bluuebunny/crossref_metadata_2025 huggingface dataset:
Credit for Comments, Comments for Credit
Authors: Sommer Robert , Sommer Barbara A.
Published: July 2011

A survey in 2 undergraduate psychology classes (N = 93) found ambivalent attitudes toward credit for classroom participation. Although students viewed credit as a way to increase interaction and improve attendance, they also believed it could stimulate irrelevant comments and penalize shy students. The following year, in a class of 49 students, halfway through the course, the instructor offered a small amount of credit for office visits and for participation, but only on alternate days. The implementation significantly increased the amount of class discussion, with students reporting an increase in discussion quality. The policy also increased office visits, but did not significantly improve class attendance
Goodbye Lecture: A Student-Led Seminar Approach for Teaching Upper Division Courses
Authors: Casteel Mark A. , Bridges K. Robert
Published: July 2011

This article describes a seminar approach for teaching small classes of advanced undergraduates modeled on graduate seminar-style courses. Students act as daily discussion leaders for assigned readings, first in small teams and later individually, and the instructor acts as facilitator. Students received evaluations based on both their active discussion and written assignments. Student survey responses revealed high levels of satisfaction for the courses and with the instructors, as well as the perceived amount of new information learned. Students also commented positively on the discussions and the seminar format. The technique is applicable to teaching any advanced undergraduate topic, appeals to students, and emphasizes the active role of student learners.
Applying Motivation Theory to Real-World Problems
Authors: Harpine Elaine Clanton
Published: July 2011

This article examines the effectiveness of incorporating an applied learning experience in an upper level undergraduate motivation theory class. In this 3-part course requirement, students (a) participated in a 2-hr field experience, (b) completed a homework assignment based on their participation, and (c) worked in groups to develop a deeper understanding of motivational interventions and possible solutions for problems observed during the applied learning experience. Students identified the field experience and the group project as effective tools for understanding and applying motivation theory in a realistic setting.
Teaching beyond the Bounds: An Interdisciplinary Introduction to Psychology and Sociology
Authors: Widner Sabina C. , Davies Kimberly A.
Published: July 2011

We describe the development and evolution of an interdisciplinary introductory course in psychology and sociology. Such a course benefits students by encouraging a wider view of the social sciences and interdisciplinary critical thinking. The challenges of a combined course include reduced content for each discipline, the selection of appropriate texts, and the negotiation of course processes between two professors. Course evaluations indicated that students appreciated thinking beyond the bounds of 1 discipline. Additionally, statistical analyses suggested that our students received similar grades in upper level psychology courses as a cohort of psychology majors who completed the traditional introduction to psychology course.
Searching under Cups for Clues about Memory: An Online Demonstration
Authors: Kahan Todd A. , Mathis Katherine M.
Published: July 2011

An online demonstration, designed to enhance comprehension of Sternberg's (1966) short-term memory scanning task, involved rapidly searching under virtual cups for a ball. We randomly assigned students to 1 of 3 groups, all of whom read the same textbook description of Sternberg's work: A demonstration group used 3 search methods to look for balls under cups (analogous to searching items in memory), a graphing control group used 3 methods to click on buttons (both groups had equivalent practice examining reaction time graphs), and there was a text-only control. The demonstration group outperformed the controls on an online quiz.
Link to the Future: Web Page Design in a Psychology Careers Course
Authors: Harris Paul B. , Queen Jennifer S.
Published: July 2011

Students in a careers in psychology course created Web pages describing career options. Student responses to a questionnaire indicated that they believed that the project reflected principles of good practice in undergraduate education (Chickering & Gamson, 1987) and also increased their knowledge of careers, Web page construction, and ways of integrating and presenting information. A 2nd group of participants from a different class navigated the Web pages and rated them as an effective and enjoyable method for learning about careers in psychology. Web page construction may be a useful pedagogical tool for a careers course because of the emphasis on current information and availability of resources on the Internet.
A Course Designed to Improve Psychological Critical Thinking
Authors: Penningroth Suzanna L. , Despain Laran H. , Gray Matt J.
Published: July 2011

We developed a 1-credit freshman-level course designed to enhance psychological critical thinking. We based the new curriculum on Stanovich's (2004) text, with an emphasis on active learning and critically evaluating claims by applying scientific concepts. To assess the effectiveness of this course, we used a pretest–posttest design with a quasi-experimental control group. At posttest, students in the psychological science course showed greater improvement on psychological critical thinking than students in a comparison group. Therefore, we recommend the techniques used in this instructional intervention to help college students improve their critical thinking skills.
Observation or Interpretation? Demonstrating Unintentional Subjectivity and Interpretive Variance
Authors: Connor-Greene Patricia A.
Published: July 2011

People often make interpretations when they believe they are providing factual descriptions. To demonstrate unintentional interpretation, I showed a brief ambiguous video clip and asked students to write descriptions of what they saw and heard. When students evaluated their responses, they discovered that 96% of the class wrote interpretations rather than strictly factual descriptions. Furthermore, the content of students' interpretations varied widely. Analyses of a qualitative measure of 3 dimensions of student learning (subsequent behavior, success at articulating the purpose of the exercise, and self-reported personal impact) supported the effectiveness of this exercise in increasing students' understanding of unintentional interpretation.
Introductory Psychology Student Performance: Weekly Quizzes Followed by a Cumulative Final Exam
Authors: Landrum R. Eric
Published: July 2011

Students in an introductory psychology course took a quiz a week over each textbook chapter, followed by a cumulative final exam. Students missing a quiz in class could make up a quiz at any time during the semester, and answers to quiz items were available to students prior to the cumulative final exam. The cumulative final exam consisted of half the items previously presented on quizzes; half of those items had the response options scrambled. The performance on similar items on the cumulative final was slightly higher than on the original quiz, and scrambling the response options had little effect. Students strongly supported the quiz a week approach.
Classic Articles as Primary Source Reading in Introductory Psychology
Authors: Griggs Richard A. , Jackson Sherri L.
Published: July 2011

Given the frequent use of primary source readings by introductory psychology teachers, especially at liberal arts colleges, we compiled the citation frequencies of classic articles in introductory textbooks to help teachers select readings for their courses. Using a random sample of 24 of the most recent introductory texts (copyright dates 2004–2006), we checked for citation of the 40 classic studies that Gorenflo and McConnell (1991) identified as cited in a simple majority of textbooks in the late 1980s. We found that 22 of these articles still met this citation criterion. We discuss the general content of these articles and ways to supplement them to comprise a sufficiently diverse set of possible readings for the introductory course.
Working with and Training Undergraduates as Teaching Assistants
Authors: Hogan Thomas P. , Norcross John C. , Cannon J. Timothy , Karpiak Christie P.
Published: July 2011

We describe a program for involving undergraduate teaching assistants (UTAs) in many types of psychology courses, as well as a 1-credit seminar for preparation of UTAs. The program, widely used by both faculty and students, has matured over a 10-year period. The seminar covers such topics as course organization, evaluation procedures, and videotaping a class presentation. UTAs sign a contract that includes ethical challenges they may encounter. We outline the potential benefits of the program for the UTAs, fellow students, the faculty, and the institution.
The GRE Analytical Writing Test: Description and Utilization
Authors: Briihl Deborah S. , Wasieleski David T.
Published: July 2011

We surveyed graduate programs to see how they use the Graduate Record Examination Analytic Writing (GRE-AW) Test. Only 35% of the graduate programs that responded use the GRE-AW test in their admission policy; of the programs not using it, most do not plan to do so. The programs using the GRE-AW rated it as medium or low in importance in their admission decisions. Few programs have cutoff scores. Approximately 8% reported using an initial validation study; about half reported considering or running an ongoing validation study. We urge program coordinators to evaluate the potential benefits of the GRE-AW as part of admissions decisions and the Educational Testing Service to help coordinators do so.
Psychology and Environmental Sustainability: A Call for Integration
Authors: Koger Susan M. , Scott Britain A.
Published: July 2011

Environmental scientists warn that the health of the planet is rapidly deteriorating, and the primary cause of the crisis is human behavior. Psychology can contribute greatly to understanding and changing behaviors that negatively impact global ecosystems; however, environmental issues are not generally included in psychology curricula, and psychology is not often represented in environmental curricula. We describe the relevance of psychology to environmental problem solving; suggest how to integrate environmental issues into psychology courses; and urge psychology faculty to collaborate with environmental studies and science faculty to strengthen the training of future policy makers, conservation scientists, and activists. We conclude that psychology has a critical role to play in creating a sustainable society.
Full-Semester and Abbreviated Summer Courses: An Evaluation of Student Performance
Authors: Anastasi Jeffrey S.
Published: July 2011

Faculty and administrators often believe that abbreviated courses are less effective than the same courses taught during a full semester. This study examined student academic performance and course evaluations for identical courses taught during abbreviated summer sessions or during regular semester sessions. Contrary to popular convention, results demonstrated that overall academic performance was similar in summer and full-semester courses. In addition, instructor ratings were comparable for regular semester and summer session courses, with summer courses rated as somewhat more challenging. Results provide empirical evidence that negative beliefs concerning abbreviated courses may be unfounded.
Service Learning in Life-Span Developmental Psychology: Higher Exam Scores and Increased Empathy
Authors: Lundy Brenda L.
Published: July 2011

This article describes research conducted to evaluate the impact of service learning on exam scores and emotional empathy in a life-span development course. Service learning was 1 of 3 project options offered in the course; others included an interview project and a research paper. With the exception of the first exam, scores were significantly higher for the service-learning students compared to those who completed other projects. In addition, only the service-learning group demonstrated a significant increase in emotional empathy as measured by the Emotional Empathetic Tendency Scale (EETS; Mehrabian & Epstein, 1972). I discuss the results in terms of the relations among practical experience, reflection, and emotional empathy.
Teaching the Psychology of Food and Culture
Authors: Cargill Kima
Published: July 2011

Increasingly, psychologists practicing as clinicians, researchers, and educators are concerned about nutrition, obesity, dieting, and body image. This article describes the development and teaching of an interdisciplinary undergraduate class on the Psychology of Food and Culture. I describe the course philosophy and curriculum as well as make recommendations to educators interested in developing a similar course. I also include recommendations for those who want to integrate components of this course into other psychology classes.
The Automatic Sweetheart: An Assignment in a History of Psychology Course
Authors: Sibicky Mark E.
Published: July 2011

This article describes an assignment in a History of Psychology course used to enhance student retention of material and increase student interest and discussion of the long-standing debate between humanistic and mechanistic models in psychology. Adapted from William James's (1955) automatic sweetheart question, the assignment asks students to imagine if they could love their sweetheart after finding out that he or she was not a conscious human being but a technologically advanced machine. Compared to a control group, students completing the assignment demonstrated improved performance on a posttest quiz. Students also reported the assignment was interesting, had educational value, and helped them understand the historical significance of a fundamental debate in the History of Psychology.
Changing Perspective: How Learning about Racism Influences Student Awareness and Emotion
Authors: Kernahan Cyndi , Davis Tricia
Published: July 2011

As students participate in diversity courses in greater numbers, it is important to understand the effects of these courses. Although other researchers have examined this topic, particularly with respect to stereotype reduction and racial attitudes, we were interested in how a diversity course might also affect students' awareness of racism and White privilege. With both quantitative and qualitative measures, our results showed increases in awareness and in feelings of racial guilt and responsibility. These findings expand the existing literature and highlight important questions for future research.
Microsoft Producer: A Software Tool for Creating Multimedia PowerPoint® Presentations
Authors: Leffingwell Thad R. , Thomas David G. , Elliott William H.
Published: July 2011

Microsoft® Producer® is a powerful yet user-friendly PowerPoint companion tool for creating on-demand multimedia presentations. Instructors can easily distribute these presentations via compact disc or streaming media over the Internet. We describe the features of the software, system requirements, and other required hardware. We also describe 3 approaches to using the software to enhance teaching of graduate and undergraduate psychology courses, offer tips on effective use of Producer, list other similar software, and note some shortcomings. Producer can be a useful tool for the teaching of psychology via both traditional and online formats.
Facilitation and inhibition caused by the orienting of attention in propositional reasoning tasks
Authors: Cherubini Paolo , Mazzocco Alberto , Minelli Stefano
Published: July 2011

In an attempt to study the orienting of attention in reasoning, we developed a set of propositional reasoning tasks structurally similar to Posner's (1980) spatial cueing paradigm, widely used to study the orienting of attention in perceptual tasks. We cued the representation in working memory of a reasoning premise, observing whether inferences drawn using that premise or a different, uncued one were facilitated, hindered, or unaffected. The results of Experiments 1a, 1b, 1c, and 1d, using semantically (1a–1c) or statistically (1d) informative cues, showed a robust, long-lasting facilitation for drawing inferences from the cued rule. In Experiment 2, using uninformative cues, inferences from the cued rule were facilitated with a short stimulus onset asynchrony (SOA), whereas they were delayed when the SOA was longer, an effect that is similar to the “inhibition of return” (IOR) in perceptual tasks. Experiment 3 used uninformative cues, three different SOAs, and inferential rules with disjunctive antecedents, replicating the IOR-like effect with the long SOAs and, at the short SOA, finding evidence of a gradient-like behaviour of the facilitation effect. Our findings show qualitative similarities to some effects typically observed in the orienting of visual attention, although the tasks did not involve spatial orienting.
Directed forgetting in the list method affects recognition memory for source
Authors: Gottlob Lawrence R. , Golding Jonathan M.
Published: July 2011

The effects of list-method directed forgetting on recognition memory were explored. In Experiment 1 ( N = 40), observers were instructed to remember words and their type-cases; in Experiment 2 ( N = 80), the instruction was to remember words and their colours. Two lists of 10 words were presented; after the first list, half of the observers ( forget) were instructed to forget that list, and the other half ( remember) were not given the forget instruction. Recognition of items (words) as well as source (encoding list + case/colour) was measured for forget and remember observers. The forget instruction affected case/colour memory more consistently than item and list memory; a multinomial analysis indicated that source information was affected by the forget instructions. The results indicated that recognition of source information may be a more sensitive indicator of forgetting than recognition of items.
Multimodal Discrimination Learning in Humans: Evidence for Configural Theory
Authors: Redhead Edward S.
Published: July 2011

Human contingency learning was used to compare the predictions of configural and elemental theories. In three experiments, participants were required to learn which indicators were associated with an increase in core temperature of a fictitious nuclear plant. Experiments 1 and 2 investigated the rate at which a triple-element stimulus (ABC) could be discriminated from either single-element stimuli (A, B, and C) or double-element stimuli (AB, BC, and AC). Experiment 1 used visual stimuli, whilst Experiment 2 used visual, auditory, and tactile stimuli. In both experiments the participants took longer to discriminate the triple-element stimulus from the more similar double-element stimuli than from the less similar single-element stimuli. Experiment 3 tested for summation with stimuli from either a single or multiple modalities, and summation was found only in the latter case. Thus, the pattern of results seen in Experiments 1 and 2 was not dependent on whether the stimuli were single modal or multimodal, nor was it dependent on whether the stimuli could elicit summation. This pattern of results is consistent with predictions derived from Pearce's (1987, 1994) configural theory.
Blocking of Human Causal Learning Involves Learned Changes in Stimulus Processing
Authors: Le Pelley M. E. , Beesley T. , Suret M. B.
Published: July 2011

Several theories of associative learning propose that blocking reflects changes in the processing devoted to learning about cues. The results of the only direct test of this suggestion in human learning (Kruschke & Blair, 2000) could equally well be explained in terms of, among others, interference in learning or memory. The present study tested this suggestion in a situation in which processing-change and interference accounts predict opposing results. Results support the idea that blocking in human learning can reflect a change in processing of the cues involved.
Separation of VUV/UV photons and reactive particles in the effluent of a He/O2atmospheric pressure plasma jet
Authors: Schneider S , Lackmann J-W , Narberhaus F , Bandow J E , Denis B , Benedikt J
Published: July 2011

Cold atmospheric pressure plasmas can be used for treatment of living tissues or for inactivation of bacteria or biological macromolecules. The treatment is usually characterized by a combined effect of UV and VUV radiation, reactive species and ions. This combination is usually beneficial for the effectiveness of the treatment but it makes the study of fundamental interaction mechanisms very difficult. Here we report on an effective separation of VUV/UV photons and heavy reactive species in the effluent of a microscale atmospheric pressure plasma jet (μ-APPJ). The separation is realized by an additional flow of helium gas under well-defined flow conditions, which deflects heavy particles in the effluent without affecting the VUV and UV photons. Both components of the effluent, the photons and the reactive species, can be used separately or in combination for sample treatment. The results of treatment of a model plasma polymer film and vegetativeBacillus subtilisandEscherichia colicells are shown and discussed. A simple model of the He gas flow and reaction kinetics of oxygen atoms in the gas phase and at the surface is used to provide a better understanding of the processes in the plasma effluent. The new jet modification, called X-Jet for its appearance, will simplify the investigation of interaction mechanisms of atmospheric pressure plasmas with biological samples.
Laser fluence effects on ion emission from a laser-generated Cu plasma
Authors: Ilyas B , Dogar A H , Ullah S , Qayyum A
Published: July 2011

We present details of an experimental facility developed for the diagnostics of highly charged ions produced during pulsed laser ablation of solid targets. A range of laser fluences (2–10 J cm−2) from a Q-switched Nd : YAG laser (wavelength = 1064 nm, pulse duration ∼10 ns) was used to generate a copper plasma. The ion diagnostics were based on the time-of-flight (TOF) methods; an ion collector and a 45° parallel plate electrostatic ion energy analyser were used. A channel electron multiplier located 1.31 m away from the Cu target was used to record the energy-resolved TOF ion spectrum. The effect of laser fluence on the total ion charge, average ion energy and charge state distribution was investigated. The estimated threshold fluence for the onset of the plasma was 2.5 J cm−2. About four times increase in both average ion energy and total ion charge was observed in the investigated laser fluence range. The maximum attainable charge state of the Cu ions increased from 1+ to 7+ with the increase in laser fluence. The correlation between relative abundance of the various ion charge states indicated that the formation of Cu
n+ occurred through ionization from Cu(n−1)+ by the impact of fast electrons or by multiphoton interactions.
The high sensitivity of InN under rare earth ion implantation at medium range energy
Authors: Lacroix B , Chauvat M P , Ruterana P , Lorenz K , Alves E , Syrkin A
Published: July 2011

In this work, the damage formation in InN layers has been investigated subsequent to europium implantation at 300 keV and room temperature. The layers of several micrometres were produced by hydride vapour phase epitaxy and used as matrices for ion implantation experiments due to their good crystalline quality. From this investigation, it is shown that InN exhibits a low stability under rare earth ion implantation. Starting at a low fluence of around 5 × 1012 Eu cm−2, an extensive modification of the surface layer takes place. The dissociation of InN and the presence of misoriented nanograins are observed in the damaged area. Analysis by electron diffraction indicates that the nanograins correspond to indium oxide In2O3.
Rolling deformation induced reduction of rate sensitivity and enhancement of hardness in nanocrystalline NiFe alloys
Authors: Cao Z H , Li P Y , Jiang Z H , Meng X K
Published: July 2011

Both hardness (H) and rate sensitivity (m) of nanocrystalline NiFe alloys were studied by nanoindentation testing. It was found that H increases, and m decreases after rolling in the alloys. It is interesting that the decrease in m by rolling is totally contrary to the conventional coarse grain alloys. The dislocation density is remarkably enhanced by rolling deformation, which leads to the hardening behaviour of the samples. The dislocation absorbed at the grain boundary (GB) and/or sub-GB and grain growth by rolling are responsible for the reduced m of the rolled alloys.
New stannite-like p-type thermoelectric material Cu3SbSe4
Authors: Yang Chongyin , Huang Fuqiang , Wu Liming , Xu Ke
Published: July 2011

The ternary chalcogenide of Cu3SbSe4 is demonstrated to be a novel p-type thermoelectric material, by doping Sn in the Sb site. The figure of merit (ZT) in Cu3Sb0.975Sn0.025Se4 reaches 0.75 at 673 K. Such excellent thermoelectric properties are attributed to the crystal structure of Cu3SbSe4, consisting of the three-dimensional Cu/Se framework
acting as the hole conduction pathway and the [SbSe4] tetrahedra. The Cu/Se framework is suitable to tune the electrical conductivity by doping. The insertion of tetrahedral [SbSe4] causes a more distorted diamond-like structure, providing a relatively lower lattice thermal conductivity and a relatively large Seebeck coefficient. The origin of the structure–electrical property relationship and ZT enhancement by Sn doping is elucidated.
Small footprint wafer-level vacuum packaging using compressible gold sealing rings
Authors: Antelius Mikael , Stemme Göran , Niklaus Frank
Published: July 2011

A novel low-temperature wafer-level vacuum packaging process is presented. The process uses plastically deformed gold rings as sealing structures in combination with flux-free soldering to provide the bond force for a sealing wafer. This process enables the separation of the sealing and the bonding functions both spatially on the wafer and temporally in different process steps, which results in reduced areas for the sealing rings and prevents outgassing from the solder process in the cavity. This enables space savings and yields improvements. We show the experimental result of the hermetic sealing. The leak rate into the packages is determined, by measuring the package lid deformation over 10 months, to be lower than 3.5 × 10−13 mbar l s−1, which is suitable for most MEMS packages. The pressure inside the produced packages is measured to be lower than 10 mbar.
Can emerging biomarkers of myocardial remodelling identify asymptomatic hypertensive patients at risk for diastolic dysfunction and diastolic heart failure?
Authors: Collier Patrick , Watson Chris J. , Voon Victor , Phelan Dermot , Jan Aftab , Mak George , Martos Ramon , Baugh John A. , Ledwidge Mark T. , McDonald Kenneth M.
Published: July 2011

Aims

Hypertension is one of the main drivers of the heart failure (HF) epidemic. The aims of this study were to profile fibro‐inflammatory biomarkers across stages of the hypertensive heart disease (HHD) spectrum and to examine whether particular biochemical profiles in asymptomatic patients identify a higher risk of evolution to HF.

Methods and results

This was a cross‐sectional observational study involving a population of 275 stable hypertensive patients divided into two different cohorts: Group 1, asymptomatic hypertension (AH) (n= 94); Group 2, HF with preserved ejection fraction  (n= 181). Asymptomatic hypertension patients were further subdivided according to left atrial volume index ≥34 mL/m2 (n= 30) and <34 mL/m2 (n= 64). Study assays involved inflammatory markers [interleukin 6 (IL6), interleukin 8 (IL8), monocyte chemoattractant protein 1 (MCP1), and tumour necrosis factor α], collagen 1 and 3 metabolic markers [carboxy‐terminal propeptide of collagen 1, amino‐terminal propeptide of collagen 1, amino‐terminal propeptide of collagen 3 (PIIINP), and carboxy‐terminal telopeptide of collagen 1 (CITP)], extra‐cellular matrix turnover markers [matrix metalloproteinase 2 (MMP2), matrix metalloproteinase 9 (MMP9), and tissue inhibitor of metalloproteinase 1 (TIMP1)], and the brain natriuretic peptide. Data were adjusted for age, sex, systolic blood pressure, and creatinine. Heart failure with preserved ejection fraction  was associated with an increased inflammatory signal (IL6, IL8, and MCP1), an increased fibrotic signal (PIIINP and CITP), and an increased matrix turnover signal (MMP2 and MMP9). Alterations in MMP and TIMP enzymes were found to be significant indicators of greater degrees of asymptomatic left ventricular diastolic dysfunction.

Conclusion

These data define varying fibro‐inflammatory profiles throughout different stages of HHD. In particular, the observations on MMP9 and TIMP1 raise the possibility of earlier detection of those at risk of evolution to HF which may help focus effective preventative strategies.
Disruption of the alsSD operon of Enterococcus faecalis impairs growth on pyruvate at low pH
Authors: Repizo Guillermo D. , Mortera Pablo , Magni Christian
Published: July 2011

Diacetyl and acetoin are pyruvate-derived metabolites excreted by many micro-organisms, and are important in their physiology. Although generation of these four-carbon (C4) compounds in Enterococcus faecalis is a well-documented phenotype, little is known about the gene regulation of their biosynthetic pathway and the physiological role of the pathway in this bacterium. In this work, we identified the genes involved in C4 compound biosynthesis in Ent. faecalis and report their transcriptional analysis. These genes are part of the alsSD bicistronic operon, which encodes α-acetolactate synthase (AlsS) and α-acetolactate decarboxylase (AlsD). Our studies showed that alsSD operon transcription levels are maximal during the exponential phase of growth, decreasing thereafter. Furthermore, we found that this transcription is enhanced upon addition of pyruvate to the growth medium. In order to study the functional role of the alsSD operon, an isogenic alsSD mutant strain was constructed. This strain lost its capacity to generate C4 compounds, confirming the role of alsSD genes in this metabolic pathway. In contrast to the wild-type strain, the alsSD-deficient strain was unable to grow in LB medium supplemented with pyruvate at an initial pH of 4.5. This dramatic reduction in growth parameters for the mutant strain was simultaneously accompanied by the inability to alkalinize the internal and external medium under these conditions. In sum, these results suggest that the decarboxylation reactions related to the C4 biosynthetic pathway give enterococcal cells a competitive advantage during pyruvate metabolism at low pH.
Non-coding nucleotides and amino acids near the active site regulate peptide deformylase expression and inhibitor susceptibility in Chlamydia trachomatis
Authors: Bao Xiaofeng , Pachikara Niseema D. , Oey Christopher B. , Balakrishnan Amit , Westblade Lars F. , Tan Ming , Chase Theodore , Nickels Bryce E. , Fan Huizhou
Published: July 2011

Chlamydia trachomatis,an obligate intracellular bacterium, is a highly prevalent human pathogen. Hydroxamic-acid-based matrix metalloprotease inhibitors can effectively inhibit the pathogen bothin vitroandin vivo, and have exhibited therapeutic potential. Here, we provide genome sequencing data indicating that peptide deformylase (PDF) is the sole target of the inhibitors in this organism. We further report molecular mechanisms that control chlamydial PDF (cPDF) expression and inhibition efficiency. In particular, we identify the σ66-dependent promoter that controls cPDF gene expression and demonstrate that point mutations in this promoter lead to resistance by increasing cPDF transcription. Furthermore, we show that substitution of two amino acids near the active site of the enzyme alters enzyme kinetics and protein stability.
Functional analysis of the nifQdctA1y4vGHIJ operon of Sinorhizobium fredii strain NGR234 using a transposon with a NifA-dependent read-out promoter
Authors: Fumeaux Coralie , Bakkou Nadia , Kopcińska Joanna , Golinowski Wladyslav , Westenberg David J. , Müller Peter , Perret Xavier
Published: July 2011

Rhizobia are a disparate collection of soil bacteria capable of reducing atmospheric nitrogen in symbiosis with legumes (Fix phenotype). Synthesis of the nitrogenase and its accessory components is under the transcriptional control of the key regulator NifA and is generally restricted to the endosymbiotic forms of rhizobia known as bacteroids. Amongst studied rhizobia, Sinorhizobium fredii strain NGR234 has the remarkable ability to fix nitrogen in association with more than 130 species in 73 legume genera that form either determinate, indeterminate or aeschynomenoid nodules. Hence, NGR234 is a model organism to study nitrogen fixation in association with a variety of legumes. The symbiotic plasmid pSfrNGR234a carries more than 50 genes that are under the transcriptional control of NifA. To facilitate the functional analysis of NifA-regulated genes a new transposable element, TnEKm-PwA, was constructed. This transposon combines the advantages of in vitro mutagenesis of cloned DNA fragments with a conditional read-out promoter from NGR234 (PwA) that reinitiates NifA-dependent transcription downstream of transposition sites. To test the characteristics of the new transposon, the nifQdctA1y4vGHIJ operon was mutated using either the Omega interposon or TnEKm-PwA. The symbiotic phenotypes on various hosts as well as the transcriptional characteristics of these mutants were analysed in detail and compared with the ineffective (Fix−) phenotype of strain NGRΔnifA, which lacks a functional copy of nifA. De novo transcription from inserted copies of TnEKm-PwA inside bacteroids was confirmed by qRT-PCR. Unexpectedly, polar mutants in dctA1 and nifQ were Fix+ on all of the hosts tested, indicating that none of the six genes of the nifQ operon of NGR234 is essential for symbiotic nitrogen fixation on plants that form nodules of either determinate or indeterminate types.
The PmrA/PmrB regulatory system controls the expression of the wzzfepE
gene involved in the O-antigen synthesis of Salmonella enterica serovar Typhimurium
Authors: Pescaretti María de las Mercedes , López Fabián E. , Morero Roberto D. , Delgado Mónica A.
Published: July 2011

The degree of polymerization of O-antigen from Salmonella enterica serovar Typhimurium is controlled by the products of the wzzs

t and wzzfepE
genes. In the present study we investigated the role of the PmrA/PmrB regulatory system in wzzfepE
transcription. We report that the direct binding of the PmrA regulator to a specific promoter site induces the expression of the wzzfepE
gene. This effect increases the amount of very long (VL) O-antigen, which is required for the resistance of Salmonella to serum human complement and polymyxin B, and for the replication of the bacteria within macrophages. The results obtained here highlight functional differences between WzzfepE and Wzzst, although the genes for both proteins are regulated in a PmrA-dependent way.
Transcriptional regulation of Pseudomonas aeruginosa rhlR: role of the CRP orthologue Vfr (virulence factor regulator) and quorum-sensing regulators LasR and RhlR
Authors: Croda-García Gerardo , Grosso-Becerra Victoria , Gonzalez-Valdez Abigail , Servín-González Luis , Soberón-Chávez Gloria
Published: July 2011

The production of many virulence factors byPseudomonas aeruginosais regulated by the quorum-sensing (QS) response. In this regulatory network LasR and RhlR, bound to their corresponding autoinducers, play a central role. The QS response has a hierarchical structure: LasR/3O-C12-HSL activates the transcription ofrhlR, and RhlR/C4-HSL activates the transcription of several genes, including therhlABoperon, which encodes the enzymes responsible for rhamnolipid synthesis. TherhlABoperon is located immediately upstream of therhlRgene.rhlRhas four transcription start sites, two of which are located in therhlBcoding region. Vfr directly activates transcription oflasR, and has been reported to be also involved inrhlRexpression. The aim of this work was to characterize the details of the mechanism ofrhlRtranscriptional regulation. We show that Vfr directly regulatesrhlRtranscription through its binding to several Vfr-binding sites (VBSs) present in therhlRpromoter region, one of which has a negative effect on transcription. Two of the VBSs overlap withlasboxes where LasR/3O-C12-HSL binds to activaterhlRtranscription. We also show thatrhlRtranscription is subject to positive-feedback autoregulation through RhlR/C4-HSL activation of therhlApromoter. This positive autoregulation plays a major role inrhlRexpression.
The Dickeya dadantii biofilm matrix consists of cellulose nanofibres, and is an emergent property dependent upon the type III secretion system and the cellulose synthesis operon
Authors: Jahn Courtney E. , Selimi Dija A. , Barak Jeri D. , Charkowski Amy O.
Published: July 2011

Dickeya dadantii is a plant-pathogenic bacterium that produces cellulose-containing biofilms, called pellicles, at the air–liquid interface of liquid cultures. D. dadantii pellicle formation appears to be an emergent property dependent upon at least three gene clusters, including cellulose synthesis, type III secretion system (T3SS) and flagellar genes. The D. dadantii cellulose synthesis operon is homologous to that of Gluconacetobacter xylinus, which is used for industrial cellulose production, and the cellulose nanofibres produced by D. dadantii were similar in diameter and branching pattern to those produced by G. xylinus. Salmonella enterica, an enterobacterium closely related to D. dadantii, encodes a second type of cellulose synthesis operon, and it produced biofilm strands that differed in width and branching pattern from those of D. dadantii and G. xylinus. Unlike any previously described cellulose fibre, the D. dadantii cellulose nanofibres were decorated with bead-like structures. Mutation of the cellulose synthesis operon genes resulted in loss of cellulose synthesis and production of a cellulase-resistant biofilm. Mutation of other genes required for pellicle formation, including those encoding FliA (a sigma factor that regulates flagella production), HrpL (a sigma factor that regulates the T3SS), and AdrA, a GGDEF protein, affected both biofilm and cell morphology. Mutation of the cellulose synthase bcsA or of bcsC resulted in decreased accumulation of the T3SS-secreted protein HrpN.
Linear plasmids mobilize linear but not circular chromosomes in Streptomyces: support for the ‘end first’ model of conjugal transfer
Authors: Lee Hsuan-Hsuan , Hsu Chin-Chen , Lin Yen-Ling , Chen Carton W.
Published: July 2011

Gram-positive bacteria of the genusStreptomycespossess linear chromosomes and linear plasmids capped by terminal proteins covalently bound to the 5′ ends of the DNA. The linearity ofStreptomyceschromosomes raises the question of how they are transferred during conjugation, particularly when the mobilizing plasmids are also linear. The classical rolling circle replication model for transfer of circular plasmids and chromosomes from an internal origin cannot be applied to this situation. Instead it has been proposed that linearStreptomycesplasmids mobilize themselves and the linear chromosomes from their telomeres using terminal-protein-primed DNA synthesis. In support of this ‘end first’ model, we found that artificially circularizedStreptomyceschromosomes could not be mobilized by linear plasmids (SLP2 and SCP1), while linear chromosomes could. In comparison, a circular plasmid (pIJ303) could mobilize both circular and linear chromosomes at the same efficiencies. Interestingly, artificially circularized SLP2 exhibited partial self-transfer capability, indicating that, being a composite replicon, it may have acquired the additional internal origin of transfer from an ancestral circular plasmid during evolution.
HXK1 regulates carbon catabolism, sporulation, fumonisin B1 production and pathogenesis in Fusarium verticillioides
Authors: Kim Hun , Smith Jonathon E. , Ridenour John B. , Woloshuk Charles P. , Bluhm Burton H.
Published: July 2011

InFusarium verticillioides, a ubiquitous pathogen of maize, virulence and mycotoxigenesis are regulated in response to the types and amounts of carbohydrates present in maize kernels. In this study, we investigated the role of a putative hexokinase-encoding gene (HXK1) in growth, development and pathogenesis. A deletion mutant (Δhxk1) ofHXK1was not able to grow when supplied with fructose as the sole carbon source, and growth was impaired when glucose, sucrose or maltotriose was provided. Additionally, the Δhxk1mutant produced unusual swollen hyphae when provided with fructose, but not glucose, as the sole carbon source. Moreover, the Δhxk1mutant was impaired in fructose uptake, although glucose uptake was unaffected. On maize kernels, the Δhxk1mutant was substantially less virulent than the wild-type, but virulence on maize stalks was not impaired, possibly indicating a metabolic response to tissue-specific differences in plant carbohydrate content. Finally, disruption ofHXK1had a pronounced effect on fungal metabolites produced during colonization of maize kernels; the Δhxk1mutant produced approximately 50 % less trehalose and 80 % less fumonisin B1(FB1) than the wild-type. The reduction in trehalose biosynthesis likely explains observations of increased sensitivity to osmotic stress in the Δhxk1mutant. In summary, this study links early events in carbohydrate sensing and glycolysis to virulence and secondary metabolism inF. verticillioides, and thus provides a new foothold from which the genetic regulatory networks that underlie pathogenesis and mycotoxigenesis can be unravelled and defined.
Identification of PTPN23 as a novel regulator of cell invasion in mammary epithelial cells from a loss-of-function screen of the ‘PTP-ome'
Authors: Lin Guang , Aranda Victoria , Muthuswamy Senthil K. , Tonks Nicholas K.
Published: July 2011

We used an RNAi-mediated loss-of-function screen to study systematically the role of the protein tyrosine phosphatase (PTP) superfamily of enzymes in mammary epithelial cell motility in the absence or presence of the oncoprotein tyrosine kinase ERBB2. We report that although shRNAs directed against most of the PTP family were without effect, suppression of three PTPs—PRPN23, PTPRG, and PTPRR—enhanced cell motility. Furthermore, we found that suppression of PTPN23, but not PTPRG or PTPRR, induced cell invasion. Suppression of PTPN23 increased E-cadherin internalization, impaired early endosome trafficking of E-cadherin, induced the expression of mesenchymal proteins, and caused cell scattering. The activity of SRC and β-catenin was elevated when PTPN23 was suppressed. Moreover, we identified SRC, E-cadherin, and β-catenin as direct substrates of PTPN23. Inhibition of SRC with the small molecular inhibitor SU6656 blocked the effects of PTPN23 depletion. These findings suggest that loss of PTPN23 may increase the activity of SRC and the phosphorylation status of the E-cadherin/β-catenin signaling complex to promote tumor growth and invasive behavior in breast cancer. In addition, our studies highlight functional specificity among PTPs and reveal new roles for PTPs in mammary epithelial cell biology.
Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression
Authors: Kim Jane C. , Nordman Jared , Xie Fang , Kashevsky Helena , Eng Thomas , Li Sharon , MacAlpine David M. , Orr-Weaver Terry L.
Published: July 2011

In metazoans, how replication origins are specified and subsequently activated is not well understood. Drosophila amplicons in follicle cells (DAFCs) are genomic regions that undergo rereplication to increase DNA copy number. We identified all DAFCs by comparative genomic hybridization, uncovering two new amplicons in addition to four known previously. The complete identification of all DAFCs enabled us to investigate these in vivo replicons with respect to parameters of transcription, localization of the origin recognition complex (ORC), and histone acetylation, yielding important insights into gene amplification as a metazoan replication model. Significantly, ORC is bound across domains spanning 10 or more kilobases at the DAFC rather than at a specific site. Additionally, ORC is bound at many regions that do not undergo amplification, and, in contrast to cell culture, these regions do not correlate with high gene expression. As a developmental strategy, gene amplification is not the predominant means of achieving high expression levels, even in cells capable of amplification. Intriguingly, we found that, in some strains, a new amplicon, DAFC-22B, does not amplify, a consequence of distant repression of ORC binding and origin activation. This repression is alleviated when a fragment containing the origin is placed in different genomic contexts.
Phosphorylation of H4 Ser 47 promotes HIRA-mediated nucleosome assembly
Authors: Kang Bin , Pu Mintie , Hu Gangqing , Wen Weihong , Dong Zigang , Zhao Keji , Stillman Bruce , Zhang Zhiguo
Published: July 2011

Histone H3 variant H3.3, while differing from canonical H3 (H3.1) by only five amino acids, is assembled into nucleosomes, along with histone H4, at genic regions by the histone chaperone HIRA, whereas H3.1 is assembled into nucleosomes in a CAF-1-dependent reaction. Here, we show that phosphorylation of histone H4 Ser 47 (H4S47ph), catalyzed by the PAK2 kinase, promotes nucleosome assembly of H3.3–H4 and inhibits nucleosome assembly of H3.1–H4 by increasing the binding affinity of HIRA to H3.3–H4 and reducing association of CAF-1 with H3.1–H4. These results reveal a mechanism whereby H4S47ph distinctly regulates nucleosome assembly of H3.1 and H3.3.
The genome of the leaf-cutting antAcromyrmex echinatiorsuggests key adaptations to advanced social life and fungus farming
Authors: Nygaard Sanne , Zhang Guojie , Schiøtt Morten , Li Cai , Wurm Yannick , Hu Haofu , Zhou Jiajian , Ji Lu , Qiu Feng , Rasmussen Morten , Pan Hailin , Hauser Frank , Krogh Anders , Grimmelikhuijzen Cornelis J.P. , Wang Jun , Boomsma Jacobus J.
Published: July 2011

We present a high-quality (>100× depth) Illumina genome sequence of the leaf-cutting antAcromyrmex echinatior, a model species for symbiosis and reproductive conflict studies. We compare this genome with three previously sequenced genomes of ants from different subfamilies and focus our analyses on aspects of the genome likely to be associated with known evolutionary changes. The first is the specialized fungal diet ofA. echinatior, where we find gene loss in the ant's arginine synthesis pathway, loss of detoxification genes, and expansion of a group of peptidase proteins. One of these is a unique ant-derived contribution to the fecal fluid, which otherwise consists of “garden manuring” fungal enzymes that are unaffected by ant digestion. The second is multiple mating of queens and ejaculate competition, which may be associated with a greatly expanded nardilysin-like peptidase gene family. The third is sex determination, where we could identify only a single homolog of thefeminizergene. As other ants and the honeybee have duplications of this gene, we hypothesize that this may partly explain the frequent production of diploid male larvae inA. echinatior. The fourth is the evolution of eusociality, where we find a highly conserved ant-specific profile of neuropeptide genes that may be related to caste determination. These first analyses of theA. echinatiorgenome indicate that considerable genetic changes are likely to have accompanied the transition from hunter-gathering to agricultural food production 50 million years ago, and the transition from single to multiple queen mating 10 million years ago.