bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcription factor WRKY46 regulates osmotic stress responses and stomatal movement independently in Arabidopsis
Authors: Ding Zhong Jie , Yan Jing Ying , Xu Xiao Yan , Yu Di Qiu , Li Gui Xin , Zhang Shu Qun , Zheng Shao Jian
Published: April 2014

Drought and salt stress severely inhibit plant growth and development; however, the regulatory mechanisms of plants in response to these stresses are not fully understood. Here we report that the expression of a WRKY transcription factor WRKY46 is rapidly induced by drought, salt and oxidative stresses. T–DNA insertion of WRKY46 leads to more sensitivity to drought and salt stress, whereas overexpression of WRKY46 (OV46) results in hypersensitivity in soil‐grown plants, with a higher water loss rate, but with increased tolerance on the sealed agar plates. Stomatal closing in the OV46 line is insensitive to ABA because of a reduced accumulation of reactive oxygen species (ROS) in the guard cells. We further find that WRKY46 is expressed in guard cells, where its expression is not affected by dehydration, and is involved in light‐dependent stomatal opening. Microarray analysis reveals that WRKY46 regulates a set of genes involved in cellular osmoprotection and redox homeostasis under dehydration stress, which is confirmed by ROS and malondialdehyde (MDA) levels in stressed seedlings. Moreover, WRKY46 modulates light‐dependent starch metabolism in guard cells via regulating QUA‐QUINE STARCH (QQS) gene expression. Taken together, we demonstrate that WRKY46 plays dual roles in regulating plant responses to drought and salt stress and light‐dependent stomatal opening in guard cells.
Small molecules that interact with RNA: riboswitch‐based gene control and its involvement in metabolic regulation in plants and algae
Authors: Bocobza Samuel E. , Aharoni Asaph
Published: April 2014

Riboswitches are RNA elements that bind small molecules and in turn regulate gene expression. This mechanism allows the cell to sense the intracellular concentration of these small molecules. A particular riboswitch typically regulates its adjacent gene by altering the transcription, the translation or the splicing of this gene. Recently, a riboswitch that binds thiamin pyrophosphate (TPP) was characterized and found to regulate thiamin biosynthesis in plants and algae. Furthermore, it appears that this element is an essential regulator of primary metabolism in plants. Manipulation of endogenous riboswitch activity resulted in metabolic phenotypes that underlined the role of these elements and their ligands in preserving metabolic homeostasis. This situation supports the hypothesis that riboswitches could be remnants of the most ancient metabolic regulators. Here, we review the mode of action of the plant and algal TPP riboswitch and its relevance to the metabolic network. We also discuss the potential engineering of riboswitches as metabolite sensors in plants and platforms for gene control. Whether additional such RNA‐based mechanisms exist in plants and in algae is still an open question, yet, the importance of these elements to metabolic regulation is beyond doubt.
A prenatal prediction model for total nucleated cell count increases the efficacy of umbilical cord blood banking
Authors: Manegold‐Brauer Gwendolin , Borner Barbara , Bucher Christoph , Hoesli Irène , Passweg Jakob , Girsberger Sabine , Schoetzau Andreas , Gisin Simona , Visca Eva
Published: April 2014

Background

The most important factor for the selection of an umbilical cord blood unit (CBU) for hematopoietic stem cell transplantation is the total nucleated cell (TNC) count as a surrogate marker for stem cell content in the CBU. At present, about one in five donors can provide a CBU with a sufficient TNC count for umbilical cord blood (UCB) banking. It is labor‐intensive to obtain consent of all eligible donors and optimization of the selection is needed. The purpose of this study was to investigate prenatal clinical predictors for TNC count that would help to identify successful UCB donors already on admission to the delivery unit.

Study Design and Methods

This study was a retrospective analysis of 758 cryopreserved CBUs, collected from 2002 to 2006. Maternal and fetal factors analyzed were maternal age, gravidity, parity, weight, height, diabetes, premature rupture of membranes, gestational age, fetal sex, and birthweight. The impact on a high TNC count (<150 × 107 vs. ≥150 × 107) of the CBU was modeled in a multivariate analysis model.

Results

Fetal birthweight was the strongest predictor (p < 0.001) of TNC count of at least 150 × 107. With a composite score of parity, gestational week, maternal weight and height, fetal sex, and birthweight, a nomogram was developed that increased banking rates from 22.7% to 31.9% while decreasing the number of banked CBUs from 149 to 79.

Conclusions

Our prenatal prediction model increases the efficacy of obtaining informed consent for UCB banking while still allowing relevant numbers of CBUs to be banked.
Foreign Direct Investment, Productivity, Demand for Skilled Labour and Wage Inequality: An Analysis of Uruguay
Authors: Peluffo Adriana
Published: April 2014

This study seeks to identify the causal effects of foreign ownership on productivity, the demand for skilled labour and wage inequality. With this aim, we use differences‐in‐differences techniques for a panel of Uruguayan manufacturing firms in the period 1997–2005. Our results seem to indicate that FDI causes higher productivity and increased demand for skilled labour. Furthermore, although average wages are higher in foreign‐owned firms than in domestic ones, the wage gap between skilled and unskilled workers is wider. It follows that promoting foreign investment enhances productivity. In addition, due to the greater demand for skilled workers, policies such as training schemes would be conducive to raising productivity still further, while other social policies could help to mitigate the wage inequality effects.
Political Connections, Government Intervention and Acquirer Performance in Cross‐border Mergers and Acquisitions: an Empirical Analysis Based on Chinese Acquirers
Authors: Yang Liuyong , Zhang Jingjing
Published: April 2014

The extant literature suggests that the political connections enjoyed by Chinese acquiring firms have both positive and negative effects on their performance in cross‐border mergers and acquisitions (CBMA). We employed firm‐level data on Chinese acquirers from 2001 to 2012, demonstrating that the effect of political connections on mergers and acquisitions performance is determined by external government intervention. Holding the level of political connections constant, the greater the degree of government intervention is, the worse the acquirer's performance in cross‐border mergers and acquisitions will be. We also demonstrated that political connections affect acquirer performance in cross‐border mergers and acquisitions through the channel of preferential access to bank financing, and the acquiring firms' high cash holdings, which are encouraged by the ease of bank financing, have a negative effect on acquirer CBMA performance. Using the Blinder‐Oaxaca decomposition, we investigated changes in the Chinese acquirers' performance following changes in the external policy environment in 2008 and the effect of political connections and other factors on this change.
Characterization of the canine urinary proteome
Authors: Brandt Laura E. , Ehrhart E. J. , Scherman Hataichanok , Olver Christine S. , Bohn Andrea A. , Prenni Jessica E.
Published: April 2014

Background

Urine is an attractive biofluid for biomarker discovery as it is easy and minimally invasive to obtain. While numerous studies have focused on the characterization of human urine, much less research has focused on canine urine.

Objectives

The objectives of this study were to characterize the universal canine urinary proteome (both soluble and exosomal), to determine the overlap between the canine proteome and a representative human urinary proteome study, to generate a resource for future canine studies, and to determine the suitability of the dog as a large animal model for human diseases.

Methods

The soluble and exosomal fractions of normal canine urine were characterized using liquid chromatography tandem mass spectrometry (LC‐MS/MS). Biological Networks Gene Ontology (BiNGO) software was utilized to assign the canine urinary proteome to respective Gene Ontology categories, such as Cellular Component, Molecular Function, and Biological Process.

Results

Over 500 proteins were confidently identified in normal canine urine. Gene Ontology analysis revealed that exosomal proteins were largely derived from an intracellular location, while soluble proteins included both extracellular and membrane proteins. Exosome proteins were assigned to metabolic processes and localization, while soluble proteins were primarily annotated to specific localization processes. Several proteins identified in normal canine urine have previously been identified in human urine where these proteins are related to various extrarenal and renal diseases.

Conclusions

The results of this study illustrate the potential of the dog as an animal model for human disease states and provide the framework for future studies of canine renal diseases.
Global Tracking Controller for Underactuated Ship via Switching Design
Authors: Wu Yuqiang , Zhang Zhongcai , Xiao Na
Published: April 2014

This paper studies the complete state tracking control of an underactuated ship with only two controls, namely, surge force and yaw moment. A novel finite-time switching controller is developed guaranteeing that the ship can track a reference trajectory generated by a virtual ship. The solution is based on the inherent cascaded interconnected structure of the ship dynamics. As opposed to the previous works, the assumptions used in this work are more relaxed in the sense that the reference surge and yaw velocities are allowed to be zero at the same time. Simulation results are given to serve the purpose of demonstrating and validating the proposed tracking methodology.
Ferroelectric phenomena in Si-doped HfO2 thin films with TiN and Ir electrodes
Authors: Lomenzo Patrick D. , Zhao Peng , Takmeel Qanit , Moghaddam Saeed , Nishida Toshikazu , Nelson Matthew , Fancher Chris M. , Grimley Everett D. , Sang Xiahan , LeBeau James M. , Jones Jacob L.
Published: April 2014

Ferroelectric HfO2 is an attractive candidate for future ferroelectric random access memory devices due to its compatibility with the complementary metal-oxide-semiconductor process, conformal deposition, and scaling ability. Crystallization of HfO2 with different dopants and annealing conditions can produce the stabilization of the monoclinic, tetragonal, cubic, or orthorhombic crystal phases. In this work, the authors observe ferroelectric behavior in Si-doped hafnium oxide with TiN and Ir electrodes. Atomic layer deposited 10 nm HfO2 capacitors doped with varying concentrations of SiO2 have been fabricated in the metal–ferroelectric–insulator–semiconductor (MFIS) structure. The ferroelectric characteristics of thin film HfO2 are compared in the MFIS and metal–ferroelectric–metal configurations. Post-metallization anneals were applied to all thin film ferroelectric HfO2 capacitors, resulting in a remanent polarization of up to 22 μC/cm2 and a range of observed coercive voltages, emphasizing the importance of the annealing conditions, electrode materials, and device structure on the ferroelectric properties of thin film HfO2.
Electrochemical etching technique: Conical-long-sharp tungsten tips for nanoapplications
Authors: Bani Milhim Alaeddin , Ben Mrad Ridha
Published: April 2014

This paper proposes an electrochemical etching technique to fabricate tungsten tips. Tips combining well-defined conical shape, a length as large as 2 mm, and sharpness with a radius of curvature of around 20 nm are fabricated using the proposed technique. These tips are needed in a variety of applications including multipoint contact measurements and nanomanipulation. The technique consists of three steps: the first is static etching, which creates a neck-in phenomenon on the wire; the second is dynamic etching, where the wire is oscillated up and down in the solution to form a long conical shape; finally, static etching is applied again to break the wire, and thus, sharp tips are produced. The best operating conditions of the process were experimentally obtained. These factors include the position of the cathode, the length of the immersed wire, and the applied voltage. The effects of these factors on the etching current and tip fidelity were also examined based on the measured etching current. In particular, the position of the cathode determines the strength of the electrical field near the air/solution interface; the immersed wire depth determines mainly the equivalent resistance of the process and thus controls the etching current; and the applied voltage defines the etching rate of the wire.
Electrostatic Deformation of Liquid Surfaces by a Charged Rod and a Van de Graaff Generator
Authors: Slisko Josip , García-Molina Rafael , Abril Isabel
Published: April 2014

Authors of physics textbooks frequently use the deflection of a thin, vertically falling water jet by a charged balloon,1–3 comb,4–6 or rod7–9 as a visually appealing and conceptually relevant example of electrostatic attraction. Nevertheless, no attempts are made to explore whether these charged bodies could cause visible deformation of a horizontal water surface. That being so, we were quite surprised when we discovered that a 19th-century French book10 contained a drawing showing an appreciable deformation of an oil surface caused by a charged rod. When we initially tried to recreate this electrostatics demonstration, we didn't succeed in reproducing the effect with a charged rod. Despite the initial unsuccessful try, we were not discouraged and we modified the demonstration a little bit, finding that it was possible to cause visible deformations of different liquid surfaces by using a Van de Graaff generator, as we will explain later.
The Sponge Resistor Model — A Hydrodynamic Analog to Illustrate Ohm's Law, the Resistor Equation R=ρℓ/A, and Resistors in Series and Parallel
Authors: Pfister Hans
Published: April 2014

Physics students encountering electric circuits for the first time often ask why adding more resistors to a circuit sometimes increases and sometimes decreases the resulting total resistance. It appears that these students have an inadequate understanding of current flow and resistance. Students who do not adopt a model of current, voltage, and resistance necessarily resort to memorizing formulas for calculating, e.g., the resistance of a resistor network. For these students, certain properties of electric circuits may remain mysterious or puzzling.
Nearly 1.4 Million High School Physics Students — Enrollments in AP and second-year courses up 26% even though number of graduates down in 2012–13
Authors: White Susan , Tesfaye Casey Langer
Published: April 2014

Since 1987, the Statistical Research Center at the American Institute of Physics has regularly conducted a nationwide survey of high school physics teachers to take a closer look at physics in U.S. high schools.1 We contact all of the teachers who teach at least one physics course at a nationally representative sample of all U.S. high schools—both public and private schools. Our most recent survey was conducted during the 2012–13 school year. While our questionnaire covers a number of areas of interest, in this article we examine the number of students enrolled in high school physics courses and the types of courses offered. We also take a closer look at the prior physics experience of students enrolled in Advanced Placement (AP) Physics classes.
Simplified Models for the Drag Coefficient of a Pitched Baseball
Authors: Kagan David , Nathan Alan M.
Published: April 2014

The classic experiment to measure the drag coefficient involves dropping coffee filters.1 Wouldn't it be more fun to try something different? In fact, an experiment on the drag force is conducted nearly 4000 times a day during the baseball season and you have free access to this PITCHf/x data!2
Experimenting with Inexpensive Plastic Springs
Authors: Perez Leander , Marques Adriana , Sánchez Iván
Published: April 2014

Acommon undergraduate laboratory experience is the determination of the elastic constant of a spring, whether studying the elongation under a static load or studying the damped harmonic motion of the spring with a suspended mass. An alternative approach to this laboratory experience has been suggested by Menezes et al.,1 aimed at studying the dependence of the elastic constant with the length of the spring. The proposal by Menezes et al.1 consists of determining the springs elastic constant K (defined as the ratio of the elongation δ and the magnitude of applied force F) using the usual method of suspending a mass m and studying the dependence of K on the springs unstretched length L. The authors vary the length of a spring by cutting pieces off the end and obtain an experimental relation K=αL−1, with α a constant depending on the spring materials and geometrical factors. In our teaching practice we have been using the experience in Ref. 1 as an opportunity for advanced students to earn extra credit after the ordinary laboratory experience. The results we have obtained so far confirm the work of Menezes et al.1 and inevitably motivate a discussion on the dependence of the elastic constant K with some other spring parameters. The present work originates from the quest of a couple of students to determine the role of the spring coil diameter D on the value of K and α.
An Unusual Exponential Graph
Authors: Syed M. Qasim , Lovatt Ian
Published: April 2014

This paper is an addition to the series of papers on the exponential function begun by Albert Bartlett.1 In particular, we ask how the graph of the exponential function y=e−t/τ would appear if y were plotted versus ln t rather than the normal practice of plotting ln y versus t. In answering this question, we find a new way to interpret the mean life (or time constant) τ using such a linear-log graph.
Why Was Kelvin's Estimate of the Earth's Age Wrong?
Authors: Lovatt Ian , Syed M. Qasim
Published: April 2014

This is a companion to our previous paper1 in which we give a published example, based primarily on Perry's work,2,3 of a graph of ln y versus t when y is an exponential function of t. This work led us to the idea that Lord Kelvin's (William Thomson's) estimate of the Earth's age was wrong not because he did not account for radioactivity, as is commonly believed,4 but because he used the wrong model for Earth's heat loss. We feel this idea is worth spreading. To this end (following England et al.2,3), we examine two questions, the first about the radioactivity part and the second about Perry's alternate model for Earth's heat loss.
Energy Theater
Authors: Daane Abigail R. , Wells Lindsay , Scherr Rachel E.
Published: April 2014

Energy Theater is a dynamic, full-body activity that engages all students in representing the flow of energy in various phenomena, such as a light bulb burning steadily or a refrigerator cooling food.1,2 In Energy Theater, each participant acts as a unit of energy that has one form at a time. Regions on the floor correspond to objects in a physical scenario, and participants move from one region to another to demonstrate the flow of energy among objects. (See Figs. 1, 3, and 4.) The goal of Energy Theater is for students to track energy transfers and transformations in real-world energy scenarios while employing the principle of energy conservation and disambiguating matter and energy. Unlike most representations of energy, which are static before-and-after accounting schemes for energy changes, Energy Theater is a dynamic representation that provides a natural stepping stone toward the more advanced ideas of energy density, energy current, and a continuity equation relating them. The fact that conservation of energy is embedded in the representation encourages students to “find the energy” in situations where it may be imperceptible. The rules of Energy Theater are listed in Fig. 2.
Motivating Students to Do Homework
Authors: Kontur Frederick J. , Terry Nathan B.
Published: April 2014

How do you motivate students to do their homework? Some instructors make students' homework scores a significant percentage of the final course grade. In that case, how much course credit is required? Some instructors do not grade homework at all, instead relying on students' intrinsic motivation to learn the course material. Will this actually work? Some instructors might motivate students by having quiz and/or exam problems closely match the assigned homework problems. In this article, we report on the effectiveness of grade incentives, homework-based quiz problems, and intrinsic motivation for 16 semesters of introductory mechanics and introductory electricity and magnetism (E&M) courses at the United States Air Force Academy (USAFA) between fall 2008 and spring 2012.
Learning Gains in Introductory Astronomy: Online Can Be as Good as Face-to-Face
Authors: Margoniner Vera
Published: April 2014

Universities and even high schools are moving more and more to online instruction as a cost-effective way to reach more students with fewer resources. This naturally raises the question: Can online learning be effective? (The question is not “Is online learning effective?” because just like face-to-face instruction, online instruction includes a diverse array of techniques.) In this paper I compare online and flipped face-to-face versions of an introductory astronomy course. Both versions were designed around student-centered learning principles, but the specific implementation of these principles varied according to the strengths of each type of instruction. Normalized Hake gains on the Star Properties Concept Inventory (SPCI) were quite similar for both classes: 56% and 58% for the online and flipped face-to-face versions, respectively. The gains obtained by students with low pre-test scores were as good as the ones achieved by students with high pre-test scores.
Decibels Via Loudness — Distance Properties of a Loudspeaker
Authors: Bates Alan
Published: April 2014

Loudness, or sound intensity level, is a human perceived or subjective measurement with units, decibels, based on the response of the human ear to different sound intensities. The response of the human ear at fixed frequency is close to being logarithmic.1,2 The experiment reported here investigates the relationship between measured sound intensity level, or loudness, and distance from a sound source such as a loudspeaker.
Scaling in Theropod Dinosaurs: Femoral Bone Dimensions
Authors: Lee Scott A.
Published: April 2014

Finding topics that inspire students is an important aspect of any physics course. Virtually everyone is fascinated by Tyrannosaurus rex, and the excitement of the class is palpable when we explore scaling effects in T. rex and other bipedal theropod dinosaurs as part of our discussion of mechanics and elasticity. In this paper, we explore the role of longitudinal stress in the femur bones due to the weight of the dinosaur in determining how the geometry of the femur changes with size of the theropod. This is one area of allometry the study of how different biological characteristics scale with size.1
Caution: Strong gravitational field present
Authors: Reif Marc
Published: April 2014

I came up with a new way to introduce the concept of a constant gravitational field near the surface of the Earth. I made “g-field detectors” (see Fig. 1) and suspended them by strings from the ceiling in a regular spacing. The detectors are cardstock arrows with a hole punched out of them and the letter “g” in the center.
Aircraft noise retrofit feasibility. I. Program objectives and scope
Authors: Koenig Robert J.
Published: April 2014

Government and the air transport industry have been faced with the problem of quieting existing low-bypass-ratio turbofan-powered aircraft which constitute nearly 90% of the current U.S. air carrier fleet. Noise had not been a design parameter for these aircraft, since they were designed prior to the noise limits specified by Federal Aircraft Regulation Part 36. This paper describes the FAA-sponsored retrofit feasibility program and related NASA-and industry-funded efforts. The program was designed to provide test data for use in determining whether the older-design aircraft could be modified for meaningful noise reduction. The modifications were required to be technologically practicable, economically reasonable, and appropriate for the aircraft type. The program included ground and flight tests of flight weight hardware capable of airworthiness certification.
Frequency Response and Spatial Fluctuations in a Room
Authors: Harrison Mark
Published: April 2014

For a constant source in a room, it is well-known that as the frequency is varied the sound pressure at a point varies erratically. Further, if the frequency is fixed and the observation point is moved, spatial fluctuations will be observed. The question arises as to the statistics of these fluctuations. In the case of high eigenvalues, one may define the concept of spatial-probability density for the acoustic pressure, and, by using an argument based upon the central-limit theorem, one may show that this probability density is Gaussian with a computable standard deviation. It is then shown that, if the observation point is fixed and the frequency is varied, for the high eigenvalue the frequency-response fluctuations are also Gaussian with a computable standard deviation. [This work has been supported by the U. S. Office of Naval Research.]
Average Control for Sinusoidal and Random-Vibration Testing
Authors: Usher Theron
Published: April 2014

Time-division multiplexers (TDM) have found application in providing control from the average of several acceleration magnitudes for swept-sinusoidal vibration tests, and also control to the average of several acceleration spectral densities for wide-band random tests. The vibration testing systems using the TDM are described. Pertinent system parameters are determined mathematically in order to limit signal harmonic distortion for the sinusoidal case, and to limit test level modulation and spectral spreading for the random case. A special case for sinusoidal testing in which a narrow-band tracking filter is used on the output of the TDM is also discussed.
Acoustic attenuation in surface-based ducts
Authors: Williams A. O. , Ryder R. D.
Published: April 2014

Attenuation of underwater sound propagated in surface-based ducts has heretofore been analyzed for a bottomless underlying ocean into which “leaked” energy vanishes—an artificial assumption, and one untenable in shallow waters. An alternative concept is proposed. Sound originally in the duct is transferred by intermodal resonances into the underlying ocean, where the acoustic energy dissipates before the return half of resonances can occur. Resonance periods are describable in terms of horizontal range r traversed in those periods. Starting at r = 0, with normal modes representing the sound as confined in the duct, each intermodal resonance is traced out to the range r of maximum transfer, and is terminated there. The ducted sound field remaining at any r is the sum of mode parts that have not yet attained half-resonance periods. A simplified model has pressure-release surface and bottom, no explicit dissipation, and three isothermal layers—a barrier of higher sound speed between the duct and an identical underlying ocean. Analytical results are encouraging. Notably, at short ranges the average ducted intensity falls off as r−2, changing at greater ranges toward r−1 behavior, thereby approximating measurements and previous theoretical calculations.
Development of noise reduction concepts for the 707 airplane
Authors: Nelsen M. D. , Callaway V. E.
Published: April 2014

Flyover noise characteristics are presented for the Boeing Model 707-300 B/C equipped with standard production nacelles and with experimental quiet nacelles modified by the addition of sound-absorbing materials. Acoustic treatment theory and technology concepts required to develop the quiet nacelles are discussed. Results from, and techniques for, certification flight testing used to demonstrate that the modified aircraft meets FAA noise regulations are presented. Comparison of noise levels due to operation of the modified aircraft and other in-service aircraft is provided. [This development work was jointly sponsored by The Boeing Company and by the FAA under Contract FA71WA-2728.]
Aircraft noise retrofit feasibility. II. Retrofit program results and applications
Authors: Koenig Robert J.
Published: April 2014

Government/Industry cooperation has lead to a successful retrofit feasibility program. Technologically feasible, economically reasonable solutions are available to the problem of quieting the JT3D- and JT8D-powered aircraft fleet. This paper reviews the results presented in previous papers and covers their potential applications. FAA rule-making activity directed toward implementation of retrofit is discussed.
Ultra-well-tempered clavier
Authors: Venderslice R.
Published: April 2014

Contrary to modern prejudices, historical tunings for fixed-pitch instruments like organs and harpsichords do not reflect fumbling efforts of our forebears to attain that acme of uniform mistuning known as equal temperament. Keyboard tuning theory has its share and then some of numerological nonsence—e. g., the “tuning/temperament” (viz., rational/irrational) distinction, pointless in view of expressed or implied tolerances—but the harshness of equal-tempered thirds is a quite palpable consequence of the procrustean approach which earlier experts eschewed. Smooth triads in a restricted subset of key signatures were achieved by just and meantone tunings; however, even within the constraint of the 12-note octave there are unequal but “correct” temperaments enabling use of all 24 major and minor signatures, with progression of tonalities. Furthermore, in the computer age the 12-note limitation can be transcended without requiring performers to face a keyboard monstrosity. The 53-note octave offers virtually just intonation in every key, with the choice of pure major thirds for harmonic, or Pythagorean ditones for melodic, purposes. The steps are 22.6 cents, roughly midway between the syntonic and ditonic commas in size. Selection of the appropriate step for each scale degree in any key could be automatic. Nor would a 53-division piano necessarily have more strings than present ones. A typology of tunings, based on Barbour's survey, graphically illustrates the tradeoffs by which at different times various of the competing desiderata have been maximized.
Arrival-time fluctuations of coherent reflections from surface gravity water waves
Authors: Badiey Mohsen , Eickmeier Justin , Song Aijun
Published: April 2014

Arrival time fluctuations of coherent reflections from surface gravity waves are examined. A two-dimensional ray model with an evolving rough sea surface is used to explain the mechanism and formation of the deterministic striation patterns due to the surface reflection. Arrival time predictions from the ray model match qualitatively well with the measurements from bidirectional acoustic transmissions in a water depth of 100 m.
A 3-D elasticity theory based model for acoustic radiation from multilayered anisotropic plates
Authors: Shen C. , Xin F. X. , Lu T. J.
Published: April 2014

A theoretical model built upon three-dimensional elasticity theory is developed to investigate the acoustic radiation from multilayered anisotropic plates subjected to a harmonic point force excitation. Fourier transform technique and stationary phase method are combined to predict the far-field radiated sound pressure of one-side water immersed plate. Compared to equivalent single-layer plate models, the present model based on elasticity theory can differentiate radiated sound pressure between dry-side and wet-side excited cases, as well as discrepancies induced by different layer sequences for multilayered anisotropic plates. These results highlight the superiority of the present theoretical model especially for handling multilayered anisotropic structures.
Molecular Method for Detection of Total Coliforms in Drinking Water Samples
Authors: Maheux Andrée F. , Boudreau Dominique K. , Bisson Marc-Antoine , Dion-Dupont Vanessa , Bouchard Sébastien , Nkuranga Martine , Bergeron Michel G. , Rodriguez Manuel J.
Published: April 2014

This work demonstrates the ability of a bacterial concentration and recovery procedure combined with three different PCR assays targeting the
lacZ
,
wecG
, and 16S rRNA genes, respectively, to detect the presence of total coliforms in 100-ml samples of potable water (presence/absence test). PCR assays were first compared to the culture-based Colilert and MI agar methods to determine their ability to detect 147 coliform strains representing 76 species of
Enterobacteriaceae
encountered in fecal and environmental settings. Results showed that 86 (58.5%) and 109 (74.1%) strains yielded a positive signal with Colilert and MI agar methods, respectively, whereas the
lacZ
,
wecG
, and 16S rRNA PCR assays detected 133 (90.5%), 111 (75.5%), and 146 (99.3%) of the 147 total coliform strains tested. These assays were then assessed by testing 122 well water samples collected in the Québec City region of Canada. Results showed that 97 (79.5%) of the samples tested by culture-based methods and 95 (77.9%), 82 (67.2%), and 98 (80.3%) of samples tested using PCR-based methods contained total coliforms, respectively. Consequently, despite the high genetic variability of the total coliform group, this study demonstrated that it is possible to use molecular assays to detect total coliforms in potable water: the 16S rRNA molecular assay was shown to be as efficient as recommended culture-based methods. This assay might be used in combination with an
Escherichia coli
molecular assay to assess drinking water quality.
Protective Effects of Lactobacillus plantarum CCFM8610 against Chronic Cadmium Toxicity in Mice Indicate Routes of Protection besides Intestinal Sequestration
Authors: Zhai Qixiao , Wang Gang , Zhao Jianxin , Liu Xiaoming , Narbad Arjan , Chen Yong Q. , Zhang Hao , Tian Fengwei , Chen Wei
Published: April 2014

Our previous study confirmed the ability of
Lactobacillus plantarum
CCFM8610 to protect against acute cadmium (Cd) toxicity in mice. This study was designed to evaluate the protective effects of CCFM8610 against chronic Cd toxicity in mice and to gain insights into the protection mode of this strain. Experimental mice were divided into two groups and exposed to Cd for 8 weeks via drinking water or intraperitoneal injection. Both groups were further divided into four subgroups, control, Cd only, CCFM8610 only, and Cd plus CCFM8610. Levels of Cd were measured in the feces, liver, and kidneys, and alterations of several biomarkers of Cd toxicity were noted. The results showed that when Cd was introduced orally, cotreatment with Cd and CCFM8610 effectively decreased intestinal Cd absorption, reduced Cd accumulation in tissue, alleviated tissue oxidative stress, reversed hepatic and renal damage, and ameliorated the corresponding histopathological changes. When Cd was introduced intraperitoneally, administration of CCFM8610 did not have an impact on tissue Cd accumulation or reverse the activities of antioxidant enzymes. However, CCFM8610 still offered protection against oxidative stress and reversed the alterations of Cd toxicity biomarkers and tissue histopathology. These results suggest that CCFM8610 is effective against chronic cadmium toxicity in mice. Besides intestinal Cd sequestration, CCFM8610 treatment offers direct protection against Cd-induced oxidative stress. We also provide evidence that the latter is unlikely to be mediated via protection against Cd-induced alteration of antioxidant enzyme activities.
300-Fold Increase in Production of the Zn
2+
-Dependent Dechlorinase TrzN in Soluble Form via Apoenzyme Stabilization
Authors: Jackson Colin J. , Coppin Christopher W. , Carr Paul D. , Aleksandrov Alexey , Wilding Matthew , Sugrue Elena , Ubels Joanna , Paks Michael , Newman Janet , Peat Thomas S. , Russell Robyn J. , Field Martin , Weik Martin , Oakeshott John G. , Scott Colin
Published: April 2014

Microbial metalloenzymes constitute a large library of biocatalysts, a number of which have already been shown to catalyze the breakdown of toxic chemicals or industrially relevant chemical transformations. However, while there is considerable interest in harnessing these catalysts for biotechnology, for many of the enzymes, their large-scale production in active, soluble form in recombinant systems is a significant barrier to their use. In this work, we demonstrate that as few as three mutations can result in a 300-fold increase in the expression of soluble TrzN, an enzyme from
Arthrobacter aurescens
with environmental applications that catalyzes the hydrolysis of triazine herbicides, in
Escherichia coli
. Using a combination of X-ray crystallography, kinetic analysis, and computational simulation, we show that the majority of the improvement in expression is due to stabilization of the apoenzyme rather than the metal ion-bound holoenzyme. This provides a structural and mechanistic explanation for the observation that many compensatory mutations can increase levels of soluble-protein production without increasing the stability of the final, active form of the enzyme. This study provides a molecular understanding of the importance of the stability of metal ion free states to the accumulation of soluble protein and shows that differences between apoenzyme and holoenzyme structures can result in mutations affecting the stability of either state differently.
Benzoate Metabolism Intermediate Benzoyl Coenzyme A Affects Gentisate Pathway Regulation in Comamonas testosteroni
Authors: Chen Dong-Wei , Zhang Yun , Jiang Cheng-Ying , Liu Shuang-Jiang
Published: April 2014

A previous study showed that benzoate was catabolized via a coenzyme A (CoA)-dependent epoxide pathway in
Azoarcus evansii
(R. Niemetz, U. Altenschmidt, S. Brucker, and G. Fuchs, Eur. J. Biochem. 227:161-168, 1995), but gentisate 1,2-dioxygenase was induced. Similarly, we found that the
Comamonas testosteroni
strain CNB-1 degraded benzoate via a CoA-dependent epoxide pathway and that gentisate 1,2-dioxygenase (GenA) was also induced when benzoate or 3-hydroxybenzoate served as a carbon source for growth. Genes encoding the CoA-dependent epoxide (
box
genes) and gentisate (
gen
genes) pathways were identified. Genetic disruption revealed that the
gen
genes were not involved in benzoate and 3-hydroxybenzoate degradation. Hence, we investigated
gen
gene regulation in the CNB-1 strain. The P

genA

promoter, a MarR-type regulator (GenR), and the GenR binding site were identified. We found that GenR took gentisate, 3-hydroxybenzoate, and benzoyl-CoA as effectors and that binding of GenR to its target DNA sequence was prohibited when these effectors were present.
In vivo
studies showed that the CNB-1 mutant that lost benzoyl-CoA synthesis was not able to activate P

genA

promoter, while transcription of
genA
was upregulated in another CNB-1 mutant that lost the ability to degrade benzoyl-CoA. The finding that benzoyl-CoA (a metabolic intermediate of benzoate degradation) and 3-hydroxybenzoate function as GenR effectors explains why GenA was induced when CNB-1 grew on benzoate or 3-hydroxybenzoate. Regulation of gentisate pathways by MarR-, LysR-, and IclR-type regulators in diverse bacterial groups is discussed in detail.
Pyruvate Formate-Lyase Is Essential for Fumarate-Independent Anaerobic Glycerol Utilization in the Enterococcus faecalis Strain W11
Authors: Doi Yuki , Ikegami Yuki
Published: April 2014

Although anaerobic glycerol metabolism in
Enterococcus faecalis
requires exogenous fumarate for NADH oxidation,
E. faecalis
strain W11 can metabolize glycerol in the absence of oxygen without exogenous fumarate. In this study, metabolic end product analyses and reporter assays probing the expression of enzymes involved in pyruvate metabolism were performed to investigate this fumarate-independent anaerobic metabolism of glycerol in W11. Under aerobic conditions, the metabolic end products of W11 cultured with glycerol were similar to those of W11 cultured with glucose. However, when W11 was cultured anaerobically, most of the glucose was converted to
l
-lactate, but glycerol was converted to ethanol and formate. During anaerobic culture with glycerol, the expression of the
l
-lactate dehydrogenase and pyruvate dehydrogenase E1αβ genes in W11 was downregulated, whereas the expression of the pyruvate formate-lyase (Pfl) and aldehyde/alcohol dehydrogenase genes was upregulated. These changes in the expression levels caused the change in the composition of end products. A
pflB
gene disruptant (Δ
pfl
mutant) of W11 could barely utilize glycerol under anaerobic conditions, but the growth of the Δ
pfl
mutant cultured with either glucose or dihydroxyacetone (DHA) under anaerobic conditions was the same as that of W11. Glucose metabolism and DHA generates one NADH molecule per pyruvate molecule, whereas glycerol metabolism in the dehydrogenation pathway generates two NADH molecules per pyruvate molecule. These findings demonstrate that NADH generated from anaerobic glycerol metabolism in the absence of fumarate is oxidized through the Pfl-ethanol fermentation pathway. Thus, Pfl is essential to avoid the accumulation of excess NADH during fumarate-independent anaerobic glycerol metabolism.
Two Different
rpf
Clusters Distributed among a Population of Stenotrophomonas maltophilia Clinical Strains Display Differential Diffusible Signal Factor Production and Virulence Regulation
Authors: Huedo Pol , Yero Daniel , Martínez-Servat Sònia , Estibariz Iratxe , Planell Raquel , Martínez Paula , Ruyra Àngels , Roher Nerea , Roca Ignasi , Vila Jordi , Daura Xavier , Gibert Isidre
Published: April 2014

The quorum-sensing (QS) system present in the emerging nosocomial pathogen
Stenotrophomonas maltophilia
is based on the signaling molecule diffusible signal factor (DSF). Production and detection of DSF are governed by the
rpf
cluster, which encodes the synthase RpfF and the sensor RpfC, among other components. Despite a well-studied system, little is known about its implication in virulence regulation in
S. maltophilia
. Here, we have analyzed the
rpfF
gene from 82
S. maltophilia
clinical isolates. Although
rpfF
was found to be present in all of the strains, it showed substantial variation, with two populations (
rpfF
-1 and
rpfF
-2) clearly distinguishable by the N-terminal region of the protein. Analysis of
rpfC
in seven complete genome sequences revealed a corresponding variability in the N-terminal transmembrane domain of its product, suggesting that each RpfF variant has an associated RpfC variant. We show that only RpfC–RpfF-1 variant strains display detectable DSF production. Heterologous
rpfF
complementation of Δ
rpfF
mutants of a representative strain of each variant suggests that RpfF-2 is, however, functional and that the observed DSF-deficient phenotype of RpfC–RpfF-2 variant strains is due to permanent repression of RpfF-2 by RpfC-2. This is corroborated by the Δ
rpfC
mutant of the RpfC–RpfF-2 representative strain. In line with this observations, deletion of
rpfF
from the RpfC–RpfF-1 strain leads to an increase in biofilm formation, a decrease in swarming motility, and relative attenuation in the
Caenorhabditis elegans
and zebrafish infection models, whereas deletion of the same gene from the representative RpfC–RpfF-2 strain has no significant effect on these virulence-related phenotypes.
The Transcription Factor Mlc Promotes Vibrio cholerae Biofilm Formation through Repression of Phosphotransferase System Components
Authors: Pickering Bradley S. , Lopilato Jane E. , Smith Daniel R. , Watnick Paula I.
Published: April 2014

The phosphoenol phosphotransferase system (PTS) is a multicomponent signal transduction cascade that regulates diverse aspects of bacterial cellular physiology in response to the availability of high-energy sugars in the environment. Many PTS components are repressed at the transcriptional level when the substrates they transport are not available. In
Escherichia
coli, the transcription factor Mlc (for
m
akes
l
arge
c
olonies) represses transcription of the genes encoding enzyme I (EI), histidine protein (HPr), and the glucose-specific enzyme IIBC (EIIBC
Glc
) in defined media that lack PTS substrates. When glucose is present, the unphosphorylated form of EIIBC
Glc
sequesters Mlc to the cell membrane, preventing its interaction with DNA. Very little is known about
Vibrio cholerae
Mlc. We found that
V. cholerae
Mlc activates biofilm formation in LB broth but not in defined medium supplemented with either pyruvate or glucose. Therefore, we questioned whether
V. cholerae
Mlc functions differently than
E. coli
Mlc. Here we have shown that, like
E. coli
Mlc,
V. cholerae
Mlc represses transcription of PTS components in both defined medium and LB broth and that
E. coli
Mlc is able to rescue the biofilm defect of a
V. cholerae
Δ
mlc
mutant. Furthermore, we provide evidence that Mlc indirectly activates transcription of the
vps
genes by repressing expression of EI. Because activation of the
vps
genes by Mlc occurs under only a subset of the conditions in which repression of PTS components is observed, we conclude that additional inputs present in LB broth are required for activation of
vps
gene transcription by Mlc.
Monitoring of Commitment, Blocking, and Continuation of Nutrient Germination of Individual Bacillus subtilis Spores
Authors: Zhang Pengfei , Liang Jintao , Yi Xuan , Setlow Peter , Li Yong-qing
Published: April 2014

Short exposures of
Bacillus
spores to nutrient germinants can commit spores to germinate when germinants are removed or their binding to the spores' nutrient germinant receptors (GRs) is inhibited.
Bacillus subtilis
spores were exposed to germinants for various periods, followed by germinant removal to prevent further commitment. Release of spore dipicolinic acid (DPA) was then measured by differential interference contrast microscopy to monitor germination of multiple individual spores, and spores did not release DPA after 1 to 2 min of germinant exposure until ∼7 min after germinant removal. With longer germinant exposures, percentages of committed spores with times for completion of DPA release (
T
release
) greater than the time of germinant removal (
T
b
) increased, while the time
T
lag
−
T
b
, where
T
lag
represents the time when rapid DPA release began, was decreased but rapid DPA release times (Δ
T
release
=
T
release
−
T
lag
) were increased; Factors affecting average
T
release
values and the percentages of committed spores were germinant exposure time, germinant concentration, sporulation conditions, and spore heat activation, as previously shown for commitment of spore populations. Surprisingly, germination of spores given a 2nd short germinant exposure 30 to 45 min after a 1st exposure of the same duration was significantly higher than after the 1st exposure, but the number of spores that germinated in the 2nd germinant exposure decreased as the interval between germinant exposures increased up to 12 h. The latter results indicate that spores have some memory, albeit transient, of their previous exposure to nutrient germinants.