bluuebunny/crossref_metadata_2025 huggingface dataset:
System Modeling and Simulation of In-Stream Hydrokinetic Turbines for Power Management and Control
Authors: Tzelepis Vasileios , VanZwieten James H. , Xiros Nikolaos I. , Sultan Cornel
Published: November 2016

Electricity generation from moving currents without using dams (i.e., in-stream hydrokinetic electricity) has the potential to introduce multiple GW of renewable power to U.S. grids. This study evaluates a control system designed to regulate the generator rotor rate (rpm) to improve power production from in-stream hydrokinetic turbines. The control algorithm is evaluated using numerical models of both a rigidly mounted tidal turbine (TT) and a moored ocean current turbine (OCT) coupled to an induction electric machine model. The moored simulation utilizes an innovative approach for coupling a multiple degrees-of-freedom (DOF) nonlinear hydrodynamic/mechanical turbine model with a nonlinear electromechanical generator model. Based on the turbine torque-speed characteristic, as well as the asynchronous machine features, a proportional–integral (PI) controller is used to generate a correction term for the frequency of the three-phase sinusoidal voltages that are supplied to the asynchronous generator. The speed control of the induction generator through the supply frequency is accomplished by a simplified voltage source inverter (VSI). The simplified VSI consists of control voltage sources (CVSs), while the comparison with a real VSI using diodes and transistors, which are controlled by pulse width modulation (PWM) technique, is also presented. Simulations are used to evaluate the developed algorithms showing that rpm fluctuations are around 0.02 for a tidal turbine operating in a wave field with a 6 m significant wave height and around 0.005 for a moored ocean current turbine operating in a wave field with a 2 m significant wave height.
Control of Blow-Down Wind Tunnel Using Combined Extended Kalman and Nonlinear Predictive Filters
Authors: Zheng Ruixiang , Li Mian , Wang Zhaoguang , Zhang Qiang
Published: November 2016

A blow-down wind tunnel is a typical nonlinear time-varying system facing the coupling effects between the pressure and temperature during the short-time test procedure. The control of blow-down wind tunnels has been discussed for a long time and a satisfactory general solution to this problem is still of interests. This paper aims to model the internal relationship of the state variables of the wind tunnel by using thermodynamic theories. With the developed model, a new control method combining extended Kalman filter (EKF) together with auxiliary nonlinear predictive filter (NPF) is proposed to improve the control performance of the blow-down wind tunnel controller, in terms of accuracy and robustness. The transient coupling effects between the pressure and temperature are fully considered in the proposed approach. The results from the simulation and experiments are consistent and demonstrate that the controller based on EKF combined together with NPF can work better than previously proposed EKF-based controller.
Audiogram of the kea parrot, Nestor notabilis
Authors: Schwing Raoul , Nelson Ximena J. , Parsons Stuart
Published: November 2016

Vocal communication requires the sender to produce a sound, which transmits through the environment and is perceived by the receiver. Perception is dependent on the quality of the received signal and the receiver's frequency and amplitude sensitivity; hearing sensitivity of animals can be tested using behavioural detection tasks, showing the physical limitations of sound perception. Kea parrots (Nestor notabilis) were tested for their ability to hear sounds that varied in terms of both frequency and amplitude by means of a simple auditory detection task. Audiograms for three kea were similar, with the region of highest sensitivity (1–5 kHz) corresponding to the frequency of the highest amplitude in kea calls. Compared with other parrots and other bird taxa, the overall shape of the kea audiogram follows a similar pattern. However, two potentially interesting differences to the audiograms of other birds were found: an increase in sensitivity at approximately 12 kHz and a decreased sensitivity to frequencies below 1 kHz.
Results From the Republic of Slovenia’s 2016 Report Card on Physical Activity for Children and Youth
Authors: Sember Vedrana , Starc Gregor , Jurak Gregor , Golobič Mojca , Kovač Marjeta , Samardžija Poljanka Pavletič , Morrison Shawnda A.
Published: November 2016

Background:

This is the first assessment of the Republic of Slovenia’s efforts to synthesize and report physical activity (PA) standards for children and youth following the Active Healthy Kids Global Alliance grading system model.

Methods:

The Republic of Slovenia Report Card relies on research findings published in peer-reviewed journals, data compiled from national databases, and government initiatives which have been monitoring physical fitness standards in schools for the past 34 years (SLOfit and ACDSi). The Report Card initiative has been jointly coordinated by the University of Primorska and the University of Ljubljana. A Research Work Group consisting of 12 representatives from various aspects of Slovenia’s public, private, and government sectors convened to evaluate evidence and assign grades for each PA indicator.

Results:

Grades (A, highest, to F, lowest; INC, incomplete) for Slovenia are as follows: Overall Physical Activity (A-), Organized Sport Participation (B-), Active Play (D), Active Transportation (C), Sedentary Behaviors (B+), Family and Peers (INC), Schools (A), Community and the Built Environment (INC), and Government (B+).

Conclusions:

This inclusive PA report indicates that overall physical activity minutes remain high in Slovenian children and youth; however, more research is needed to determine the effects of family life, peer influences, and the built environment on active play behaviors.
Results From Japan’s 2016 Report Card on Physical Activity for Children and Youth
Authors: Tanaka Chiaki , Tanaka Shigeho , Inoue Shigeru , Miyachi Motohiko , Suzuki Koya , Reilly John J.
Published: November 2016

Background:

The Report Card on Physical Activity for Children and Youth aims to consolidate existing evidence, encourage greater evidence-informed physical activity, and improve surveillance of physical activity.

Methods:

The Japan report card followed the methodology of the Canadian and Scottish report cards, but was adapted to reflect the Japanese context. Nationally representative data were used to score each of the respective indicators.

Results:

The 2016 Japan Report Card on Physical Activity for Children and Youth consists of Health Behaviors and Outcomes (7 indicators), and Influences on Health Behaviors (4 indicators). Three Health Behaviors and Outcomes received C grades (Participation in Sport; Sedentary Behavior; Recreational Screen Time; Physical Fitness), while 2 indicators could not be graded (Overall Physical Activity, and Active Play). The indicators Active Transportation (B) and Weight Status were favorable (A). In the Influences domain, Family Influence and Community and the Built Environment were graded as D, while School and Government Strategies and Investments were favorable (B).

Conclusions:

The Japan report card illustrated some favorable health behaviors, health outcomes, and influences. There is a need for more evidence especially on overall physical activity levels, active play, and community and the built environment.
Results From Zimbabwe’s 2016 Report Card on Physical Activity for Children and Youth
Authors: Manyanga Taru , Makaza Daga , Mahachi Carol , Mlalazi Tholumusa F. , Masocha Vincent , Makoni Paul , Tapera Eberhard , Khumalo Bhekuzulu , Rutsate Sipho H. , Tremblay Mark S.
Published: November 2016

Background:

The report card was a synthesis of the best available evidence on the performance of Zimbabwean children and youth on key physical activity (PA) indicators. The aim of this article was to summarize the results from the 2016 Zimbabwe Report Card.

Methods:

The Report Card Working Group gathered and synthesized the best available evidence, met, discussed and assigned grades to 10 indicators based on the Active Healthy Kids Global Alliance global matrix grading system.

Results:

The indicators were graded as follows: overall PA (C+), organized sport participation (B), active play (D+), active transportation (A-), sedentary behaviors (B), school (D), family and peers (Incomplete), community and the built environment (F), government (D) and nongovernmental organizations (Incomplete).

Conclusions:

Although the majority of children used active transport, played organized sports and engaged in acceptable levels of PA, most of them did not meet the recommended hours of unstructured/unorganized play per day. At present, there are limited data to accurately inform the Zimbabwe Report Card therefore studies employing robust research designs with representative samples are needed. Zimbabwe also needs to prioritize policies and investments that promote greater and safe participation in PA among children and youth.
Results From the United States of America’s 2016 Report Card on Physical Activity for Children and Youth
Authors: Katzmarzyk Peter T. , Denstel Kara D. , Beals Kim , Bolling Christopher , Wright Carly , Crouter Scott E. , McKenzie Thomas L. , Pate Russell R. , Saelens Brian E. , Staiano Amanda E. , Stanish Heidi I. , Sisson Susan B.
Published: November 2016

Background:

The 2016 United States (U.S.) Report Card on Physical Activity for Children and Youth provides a comprehensive evaluation of physical activity levels and factors influencing physical activity among children and youth.

Methods:

The report card includes 10 indicators: Overall Physical Activity, Sedentary Behavior, Active Transportation, Organized Sport Participation, Active Play, Health-related Fitness, Family and Peers, School, Community and the Built Environment, and Government Strategies and Investments. Nationally representative data were used to evaluate the indicators using a standard grading rubric.

Results:

Sufficient data were available to assign grades to 7 of the indicators, and these ranged from B- for Community and the Built Environment to F for Active Transportation. Overall Physical Activity received a grade of D- due to the low prevalence of meeting physical activity guidelines. A grade of D was assigned to Health-related Fitness, reflecting the low prevalence of meeting cardiorespiratory fitness standards. Disparities across age, gender, racial/ethnic and socioeconomic groups were observed for several indicators.

Conclusions:

Continued poor grades suggest that additional work is required to provide opportunities for U.S. children to be physically active. The observed disparities indicate that special attention should be given to girls, minorities, and those from lower socioeconomic groups when implementing intervention strategies.
Results From Australia’s 2016 Report Card on Physical Activity for Children and Youth
Authors: Schranz Natasha K. , Olds Timothy , Boyd Roslyn , Evans John , Gomersall Sjaan R. , Hardy Louise , Hesketh Kylie , Lubans David R. , Ridgers Nicola D. , Straker Leon , Vella Stewart , Ziviani Jenny , Tomkinson Grant R.
Published: November 2016

Background:

Two years on from the inaugural Active Healthy Kids Australia (AHKA) Physical Activity Report Card, there has been little to no change with the majority of Australian children still insufficiently active.

Methods:

The 2016 AHKA Report Card was developed using the best available national- and state-based physical activity data, which were evaluated by the AHKA Research Working Group using predetermined weighting criteria and benchmarks to assign letter grades to the 12 Report Card indicators.

Results:

In comparison with 2014, Overall Physical Activity Levels was again assigned a D- with Organized Sport and Physical Activity Participation increasing to a B (was B-) and Active Transport declining to a C- (was C). The settings and sources of influence again performed well (A- to a C+), however Government Strategies and Investments saw a decline (C+ to a D). The traits associated with physical activity were also graded poorly (C- to a D).

Conclusions:

Australian youth are insufficiently active and engage in high levels of screen-based sedentary behaviors. While a range of support structures exist, Australia lacks an overarching National Physical Activity Plan that would unify the country and encourage the cultural shift needed to face the inactivity crisis head on.
Results From Mexico’s 2016 Report Card on Physical Activity for Children and Youth
Authors: Galaviz Karla I. , Arroyo Mabel Aguilar , González-Casanova Inés , Villalobos Martín Francisco González , Jáuregui Alejandra , Ulloa Edtna Jáuregui , Miranda Selene Pacheco , Rodríguez Marcela Pérez , Pelayo Ricardo Alejandro Retano , López-Taylor Juan Ricardo
Published: November 2016

Background:

The 2016 Mexican Report Card on Physical Activity for Children and Youth aims to assess how Mexico is doing in terms of providing physical activity (PA) opportunities for Mexican children and youth. The purpose of this article is to summarize results from the Mexican 2016 Report Card.

Methods:

A literature search was conducted in Spanish and English languages using major databases, and complemented with a review of government/nongovernment documents, websites, and national health surveys. Information on the 9 indicators outlined in the Global Matrix of Report Card Grades was extracted. A team of Mexican experts met to discuss and assign a grade on each indicator based on the best available evidence and established benchmarks.

Results:

Daily behaviors grades were Overall PA (C), Organized Sport Participation (D), Active Play (D-), Active Transportation (C), and Sedentary Behavior (D). For Settings and Sources of Influence, grades were Family and Peers (INC), School (D-), and Community and Environment (D). Strategies and Investments grades were Government Strategies (C) and Non-Government (F).

Conclusions:

PA and sedentary behaviors among Mexican children and youth remain below the recommended levels. Government and communities are far from providing appropriate and sufficient physical activity opportunities for children and youth.
Results From Colombia’s 2016 Report Card on Physical Activity for Children and Youth
Authors: González Silvia A. , Castiblanco Maria A , Arias-Gómez Luis F. , Martinez-Ospina Andrea , Cohen Daniel D. , Holguin Gustavo A. , Almanza Adriana , Lemos Diana Marina Camargo , Correa-Bautista Jorge Enrique , Escobar Iván D. , García Johnattan , Gámez Rocio , Garzon Mauricio , Beltrán Yaneth Herazo , Hurtado Hernan , Lozano Oscar , Páez Diana C. , Ramírez-Vélez Robinson , Ruiz Nubia , Tovar Gustavo , Sarmiento Olga L.
Published: November 2016

Background:

Physical activity (PA) is vital to the holistic development of young people. Regular participation in PA is associated with substantial benefits for health, cognitive function, and social inclusion. Recognizing the potential of PA in the context of the current peace process in Colombia, the purpose of this article is to present the methodology and results of Colombia’s second Report Card on PA for children and youth.

Methods:

A group of experts on PA graded 14 PA indicators based on data from national surveys and policy documents.

Results:

National and departmental policy indicators received a grade of B, while organized sport participation, overweight, obesity, community influence, and nongovernment initiatives indicators received a grade of C. Overall PA levels, active transportation, sedentary behaviors, and school influence received a grade of D. Active play, low physical fitness, and family influence received an Incomplete grade.

Conclusions:

PA levels are low and sedentary behaviors are high in Colombian children and youth, with notable geographic differences. A broad policy framework translated into specific actions could provide unique opportunities to bridge the gap between knowledge and practice, and contribute to social integration goals in a postconflict setting.
Results From Poland’s 2016 Report Card on Physical Activity for Children and Youth
Authors: Zembura Pawel , Goldys Aleksandra , Nalecz Hanna
Published: November 2016

Background:

Poland’s 2016 Report Card on Physical Activity for Children and Youth is the first assessment of child and youth physical activity (PA) in Poland using the Active Healthy Kids Global Alliance grading system. The main goal was to summarize and describe the current state of child and youth PA to increase awareness and surveillance.

Methods:

The systematic methodology that underpins the Active Healthy Kids Canada Report Card was adapted and applied to the Polish report card. The best available data were consolidated, reviewed by a group of experts, and used to assign the letter grades to 9 core PA indicators on a scale ranging from A (highest) to F (lowest).

Results:

The 9 indicators were graded as such: 1) Overall Physical Activity (D), 2) Organized Sport Participation (C), 3) Active Play (INC), 4) Active Transportation (C), 5) Sedentary Behaviors (D), 6) Family and Peers (C), 7) School (B), 8) Community and the Built Environment (C), and 9) Government Strategies and Investments (C).

Conclusions:

The final grades show a strong role of school in providing PA for children and youth in Poland. However, promotion of school-based sport participation appears to be insufficient by itself to sustainably promote PA in this group.
Science Signaling
Podcast for 15 November 2016: A new type of kinase inhibitor
Authors: Eldar-Finkelman Hagit , VanHook Annalisa M.
Published: November 2016

A peptide that inhibits the kinase GSK-3 improves symptoms in a mouse model of Alzheimer’s disease (Licht-Murava
et al
., in 15 November 2016 issue).
Paper of note in
Science Translational Medicine
Authors: Ferrarelli Leslie K.
Published: November 2016

This week’s paper describes how a CXCL12-trapping nanoparticle may prevent liver metastasis.
Paper of note in
Science Immunology
Authors: Foley John F.
Published: November 2016

This week’s article shows that by inducing expression of the gene encoding the transcription factor Blimp-1, the cytokine IL-10 restrains autoimmune responses.
A tRNA synthetase protects MAVS
Authors: Foley John F.
Published: November 2016

A tRNA synthetase enhances the immune response to RNA viruses by protecting the antiviral signaling protein MAVS from degradation.
Isolation and characterization of a new mutant of Saccharomyces cerevisiae with altered synthesis of 5-aminolevulinic acid
Authors: Carvajal E , Panek A D , Mattoon J R
Published: November 2016

A new gene, RHM1, required for normal production of 5-aminolevulinic acid by Saccharomyces cerevisiae, was identified by a novel screening method. Ethyl methanesulfonate treatment of a fluorescent porphyric strain bearing the pop3-1 mutation produced nonfluorescent or weakly fluorescent mutants with defects in early stages of tetrapyrrole biosynthesis. Class I mutants defective in synthesis of 5-aminolevulinate regained fluorescence when grown on medium supplemented with 5-aminolevulinate, whereas class II mutants altered in later biosynthetic steps did not. Among six recessive class I mutants, at least three complementation groups were found. One mutant contained an allele of HEM1, the structural gene for 5-aminolevulinate synthase, and two mutants contained alleles of the regulatory gene CYC4. The remaining mutants contained genes complementary to both hem1 and cyc4. Mutant strain DA3-RS3/68 contained mutant gene rhm1, which segregated independently of hem1 and cyc4 during meiosis. 5-Aminolevulinate synthase activity of the rhm1 mutant was 35 to 40% of that of the parental pop3-1 strain, whereas intracellular 5-aminolevulinate concentration was only 3 to 4% of the parental value. Transformation of an rhm1 strain with a multicopy plasmid containing the cloned HEM1 gene restored normal levels of 5-aminolevulinate synthase activity, but intracellular 5-aminolevulinate was increased to only 9 to 10% of normal. We concluded that RHM1 could control either targeting of 5-aminolevulinate synthase to the mitochondrial matrix or the activity of the enzyme in vivo.
Cloning of Pseudomonas aeruginosa algG, which controls alginate structure
Authors: Chitnis C E , Ohman D E
Published: November 2016

The biochemical mechanism by which alpha-L-guluronate (G) residues are incorporated into alginate by Pseudomonas aeruginosa is not understood. P. aeruginosa first synthesizes GDP-mannuronate, which is used to incorporate beta-D-mannuronate residues into the polymer. It is likely that the conversion of some beta-D-mannuronate residues to G occurs by the action of a C-5 epimerase at either the monomer (e.g., sugar-nucleotide) or the polymer level. This study describes the results of a molecular genetic approach to identify a gene involved in the formation or incorporation of G residues into alginate by P. aeruginosa. Mucoid P. aeruginosa FRD1 was chemically mutagenized, and mutants FRD462 and FRD465, which were incapable of incorporating G residues into alginate, were independently isolated. Assays using a G-specific alginate lyase from Klebsiella aerogenes and 1H-nuclear magnetic resonance analyses showed that G residues were absent in the alginates secreted by these mutants. 1H-nuclear magnetic resonance analyses also showed that alginate from wild-type P. aeruginosa contained no detectable blocks of G. The mutations responsible for defective incorporation of G residues into alginate in the mutants FRD462 and FRD465 were designated algG4 and algG7, respectively. Genetic mapping experiments revealed that algG was closely linked (greater than 90%) to argF, which lies at 34 min on the P. aeruginosa chromosome and is adjacent to a cluster of genes required for alginate biosynthesis. The clone pALG2, which contained 35 kilobases of P. aeruginosa DNA that included the algG and argF wild-type alleles, was identified from a P. aeruginosa gene bank by a screening method that involved gene replacement. A DNA fragment carrying algG was shown to complement algG4 and algG7 in trans. The algG gene was physically mapped on the alginate gene cluster by subcloning and Tn501 mutagenesis.
Cloning and nucleotide sequence of luxR, a regulatory gene controlling bioluminescence in Vibrio harveyi
Authors: Showalter R E , Martin M O , Silverman M R
Published: November 2016

Mutagenesis with transposon mini-Mulac was used previously to identify a regulatory locus necessary for expression of bioluminescence genes, lux, in Vibrio harveyi (M. Martin, R. Showalter, and M. Silverman, J. Bacteriol. 171:2406-2414, 1989). Mutants with transposon insertions in this regulatory locus were used to construct a hybridization probe which was used in this study to detect recombinants in a cosmid library containing the homologous DNA. Recombinant cosmids with this DNA stimulated expression of the genes encoding enzymes for luminescence, i.e., the luxCDABE operon, which were positioned in trans on a compatible replicon in Escherichia coli. Transposon mutagenesis and analysis of the DNA sequence of the cloned DNA indicated that regulatory function resided in a single gene of about 0.6-kilobases named luxR. Expression of bioluminescence in V. harveyi and in the fish light-organ symbiont Vibrio fischeri is controlled by density-sensing mechanisms involving the accumulation of small signal molecules called autoinducers, but similarity of the two luminescence systems at the molecular level was not apparent in this study. The amino acid sequence of the LuxR product of V. harveyi, which indicates a structural relationship to some DNA-binding proteins, is not similar to the sequence of the protein that regulates expression of luminescence in V. fischeri. In addition, reconstitution of autoinducer-controlled luminescence in recombinant E. coli, already achieved with lux genes cloned from V. fischeri, was not accomplished with the isolation of luxR from V. harveyi, suggesting a requirement for an additional regulatory component.
Specificity of the mutator effect caused by disruption of the RAD1 excision repair gene of Saccharomyces cerevisiae
Authors: Kunz B A , Kohalmi L , Kang X L , Magnusson K A
Published: November 2016

Disruption of RAD1, a gene controlling excision repair in the yeast Saccharomyces cerevisiae, increased the frequency of spontaneous forward mutation in a plasmid-borne copy of the SUP4-o gene. To characterize this effect in detail, a collection of 249 SUP4-o mutations arising spontaneously in the rad1 strain was analyzed by DNA sequencing. The resulting mutational spectrum was compared with that derived from an examination of 322 spontaneous SUP4-o mutations selected in an isogenic wild-type (RAD1) strain. This comparison revealed that the rad1 mutator phenotype was associated with increases in the frequencies of single-base-pair substitution, single-base-pair deletion, and insertion of the yeast retrotransposon Ty. In the rad1 strain, the relative fractions of these events and their distributions within SUP4-o exhibited features similar to those for spontaneous mutagenesis in the isogenic RAD1 background. The increase in the frequency of Ty insertion argues that Ty transposition can be activated by unrepaired spontaneous DNA damage, which normally would be removed by excision repair. We discuss the possibilities that either translesion synthesis, a reduced fidelity of DNA replication, or a deficiency in mismatch correction might be responsible for the majority of single-base-pair events in the rad1 strain.
Surface-active novel glycolipid and linked 3-hydroxy fatty acids produced by Serratia rubidaea
Authors: Matsuyama T , Kaneda K , Ishizuka I , Toida T , Yano I
Published: November 2016

A Serratia rubidaea isolate with wetting activity when grown at 30 but not 37 degrees C was examined for the production of specific lipids. Two novel lipids (rubiwettins R1 and RG1) were isolated and shown to be able to lower the surface tension of saline to 26 mN/m. These lipids were located in extracellular vesicles found in a 30 degrees C culture of S. rubidaea. Chemical structures of these biosurfactants were determined by degradation product analyses, infrared spectroscopy, mass spectrometry, and proton nuclear magnetic resonance spectroscopy. Rubiwettin R1 was proposed to be a mixture of 3-(3'-hydroxytetradecanoyloxy)decanoate, 3-(3'-hydroxyhexadecenoyloxy)decanoate, and minor molecular isomers. The structure of rubiwettin RG1 was proposed to be beta-D-glucopyranosyl 3-(3'-hydroxytetradecanoyloxy)decanoate. The importance of such surface-active exolipids in bacterial occupancy on surfaces was suggested.
Carboxyphosphonoenolpyruvate phosphonomutase, a novel enzyme catalyzing C-P bond formation
Authors: Hidaka T , Imai S , Hara O , Anzai H , Murakami T , Nagaoka K , Seto H
Published: November 2016

An enzyme catalyzing the formation of an unusual C-P bond that is involved in the biosynthesis of the antibiotic bialaphos (BA) was isolated from the cell extract of a mutant (NP71) of Streptomyces hygroscopicus SF1293. This enzyme, carboxyphosphonoenolpyruvate (CPEP) phosphonomutase, was first identified as a protein lacking in a mutant (NP213) defective in one of the steps in the pathway to BA. The first 30 residues of the amino terminus of this protein were identical to those predicted by the nucleotide sequence of the gene that restored BA production to NP213. The substrate of the enzyme, a P-carboxylated derivative of phosphoenolpyruvate named CPEP, was also isolated from the broth filtrate of NP213 as a new biosynthetic intermediate of BA. CPEP phosphonomutase catalyzes the rearrangement of the carboxyphosphono group of CPEP to form the C-P bond of phosphinopyruvate.
A segment of Myxococcus xanthus ops DNA functions as an upstream activation site for tps gene transcription
Authors: Kil K S , Brown G L , Downard J S
Published: November 2016

A segment of DNA located between 131 and 311 base pairs (bp) upstream from the transcriptional start of the Myxococcus xanthus ops gene (-131 to -311) was shown to function as an upstream activation site (UAS) for developmentally regulated transcription from the tps gene promoter region. The activation of early developmental transcription by the ops UAS was independent of orientation and could be increased by the addition of a second copy of the UAS. The ops UAS segment continued to function when placed 1.5 kbp upstream from the transcription initiation site. DNA from the tps promoter region was required for transcriptional activation by the ops UAS, and a specific requirement for the sequence of tps DNA between -34 and -66 was demonstrated. Several specific ops UAS DNA-protein complexes were observed after incubation of this DNA segment with an extract of early developmental M. xanthus cells. Extracts of vegetative cells contained much less ops UAS-specific DNA-binding activity. When the distance between the tps and ops genes was increased from 2 to 15 kbp by insertion of a transduced segment of DNA, the amount of developmentally induced tps RNA was found to be about one-third that found in wild-type M. xanthus. Our observations suggest that the regulatory region of the ops gene functions not only to control ops gene expression but also to increase early developmental expression of the tps gene located about 2 kbp downstream on the M. xanthus chromosome.
Manganese regulates expression of manganese peroxidase by Phanerochaete chrysosporium
Authors: Brown J A , Glenn J K , Gold M H
Published: November 2016

The appearance of manganese peroxidase (MnP) activity in nitrogen-limited cultures of Phanerochaete chrysosporium is dependent on the presence of manganese. Cultures grown in the absence of Mn developed normally and produced normal levels of the secondary metabolite veratryl alcohol but produced no MnP activity. Immunoblot analysis indicated that appearance of MnP protein in the extracellular medium was also dependent on the presence of Mn. Intracellular MnP protein was detectable only in cells grown in the presence of Mn. MnP mRNA was detected by Northern (RNA) blot analysis only in cells grown in the presence of Mn. If Mn was added to 4-day-old nitrogen-limited Mn-deficient cultures, extracellular MnP activity appeared after 6 h and reached a maximum after 18 h. Both actinomycin D and cycloheximide inhibited the induction of MnP activity by Mn. These results indicate that Mn, the substrate of the enzyme, is involved in the transcriptional regulation of the MnP gene.
A phoA structural gene mutation that conditionally affects formation of the enzyme bacterial alkaline phosphatase
Authors: Agrawal D K , Wanner B L
Published: November 2016

The phoA503 mutant was identified as a mutant that shows a novel phoA regulatory phenotype. The phoA503 allele dramatically reduces the synthesis of bacterial alkaline phosphatase activity during Pi starvation in an otherwise wild-type host and during the logarithmic growth phase in a phoR or phoU background. Near-normal amounts of enzyme activity are found in phoR phoA503 or phoU phoA503 mutants when starved for carbon, nitrogen, or sulfur or during the stationary phase, however. Marker rescue and DNA sequence analysis located the phoA503 mutation to the phoA coding region. It is a C-to-T transition that would cause a substitution of Val for Ala-22 in the mature protein. Transcriptional and translational lacZ fusions to both wild-type and mutant alleles demonstrated that phoA gene expression is unaltered. Also, the mutant protein was secreted and processed as efficiently as the wild type. Furthermore, the subunits appeared to dimerize and to be stable in the periplasm. But, greater than 98% of the dimers were inactive and found exclusively as isozyme 1. An activation of preformed phoA503 dimers occurred during the stationary phase with the concomitant conversion into isozymes 2 and 3. We propose that the phoA503 mutation affects a late stage in the formation of active enzyme. An unknown change when Pi is present during stationary-phase growth leads to formation of active dimers, which is responsible for this new conditional phenotype.
Regulation of Escherichia coli pyrC by the purine regulon repressor protein
Authors: Choi K Y , Zalkin H
Published: November 2016

The purine regulon repressor, PurR, was identified as a component of the Escherichia coli regulatory system for pyrC, the gene that encodes dihydroorotase, an enzyme in de novo pyrimidine nucleotide synthesis. PurR binds to a pyrC control site that resembles a pur regulon operator and represses expression by twofold. Mutations that increase binding of PurR to the control site in vitro concomitantly increase in vivo regulation. There are completely independent mechanisms for regulation of pyrC by purine and pyrimidine nucleotides. Cross pathway regulation of pyrC by PurR may provide one mechanism to coordinate synthesis of purine and pyrimidine nucleotides.
Direct involvement of IS26 in an antibiotic resistance operon
Authors: Lee K Y , Hopkins J D , Syvanen M
Published: November 2016

The plasmid pBWH77, originally found in an isolate of Klebsiella pneumoniae, harbors a new antibiotic resistance operon containing two resistance genes transcribed from an IS26-hybrid promoter, as shown by nucleotide sequencing, mRNA mapping, and the effect of inserting a transcription terminator within the promoter-proximal gene. The nucleotide sequence of this region revealed that the operon (IAB) is made up of three sections that are closely related to previously described genetic elements. The -35 region of the promoter, together with the adjacent sequence, is identical to sequences of the IS26 element. One of the resistance genes, aphA7, which is located next to the hybrid promoter, confers assistance to neomycin and structurally related aminoglycosides. This aphA7 gene is highly homologous to aphA1 of Tn903, with five nucleotide differences. The second gene, blaS2A, encodes an evolved SHV-type beta-lactamase with a pI of 7.6 that confers resistance to the broad-spectrum cephalosporins cefotaxime and ceftizoxime. The deduced amino acid sequence of SHV-2A shows that amino acid 238 is a serine, a residue reported to confer resistance to cefotaxime. We discuss how the operon may have evolved by a combination of insertion sequence-mediated genetic rearrangements and acquisitive evolution. Using phylogenetic parsimony, we show that aphA7 in the IAB operon evolved from an ancestral form similar to aphA1 in Tn903 and that blaS2A evolved from an ancestral form similar to blaS1.
In vivo cloning and characterization of the gabCTDP gene cluster of Escherichia coli K-12
Authors: Metzer E , Halpern Y S
Published: November 2016

The gabCTDP gene cluster, which specifies and regulates synthesis of the gamma-aminobutyrate (GABA) transport carrier, of glutamate-succinic semialdehyde transaminase, and of succinic semialdehyde dehydrogenase, responsible for the uptake and metabolism of gamma-aminobutyric acid in Escherichia coli K-12, was cloned in vivo, using the mini-Mu replicon bacteriophage Mu dI5086 as the vector. A subclone containing a 7.8-kilobase (kb) EcoRI-HindIII fragment complemented all of our Gab- mutants. By restriction mapping, this DNA fragment was located at kb 2800.5 to 2808.5 on the physical map of the E. coli K-12 chromosome. A subclone containing a 1.8-kb EcoRI-SalI fragment complemented the gab-repressed strain CS101A (wild-type gabC) but did not complement any gab structural gene mutants. The gab genes are divergently transcribed from promoters located in the vicinity of the unique BamHI site. Transcription in both directions is under dual control of catabolite repression and nitrogen regulation. Using a procaryotic DNA-directed translation system, we observed three insert-coded polypeptide bands of 53 to 55, 45 to 48, and 40 to 43 kilodaltons (kDa). In vivo studies with subcloned fragments of the gab DNA identified the 53- to 55- and 45- to 48-kDa bands as products of the BamHI-SalI fragment and the 40- to 43-kDa band as the product of the EcoRI-SalI fragment. An additional 26- to 28-kDa band was identified as the product of the BamHI-HindIII fragment. Furthermore, the BamHI-SalI fragment was shown to specify synthesis of the two GABA enzymes, whereas synthesis of the GABA carrier was specified by the BamHI-HindIII fragment. No catalytic function in addition to its regulatory role could be attributed to the EcoRI-SalI gene product.
Isolation and characterization of the 5S rRNA gene of Leptospira interrogans
Authors: Fukunaga M , Horie I , Mifuchi I
Published: November 2016

The gene encoding the 5S rRNA for Leptospira interrogans serovar canicola strain Moulton was isolated and sequenced. The 5S rRNA gene occurs as a single copy within the genome and encodes a 117-nucleotide-long RNA molecule. The 5S rRNA gene is flanked at both the 5' and 3' ends by regions of A + T-rich sequences, and the 5'-flanking region contains a promoter sequence. L. interrogans has a unique and remarkable organization of the 5S rRNA gene. The 5S rRNA molecule exhibits a strong similarity to typical eubacterial 5S rRNA in terms of overall secondary structure, while the primary sequence is conserved to a lesser degree. Restriction analysis of the 5S rRNA gene indicated that the DNA sequence including the 5S rRNA gene is highly conserved in the genomes of parasitic leptospires.
Molecular cloning and characterization of an Erwinia carotovora subsp. carotovora pectin lyase gene that responds to DNA-damaging agents
Authors: McEvoy J L , Murata H , Chatterjee A K
Published: November 2016

recA-mediated production of pectin lyase (PNL) and the bacteriocin carotovoricin occurs in Erwinia carotovora subsp. carotovora 71 when this organism is subjected to agents that damage or inhibit the synthesis of DNA. The structural gene pnlA was isolated from a strain 71 cosmid gene library following mobilization of the cosmids into a moderate PNL producer, strain 193. The cosmid complemented pnl::Tn5 but not ctv::Tn5 mutations. A constitutive level of PNL activity was detected in RecA+ and RecA- Escherichia coli strains carrying the pnlA+ gene on the high-copy-number plasmid pBluescript SK-. Mappings of Mu dI1734 (Km lac'ZYA) insertions in pnlA and unidirectional deletion analyses allowed localization of the gene to approximately 1.4 kilobases of DNA. A typical pnlA-lacZ transcriptional fusion was inducible in a RecA+ but not a RecA- derivative of strain 71. In contrast, the pnlA-lacZ fusion was not inducible in a RecA+ E. coli strain. DNA sequences homologous to pnlA were detected in E. carotovora subsp. carotovora and E. carotovora subsp. atroseptica strains and in one of four Erwinia rhapontici strains but not in Erwinia chrysanthemi.
Citrate as a siderophore in Bradyrhizobium japonicum
Authors: Guerinot M L , Meidl E J , Plessner O
Published: November 2016

Under iron-limiting conditions, many bacteria secrete ferric iron-specific ligands, generically termed siderophores, to aid in the sequestering and transport of iron. One strain of the nitrogen-fixing soybean symbiont Bradyrhizobium japonicum, 61A152, was shown to produce a siderophore when 20 B. japonicum strains were screened with all six chemical assays commonly used to detect such production. Production by strain 61A152 was detected via the chrome azurol S assay, a general test for siderophores which is independent of siderophore structure. The iron-chelating compound was neither a catechol nor a hydroxamate and was ninhydrin negative. It was determined to be citric acid via a combination of thin-layer chromatography and high-voltage paper electrophoresis; this identification was verified by a specific enzymatic assay for citric acid. The inverse correlation which was observed between citric acid release and the iron content of the medium suggested that ferric citrate could serve as an iron source. This was confirmed via growth and transport assays. Exogenously added ferric citrate could be used to overcome iron starvation, and iron-deficient cells actively transported radiolabeled ferric citrate. These results, taken together, indicate a role for ferric citrate in the iron nutrition of this strain, which has been shown to be an efficient nitrogen-fixing strain on a variety of soybean cultivars.
Sulfate and thiosulfate transport in Escherichia coli K-12: identification of a gene encoding a novel protein involved in thiosulfate binding
Authors: Hryniewicz M , Sirko A , Pałucha A , Böck A , Hulanicka D
Published: November 2016

The sequence of 1,973 nucleotides encompassing the region at and directly adjacent to the CysB-dependent promoter controlling expression and synthesis of the sulfate-thiosulfate transport system of Escherichia coli has been determined. The transcription start site has been mapped by primer extension. One open reading frame representing the first gene of the presumed sulfate transport operon was identified and designated cysP. The deduced amino acid sequence of the CysP polypeptide indicates the presence of a signal peptide. Expression of the cysP gene in the T7 promoter-polymerase system revealed the location of the gene product in the periplasm. Construction of a cysP insertional mutant and assays of binding and uptake of sulfate and thiosulfate by this mutant allowed the identification of the cysP gene product as a thiosulfate-binding protein. The TGA termination codon of cysP was found to overlap the putative ATG initiation codon of the next open reading frame, inferred as being essential for the sulfate transport system, and it was designated cysT. Preliminary sequence data from the corresponding region of the Salmonella typhimurium chromosome showed strictly homologous counterparts of the E. coli cysP and cysT genes.
In vivo phosphorylation of OmpR, the transcription activator of the ompF and ompC genes in Escherichia coli
Authors: Forst S , Delgado J , Rampersaud A , Inouye M
Published: November 2016

An in vivo approach was taken to assess whether the phosphorylated state of the transcription activator OmpR was affected by changes in the osmolarity of the growth medium or by mutations in envZ, the gene encoding the inner membrane histidine kinase that phosphorylates OmpR. We present results that support the view that increased phosphorylation of OmpR is correlated with enhanced expression of ompC. The in vivo phosphorylation approach was also used to show that OmpR can be phosphorylated in an envZ null strain. This result indicates that phosphorylation cross talk can occur in vivo between OmpR and a kinase(s) that is functionally homologous to envZ.
DNA cloning and organization of the Staphylococcus aureus gyrA and gyrB genes: close homology among gyrase proteins and implications for 4-quinolone action and resistance
Authors: Hopewell R , Oram M , Briesewitz R , Fisher L M
Published: November 2016

Staphylococcus aureus gyrA and gyrB genes, which encode the DNA gyrase A and B proteins, have been isolated and found to map contiguously. DNA sequence analysis revealed close homology between the S. aureus gyrase subunits and their counterparts in Bacillus subtilis and Escherichia coli, including several conserved amino acid residues whose substitution in E. coli confers resistance to 4-quinolones. These results are discussed in regard to quinolone resistance mechanisms in S. aureus.
Cloning and sequence analysis of tryptophan synthetase genes of an extreme thermophile, Thermus thermophilus HB27: plasmid transfer from replica-plated Escherichia coli recombinant colonies to competent T. thermophilus cells
Authors: Koyama Y , Furukawa K
Published: November 2016

Tryptophan synthetase genes (trpBA) of the extreme thermophile Thermus thermophilus HB27 were cloned by a novel method of direct plasmid transfer from replica-plated Escherichia coli recombinant colonies to competent T. thermophilus HB27 trpB cells. The nucleotide sequences of the trpBA genes were determined. The amino acid sequences deduced from the nucleotide sequences of Thermus trpB and trpA were found to have identities of 54.8 and 28.7%, respectively, with those of E. coli trpB and trpA genes. Low cysteine content (one in trpB; zero in trpA) is a striking feature of these proteins, which may contribute to their thermostability.
Characterization of an inducible oxidative stress system in Bacillus subtilis
Authors: Bol D K , Yasbin R E
Published: November 2016

Exponentially growing cells of Bacillus subtilis demonstrated inducible protection against killing by hydrogen peroxide when prechallenged with a nonlethal dose of this oxidative agent. Cells deficient in a functional recE+ gene product were as much as 100 times more sensitive to the H2O2 but still exhibited an inducible protective response. Exposure to hydrogen peroxide also induced the recE(+)-dependent DNA damage-inducible (din) genes, the resident prophage, and the product of the recE+ gene itself. Thus hydrogen peroxide is capable of inducing the SOS-like or SOB system of B. subtilis. However, the induction of this DNA repair system by other DNA-damaging agents is not sufficient to activate the protective response to hydrogen peroxide. Therefore, at least one more regulatory network (besides the SOB system) that responds to oxidative stress must exist. Furthermore, the data presented indicate that a functional catalase gene is necessary for this protective response.
A trans-unsaturated fatty acid in a psychrophilic bacterium, Vibrio sp. strain ABE-1
Authors: Okuyama H , Sasaki S , Higashi S , Murata N
Published: November 2016

A high level of a trans-unsaturated fatty acid was found in the phospholipids of a psychrophilic bacterium, Vibrio sp. strain ABE-1. This fatty acid was identified as 9-trans-hexadecenoic acid (C16:19t) by gas-liquid chromatography and infrared absorption spectrometry. C16:1(9)t accounted for less than 1% of the total fatty acids in cells grown at 5 degrees C and reached 12% of the total at 20 degrees C. We suggest that the increase in the level of the trans-unsaturated fatty acid is related to the high growth rate of this bacterium at elevated temperatures. Possible biological roles of the trans-unsaturated fatty acid in the adaptation of the microorganism to the ambient temperature are discussed.
Genetic analysis of a plasmid-encoded, host genotype-specific enhancement of bacterial fitness
Authors: Lenski R E , Simpson S C , Nguyen T T
Published: November 2016

In the absence of antibiotics, carriage of pACYC184 reduces the competitive fitness of an Escherichia coli B genotype that was not previously selected for plasmid carriage, relative to that of an isogenic plasmid-free competitor. However, a host genotype propagated with the plasmid for 500 generations evolved an unexpected competitive advantage from plasmid carriage, relative to its own isogenic plasmid-free segregant. We manipulated the pACYC184 genome in order to identify the plasmid-encoded function that was required for the enhancement of the coevolved host genotype's competitive fitness. Inactivation of the plasmid-encoded tetracycline resistance gene, by deletion of either the promoter region or the entire gene, eliminated the beneficial effect of plasmid carriage for the coevolved host. This beneficial effect for the coevolved host was also manifest with pBR322, which contains a tetracycline resistance gene identical to that of pACYC184 but is otherwise heterologous.