular organism to provide a means for more in-depth studies of its fatty acid production potential.
Draft Genome Sequence of
Cryptococcus terricola
JCM 24523, an Oleaginous Yeast Capable of Expressing Exogenous DNA
Authors: Close Dan , Ojumu John , Zhang Gui
Published: November 2016

Cryptococcus terricola
JCM 24523 has recently been identified as an oleaginous yeast capable of converting starch into fatty acids. This draft genome sequence provides a platform for elucidating its fatty acid production potential and supporting comparisons with other oleaginous species.
Complete Genome Sequence of the Neonatal Meningitis-Causing Escherichia coli Strain NMEC O18
Authors: Nicholson Bryon A. , Wannemuehler Yvonne M. , Logue Catherine M. , Li Ganwu , Nolan Lisa K.
Published: November 2016

Neonatal meningitis
Escherichia coli
(NMEC) is a common agent of neonatal bacterial meningitis, causing high neonatal mortality and neurologic sequelae in its victims. Here, we present the complete genome sequence of NMEC O18 (also known as NMEC 58), a highly virulent (O18ac:K1, ST416) strain.
Hydrogen metabolism in Escherichia coli: biochemical and genetic evidence for a hydF gene
Authors: Sankar P , Shanmugam K T
Published: November 2016

A new gene whose product is essential for production of all three hydrogenase isoenzymes in Escherichia coli has been identified. This gene, termed hydF, mapped at 59 min in the E. coli chromosome and resided next to the hydB gene. The map order of these genes was hydE, hydF, hydB, fhlA, and fdv. The hydF gene was transcribed from its own promoter and coded for a protein with an apparent molecular weight of 43,000 to 44,000. Expression of the hydF operon was enhanced by anaerobic growth conditions. Partial products of the hydF gene were capable of supporting various levels of hydrogenase activity in a hydF mutant in the presence of the fhlA gene product, also produced from multicopy plasmids. In the presence of a second mutation in an unidentified, unlinked gene, hydrogenase activity in a hydF mutant was restored by plasmids which carried incomplete hydF and hydB+ genes. These results suggest that the products of hydF and fhlA interact with each other and with yet one other gene product.
Mutational analysis of the catalytic and feedback sites of the tryptophan-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase of Escherichia coli
Authors: Ray J M , Yanofsky C , Bauerle R
Published: November 2016

The nucleotide sequence of aroH, the structural gene for the tryptophan-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase [DAHPS(Trp)], is presented, and the deduced amino acid sequence of AroH is compared with that of the tyrosine-sensitive (AroF) and phenylalanine-sensitive (AroG) DAHPS isoenzymes. The high degree of sequence similarity among the three isoenzymes strongly indicates that they have a common evolutionary origin. In vitro chemical mutagenesis of the cloned aroH gene was used to identify residues and regions of the polypeptide essential for catalytic activity and for tryptophan feedback regulation. Missense mutations leading either to loss of catalytic activity or to feedback resistance were found interspersed throughout the polypeptide, suggesting overlapping catalytic and regulatory sites in DAHPS(Trp). We conclude that the specificity of feedback regulation of the isoenzymes was probably acquired by the duplication and divergent evolution of an ancestral gene, rather than by domain recruitment.
Gene encoding a minor extracellular protease in Bacillus subtilis
Authors: Sloma A , Ally A , Ally D , Pero J
Published: November 2016

The gene for a minor, extracellular protease has been identified in Bacillus subtilis. The gene (epr) encoded a primary product of 645 amino acids that was partially homologous to both subtilisin (Apr) and the major internal serine protease (ISP-1) of B. subtilis. Deletion analysis indicated that the C-terminal 240 amino acids of Epr were not necessary for activity. This C-terminal region exhibited several unusual features, including a high abundance of lysine residues and the presence of a partially homologous sequence of 44 amino acids that was directly repeated five times. The epr gene mapped near sacA and was not required for growth or sporulation.
Role of the leader peptide of maltose-binding protein in two steps of the export process
Authors: Thom J R , Randall L L
Published: November 2016

During the process of export of maltose-binding protein to the periplasm of Escherichia coli, the leader peptide is involved in at least two steps. The presence of the leader portion of maltose-binding protein was shown to be necessary to mediate initial binding of the precursor to the membrane. However, the presence of a mutationally altered leader which does not sustain export in vivo was sufficient to allow this interaction. Thus, the defect in export which is manifested in vivo by this mutational substitution occurs at a step that follows membrane association, most likely the translocation step. Translocation occurs at discrete sites that are not uniformly distributed over the cytoplasmic membrane. A large proportion of the membrane involved in translocation has a higher density than that of bulk cytoplasmic membrane.
Motility response of Rhodobacter sphaeroides to chemotactic stimulation
Authors: Poole P S , Armitage J P
Published: November 2016

Tethered rotating cells of Rhodobacter sphaeroides varied widely in their stopping frequency; 45% of cells showed no stops of longer than 1 s, whereas others showed stops of up to several seconds. Individual cells alternated between stops and rotation at a fairly constant rate, without continuous variation. Addition of the chemoattractant propionate to free-swimming cells of R. sphaeroides increased the mean population swimming speed from 15 to 23 microns s-1. After correction for nonmotile cells, the percentage swimming at less than 5 microns s-1 dropped from approximately 22 to 8, whereas the percentage swimming at greater than 50 microns s-1 increased from 6 to 15. However, cells already swimming did not swim faster after propionate addition; the increase in the mean population speed after propionate addition was caused by an increase in the mean run length between stops from 25 to 101 microns. The increased run length was the result of a drop in both the stopping frequency and the length of a stop. Addition of propionate over the range of 10 microM to 1 mM decreased the stopping frequency; this decrease was almost entirely blocked by benzoate, a competitive inhibitor of propionate transport. The chemoattractants acetate and potassium had the same effect as propionate on the distribution of stopping frequency, which demonstrated that this is a general behavioral response to chemotactic stimulation. Adaptation to propionate stimulation was slow and very variable, cultures frequently showing little adaptation over 30 min. This characteristic may be the result of the lack of a highly specific chemosensory system in R. sphaeroides.
Cell surface properties correlated with cohesion in Myxococcus xanthus
Authors: Arnold J W , Shimkets L J
Published: November 2016

The gliding behavior of Myxococcus xanthus cells is controlled by two multigene systems, A and S, which encode information for adventurous and social behaviors, respectively. The S system can be genetically disrupted through mutation, such as a dsp mutation, or phenotypically disrupted by treating cells with the diazo dye Congo red (Arnold and Shimkets, J. Bacteriol. 170:5765-5770, 1988). One of the functions controlled by the S system is cell agglutination. Immediately after the induction of agglutination, wild-type cells begin to form aggregates, and within 30 min the cells are packed side-to-side in clumps containing thousands of cells. Changes in the cohesive properties of S+ cells are correlated with changes in the topology of the cell surface observed by electron microscopy. Two types of cell-associated appendages were observed on wild-type cells: thin filaments (ca. 5 nm in diameter), which have been called fimbriae or pili, at one cell pole, and thick, flaccid filaments (ca. 50 nm in diameter), referred to as fibrils, at both the sides and tips of cells. Cohesion was correlated with the secretion of the thick fibrils, which coat the cell surface and form an extracellular matrix in which the cells are interconnected. Several lines of evidence suggest that these thick fibrils are involved in cohesion. First, Dsp cells were unable to agglutinate or secrete this extracellular material. Second, wild-type cells which were treated with Congo red neither agglutinated nor secreted the extracellular fibrils. Finally, removal of the Congo red from wild-type cells restored cohesion and also restored production of the thick fibrils. Attempts to estimate the efficiency with which two cells cohered following collision suggested that under optimal conditions, one in three collisions resulted in stable contact. The collision efficiency decreased linearly as the cell density increased, suggesting a cell density-dependent regulation of cohesion. Some aspects of gliding behavior can be explained in terms of an inducer and an inhibitor of S motility.
Cloning of the Alcaligenes eutrophus genes for synthesis of poly-beta-hydroxybutyric acid (PHB) and synthesis of PHB in Escherichia coli
Authors: Schubert P , Steinbüchel A , Schlegel H G
Published: November 2016

Eight mutants of Alcaligenes eutrophus defective in the intracellular accumulation of poly-beta-hydroxybutyric acid (PHB) were isolated after transposon Tn5 mutagenesis with the suicide vector pSUP5011. EcoRI fragments which harbor Tn5-mob were isolated from pHC79 cosmid gene banks. One of them, PPT1, was used as a probe to detect the intact 12.5-kilobase-pair EcoRI fragment PP1 in a lambda L47 gene bank of A. eutrophus genomic DNA. In six of these mutants (PSI, API, GPI, GPIV, GPV, and GPVI) the insertion of Tn5-mob was physically mapped within a region of approximately 1.2 kilobase pairs in PP1; in mutant API, cointegration of vector DNA has occurred. In two other mutants (GPII and GPIII), most probably only the insertion element had inserted into PP1. All PHB-negative mutants were completely impaired in the formation of active PHB synthase, which was measured by a radiometric assay. In addition, activities of beta-ketothiolase and of NADPH-dependent acetoacetyl coenzyme A (acetoacetyl-CoA) reductase were diminished, whereas the activity of NADPH-dependent acetoacetyl-CoA reductase was unaffected. In all PHB-negative mutants the ability to accumulate PHB was restored upon complementation in trans with PP1. The PHB-synthetic pathway of A. eutrophus was heterologously expressed in Escherichia coli. Recombinant strains of E. coli JM83 and K-12, which harbor pUC9-1::PP1, pSUP202::PP1, or pVK101::PP1, accumulated PHB up to 30% of the cellular dry weight. Crude extracts of these cells had significant activities of the enzymes PHB synthase, beta-ketothiolase, and NADPH-dependent acetoacetyl-CoA reductase. Therefore, PP1 most probably encodes all three genes of the PHB-synthetic pathway in A. eutrophus. In addition to PHB-negative mutants, we isolated mutants which accumulate PHB at a much lower rate than the wild type does. These PHB-leaky mutants exhibited activities of all three PHB-synthetic enzymes; Tn5-mob had not inserted into PP1, and the phenotype of the wild type could not be restored with fragment PP1. The rationale for this mutant type remains unknown.
Reduction of Mo6+ with elemental sulfur by Thiobacillus ferrooxidans
Authors: Sugio T , Tsujita Y , Katagiri T , Inagaki K , Tano T
Published: November 2016

In the presence of phosphate ions, molybdic ions (Mo6+) were reduced enzymatically with elemental sulfur by washed intact cells of Thiobacillus ferrooxidans to give molybdenum blue. The whole-cell activity that reduced Mo6+ was totally due to cellular sulfur:ferric ion oxidoreductase (SFORase) (T. Sugio, W. Mizunashi, K. Inagaki, and T. Tano, J. Bacteriol. 169:4916-4922, 1987). The activity of M06+ reduction with elemental sulfur was competitively inhibited by Fe3+, Cu2+, and Co2+. The Michaelis constant of SFORase for Mo6+ was 7.6 mM, and the inhibition constants for Fe3+, Cu2+, and Co2+ were 0.084, 0.015, and 0.17 mM, respectively, suggesting that SFORase can reduce not only Fe3+ and Mo6+ but also Cu2+ and Co2+ with elemental sulfur.
Effect of lipopolysaccharide structure on reactivity of antiporin monoclonal antibodies with the bacterial cell surface
Authors: Bentley A T , Klebba P E
Published: November 2016

We studied the reactivity of 66 anti-Escherichia coli B/r porin monoclonal antibodies (MAbs) with several E. coli and Salmonella typhimurium strains. Western immunoblots showed complete immunological cross-reactivity between E. coli B/r and K-12; among 34 MAbs which recognized porin in immunoblots of denatured outer membranes of E. coli B/r, all reacted with OmpF in denatured outer membranes of E. coli K-12. Extensive reactivity, although less than that for strain B/r (31 of 34 MAbs), occurred for porin from a wild-type isolate, E. coli O8:K27. Only one of the MAbs reacted with porin in denatured outer membranes of S. typhimurium. Even with immunochemical amplification of the Western immunoblot technique, only six MAbs recognized S. typhimurium porin (OmpD), demonstrating that there is significant immunological divergence between the porins of these species. Antibody binding to the bacterial surface, which was analyzed by cytofluorimetry, was strongly influenced by lipopolysaccharide (LPS) structure. An intact O antigen, as in E. coli O8:K27, blocked adsorption of all 20 MAbs in the test panel. rfa+ E. coli K-12, without an O antigen but with an intact LPS core, bound seven MAbs. When assayed against a series of rfa E. coli K-12 mutants, the number of MAbs that recognized porin surface epitopes increased sequentially as the LPS core became shorter. A total of 17 MAbs bound porin in a deep rough rfaD strain. Similar results were obtained with S. typhimurium. None of the anti-E. coli B/r porin MAbs adsorbed to a smooth strain, but three antibodies recognized porin on deep rough (rfaF, rfaE) mutants. These data define six distinct porin surface epitopes that are shielded by LPS from reaction with antibodies.
Physiological and structural analysis of light-harvesting mutants of Rhodobacter sphaeroides
Authors: Kiley P J , Varga A , Kaplan S
Published: November 2016

Two mutants of Rhodobacter sphaeroides defective in formation of light-harvesting spectral complexes were examined in detail. Mutant RS103 lacked the B875 spectral complex despite the fact that substantial levels of the B875-alpha polypeptide (and presumably the beta polypeptide) were present. The B800-850 spectral complex was derepressed in RS103, even at high light intensities, and the growth rate was near normal at high light intensity but decreased relative to the wild type as the light intensity used for growth decreased. Mutant RS104 lacked colored carotenoids and the B800-850 spectral complex, as well as the cognate apoproteins. This strain grew normally at high light intensity and, as with RS103, the growth rate decreased as the light intensity used for growth decreased. At very low light intensities, however, RS104 would grow, whereas RS103 would not. Structural analysis of these mutants as well as others revealed that the morphology of the intracytoplasmic membrane invaginations is associated with the presence or absence of the B800-850 complex as well as of carotenoids. A low-molecular-weight intracytoplasmic membrane polypeptide, which may play a role in B800-850 complex formation, is described, as is a 62,000-dalton polypeptide whose abundance is directly related to light intensity as well as the absence of either of the light-harvesting spectral complexes. These data, obtained from studies of mutant strains and the wild type, are discussed in light of photosynthetic membrane formation and the abundance of spectral complexes per unit area of membrane. Finally, a method for the bulk preparation of the B875 complex from wild-type strain 2.4.1 is reported.
Transcriptional regulation, nucleotide sequence, and localization of the promoter of the catBC operon in Pseudomonas putida
Authors: Aldrich T L , Chakrabarty A M
Published: November 2016

The catB and catC genes encode cis,cis-muconate lactonizing enzyme I (EC 5.5.1.1) and muconolactone isomerase (EC 5.3.3.4), respectively. These enzymes are required for the dissimilation of benzoate to beta-ketoadipate by Pseudomonas putida and are under coordinate transcriptional regulation. By deletion analysis and the use of pKT240 as a promoter probe vector, we located a single promoter region for the catBC operon upstream of catB. RNA-DNA hybridization studies, together with reverse transcriptase mapping, demonstrated that this promoter must be activated in the presence of an inducer molecule for effective transcription of the operon. In addition, the transcription initiation site was located 64 base pairs upstream of the catB initiation codon, and sequences upstream of -43 were required for promoter function. The catBC promoter was compared with other positively regulated procaryotic promoters to identify possible consensus sequences.